Biomedical subjects

W R Bauer

Publications and source records attributed to W R Bauer.

At least 55 records · Page 3Linked to original sources

PubMed1994

Effects of postnatal blockade of cortical activity with tetrodotoxin upon the development and plasticity of vibrissa-related patterns in the somatosensory cortex of hamsters.

Several previous studies have shown that postnatal blockade of thalamocortical activity with either tetrodotoxin (TTX) or the N-methyl-D-aspartate (NMDA) receptor antagonist D,L-2-amino-5-phosphonovalerate (APV) does not prevent the formation of vibrissa-related patterns in the primary somatosensory cortex of rats. One limitation of these studies is that this pattern forms very shortly after birth in rats, and there may be only a very limited time over which it may be influenced by activity blockade. In the present study, the effect of activity blockade was evaluated in a more altricial rodent, the hamster. The present study showed that a pattern of thalamocortical afferents corresponding to the vibrissae is not observed until the fourth postnatal day in hamsters. Nevertheless, application of TTX-impregnated implants to the cortices of newborn hamsters had no qualitative or quantitative effect upon vibrissa-related patterns in the primary somatosensory cortices of these animals. Moreover, TTX implants did not prevent the changes in patterns that followed cauterization of a row of vibrissa follicles.

Afferent Pathways↗

PubMed1993

The free energy, enthalpy and entropy of native and of partially denatured closed circular DNA.

We have used gel electrophoresis to measure the progress of local denaturation in closed circular pBR322 DNA as a function of temperature and linking deficiency, delta Lk. Local denaturation is closely coupled to supercoiling in closed DNA, requiring statistical mechanical methods for analysis. We have applied these methods to the experimental data to evaluate the free energies for three associated molecular processes. These processes are changes in the residual linking deficiency, delta Lkr, initiation of local denaturation, and twisting of denatured strands about one another. Our results confirm the quadratic dependence of the supercoiling free energy upon delta Lk, with a free energy coefficient of 740/N kcal/mol at 37 degrees C, where N is the number of base-pairs. The free energy of initiation of denaturation is 10.2(+/- 0.7) kcal/mol. The free energy of interstrand twisting of denatured regions varies with the square of the twist density, with proportionality coefficient C tau = 1.62 (+/- 0.11) kcal/rad2 at 37 degrees C. We have also calculated the entropy and enthalpy of these three processes, using the temperature dependence of the respective free energies. We find that both the entropy and the enthalpy of supercoiling are positive and vary quadratically with delta Lk. The free energy of initiation of denaturation is independent of temperature, hence arises primarily from a change in enthalpy. The entropy and enthalpy of interstrand twisting of denatured regions are both positive, and the twisting force constant decreases with temperature. These results differ considerably from expectations based solely upon considerations of chain configuration in vacuo, indicating the importance of solvent-dependent factors in determining the structure of closed circular DNA.

DNA, Circular↗

PubMed1993

Twist and writhe of a DNA loop containing intrinsic bends.

The finite-element method of solid mechanics is applied to calculation of the three-dimensional structure of closed circular DNA, modeled as an elastic rod subject to large motions. The results predict the minimum elastic energy conformation of a closed loop of DNA as a function of relaxed equilibrium configuration and linking number (Lk). We apply the method to four different starting states: a straight rod, two rods containing either one or two 20 degrees bends, and a circular O-ring. The results, here at low superhelix density, show the changes in writhe (Wr) and in twist (Tw) as Lk is progressively lowered. The presence of even a single intrinsic bend reduces significantly the linking number change at which Wr first appears, compared to an initially straight, bend-free rod. The presence of two in-phase bends, situated at opposite ends of a diameter, leads to the formation of at least two distinct regions of different but relatively uniform Tw increment. The O-ring begins to writhe immediately upon reduction of Lk, and the Tw increment distribution is sinusoidal along the rod. The mechanics calculations, unlike other theoretical approaches, permit us to calculate Tw and Wr independent of the constraint of constant Lk.

DNA↗

PubMed1993

Prenatal development of the receptive fields of individual trigeminal ganglion cells in the rat.

