Fluorescence quenching: A tool for single-molecule protein-folding study

By using titin as a model system, we have demonstrated that fluorescence quenching can be used to study protein folding at the single molecule level. The unfolded titin molecules with multiple dye molecules attached are able to fold to the native state. In the native folded state, the fluorescence from dye molecules is quenched due to the close proximity between the dye molecules. Unfolding of the titin leads to a dramatic increase in the fluorescence intensity. Such a change makes the folded and unfolded states of a single titin molecule clearly distinguishable and allows us to measure the folding dynamics of individual titin molecules in real time. We have also shown that fluorescence quenching can signal folding and unfolding of a small protein with only one immunoglobulin domain.

Requirement for presenilin 1 in facilitating lagged 2-mediated endoproteolysis and signaling of notch 1

Presenilin 1 (PS1), a polytopic membrane protein, is required for endoproteolytic processing at gamma-secretase site within the transmembrane domain of amyloid precursor proteins (APP). In addition, PS1 and its orthologues facilitate signaling of Notch family members, cell-surface receptors that specify cell fates during development. To clarify the mechanism(s) by which PS facilitates Notch signaling, we examined human Jagged-2-dependent metabolism and activity of a chimeric full-length Notchl-GFP molecule expressed in fibroblasts with heterozygous, or homozygous deletions of PS1. We demonstrate that PS1 is required for facilitating Jagged 2-mediated proteolysis and that translocation and accumulation of NICD in the nucleus correlates with signaling activity. Moreover, in a ligand-independent, Ca2+-depletion paradigm, we demonstrate that PS1 facilitates endoproteolysis of a plasma-membrane-associated, Notch1-GFP derivative. Finally, we report that NICD production is inhibited by L-685,458, a potent and selective inhibitor that blocks solubilized gamma-secretase activity and Abeta production in cultured cells. These findings strongly suggest that intramembranous processing of APP and Notch 1 are mediated by similar, if not identical, proteases that require PS1 for their activation.

Stimulation of MCF-7 cell proliferation by low concentrations of Chinese domestic polychlorinated biphenyls

The simple and sensitive in vitro MCF-7 human breast cancer cell proliferation assay was used to examine the proliferation abilities of two Chinese commercial polychlorinated biphenyl (PCB) mixtures made in the 1960s. Chinese PCB3 and Chinese PCB5 were compared with 17 beta-estradiol (E2). All of the positive activities of these types of Chinese PCBs were significantly different compared to controls with respect to MCF-7 cell doubling time. At lower levels of 7.8 pg/ml and 182 pg/ml, the Chinese PCB3 showed 94% and 86% of relative proliferation effects compared to 17 beta-estradiol, respectively. Chinese PCB5, also showed higher cell proliferation activity at lower level of 8.3 pg/ml, with relative proliferation effect as high as 107% in comparison to 17 beta-estradiol. Thus, both PCBs seem to be different from corresponding Aroclor mixtures. However, Chinese PCBs did not express cell proliferation effects at higher levels of 9.1 ng/ml for Chinese PCB3 and 166 pg/ml and 8.3 ng/ml for Chinese PCB3. This may be due to cytotoxicity and/or antiestrogenic compounds in the mixtures.

High resolution feshbach spectroscopy of cesium

We measure high-resolution Feshbach resonance spectra for ultracold cesium atoms colliding in different hyperfine and magnetic sublevels. More than 25 resonances are observed for magnetic fields up to 230 G and their positions are measured with an accuracy down to 0.03 G. From these spectra several ground-state molecular interaction parameters can be extracted with sufficient accuracy to permit for the first time an unambiguous and accurate determination of cesium's ultracold collision properties [P. J. Leo, C. J. Williams, and P. S. Julienne, following Letter, Phys. Rev. Lett. 85, 2721 (2000)].

Analysis of scar tissue distribution on rat palates: a laser Doppler flowmetric study

OBJECTIVE

The aim of this study was to evaluate the effectiveness of laser Doppler flowmetry (LDF) to discriminate postoperative scar tissue distribution on the palate.

