RFLP-based phylogenetic analysis of wide compatibility varieties in Oryza sativa L

Twenty-one wide compatibility varieties (WCVs) of rice together with three indica and three japonica testers were assayed with 160 DNA probes that were selected to represent the entire RFLP map at an average interval of 11 cM. On the basis of four enzyme digestion 125 probes detected polymorphisms among the WCVs and subspecies' testers. Among these polymorphic probes there were 68 that could distinguish the indica from the japonica testers. Two dendrograms were constructed on the basis of 398 polymorphic fragments of 125 probes and 139 polymorphic fragments of 68 subspecies' differentiating probes in combination with single enzymes, respectively. The reliability and representativeness of the testers and the levels of DNA variations among WCVs were estimated. The potential of WCVs in the utilization of intersubspecific heterosis is discussed.

Inactivation of the Streptococcus mutans wall-associated protein A gene (wapA) results in a decrease in sucrose-dependent adherence and aggregation

A 0.8-kb HindIII-BamHI internal fragment of the Streptococcus mutans wall-associated protein A gene (wapA) was ligated to the 5.1-kb HindIII-BamHI fragment of the chimeric Streptococcus-Escherichia coli plasmid pVA891 (Emr Cmr). The resulting construct was used to transform S. mutans GS-5, and erythromycin-resistant mutants were isolated and analyzed. Directed mutagenesis of the wapA gene by plasmid insertion through homologous recombination was demonstrated by Southern blot hybridization with the wapA and pVA891 probes. Stable mutants were obtained, and the alteration of the wapA gene by insertional inactivation was associated with a significant decrease in S. mutans sucrose-dependent aggregation and binding to smooth surfaces. Thus, WapA may play an important role in the colonization of the tooth surface by S. mutans and in the buildup of dental plaque. These findings provided an explanation for previous studies which indicated that WapA was effective in the prevention of dental caries in animal models. Thus, the use of recombinant WapA in the preparation of a safe and effective human dental vaccine should be investigated further.

Single-residue substitution in homopolypeptides: perturbative helix-coil theory at a single site

Based on Lifson-Roig's helix-coil transition theory, substitution of a single heteroresidue into a homopolymer host is studied. This study models recent experiments that substitute a single amino acid into a small peptide in water [A. Chakrabartty, J. A. Schellman, and R. L. Baldwin (1991), Nature, Vol. 351, pp. 586-688]. Our formalism, which is based on a perturbation method, differs from the existing theory for sequenced polymers and is naturally analogous, hence likely to be useful, to substitution experiments in the laboratory. It is shown that the intrinsic helix propensity w is directly proportional to the equilibrium constant for the helix-coil equilibrium of a single residue in a host peptide. This intuitive new result will simplify experimental data interpretations for measurements of the helical conformation on the single amino acid level. It is also shown that substitution affects the total helicity of the host peptide according to two considerations: the helicity of the replaced residue prior to the substitution, and the sensitivity of the site, a measure of neighboring interactions. The relationship between substitution stability and thermal stability is explored.

The energetics of ion-pair and hydrogen-bonding interactions in a helical peptide

A single pair of Glu and Lys residues has been placed at four different spacings, and in both orientations, in an otherwise neutral alanine-glutamine peptide helix, and the contribution to helix stability of the different Glu-Lys interactions has been measured. The contribution from the interaction of each charged side chain with the helix macrodipole has also been determined. A side-chain interaction between Gln and Glu, when the spacing is (i,i+4), has been detected and quantified. The interactions have been divided into contributions from hydrogen bonds (independent of the concentration of NaCl) and from electrostatic interactions (present in 10 mM NaCl, absent in 2.5 M NaCl). The major results are as follows: (1) The (i,i+3) and (i,i+4) Glu-Lys interactions are helix-stabilizing and are similar in strength to each other, regardless of the orientation of the side chains. (2) Hydrogen bonds provide the major contribution to these side-chain interactions, as shown by the following facts. First, the major part of the interaction observed in 10 mM NaCl, pH 7, is still present in 2.5 M NaCl. Second, the interaction found at pH 2 is equally as strong as that found in 2.5 M NaCl at pH 7. (3) The (i,i+4) Gln-Glu side-chain hydrogen bond is as strong as the hydrogen-bond component of the Glu-Lys interaction at both pH 2 and pH 7. The Gln-Glu interaction differs from the Glu-Lys interaction in being specific both for the orientation and the spacing of the residues. (4) No significant hydrogen-bonding interaction was found for the (i,i+1) or (i, i+2) Glu-Lys spacings, either at pH 2 or at pH 7, in 2.5 M NaCl. At 10 mM NaCl and pH 7, these spacings show a helix-destabilizing electrostatic interaction which probably results from stabilization of the coil conformation.