1. Extracellular single-unit recording and receptive-field mapping techniques were used to evaluate the response characteristics of trigeminal (V) ganglion cells in unanesthetized, decerebrate, fetal rats between the ages of embryonic (E-) day 15 and E-20 (E-0 is the day of conception). 2. The receptive-field properties of the cells (n = 282) recorded at all of these ages except E-15 were remarkably similar; V primary afferents were generally silent in the absence of peripheral stimulation (94.3%) and gave rapidly adapting responses to innocuous tactile stimuli (97.5%). Rapid response decrements to repeated stimuli were observed in 9 of the 14 cells (64%) tested. 3. None of the cells recorded were activated by either heat or cold. No attempt was made to evaluate responses to noxious mechanical stimuli. 4. Particular attention was paid to neurons whose receptive fields involved mystacial vibrissae follicles. At all ages, neurons were recorded that responded to indentation of the skin at the base of the vibrissae, but vibrissa deflection was not an adequate stimulus for any of the cells tested. At all ages, nearly all (89.0%) of the 127 cells with vibrissa-related receptive fields responded to indentation of one and only one follicle. 5. These results indicate that the response properties (e.g., adaptation characteristics, ability to respond to repeated stimuli) of V primary afferents in fetal rats differ substantially from those of V ganglion cells in adult animals, but that the receptive-field size for these neurons in prenatal rats is, with very rare exceptions, adult-like from the earliest age at which they can be recorded. 6. These results, when considered together with the results of previous retrograde tracing experiments in fetal animals, suggest that the initial projections of V primary afferents to their peripheral targets may be quite accurate.

Animals↗

PubMed1992

Effects of neonatal transection of the infraorbital nerve upon the structural and functional organization of the ventral posteromedial nucleus in the rat.

The present study examined the way in which an indirect partial deafferentation of the medial portion of the ventrobasal complex (VPM/VPL) induced by neonatal transection of the infraorbital nerve (ION) altered the structural and functional properties of its constituent neurons. This manipulation significantly reduced the volume of the contralateral VPM/VPL. In addition, cell counts in Nissl-stained material revealed a significant reduction of the number of VPM/VPL neurons contralateral to neonatal ION transection. We also analyzed the effect of neonatal ION transection on the soma-dendritic morphology of individual neurons in the ventral posteromedial nucleus of the thalamus (VPM) by intracellular injection of horseradish peroxidase (HRP) in vivo and Lucifer yellow in fixed slices. Neonatal transection of the ION resulted in increased dendritic length, area, and volume of VPM neurons in both preparations; however only the changes observed in fixed slices reached statistical significance. Alterations in the functional characteristics of VPM neurons were also observed following neonatal nerve damage. There was a significant decrease in the percentage of vibrissae-sensitive neurons and a corresponding increase in the percentages of neurons responsive to guard hair deflection or that were unresponsive to peripheral stimulation. Neonatal nerve damage also resulted in significantly longer latencies of VPM cells after stimulation of either trigeminal nucleus principalis or subnucleus interpolaris. The present results indicate that the development of normal response properties and soma-dendritic morphology of VPM neurons is dependent upon intact afferent input during development. Indirect partial deafferentation of VPM/VPL by neonatal transection of the ION results in reduced neuron number, which may result in decreased competition among the dendrites of these neurons. This proposal is consistent with observations of increased dendritic dimensions of VPM neurons contralateral to neonatal ION damage.

Animals↗

PubMed1992

Postnatal blockade of cortical activity by tetrodotoxin does not disrupt the formation of vibrissa-related patterns in the rat's somatosensory cortex.

Neuronal activity has been shown to influence pattern formation in the visual system. In the present study, we determined whether or not this was also true in the somatosensory system by silencing the primary somatosensory cortex of rats with tetrodotoxin (TTX) for the first 7-11 days of life. Application of TTX during this period did not prevent the formation of the normal vibrissa-related pattern in S-I as visualized by either staining cortical sections for cytochrome oxidase, demonstration of the pattern with an antibody directed against serotonin, or labelling of thalamocortical axons with the carbocyanine dye, Di-I. These results indicate that neither peripherally evoked nor spontaneous activity are required for qualitatively normal pattern formation in the rat's primary somatosensory cortex.

