Biomedical subjects

R E Jacobs

Publications and source records attributed to R E Jacobs.

At least 19 recordsLinked to original sources

PubMed2001

Kir4.1 potassium channel subunit is crucial for oligodendrocyte development and in vivo myelination.

To understand the cellular and in vivo functions of specific K(+) channels in glia, we have studied mice with a null mutation in the weakly inwardly rectifying K(+) channel subunit Kir4.1. Kir4.1-/- mice display marked motor impairment, and the cellular basis is hypomyelination in the spinal cord, accompanied by severe spongiform vacuolation, axonal swellings, and degeneration. Immunostaining in the spinal cord of wild-type mice up to postnatal day 18 reveals that Kir4.1 is expressed in myelin-synthesizing oligodendrocytes, but probably not in neurons or glial fibrillary acidic protein-positive (GFAP-positive) astrocytes. Cultured oligodendrocytes from developing spinal cord of Kir4.1-/- mice lack most of the wild-type K(+) conductance, have depolarized membrane potentials, and display immature morphology. By contrast, cultured neurons from spinal cord of Kir4.1-/- mice have normal physiological characteristics. We conclude that Kir4.1 forms the major K(+) conductance of oligodendrocytes and is therefore crucial for myelination. The Kir4.1 knock-out mouse is one of the few CNS dysmyelinating or demyelinating phenotypes that does not involve a gene directly involved in the structure, synthesis, degradation, or immune response to myelin. Therefore, this mouse shows how an ion channel mutation could contribute to the polygenic demyelinating diseases.

Animals↗

PubMed2001

Three-dimensional digital mouse atlas using high-resolution MRI.

We present an archetypal digital atlas of the mouse embryo based on microscopic magnetic resonance imaging. The atlas is composed of three modules: (1) images of fixed embryos 6 to 15.5 days postconception (dpc) [Theiler Stages (TS) 8 to 24]; (2) an annotated atlas of the anterior portion of a 13.5 dpc (TS 22) mouse with anatomical structures delineated and linked to explanatory files; and (3) three-dimensional renderings of the entire 13.5 dpc embryo and specific organ systems. The explanatory files include brief descriptions of the structure at each volume element in the image and links to 3D reconstructions, allowing visualization of the shape of the isolated structures. These files can also contain or be linked to other types of information and data including detailed anatomical and physiological information about structures with pointers to online references, relationships between structures, temporal characteristics (cell lineage patterns, size, and shape changes), and gene expression patterns (both spatial and temporal). As an example, we have "painted" in the expression pattern of Dlx5/Dlx6 genes. This digital atlas provides a means to put specific data within the context of normal specimen anatomy, to analyze the information in 3D, and to examine relationships between different types of information.

Animals↗

PubMed2001

MR imaging with phase encoding of intermolecular multiple quantum coherences.

Novel 2D and 3D pulse sequences producing images through the phase encoding of intermolecular multiple quantum coherences (i-MQCs) are presented. The signal acquired with these sequences is free from intermolecular zero quantum coherences (i-ZQCs) which are not phase encoded and additional phase cycling eliminates artifacts. Phase encoding during the n-quantum evolution period provides n times the resolution expected from equivalent phase encoding of the reconverted single quantum coherences. These sequences have potential applications for producing i-MQC images of biological tissues as well as nonbiological materials with substantial amounts of water.

Magnetic Resonance Imaging↗

PubMed2001

Complementary emerging techniques: high-resolution PET and MRI.

Noninvasive imaging technologies provide a unique window on the anatomy, physiology and function of living organisms. Imaging systems and methods have been developed for the study of small animal model systems that offer exciting new possibilities in neuroscience. Advances in magnetic resonance microscopy and positron emission tomography, and their applications in brain imaging, have provided many benefits to neurobiology, ranging from detailed in vivo neuroanatomy to the measurement of specific molecular targets.

Animals↗

PubMed2000

In vivo visualization of gene expression using magnetic resonance imaging.