METHODS

Nineteen male Wistar rats at the 20th postnatal day were divided into experimental and control groups. In the experimental group, lateral palatal mucoperiosteum was excised to form scar tissue on the palate. At the 11th postnatal week, changes in the palatal blood flow were recorded with LDF in both groups by occluding exposed common carotid arteries. Perfusion values of nonoccluded (stable) and occluded states and the ratio of occluded to stable states were compared for scar tissue and normal tissue areas, and also for the normal tissue areas. After the LDF measurements, India ink-injected specimens and tissue sections were prepared for histological observations.

RESULTS AND CONCLUSIONS

Scar tissue areas showed lower perfusion values both in the stable and occluded states, reflecting a lower vascular density in the scar tissue. The ratio of the occluded to stable states was higher in the scar tissue than in the normal tissue areas. In normal tissue areas, perfusion values of both the stable and occluded states appeared to vary, but the ratio did not vary among the areas. In the LDF study, the ratio of the occluded to stable states was considered to be the better parameter for discriminating scar tissue from normal tissue.

Relating the microscopic and macroscopic response of a polymeric fluid in a shearing flow

The microscopic and macroscopic response of a polymer solution in start-up shear flow was investigated using fluorescence microscopy of single molecules, bulk viscosity measurements, and Brownian dynamics simulations. An overshoot in viscosity was observed upon flow inception and understood via the observed molecular extension and by simulation findings. Increasing the polymer concentration up to six times the overlap concentration ( C(*)) has no effect on the character of the dynamics of individual molecules.

The distribution of cells containing estrogen receptor-alpha (ERalpha) and ERbeta messenger ribonucleic acid in the preoptic area and hypothalamus of the sheep: comparison of males and females

We have used in situ hybridization to compare the distributions of estrogen receptor alpha (ERalpha) and ERbeta messenger RNA (mRNA)-containing cells in the preoptic area and hypothalamus of ewes and rams. Perfusion-fixed brain tissue was collected from luteal phase ewes and intact rams (n = 4) during the breeding season. Matched pairs of sections were hybridized with sheep-specific, 35S-labeled riboprobes, and semiquantitative image analysis was performed on emulsion-dipped slides. A number of sex differences were observed, with females having a greater density of labeled cells than males (P < 0.001) and a greater number of silver grains per cell (P < 0.01) in the ventromedial nucleus for both ER subtypes. In addition, in the retrochiasmatic area, males had a greater (P < 0.05) cell density for ERalpha mRNA-containing cells than females, whereas in the paraventricular nucleus, females had a greater density (P < 0.05) of ERalpha mRNA-containing cells than males. There was a trend (P = 0.068) in the arcuate nucleus for males to have a greater number of silver grains per cell labeled for ERalpha mRNA. In both sexes, there was considerable overlap in the distributions of ERalpha and ERbeta mRNA-containing cells, but the density of labeled cells within each nucleus differed in a number of instances. Nuclei that contained a higher (P < 0.001) density of ERalpha than ERbeta mRNA-containing cells included the preoptic area, bed nucleus of the stria terminalis, and ventromedial nucleus, whereas the subfornical organ (P < 0.001), paraventricular nucleus (males only, P < 0.05), and retrochiasmatic nucleus (females only, P < 0.05) had a greater density of ERalpha than ERbeta mRNA-containing cells. The anterior hypothalamic area and supraoptic nucleus had similar densities of cells containing both ER subtypes. The lateral septum and arcuate nucleus contained only ERalpha, whereas only ERbeta mRNA-containing cells were seen in the zona incerta. The sex differences in the populations of ER mRNA-containing cells in the ventromedial and arcuate nuclei may explain in part the sex differences in the neuroendocrine and behavioral responses to localized estrogen treatment in these nuclei. Within sexes, the differences between the distributions of ERalpha and ERbeta mRNA-containing cells may reflect differential regulation of the actions of estrogen in the sheep hypothalamus. Low levels of ERbeta mRNA in the preoptic area and ventromedial and arcuate nuclei, regions known to be important for the regulation of reproduction, suggest that ERbeta may not be involved in these functions.

Syntheses and binding affinities of 6-nitroquipazine analogues for serotonin transporter. Part 1

6-Nitroquipazine has been known as one of the most potent and selective inhibitors of serotonin transporter in vitro and in vivo. Nine derivatives of 6-nitroquipazine were synthesized and tested for their potential abilities to displace [3H]citalopram binding to the rat cortical membranes.