Animals↗

PubMed1992

Torsional rigidity of positively and negatively supercoiled DNA.

Time-correlated single-photon counting of intercalated ethidium bromide was used to measure the torsion constants of positively supercoiled, relaxed, and negatively supercoiled pBR322 DNA, which range in superhelix density from +0.042 to -0.123. DNA behaves as coupled, nonlinear torsional pendulums under superhelical stress, and the anharmonic term in the Hamiltonian is approximately 15 percent for root-mean-square fluctuations in twist at room temperature. At the level of secondary structure, positively supercoiled DNA is significantly more flexible than negatively supercoiled DNA. These results exclude certain models that account for differential binding affinity of proteins to positively and negatively supercoiled DNA.

DNA, Superhelical↗

PubMed1992

Theory of contrast agents in magnetic resonance imaging: coupling of spin relaxation and transport.

The role of diffusive transport on the enhancement of nuclear spin relaxation through NMR contrast agents is described by means of diffusion-Bloch equations. These equations are solved in the mean relaxation time approximation [W. Nadler and K. Schulten, J. Chem. Phys. 82, 151-160 (1985)]. A model presented considers relaxation enhancement in tissue in which contrast agents confined to intravascular spaces affect nuclear spin in the extravascular volume. We show how the mean relaxation time depends on capillary density, on permeability, and on diffusion. A second model describes enhanced phase relaxation of liver tissue in the presence of magnetic particles in Kupffer cells. The relationship between relaxation rate and density of Kupffer cells is investigated. The diagnostic value of enhanced nuclear relaxation in the presence of contrast agents is discussed on the basis of the systematic mathematical results obtained.

Contrast Media↗

PubMed1992

Direct measurement of spin-lattice relaxation times of phosphorus metabolites in human myocardium.

T1 values of phosphorus metabolites visible in human cardiac 31P-MR spectra were determined in 12 volunteers at 1.5 T. Consecutive spectra were acquired with varying pulse repetition time (TR) from 1.6 to 24 s; volume selection was achieved with ISIS. T1's of creatine phosphate (CP), [gamma-P], [alpha-P], and [beta-P]ATP, 2-3 diphosphoglycerate, and phosphodiesters were 6.1 +/- 0.5, 5.4 +/- 0.5, 5.5 +/- 0.5, 5.8 +/- 1.0, 7.6 +/- 1.0, and 5.0 +/- 1.0 s, respectively. CP/ATP ratios showed little change with varying TR; linear regression of CP/ATP vs TR was of borderline significance (r = 0.28, P = 0.06). T1's for CP and ATP were also determined in standard solution (20 mM CP, 10 mM ATP) yielding T1CP of 8.7 +/- 0.2 and T1[gamma-P]-ATP of 9.9 +/- 0.7 s. Thus, T1's for CP and ATP were similar at 1.5 T in both human heart and standard solution. In human cardiac 31P-MR spectra, CP/ATP ratios may need little correction for partial saturation.

2,3-Diphosphoglycerate↗

PubMed1992

Closed circular DNA as a probe for protein-induced structural changes.

Biological systems are replete with examples of DNA formed into a closed loop structure, either alone or in close association with proteins. Such closed circular DNA molecules are subject to a topological constraint that modifies, often in a major way, the structure and reactivity of the DNA. The topological constraint also permits closed circular DNAs to be used as analytical tools to learn about the structure of DNA-protein complexes.

DNA Probes↗

PubMed1989

Dependence of the linking deficiency of supercoiled minichromosomes upon nucleosome distortion.

The contribution from each nucleosome to the linking number of minichrosome DNA depends on two factors. These are the wrapping number, omega, which is the number of times the DNA wraps about the axis of the nucleosome; and the winding number, phi, which is the number of base pairs on the nucleosome divided by the helical repeat of the DNA. If the nucleosome is distorted with DNA surface contacts being preserved, phi remains unchanged. The wrapping number may still change, however, depending on the extent of the distortion. For example, if the usual cylindrical shape of the nucleosome is deformed into an ellipsoid while preserving the equatorial radius, then the wrapping number will increase. We apply these concepts to minichromosomes torsionally stressed by supercoiling with, for example, DNA gyrase. We analyze the experimental result that the maximum amount of supercoiling obtained by gyrase treatment of minichromosomes is the same as that of naked DNA. In particular, we show that this phenomenon can be explained by a relatively slight distortion of the nucleosome core while maintaining the surface contacts of the DNA on the core.