High-resolution in vivo imaging of gene expression is not possible in opaque animals by existing techniques. Here we present a new approach for obtaining such images by magnetic resonance imaging (MRI) using an MRI contrast agent that can indicate reporter gene expression in living animals. We have prepared MRI contrast agents in which the access of water to the first coordination sphere of a chelated paramagnetic ion is blocked with a substrate that can be removed by enzymatic cleavage. Following cleavage, the paramagnetic ion can interact directly with water protons to increase the MR signal. Here, we report an agent where galactopyranose is the blocking group. This group renders the MRI contrast agent sensitive to expression of the commonly used marker gene, beta-galactosidase. To cellular resolution, regions of higher intensity in the MR image correlate with regions expressing marker enzyme. These results offer the promise of in vivo mapping of gene expression in transgenic animals and validate a general approach for constructing a family of MRI contrast agents that respond to biological activity.

Animals↗

PubMed1999

Magnetic resonance microscopy of iron in the basal forebrain cholinergic structures of the aged mouse lemur.

Increased non-heme iron levels in the brain of Alzheimer's disease (AD) patients are higher than the levels observed in age matched normal subjects. Iron level in structures that are highly relevant for AD, such as the basal forebrain, can be detected post mortem with histochemistry. Because of the small size of these structures, in vivo MR detection is very difficult at conventional field magnets (1.5 and 4 T). In this study, we observed iron deposits with histochemistry and MR microscopy at 11.7 T in the brain of the mouse lemur, a strepsirhine primate which is the only known animal model of aging presenting both senile plaques and neurofibrillary degeneration. We also examined a related species, the dwarf lemur. Iron distribution in aged animals (8 to 15 years old) agrees with previous findings in humans. In addition, the high iron levels of the globus pallidus is paralleled by a comparable contrast in basal forebrain cholinergic structures. Because of the enhancement of iron-dependent contrast with increasing field strength, microscopic magnetic resonance imaging of the mouse lemur appears to be an ideal model system for studying in vivo iron changes in the basal forebrain in relation to aging and neurodegeneration.

Animals↗

PubMed1999

Topographical localization of lipofuscin pigment in the brain of the aged fat-tailed dwarf lemur (Cheirogaleus medius) and grey lesser mouse lemur (Microcebus murinus): comparison to iron localization.

The present study was undertaken to explore the distribution of lipofuscin in the brain of cheirogaleids by autofluorescence and compare it to other studies of iron distribution. Aged dwarf (Cheirogaleus medius) and mouse (Microcebus murinus) lemurs provide a reliable model for the study of normal and pathological cerebral aging. Accumulation of lipofuscin, an age pigment derived by lipid peroxidation, constitutes the most reliable cytological change correlated with neuronal aging. Brain sections of four aged (8-15 year old) and 3 young (2-3 year old) animals were examined. Lipofuscin accumulation was observed in the aged animals but not in the young ones. Affected regions include the hippocampus (granular and pyramidal cells), where no iron accumulation was observed, the olfactory nucleus and the olfactory bulb (mitral cells), the basal forebrain, the hypothalamus, the cerebellum (Purkinje cells), the neocortex (essentially in the pyramidal cells), and the brainstem. Even though iron is known to catalyse lipid oxidation, our data indicate that iron deposits and lipofuscin accumulation are not coincident. Different biochemical and morphological cellular compartments might be involved in iron and lipofuscin deposition. The nonuniform distribution of lipofuscin indicates that brain structures are not equally sensitive to the factors causing lipofuscin accumulation. The small size, the rapid maturity, and the relatively short life expectancy of the cheirogaleids make them a good model system in which to investigate the mechanisms of lipofuscinogenesis in primates.

Animals↗

PubMed1999

Looking deeper into vertebrate development.

Magnetic resonance imaging (MRI) is a non-invasive imaging method that provides three-dimensional (3-D) images of the internal structure of opaque objects, such as humans and mice. In optimal situations, spatial resolution can approach the micron level. Arbitrarily oriented single-slice images can be obtained in seconds, with full 3-D volume images taking tens of minutes to collect. The exquisite sensitivity of MRI to the local physical and chemical environment provides a wide range of mechanisms giving rise to intrinsic contrast in the MR experiment, thus providing images with dramatic differences between different tissue types (e.g. white vs grey matter, myelinated vs unmyelinated fibres, and brain parenchyma vs ventricles). The recent advent of physiologically sensitive MRI contrast agents opens up a wealth of new avenues of study, even including the in vivo imaging of gene expression.