Evidence for hemi-gap junctional channels in isolated horizontal cells of the skate retina

Prolonged depolarization of isolated, voltage-clamped skate retinal horizontal cells produces an outward current that exhibit a late onset and develops slowly with time. This current, which we refer to as the Q-current, is associated with an increase in membrane conductance, and is present when other voltage-gated conductances have been pharmacologically blocked. The reversal potential for the Q-current, obtained using tail current analysis, was close to 0 mV. The magnitude of the current was greatly reduced by superfusion with 25 mM acetate, and by 4 mM cobalt chloride, 2 mM 1-octanol, and a saturated solution of the general anesthetic halothane. In addition, the low-molecular weight fluorescent dye Lucifer yellow, applied extracellularly, entered the cells during activation of the Q-current, whereas a 3 kD dextran-fluorescein complex did not cross the cell membrane. The effects of divalent cations, the non-specific nature of the ionic current suggested by its reversal potential, the entry of Lucifer yellow, and the ability of acetate, halothane, cobalt, and octanol to block the current lead us to hypothesize that the Q-current results from the opening of hemi-gap junctional channels that mediate electrical coupling between skate horizontal cells.

The effects of lowered extracellular sodium on gamma-aminobutyric acid (GABA)-induced currents of Muller (glial) cells of the skate retina

1. The effects of external sodium on GABA-induced chloride currents were examined with whole-cell voltage-clamp recordings obtained from enzymatically dissociated solitary Muller cells in culture. Our goal was to determine whether a sodium-dependent GABA uptake mechanism influences the GABAa-mediated responses of skate Muller cells. 2. At low concentrations of GABA (0.01 to 0.5 microM), removal of sodium from the external solution resulted in a marked increase in the ligand-gated currents mediated by activation of GABAa receptors. The enhancement by lowered sodium was greatest at hyperpolarizing potentials and decreased progressively as the cell was depolarized. 3. The reversal potential for the GABA-induced response was not significantly altered by the removal of sodium, suggesting that sodium ions did not directly contribute to the GABAa-mediated current. 4. Lowering external sodium had no effect on the currents induced by the GABAa-agonist muscimol, consistent with its much lower affinity for the GABA transport carrier. 5. Application of the GABA uptake blocker nipecotic acid also abolished the effects of lowered sodium. 6. These findings suggest that the effects of lowered external sodium resulted from a decrease in the uptake of GABA into the Muller cells, thus raising the effective concentration of GABA acting upon the GABAa receptors.

Gap-junctional properties of electrically coupled skate horizontal cells in culture

Whole-cell voltage-clamp recordings were used to examine the unusual pharmacological properties of the electrical coupling between rod-driven horizontal cells in skate retina as revealed previously by receptive-field measurements (Qian & Ripps, 1992). The junctional resistance was measured in electrically coupled cell pairs that had been enzymatically isolated and maintained in culture; the typical value was about 19.92 M omega (n = 45), more than an order of magnitude lower than the nonjunctional membrane resistance. These data and the intercellular spread of the fluorescent dye Lucifer Yellow provide a good indication that skate horizontal cells are well coupled. The junctional conductance between cells was not modulated by the neurotransmitters dopamine (200 microM) or GABA (1 mM), nor was it affected by the membrane-permeable analogues of cAMP or cGMP, or the adenylate cyclase activator, forskolin. Although resistant to agents that have been reported to alter horizontal-cell coupling in cone-driven horizontal cells, the junctional conductance between paired horizontal cells of skate was greatly reduced by the application of 20 mM acetate, which is known to effectively reduce intracellular pH. Together with the results obtained in situ on the receptive-field properties of skate horizontal cells, these findings indicate that the gap-junctional properties of rod-driven horizontal cells of the skate are fundamentally different from those of cone-driven horizontal cells in other species. This raises the possibility that there is more than one class of electrical synapse on vertebrate horizontal cells.