Chromosomes↗

PubMed1989

Effect of nucleosome distortion on the linking deficiency in relaxed minichromosomes.

The wrapping of closed circular DNA on a protein surface, followed by relaxation with a topoisomerase and removal of proteins, produces a characteristic DNA linking deficiency, delta Lk. We show that the magnitude of delta Lk depends upon the surface shape, and we calculate changes in delta Lk caused by particular distortions of the protein wrapping surface. If the DNA remains attached to the surface during distortion, the DNA winding number, phi, is not altered. The change in delta Lk is then equal to the change in the surface linking number, SLk, which is a straightforward measure of the wrapping of the DNA around the surface. For left-handed wrapping, as in a nucleosome, SLk = -n, the number of times that the DNA axis winds around the axis of the protein complex. We calculate values of SLk for the helical wrapping of a constant length of DNA on protein surfaces having the shapes of cylinders and of ellipsoids and hyperboloids of revolution. If the equatorial radius of the protein is fixed, change in shape from a cylinder to a hyperboloid increases SLk, while the corresponding change to an ellipsoid reduces SLk. We apply the general results to the interpretation of experiments in which minichromosomes are relaxed with topoisomerase at various temperatures and delta Lk is determined. The result is that a distortion of the nucleosome core by at most 5% (the change in the radius at the axial extremity relative to the equator) is sufficient to explain the observed delta Lk changes.

Animals↗

PubMed1989

Activation of the vaccinia virus nicking-joining enzyme by trypsinization.

The vaccinia virus nicking-joining (NJ) enzyme has been purified to homogeneity from a preparation of virus cores. The virus-specific DNA-dependent enzyme, which does not require ATP, is a single polypeptide of Mr 50,000 and possesses both endonuclease and ligase activities. The principal end product of the enzyme activity, following incubation with closed circular DNA of sufficient linking deficiency, is a linear DNA in which one of the termini has become cross-linked by the in vitro formation of a hairpin. The ability of the NJ enzyme to cross-link DNA is significantly enhanced by in vitro proteolysis. The enzymatic properties of the proteolytic digestion product, a 44-kDa polypeptide, differ in several other ways from the intact NJ enzyme. In particular, the specific activity is enhanced and the ionic strength optimum is shifted toward higher salt concentrations. It is suggested that the purified 50-kDa species is a pronuclease that is activated by proteolytic processing.

Chromatography, Affinity↗

PubMed1988

Helical repeat and linking number of surface-wrapped DNA.

The geometric properties of duplex DNA are systematically altered when the DNA is wrapped on a protein surface. The linking number of surface-wrapped closed circular DNA is the sum of two integers: the winding number, phi, a function of the helical repeat; and the surface linking number, SLk, a newly defined geometric constant that accounts for the effects of surface geometry on the twist and writhe of DNA. Changes in the helical repeat, h, and in the winding number can be deduced solely from surface geometry and superhelix density, sigma. This treatment relates the theoretically important properties twist and writhe to the more experimentally accessible quantities phi, h, SLk, and sigma. The analysis is applied to three biologically important cases: interwinding of DNA in a plectonemic superhelix, catenated DNA, and minichromosomes.

Chromosomes↗

PubMed1988

Applications of the twist difference to DNA structural analysis.