Animals↗

PubMed1998

A model for MRI contrast enhancement using T1 agents.

Contrast in MRI relies on differences in the local environment of water and is often enhanced by using contrast agents. We present a simple model for evaluating the minimal contrast agent concentration required to produce "satisfactory" contrast enhancement in magnetic resonance images. Previous strategies have been based largely on empirical results for specific systems. The present tissue contrast model (TCM) can be applied to "conventional," targeted, or biochemically responsive agents. The model results are formulated so that only a small number of parameters are required to analyze a given scenario. The TCM is a particularly useful tool in the development of new classes of magnetic resonance contrast media. These agents will have the ability to target specific cells or tissue, and perhaps be able to report on their physiological status. As an example of the applicability of the TCM, we test it against in vivo magnetic resonance microscopy results in frog embryos that have focal cell populations labeled with contrast agent by using calibrated single-cell microinjection techniques.

Animals↗

PubMed1998

Topographical localization of iron in brains of the aged fat-tailed dwarf lemur (Cheirogaleus medius) and gray lesser mouse lemur (Microcebus murinus).

Iron deposits in the human brain are characteristic of normal aging but have also been implicated in various neurodegenerative diseases. Among nonhuman primates, strepsirhines are of particular interest because hemosiderosis has been consistently observed in captive aged animals. In particular, the cheirogaleids, because of their small size, rapid maturity, fecundity, and relatively short life expectancy, are a useful model system for the study of normal and pathological cerebral aging. This study was therefore undertaken to explore iron localization in the brain of aged cheirogaleids (mouse and dwarf lemurs) with histochemistry and magnetic resonance microscopy. Results obtained with both techniques were comparable. There was no difference between old animals in the two species. The young animals (3 years old) showed no iron deposits. In the old animals (8-15 years old), iron pigments were mainly localized in the globus pallidus, the substantia nigra, the neocortical and cerebellar white matter, and anterior forebrain structures, including the nucleus basalis of Meynert. This distribution agrees with previous findings in monkeys and humans. In addition, we observed iron in the thalamus of these aged non-human primates. Microscopic NMR images clearly reveal many features seen with the histochemical procedure, and magnetic resonance microscopy is a powerful method for visualizing age-related changes in brain iron.

Aging↗

PubMed1998

MR microscopy of transgenic mice that spontaneously acquire experimental allergic encephalomyelitis.

Pathology of fixed spinal cords from transgenic mice with a myelin basic protein (MBP) specific T cell receptor was investigated. These mice spontaneously acquire the demyelinating disease experimental allergic encephalomyelitis (EAE). Several complementary imaging modalities, all on the same tissues, were used to visualize lesions; these included high-field (11.7-T) microscopic diffusion tensor imaging (DTI), T2*-weighted imaging, and optical microscopy on histological sections. Lesions were predominantly in white matter around meninges and vasculature and appeared hyperintense in anatomical images. DTIs showed reduced diffusion anisotropy in the same hyperintense regions, consistent with inflammation and edema. Histology in the same tissues exhibited the characteristic pathology of EAE. Two techniques for visualizing the effective diffusion tensor fields are presented, which display direction, organization, and integrity of neuronal fibers. It is shown that DTI offers intriguing possibilities for visualizing axonal organization and lesions within white matter.

Algorithms↗

PubMed1994

Magnetic resonance microscopy of embryonic cell lineages and movements.

Key events in vertebrate embryogenesis are difficult to observe in many species. High-resolution magnetic resonance imaging was used to follow cell movements and lineages in developing frog embryos. A single cell was injected at the 16-cell stage with a contrast agent, based on the gadolinium chelate gadolinium-diethylenetriamine pentaacetic acid-dextran. The labeled progeny cells could be followed uniquely in three-dimensional magnetic resonance images, acquired from the embryo over several days. The results show that external ectodermal and internal mesodermal tissues extend at different rates during amphibian gastrulation and neurulation.

Animals↗

PubMed1994

Mouse lemur microscopic MRI brain atlas.