Novel GABA responses from rod-driven retinal horizontal cells

gamma-Aminobutyric acid (GABA) is the main inhibitory neurotransmitter in the central nervous system. Two classes of GABA receptors (GABAA and GABAB) have been identified. GABAA receptors are ligand-gated chloride channels that are competitively antagonized by bicuculline, noncompetitively blocked by picrotoxin, and often allosterically modulated by barbiturates and benzodiazepines. GABAB receptors regulate potassium and calcium channels through G-protein and intracellular second-messenger pathways, are selectively activated by baclofen, and are antagonized by phaclofen and 2-hydroxysaclofen. For some years, evidence has accumulated that there are GABA receptors, especially prominent along visual pathways, which are neither antagonized by bicuculline nor activated by baclofen, but are activated by certain conformationally restricted analogues of GABA, including cis-4-aminocrotonic acid (CACA). These receptors have been designated GABAC receptors. As yet, membrane current responses from isolated neurons that reflect this novel pharmacology have not been reported, although such responses have been recorded from oocytes injected with retinal messenger RNA. Here we describe a chloride-mediated current response from isolated rod-driven horizontal cells (H4) of the white perch retina that has this novel pharmacology.

Receptive field properties of rod-driven horizontal cells in the skate retina

The large receptive fields of retinal horizontal cells result primarily from extensive intercellular coupling via gap (electrical) junctions; thus, the extent of the receptive field provides an index of the degree to which the cells are electrically coupled. For rod-driven horizontal cells in the dark-adapted skate retina, a space constant of 1.18 +/- 0.15 mm (SD) was obtained from measurements with a moving slit stimulus, and a comparable value (1.43 +/- 0.55 mm) was obtained with variation in spot diameter. These values, and the extensive spread of a fluorescent dye (Lucifer Yellow) from the site of injection to neighboring cells, indicate that the horizontal cells of the all-rod retina of skate are well coupled electrically. Neither the receptive field properties nor the gap-junctional features of skate horizontal cells were influenced by the adaptive state of the retina: (a) the receptive field organization was unaffected by light adaptation, (b) similar dye coupling was seen in both dark- and light-adapted retinae, and (c) no significant differences were found in the gap-junctional particle densities measured in dark- and light-adapted retinas, i.e., 3,184 +/- 286/microns 2 (n = 8) and 3,073 +/- 494/microns 2 (n = 11), respectively. Moreover, the receptive fields of skate horizontal cells were not altered by either dopamine, glycine, GABA, or the GABAA receptor antagonists bicuculline and picrotoxin. We conclude that the rod-driven horizontal cells of the skate retina are tightly coupled to one another, and that the coupling is not affected by photic and pharmacological conditions that are known to modulate intercellular coupling between cone-driven horizontal cells in other species.

Clinical evaluation of radioimmunoimaging with 131I-C0C183B2 monoclonal antibody against ovarian carcinoma by intraperitoneal injection

Forty-eight cases subjected to radioimmunoimaging (RII) by intraperitoneal injection with 131I-C0C183B2 monoclonal antibody (MAb) prepared in our laboratory were studied. Thirteen of 14 cases of proved primary ovarian carcinoma were positive. In 11 follow-up cases of ovarian carcinoma after initial surgery and chemotherapy, 5 recurrences were positive and 6 cases without recurrence were negative; all were confirmed histopathologically after a second operation. One false negative was ovarian mucinous adenocarcinoma, which also negatively stained with C0C183B2 by the peroxidase anti-peroxidase method. Twenty of 23 cases of nonepithelial or metastatic carcinoma of the ovary, benign tumors, and benign diseases were negative. The sensitivity and specificity were 94.7 and 89.7%, respectively. If patients had complications with ascites, the MAb which positively stained with the cancer cells in the ascites was chosen for RII. For follow-up cases PAP staining with the tumor tissue from the initial surgery and the MAb should be done before RII. These are the principal factors that increase the positive rate and accuracy of RII. The intraperitoneal route seems to be a valuable method for clinical staging and tumor localization as well as for follow-up use.