A three-tier clinical information systems design model

Modern health care institutions are often multi-site organisations that implement heterogeneous information management systems interacting with distributed databases. Advances in treatment modality/technology and rapidly changing information technology create increasing demand for changes/redevelopment of many health information applications. These features spawn the need for solutions to (a) guarantee data exchange across different types of applications and database management systems, and (b) reduce the costs of systems development and modification. This paper explores the concept of 'middleware services' as a solution to achieve these goals. It reports on the successful application of a component-based 3-tier system architecture to develop a computerised clinical pathways management system. The implementation experience confirms a number of significant benefits of the 3-tier structure including, reusability, flexibility, significant reduction in costs and efforts of systems development, and provision of easy, open migration pathway for future change of technology and system redevelopment.

A single-molecule study of RNA catalysis and folding

Using fluorescence microscopy, we studied the catalysis by and folding of individual Tetrahymena thermophila ribozyme molecules. The dye-labeled and surface-immobilized ribozymes used were shown to be functionally indistinguishable from the unmodified free ribozyme in solution. A reversible local folding step in which a duplex docks and undocks from the ribozyme core was observed directly in single-molecule time trajectories, allowing the determination of the rate constants and characterization of the transition state. A rarely populated docked state, not measurable by ensemble methods, was observed. In the overall folding process, intermediate folding states and multiple folding pathways were observed. In addition to observing previously established folding pathways, a pathway with an observed folding rate constant of 1 per second was discovered. These results establish single-molecule fluorescence as a powerful tool for examining RNA folding.

PPARgamma: observations in the hematopoietic system

Human Peroxisome Proliferator-Activated Receptor gamma (PPARgamma) was originally cloned from a human bone marrow library. What role does this ligand activated transcription factor play in hematopoiesis and the immune system? We note that: a) PPARgamma has potential to interact/interfere or synergize with retinoid biology, b) fatty acids and a prostaglandin have been identified as ligands, and c) lymphocytes, monocytes and neutrophils use fatty acids as a major source of energy production, d) PPARgamma has been shown to oppose TNFalpha and down regulate cytokine production in monocytes. Therefore, we undertook a review of the literature and an expression survey of PPARgamma in a number of major organs and cells involved in the hematopoietic system, for the purpose of building a database towards understanding the role and function of PPARgamma gene regulation in the developing blood and immune systems. PPARgamma is expressed before mesodermal induction in tissue in and around Speymann's organizer in the xenopus blastocyst, in erythroid precursors of blood islands and in the circulation of the day 10.0 murine embryo, in human 19 week fetal liver, in some but not all murine and human bone marrow erythroid, myeloid, and monocytoid progenitors, bone marrow stromal cells and adipocytes, osteoblasts, endothelial cells, some T, and B lymphocytes, monocytes, macrophages, and other monocytic derivatives. It can be found in the cells of Peyer's patches, lymphoid follicles, spleen, and thymus. It is not clear if it is ever or transiently expressed in megakaryocytes, mast cells, or neutrophils. Based on the above data and a review of the literature, PPARgamma seems to play a role during the elicitation of immune responses. We propose PPARgamma may be involved in changes in energy states required during activation and development of many cell types involved, and has additional immunologically relevant effects in erythroid, myeloid, monocytic, T and B lymphocytic, stromal, and endothelial cell function.

Long live Proust: the odour-cued autobiographical memory bump

The autobiographical memory bump is an increase in the frequency of reported autobiographical memories (AMs) from a particular age range, and has been reported by numerous investigators (for reviews, see Conway, M. A. & Rubin, D. C. (1993). The structure of autobiographical memory. In A. F. Collins, S. E. Gathercole, M. A. Conway & P. E. Morris, Theories of memory. Hove: Lawrence Erlbaum; Rubin, D. C., Rahhal, T. A. & Poon, L. W. (1998). Things learned in early adulthood are remembered best. Memory and Cognition, 26, 3-19) to occur in the second and third decades of life. Invariably, word labels have been used as AM cues but, given that a popular interpretation of the anecdotal 'Proust phenomenon' is that odours evoke AMs which are especially aged, we wondered if a different pattern in the AM bump might emerge if AMs were cued by odours rather than labels. Here we report an attempt to substantiate this aspect of the 'Proust phenomenon' by comparing the distributions of memories across the lifespan when cued by odour and label. Data showed that, in line with previous studies, the bump for label cues was found to peak between ages 11 and 25 years and was confirmed to be quadratic in form. In contrast, the odour-cued memory distribution peaked at 6-10 years and decreased linearly thereafter. In the earliest age interval, 6-10 years, the proportion of AMs retrieved in response to odour cues was significantly greater than that for the label cues. These results provide empirical support for the Proust phenomenon, and have more general implications for the structure and age distribution of stored AMs.