We present a three-dimensional (3D) digital atlas of a mouse lemur head at 60-micron cubic voxel isotropic resolution. It was constructed from a 3D proton magnetic resonance image (MRI) acquired at 500 MHz. It shows views of 3D volume-rendering and movies of contiguous 2D plane cuts in three orthogonal directions. This MR data set was acquired using a spin-echo pulse sequence under conditions of strong T2 and significant diffusion weighting. Experimental parameters were optimized to provide strong intrinsic contrast between gray and white matter. Familiar anatomical structures are clearly identifiable. Fine fiber tracts, laminations of cortices, details of the inner ears, and layering in the lateral geniculate nuclei are all visible. Anatomical identifications of structures in representative slices selected from the atlas are presented. We also describe some difficulties and trade-offs encountered in microscopic resolution MRI. We note that this type of atlas does not suffer from the spatial distortions and slice registration problems introduced by standard histological techniques. Future in vivo longitudinal studies will provide atlases describing in detail the development of the primate brain.

Animals↗

PubMed1994

Imaging neuronal development with magnetic resonance imaging (NMR) microscopy.

An ideal technique for following the development of the vertebrate nervous system would allow cells to be followed at the resolution of light microscopy at depths of several millimeters into the tissue. This would permit critical events to be followed at cellular or sub-cellular resolution even deep within the developing organism. To date, no technique has emerged with all of the needed properties. Light microscopy can follow a cell and its descendants after they have been labeled by either the infection of embryonic cells with a recombinant retrovirus or the microinjection of individual precursor cells with enzymes or fluorescent dyes. However, light microscopy cannot image events deeper than a few hundred micrometers within an embryo due to light scattering and aberrations in the objective lenses and other optics. Magnetic resonance imaging (MRI) does not suffer from these limitations, routinely being used to image in 3 dimensions through specimens as large as adult humans. However, it is relatively slow and, as implemented to date, it cannot routinely achieve cellular resolution. Here, we present our attempts to meet the technical challenges posed by in vivo MRI microscopy. As an example of both the progress and the future challenges, we present images of cells within the developing frog embryo over a several day time course.

Animals↗

PubMed1993

The evolution of proteins from random amino acid sequences. I. Evidence from the lengthwise distribution of amino acids in modern protein sequences.

We examine in this paper one of the expected consequences of the hypothesis that modern proteins evolved from random heteropeptide sequences. Specifically, we investigate the lengthwise distributions of amino acids in a set of 1,789 protein sequences with little sequence identify using the run test statistic (ro) of Mood (1940, Ann. Math. Stat. 11, 367-392). The probability density of ro for a collection of random sequences has mean = 0 and variance = 1 [the N(0,1) distribution] and can be used to measure the tendency of amino acids of a given type to cluster together in a sequence relative to that of a random sequence. We implement the run test using binary representations of protein sequences in which the amino acids of interest are assigned a value of 1 and all others a value of 0. We consider individual amino acids and sets of various combinations of them based upon hydrophobicity (4 sets), charge (3 sets), volume (4 sets), and secondary structure propensity (3 sets). We find that any sequence chosen randomly has a 90% or greater chance of having a lengthwise distribution of amino acids that is indistinguishable from the random expectation regardless of amino acid type. We regard this as strong support for the random-origin hypothesis. However, we do observe significant deviations from the random expectation as might be expected after billions years of evolution. Two important global trends are found: (1) Amino acids with a strong alpha-helix propensity show a strong tendency to cluster whereas those with beta-sheet or reverse-turn propensity do not. (2) Clustered rather than evenly distributed patterns tend to be preferred by the individual amino acids and this is particularly so for methionine. Finally, we consider the problem of reconciling the random nature of protein sequences with structurally meaningful periodic "patterns" that can be detected by sliding-window, autocorrelation, and Fourier analyses. Two examples, rhodopsin and bacteriorhodopsin, show that such patterns are a natural feature of random sequences.

Amino Acid Sequence↗

PubMed1990

Observations concerning topology and locations of helix ends of membrane proteins of known structure.