Studies on the structure of actin gels using time correlation spectroscopy of fluorescent beads

Fluorescence correlation spectroscopy (FCS) has been used to measure the diffusion of fluorescently labeled beads in solutions of polymerized actin or buffer. The results, obtained at actin concentrations of 1 mg/ml, show that small beads (0.09 micron in diameter) diffuse nearly as rapidly in the actin gel as in buffer, whereas the largest beads tested (0.5 micron in diameter) are immobilized. Measured autocorrelation times for motions of beads with intermediate sizes show that the diffusion is retarded (relative to buffer) and that the time behavior cannot be represented as a single diffusive process. In addition to the retarded diffusion observed over distances > 1 micron, 0.23-micron beads also show a faster motion over smaller distances. Based on the measured rate of this faster motion, we estimate that the beads may be constrained within a cage approximately 0.67 micron on a side, equal to a filament length of approximately 250 subunits. Fluorescence correlation spectroscopy measurements made in the same small spot (radius of 1.4 microns) of the gel vary over time. From the variations of both the autocorrelation functions and the mean fluorescence, we conclude that, corresponding to a spatial scale of 1.4 microns, the actin gel is a dynamic structure with slow rearrangement of the gel occurring over periods of 20-50 s at 21-22 degrees C. This rearrangement may result from local reorganization of the actin matrix. Data for the retardation of beads by the actin gel are consistent with a detailed theory of the diffusion of particles through solutions of rigid rods that have longitudinal diffusion coefficients much less than that of the particles (Ogston, A. G., B. N. Preston, and J. D. Wells. 1973. Proc. R. Soc. Lond. A. 333:297-316).

Parameters of helix-coil transition theory for alanine-based peptides of varying chain lengths in water

Thermal unfolding curves have been measured for a series of short alanine-based peptides that contain repeating sequences and varying chain lengths. Standard helix-coil theory successfully fits the observed transition curves, even for these short peptides. The results provide values for sigma, the helix nucleation constant, delta H0, the enthalpy change on helix formation, and for s (0 degree C), the average helix propagation parameter at 0 degree C. The enthalpy change agrees with the value determined calorimetrically. The success of helix-coil theory in describing the unfolding transitions of short peptides in water indicates that helical propensities, or s values, can be determined from substitution experiments in short alanine-based peptides.

Single particle tracking. Analysis of diffusion and flow in two-dimensional systems

Analysis of the trajectories of small particles at high spatial and temporal resolution using video enhanced contrast microscopy provides a powerful approach to characterizing the mechanisms of particle motion in living cells and in other systems. We present here the theoretical basis for the analysis of these trajectories for particles undergoing random diffusion and/or systematic transport at uniform velocity in two-dimensional systems. The single particle tracking method, based on observations of the trajectories of individual particles, is compared with methods that characterize the motions of a large collection of particles such as fluorescence photobleaching recovery. Determination of diffusion coefficients or transport velocities either from correlation of positions or of velocities of the particles is discussed. A result of practical importance is an analysis of the dependence of the expected statistical uncertainty of these determinations on the number of position measurements. This provides a way of judging the accuracy of the diffusion coefficients and transport velocities obtained using this approach.

Analysis of confocal laser-microscope optics for 3-D fluorescence correlation spectroscopy

Quantitative fluorescence correlation spectroscopy (FCS) and fluorescence photobleaching recovery (FPR) measurements in bulk solution require a well characterized confocal laser microscope optical system. The introduction of a characteristic function, the collection efficiency function (CEF), provides a quantitative theoretical analysis of this system, which yields an interpretation of the FCS and FPR measurements in three dimensions. We demonstrate that when the proper field diaphragm is introduced, the 3-D FCS measurements can be mimicked by a 2-D theory with only minor error. The FPR characteristic recovery time for diffusion is expected to be slightly longer than the corresponding time measured by FCS in the same conditions. This is because the profile of the laser beam used for photobleaching is not affected by the field diaphragm. The CEF is also important for quantitative analysis of standard scanning confocal microscopy when it is carried out using a finite detection pinhole.