pH heterogeneity at intracellular and extracellular plasma membrane sites in HT29-C1 cell monolayers

In the colonic mucosa, short-chain fatty acids change intracellular pH (pH(i)) and extracellular pH (pH(e)). In this report, confocal microscopy and dual-emission ratio imaging of carboxyseminaphthorhodofluor-1 were used for direct evaluation of pH(i) and pH(e) in a simple model epithelium, HT29-C1 cells. Live cell imaging along the apical-to-basal axis of filter-grown cells allowed simultaneous measurement of pH in the aqueous environment near the apical membrane, the lateral membrane, and the basal membrane. Subapical cytoplasm reported the largest changes in pH(i) after isosmotic addition of 130 mM propionate or 30 mM NH(4)Cl. In resting cells and cells with an imposed acid load, lateral membranes had pH(i) values intermediate between the relatively acidic subapical region (pH 6.3-6.9) and the relatively alkaline basal pole of the cells (pH 7.4-7.1). Transcellular pH(i) gradients were diminished or eliminated during an induced alkaline load. Propionate differentially altered pH(e) near the apical membrane, in lateral intracellular spaces between adjacent cells, and near the basal membrane. Luminal or serosal propionate caused alkalinization of the cis compartment (where propionate was added) but acidification of the trans compartment only in response to luminal propionate. Addition of NH(4)Cl produced qualitatively opposite pH(e) excursions. The microscopic values of pH(i) and pH(e) can explain a portion of the selective activation of polarized Na/H exchangers observed in HT29-C1 cells in the presence of transepithelial propionate gradients.

Laser cooling of atoms, ions, or molecules by coherent scattering

We point out a laser cooling method for atoms, molecules, or ions at low saturation and large detuning from the particles' resonances. The moving particle modifies the field inside a cavity with a time delay characteristic of the cavity linewidth, while the field acts on the particle via the light shift. The dissipative mechanism can be interpreted as Doppler cooling based on preferential scattering rather than preferential absorption. It depends on particle properties only through the coherent scattering rate, opening new possibilities for optically cooling molecules or interacting atoms.

Dentoalveolar compensation in negative overjet cases

The purpose of this study was to investigate dentoalveolar compensation in negative overjet cases. Eighty-eight adult females with either skeletal Class I or skeletal Class III jaw relationships were examined. Of the total, 44 cases showed anterior crossbite and the remaining 44 cases had normal incisor relationships. Four cephalometric parameters were measured: the sagittal jaw relationship, maxillary and mandibular incisor inclination, and the occlusal plane angulation. In the negative overjet cases, correlation analysis was performed between the skeletal and dental measurements. Stepwise discriminate analysis was carried out to separate the negative and normal overjet cases. Compensatory changes for sagittal jaw discrepancies in the negative overjet cases were statistically confirmed for both incisor inclination and occlusal plane angulation. However, the compensatory effects were weaker than in the normal overjet cases. The discriminate analysis successfully separated the normal and negative overjet cases, suggesting that negative overjet results from insufficient dentoalveolar compensation for variations in the sagittal jaw relationships.

