Effects of Na+ and Mg2+ on the structures of supercoiled DNAs: comparison of simulations with experiments

Recent cryo-electron microscopy (cryo-EM) results suggest that sufficient NaCl concentration (> or approximately 0.1 M) and superhelix density (> or approximately-0.05) cause circular DNAs to adopt highly extended, tightly interwound configurations, in which the strands are laterally contiguous along almost their entire length. Millimolar levels of MgCl2 reportedly act synergistically with NaCl to produce similar conformations. However, Monte Carlo simulations with purely repulsive interduplex forces failed to reproduce such structures. In the present work, solution measurements of particular physical properties were performed both to characterize the effects of Na+ and Mg2+ on DNA structure and to provide quantitative tests of Monte Carlo simulations of circular DNAs. Supercoiled p30 delta DNAs in 10 mM Tris plus 0, 0.122, and 0.1 M NaCl, and 0.1 M NaCl plus 4 mM Mg2+ were examined by static and dynamic light scattering (LS and DLS), time-resolved fluorescence polarization anisotropy (FPA) of intercalated ethidium, and circular dichroism (CD) spectroscopy. Upon addition of 0.122 M NaCl, the radius of gyration (Rg) decreased substantially, which indicates that p30 delta adopts a more compact structure. This contradicts the cryo-EM studies, where molecular extension and Rg both increase upon adding 0.1 M NaCl. In 0.1 M NaCl, the torsion constant measured by FPA is practically invariant to superhelix density, and the plateau diffusion coefficient at large scattering vector (Dplat) is likewise nearly the same at both relaxed and native superhelix densities. Such invariance is difficult to reconcile with any transition from relaxed circles to tightly interwound structures with laterally contiguous strands. Metropolis Monte Carlo simulations were performed to generate canonically distributed sets of structures, from which average Do values and scattered intensity ratios, [symbol: see text]I (zero) [symbol: see text]/[symbol: see text] l(k) [symbol: see text], were calculated. Agreement between simulations and experiments in regard to [symbol: see text] I(O) [symbol: see text] /[symbol: see text] I(k) [symbol: see text], D(zero) and the supercoiling free energy, delta Gsc (delta l), is remarkably good for the most extensively studied p30 delta samples. The simulated structures exhibit no sign of very tight interwinding with extensive lateral contacts, but instead exhibit most probable superhelix diameters of 85 to 90 A. When 4 mM Mg2+ was added to native supercoiled p30 delta in 0.1 M NaCl, Rg decreased, D(zero) increased, and the longest internal relaxation rate (1/tau 2(zero)) increased, all of which indicate a further overall contraction of the molecular envelope. The torsion constant exhibited a slight increase that is hardly statistically significant. In this case, agreement between the simulations and experiments was only semi-quantitative for most samples investigated, although the predicted contraction was exhibited by all five samples of p30 delta and one of pBR322 DNA. The simulated structures in 0.1 M NaCl plus 4 mM Mg2+ again showed no sign of extensive lateral contacts. A plausible explanation is proposed for the highly extended, tightly interwound structures seen in cryo-EM, and explicitly tested by Monte Carlo simulations of a 1000 bp circular DNA at +25 and -50 degrees C. Structures identical to those seen in cryo-EM are in fact the equilibrium structures in the simulations at -50 degrees C, and the estimated time for equilibration (2.3 x 10(-6) second) is much smaller than the estimated time for vitrification (1 x 10(-4) second).     

Middle cerebral artery main stem thrombosis in two siblings with familial thrombotic thrombocytopenic purpura

Idiopathic thrombotic thrombocytopenic purpura (TTP) is frequently complicated by microinfarcts in cerebral cortex and subcortical white matter. We describe two sisters who suffered massive hemispheric infarction due to thrombosis of the middle cerebral artery main stem during exacerbations of TTP. Acute TTP may be associated with intraluminal thrombosis of large-diameter arteries in addition to arterioles and capillaries.     