[A clinical and pathological study of 24 cases of primary non-Hodgkin's lymphoma of the orbit]

Primary non-Hodgkin's lymphoma of the orbit predominantly consists of the small lymphocytic, the lympho-plasmacytic, and the schistocytic types. Because of fair cellular differentiation, the tumor shows low or medium atypia as if benign. Hence, differential diagnosis from inflammation pseudotumor or lymphocytic hyperplasia is important. Follow-up of 18 of the present 24 cases showed that the tumor usually began insidiously and was long confined to the orbit. 44% (8/18) of the patients had relapses and 22% (4/18) died of systemic dissemination 2-6 years after confirmed diagnosis, a finding in agreement with Kinyh et al, who reported a 5 year survival rate of 75% and a 8 year survival rate of 50%. The prognosis was better than that of intranodal or extranodal non-Hodgkin's lymphoma in other locations.

On the statistics of fluorescence correlation spectroscopy

I present a detailed statistical analysis of fluorescence correlation spectroscopy (FCS) which is a natural extension of an early work. This analysis more realistically takes account of the following issues. (1) A spatial Gaussian laser excitation of fluorescence, (2) the effect of a small number of fluorescent molecules in the observation volume, (3) the shot noise effect due to random emission of fluorescent photons, and (4) a hyperbolic form for the fluorescence autocorrelation function obtained in the case of diffusion. Based on these assumptions, the results differ from the earlier work in several respects, in particular, the dependence of the signal-to-noise ratio on sample concentration and the understanding of shot noise in fluorescence fluctuation moments.

Distribution of molecular aggregation by analysis of fluctuation moments

The fluorescence from an open volume of a solution of fluorescent molecules fluctuates as the molecules randomly diffuse into and out of the volume. The distribution of degrees of aggregation or polymerization of the fluorescent molecules can be characterized without perturbing the system by measuring either the moments or the amplitude distribution of these fluctuations. We present an experimental verification of this approach applied to simple model systems consisting of solutions of fluorescent particles of well-defined size. We have also characterized the response of the photon-detection device (typically a photomultiplier), which is essential to the analysis of the fluorescence fluctuations, and have compared two methods for determining shot-noise contributions.

On the analysis of high order moments of fluorescence fluctuations

A simple, straightforward analysis to characterize the distribution of aggregate sizes in a reversible aggregation system at equilibrium is presented. The method, an extension of fluorescence correlation spectroscopy (FCS), is based on measurements of higher order moments of spontaneous fluctuations of fluorescence intensity emitted from a defined open region of the sample. These fluctuations indicate fluctuations of the numbers of the fluorescent molecules in the observation region. Shot noise resulting from the random character of fluorescence emission and from the photoelectric detection system is modeled as a Poisson distribution and is subtracted from the measured photon count fluctuation moments to yield the desired fluorescence fluctuation moments. This analysis can also be used to estimate the fraction of immobile fluorophores in FCS measurements.

Nanometre-level analysis demonstrates that lipid flow does not drive membrane glycoprotein movements

Nanometre-level analyses of the movements of membrane glycoproteins tagged with gold particles demonstrate that diffusing particles are not under the influence of a lipid flow, although a subset of particles which appear attached to the cytoskeleton are moving rearward.

[Pathologic analysis of lobular carcinoma of the breast--report of 36 cases]