Estrogen receptor isoform gene expression in ovarian stromal and epithelial tumors

The factors involved in the pathogenesis of ovarian cancers remain unclear, and the response of these tumors to hormonal therapy is limited. The identification of a second estrogen receptor gene (ERbeta), expressed predominantly in ovarian granulosa cells, led us to explore its possible role in ovarian cancer, particularly in granulosa cell tumors (GCT). Several isoforms of ERbeta have been identified. We sought to define the patterns of both ERalpha and ERbeta gene expression in a panel of ovarian tumors consisting of GCT and serous and mucinous cystadenocarcinomas as well as in normal ovary. Expression was determined by RT-PCR using gene- and isoform-specific primers and probes combined with Southern blot analysis of the PCR products. Widespread expression of ERalpha was observed in all tumor types, but at relatively low levels. ERbeta is expressed predominantly in GCT, with lower levels in mucinous tumors and very low levels in serous tumors. The ERbeta2 splice variant previously reported in rodents was not observed. Only very low levels of the exon 5, exon 6, and exon 5/6 deletion variants were detected. The C-terminal truncation variant ERbeta(cx), however, exhibited widespread expression across all the tumor types. As ERbeta(cx) has been shown to be a ligand-independent antagonist of ERalpha action, the relative ratios of ERbeta(cx), ERalpha, and ERbeta may influence the response of a tumor to antiestrogen therapy.

Odour-evoked autobiographical memories: psychological investigations of proustian phenomena

Folk wisdom dictates that odours are especially powerful reminders of autobiographical experience, an effect which has become known as the Proust phenomenon. This paper reviews the relevant literature to determine whether there is any substantive evidence to support this view. Different methodologies have been adopted in addressing this issue, but the most revealing and ecologically valid have been the few studies which have examined naturally formed autobiographical memories. From these data, there is at least preliminary evidence that olfactory stimuli can cue autobiographical memories more effectively than cues from other sensory modalities. Explanations for these effects can be invoked from accepted principles in contemporary cognitive psychology.

Retinal degeneration but not obesity is observed in null mutants of the tubby-like protein 1 gene

The tub gene is a member of a small, well conserved neuronal gene family of unknown function. Mutations within this gene lead to early-onset blindness and deafness, as well as late-onset obesity and insulin resistance. To test the hypothesis that mutations within other members of this gene family would lead to similar phenotypes as observed in tubby mice, and hence have similar functional properties, we have generated null mutants of the tubby-like protein ( Tulp ) 1 gene by homologous recombination. Similarly to tubby mice, Tulp1 (-/-)mice exhibit an early-onset retinal degeneration with a progressive, rapid loss of photoreceptors, further supporting the notion that previously identified mutations within the human TULP1 gene are indeed causative of retinitis pigmentosa. However, in contrast to tubby mice, Tulp1 (-/-)mice exhibited normal hearing ability and, surprisingly, normal body weight despite the fact that both TUB and TULP1 are expressed in the same neurons within the hypothalamus in areas known to be involved in feeding behavior and energy homeo stasis. However, TUB and TULP1 show a distinctly different staining pattern in the nucleus of these neurons, perhaps explaining the difference in body weight between the Tulp1 (-/-)and tubby mutant mice.

Beyond optical molasses: 3D raman sideband cooling of atomic cesium to high phase-space density

We demonstrate a simple, general purpose method to cool neutral atoms. A sample containing 3x10(8) cesium atoms prepared in a magneto-optical trap is cooled and simultaneously spin polarized in 10 ms at a density of 1.1x10(11) cm (-3) to a phase space density nlambda(3)(dB) = 1/500, which is almost 3 orders of magnitude higher than attainable in free space with optical molasses. The technique is based on 3D degenerate Raman sideband cooling in optical lattices and remains efficient even at densities where the mean lattice site occupation is close to unity.

Subcutaneous emphysema in advanced cancer

Spontaneous subcutaneous emphysema is a rare and usually benign entity that may occasionally be symptomatic. We report a case of a patient with advanced cancer who developed extensive but asymptomatic subcutaneous emphysema shortly before death. Perforation of the lower gastrointestinal tract, perhaps as a result of straining due to severe unrelieved constipation or due to fistula formation, is suspected to have been the mechanism. The causes, treatment, and implications for management of this condition are discussed.