Hydropathy plots of amino acid sequences reveal the approximate locations of the transbilayer helices of membrane proteins of known structure and are thus used to predict the helices of proteins of unknown structure. Because the three-dimensional structures of membrane proteins are difficult to obtain, it is important to be able to extract as much information as possible from hydropathy plots. We describe an "augmented" hydropathy plot analysis of the three membrane proteins of known structure, which should be useful for the systematic examination and comparison of membrane proteins of unknown structure. The sliding-window analysis utilizes the floating interfacial hydrophobicity scale [IFH(h)] of Jacobs and White (Jacobs, R.E., White, S. H., 1989. Biochemistry 28:3421-3437) and the reverse-turn (RT) frequencies of Levitt (Levitt, M., 1977, Biochemistry 17:4277-4285). The IFH(h) scale allows one to examine the consequences of different assumptions about the average hydrogen bond status (h = 0 to 1) of polar side chains. Hydrophobicity plots of the three proteins show that (i) the intracellular helix-connecting links and chain ends can be distinguished from the extracellular ones and (ii) the main peaks of hydrophobicity are bounded by minor ones which bracket the helix ends. RT frequency plots show that (iii) the centers of helices are usually very close to wide-window minima of average RT frequency and (iv) helices are always bounded by narrow-window maxima of average RT frequency. The analysis suggests that side-chain hydrogen bonding with membrane components during folding may play a key role in insertion.

Amino Acid Sequence↗

PubMed1990

Statistical distribution of hydrophobic residues along the length of protein chains. Implications for protein folding and evolution.

We consider in this paper the statistical distribution of hydrophobic residues along the length of protein chains. For this purpose we used a binary hydrophobicity scale which assigns hydrophobic residues a value of one and non-hydrophobes a value of zero. The resulting binary sequences are tested for randomness using the standard run test. For the majority of the 5,247 proteins examined, the distribution of hydrophobic residues along a sequence cannot be distinguished from that expected for a random distribution. This suggests that (a) functional proteins may have originated from random sequences, (b) the folding of proteins into compact structures may be much more permissive with less sequence specificity than previously thought, and (c) the clusters of hydrophobic residues along chains which are revealed by hydrophobicity plots are a natural consequence of a random distribution and can be conveniently described by binomial statistics.

Amino Acids↗

PubMed1989

The nature of the hydrophobic binding of small peptides at the bilayer interface: implications for the insertion of transbilayer helices.

One method of obtaining useful information about the physical chemistry of peptide/bilayer interactions is to relate thermodynamic parameters of the interactions to structural parameters obtained by diffraction methods. We report here the results of the application of this approach to interactions of hydrophobic tripeptides of the form Ala-X-Ala-O-tert-butyl with lipid bilayers. The thermodynamic constants (delta Gt, delta Ht, and delta St) for the transfer of the tripeptides from water into DMPC vesicles were determined for X = Leu, Phe, and Trp and found to be consistent with those expected for hydrophobic interactions above the phase transition of DMPC. Combining these results with the earlier ones of Jacobs and White [(1986) Biochemistry 25, 2605-2612], the favorable free energies of transfer with different amino acids in the -X- position increase in the order Gly less than Ala less than Leu less than Phe less than Trp in agreement with the Nozaki and Tanford [(1971) J. Biol. Chem. 246, 2211-2217] hydrophobicity scale. Determination of the location of Ala-[2H5]Trp-Ala-O-tert-butyl in oriented DOPC bilayers by neutron diffraction shows that the most hydrophobic peptide of the series is confined to the bilayer headgroup/water region. Refinement of the diffraction measurements shows that only 13% of the tryptophan is associated with the hydrocarbon core. The distribution of the water tends to mirror that of the peptide. Unlike peptide-free bilayers, 5% of the water penetrates the hydrocarbon, which is about 100-fold greater than expected. A quantitative thermodynamic analysis of the interfacial binding of the peptides suggests that (1) the hydrophobic interactions are 60-70% complete upon binding at the bilayer interface, (2) the interface is likely to play an important role in helix formation and insertion, (3) the hydrogen bond status of amino acid side chains is crucial to insertion, and (4) an a priori lack of knowledge of the status of such bonds could limit the precision of hydrophobicity plots. We introduce an interfacial hydrophobicity scale, IFH(h), with a variable hydrogen bond parameter (h) that permits one to consider explicitly hydrogen bonding in transbilayer helix searches.

Amino Acids↗