Thirty-six cases of lobular carcinoma of the breast are reported. It comprised 11% of all the breast carcinomas. All patients were female. There were 6 cases of lobular carcinoma in situ (LCIS) with a mean age of 42 years and 30 cases of infiltrating lobular carcinoma (ILC) with a mean age of 51 years. LCIS was small, millet-size lesion which was usually accompanied with fibrocystic disease of the breast and often accidentally observed by pathologic examination. LCIS was prone to multicentricity, bilateral involvement and developing into ILC. Histologically, LCIS was characterized by intralobular proliferation of the cells lining the acini. The lumen became packed with these cells and progressively disappeared as the lobule became more and more distended. Pleomorphism of the cells was usually minimal. Necrosis was absent and mitosis was extremely rare. When the basement membrane of the acini was destroyed, two types of invasion were observed: first, the cells invaded into the stroma between the acini within the same lobule-so called LCIS with invasion, then the cells spread out of the boundary of the involved lobule and presented as threadlike strands or small nests infiltrated in a dense fibrous matrix. Sometimes the cells formed concentric rings around an apparently dilated duct. It should be pointed out that the mistakes made by pathologists in practics are overlooking LCIS and misinterpreting ILC.(ABSTRACT TRUNCATED AT 250 WORDS)

Cell poking: quantitative analysis of indentation of thick viscoelastic layers

A recently introduced device, the cell poker, measures the force required to indent the exposed surface of a cell adherent to a rigid substratum. The cell poker has provided phenomenological information about the viscoelastic properties of several different types of cells, about mechanical changes triggered by external stimuli, and about the role of the cytoskeleton in these mechanical functions. Except in special cases, however, it has not been possible to extract quantitative estimates of viscosity and elasticity moduli from cell poker measurements. This paper presents cell poker measurements of well characterized viscoelastic polymeric materials, polydimethylsiloxanes of different degrees of polymerization, in a simple shape, a flat, thick layer, which for our purposes can be treated as a half space. Analysis of the measurements in terms of a linear viscoelasticity theory yields viscosity values for three polymer samples in agreement with those determined by measurements on a macroscopic scale. Theoretical analysis further indicates that the measured limiting static elasticity of the layers may result from the tension generated at the interface between the polymer and water. This work demonstrates the possibility of obtaining quantitative viscoelastic material properties from cell poker measurements and represents the first step in extending these quantitative studies to more complicated structures including cells.

Interpretation of fluorescence correlation spectroscopy and photobleaching recovery in terms of molecular interactions

The theoretical basis and experimental implementation of FCS and FPR measurements are now well established. Because of the requirements for system stability and long data acquisition times FCS is relatively rarely used. But FCS can provide unique information, especially about extents of aggregation or polymerization and therefore is a useful supplement to FPR for certain applications. FPR measurements are now carried out routinely in many laboratories in a variety of formats using different beam profiles, optical systems, and analytical schemes. A particular version may be better adapted to a specific application. The spot photobleaching approach, however, seems simplest and most versatile for cellular studies and is now most often used. Important experimental considerations in setting up a spot photobleaching instrument are discussed in detail in Chapter 10 by Wolf (this volume) and elsewhere (Petersen et al., 1986a). In interpreting FPR measurements it is also important to take into account the possibility of systematic errors from a number of sources. In Chapter 10 in this volume, Wolf discusses many factors that must be properly controlled in carrying out FPR measurements. Additional consideration of some of these points is presented by Petersen et al. (1986a). One potentially troublesome type of error arises from the possibility that chemical reactions initiated by the photobleaching pulse or during the measurement of recovery could significantly perturb the system. Evidence from a variety of sources [summarized, for example, in Petersen et al. (1986a)] indicates that photobleaching fluorophores can induce chemical cross-linking of cellular proteins under some conditions. But measurements in a number of different systems have demonstrated that, even if these types of reactions occur in FPR measurements, nevertheless they do not perturb the measured mobilities. If possible, however, this point should be checked for each new system because variations in structure or environmental conditions could enhance the chemical cross-linking reactions mediated by photogenerated free radicals. In practice, the principal difficulty in carrying out FPR measurements on cells is frequently the low intensity of the fluorescent signal which can be obtained from specifically labeled cell surface ligands or microinjected components. This low intensity results from the typically low capacity of an individual cell for the specifically labeled macromolecule. Even in the absence of systematic errors, low emission intensity will reduce the accuracy of measurements due to shot noise. This is an important practical limitation on measuring accuracy. Low measurement accuracy severely limits the extent to which the data can be interpreted mechanistically. Precision can be improved by averaging many recovery experiments.(ABSTRACT TRUNCATED AT 400 WORDS)