Structural determinants of aldosterone binding selectivity in the mineralocorticoid receptor

The structural determinants of aldosterone binding specificity in the mineralocorticoid receptor (MR) have not been determined. The MR has greatest sequence identity with the better characterized glucocorticoid receptor (GR), which is reflected in their overlapping ligand binding specificities. There must be subtle sequence differences that can account for the MR-specific binding of aldosterone and the shared binding of cortisol. To characterize ligand binding specificity, chimeras were made between the human MR and GR ligand-binding domains (LBDs). Three points were chosen as break points to generate a total of 16 different constructs. These chimeric LBDs were placed in a human GR expression vector containing the GR DNA-binding and N-terminal domains and assayed by co-transfection into CV-1 cells with the mouse mammary tumor virus-luciferase reporter plasmid. Binding of [(3)H]aldosterone and [(3)H]dexamethasone was also measured. All of the constructs that are potently activated by aldosterone contain amino acids 804-874 of the MR. The results of the ligand binding experiments using [(3)H]aldosterone were consistent with the transactivation assay. Cortisol activation of the chimeras was surprisingly complex. Constructs that are activated by cortisol contain either amino acids 804-874 and 932-984 of the MR or amino acids 598-668 and 726-777 of the GR. However, all of the chimeras retained the ability to bind the synthetic glucocorticoid [(3)H]dexamethasone, and cortisol was able to displace [(3)H]dexamethasone binding, suggesting that the differential effects of cortisol on transcriptional activation are caused by an effect that occurs downstream of ligand binding. These results identify a subregion of the MR LBD that confers specificity of aldosterone binding, which contrasts with cortisol binding where differential effects between chimeras appear to be mediated by interactions distal to ligand binding.

Dentoalveolar growth inhibition induced by bone denudation on palates: a study of two isolated cleft palates with asymmetric scar tissue distribution

OBJECTIVE

This report presents two cases of isolated cleft palate with asymmetric distribution of postsurgical scar tissue determined by laser Doppler flowmetry. To determine the effect of mucoperiosteal denudation of the bone on maxillary alveolar growth, the analysis of dentoalveolar structures compared the affected side to the unaffected side of each case.

METHOD

Two Japanese girls with isolated cleft palates were examined. Both subjects had undergone pushback operations (a modified version of the procedure of Wardill) for palatal repair at 18 months of age. Palatal blood flow was examined by laser Doppler flowmetry when the girls were 12 years old to determine the extent of postsurgical scar tissue over the denuded bone. To analyze the maxillary dentoalveolar structures three dimensionally, the whole surface of the upper dental cast was measured and recorded by an optical measuring device when the girls were 7 years old.

RESULTS AND CONCLUSIONS

Analysis via flowmetry showed that the palatal scar tissue area was limited to the anterior tooth region on the right (unaffected) side but extended posteriorly to the premolar region on the left (affected) side in both subjects. The two girls had similar dentoalveolar structures, with the dental and alveolar arches deflected lingually at the deciduous molar area on the affected side. There were no differences in the buccolingual inclination of deciduous molars or in the vertical growth of the alveolar processes between the affected and unaffected sides. In both girls, bone denudation in the premolar region appeared to result in less than 3 mm of displacement of the teeth palatally, with no change in lingual inclination. Any effects of scar tissue on the vertical development of the alveolus were not substantiated.

Ligand-induced conformational changes observed in single RNA molecules

We present the first demonstration that fluorescence resonance energy transfer can be used to track the motion of a single molecule undergoing conformational changes. As a model system, the conformational changes of individual three-helix junction RNA molecules induced by the binding of ribosomal protein S15 or Mg(2+) ions were studied by changes in single-molecule fluorescence. The transition from an open to a folded configuration was monitored by the change of fluorescence resonance energy transfer between two different dye molecules attached to the ends of two helices in the RNA junction. Averaged behavior of RNA molecules closely resembles that of unlabeled molecules in solution determined by other bulk assays, proving that this approach is viable and suggesting new opportunities for studying protein-nucleic acids interactions. Surprisingly, we observed an anomalously broad distribution of RNA conformations at intermediate ion concentrations that may be attributed to foldability differences among RNA molecules. In addition, an experimental scheme was developed where the real-time response of single molecules can be followed under changing environments. As a demonstration, we repeatedly changed Mg(2+) concentration in the buffer while monitoring single RNA molecules and showed that individual RNA molecules can measure the instantaneous Mg(2+) concentration with 20-ms time resolution, making it the world's smallest Mg(2+) meter.