The twist is a fundamental geometric property of nucleic acids. Calculation of the twist in the most general case requires detailed specification of the three-dimensional path of each strand, but many important cases may be analyzed by considering only the twist difference. If C1, C2, and C3 are three distinct space curves, the twist difference about C1 is defined as Tw(C3, C1) - Tw(C2, C1). We show here that this difference measures the rotation of the correspondence surface joining C1 to C2 about the correspondence surface joining C1 to C3. This result has application to DNA containing local nonuniformities, such as denatured regions, cruciforms, and other altered structures. It also facilitates the calculation of twist for three-stranded structures, including D-loops in mitochondrial DNA and replication and transcription intermediates. The twist difference may also be used to simplify greatly the analysis of twist changes in duplex DNA due to winding on surfaces, such as histones and certain enzymes. In such cases the strand-axis twist of DNA divides into two independent terms. The first term arises from the twist of the local reference frame, and the second arises from the rotation of either strand about the duplex axis as measured in the local reference frame. Twist changes consequent to nucleosome winding, for example, arise from the twist of the nucleosome axis, a straight line, about the DNA axis plus the rotation of either strand of the DNA about its axis in the reference frame of the cylinder.

DNA, Superhelical↗

PubMed1988

Purification and characterization of vaccinia virus structural protein VP8.

A major vaccinia virus core protein, designated VP8, has been purified from virions to homogeneity through DEAE-cellulose, CM-cellulose, and hydroxyapatite chromatography. VP8 migrates as a 25-kDa band in SDS-polyacrylamide gel electrophoresis and sediments as a monomeric species in neutral sucrose gradient centrifugation. This protein is a significant constitutent of the virion, comprising about 6.5% of the total viral polypeptides by mass. Analysis by filter binding and by sucrose gradient centrifugation shows that VP8 binds to double-stranded as well as to single-stranded DNA at low salt concentrations (25 mM NaCl). At higher salt concentrations (100 mM NaCl), the protein binds with a relatively greater affinity to single-stranded DNA. The results from sucrose gradient centrifugation indicate that VP8 probably binds noncooperatively to all structural forms of DNA. The protein is likely to be a component of the viral nucleoprotein complex.

Binding, Competitive↗

PubMed1988

Biosynthesis and post-translational cleavage of vaccinia virus structural protein VP8.

We have obtained antiserum against highly purified vaccinia virus structural protein VP8, a major DNA binding protein present in the viral core particle. The antiserum has been used to monitor the course of the biosynthesis of this protein. The protein can first be detected in extracts of infected cells at 4 hr postinfection (p.i.). Its synthesis increases significantly at 5 hr p.i. and is maintained at about the same level up to 11 hr. The requirement of viral DNA replication for VP8 synthesis indicates that it is a viral late protein. This protein is synthesized in the form of a 28-kDa precursor, which is then processed to a 25-kDa product. The half-life of the precursor is about 2 hr. Comparing the N-terminal amino acid sequence of this purified protein with those derived from the published DNA sequence of the vaccinia viral genome [J.P. Weir and B. Moss (1984) J. Virol. 51, 662-669], it is found that VP8 maps to the HindIII L fragment of the viral genome. The cleavage site at which processing takes place lies between amino acids 32 (Gly) and 33 (Ala) from the N-terminal end of the precursor.

Amino Acid Sequence↗

PubMed1987

Superhelical DNA with local substructures. A generalization of the topological constraint in terms of the intersection number and the ladder-like correspondence surface.

The presence of certain local structural elements in superhelical DNA, such as cruciforms and denatured loops, complicates the topological and geometric analysis of these molecules. In particular, the duplex axis is often difficult to define. In consequence, the usual conservation condition, Lk = Tw + Wr, is often inapplicable as formulated in terms of the winding of either strand of the DNA about the duplex axis. We present here a more general formulation of the topological conservation condition in terms of a model in which the two strands of DNA are regarded as twisting about one another, and in which one of the two strands is considered to writhe. We define a ladder-like correspondence surface, which connects the two strands nd is independent of whether or not a unique duplex axis is locally available. These considerations lead to the definition of a new topological property of superhelical DNA, the intersection number, In. This quantity describes the complexity of a local structural element; in the case of a cruciform, for example, the intersection number is a measure of the number of duplex turns removed from the major segment of the DNA by the cruciform formation. In more general terms, the topological constraint applicable to closed circular DNA is given by Lk(W,C) + In(S,C) = Tw(W,C) + Wr (C), where W and C represent the two strands of the DNA and S is the ladder-like correspondence surface that connects the two strands.

DNA, Superhelical↗