The use of force modulation microscopy to investigate block copolymer morphology

Force modulation microscopy (FMM) is used to characterize the external surface and internal fracture surface morphologies of three different block copolymer samples. A roll-cast poly(styrene-butadiene-styrene) triblock copolymer film, spin-coated poly(styrene-b-methyl methacrylate) thin films, and an ultrathin poly(styrene-b-hexyl isocyanate) rod-coil block copolymer film were investigated. For each sample, height and elasticity images were obtained for the same areas allowing direct comparison. The elasticity images obtained using force modulation microscopy were independent of surface roughness and found to exhibit better contrast and spatial resolution of the respective block copolymer domains than the height images. The lateral resolution of the elasticity images was sufficient to show microphase separated domains having length scales as small as about 10 nm. The poly(styrene-b-methyl methacrylate) samples demonstrate that FMM can even be successfully used to study block copolymers in which both blocks are glassy under the conditions of measurement.     

Conservation surgery for breast cancer: selection criteria and technical considerations

Patients with stage I or II breast cancer are candidates for either modified radical mastectomy or breast preservation therapy involving limited resection of the primary tumor, axillary dissection, and breast irradiation. The overall survival rates of both these approaches are comparable according to retrospective reviews and ongoing clinical trials, and long-term follow-up confirms the earlier findings. Thus, patients should be given the choice between these two options by surgeons, radiation therapists, and other physicians involved in their care. However, not all breast cancer patients will choose breast preservation surgery, and because of tumor-related and other factors not all patients are candidates. The patient selection criteria are discussed herein and the optimal surgical techniques are reviewed.     

Software for dynamic reconfigurable order picking systems

This paper describes an approach, conceptual framework, and software architecture for dynamic reconfiguration of the order picking system. The research and development project was sponsored by the Material Handling Research Center (MHRC), a National Science Foundation sponsored Cooperative Industry/University Research Center. The storage configuration is assumed to be an in-the-aisle order picking system in which stockkeeping units (SKUs) can occupy variable capacity storage locations and stock-splitting is allowed among zones (clusters). The product mix may include multiple product families with different life cycles, correlated demand within families and commonality of demand across families.     

The bone marrow stromal environment is a major factor in myeloma cell resistance to dexamethasone

The expression of several markers of epithelial cell proliferation was analyzed to establish baseline data for future chemoprevention studies of oral premalignant lesions. Punch biopsies (n = 60) from three different sites of oral mucosa (bucca, lateral tongue, and the floor of the mouth) were obtained from 20 normal donors of both sexes. After formaldehyde fixation and paraffin embedding, immunohistochemistry was used to detect the proliferation markers Mib-1, cyclin D1, and centromere-associated protein CENP-F. Analysis of sections stained for the three markers showed similar patterns, i.e., a low labeling index (LI) in the basal layer and a high LI in the parabasal layer at all three intraoral sites. No proliferative activity was seen above the parabasal layer (superficial layer). All sites showed similar Mib-1 LI values for the proliferative markers. The tongue epithelium exhibited higher parabasal LIs of cyclin D1 and CENP-F than did the other two sites. No significant differences were detected between smokers and nonsmokers. The data from normal mucosa were compared with those from low (n = 30)- and high (n = 17)-grade dysplastic leukoplakias. The Mib-1 LI showed a very significant change, with a 9-fold increase in the basal layer LI in dysplastic leukoplakias. Cyclin D1 and CENP-F showed similar trends with increments of up to 7-fold in the basal layer of high-grade dysplasia. Although the proliferative activity of the parabasal layer was similar in normal and leukoplakic epithelia, the superficial layer showed a significant increment in proliferative activity mainly in high-grade leukoplakia. These studies suggest that proliferation markers in the basal and superficial cells of premalignant lesions may serve as surrogate end point biomarkers for chemoprevention trials.     

Non-redundant data clustering

Data clustering is a popular approach for automatically finding classes, concepts, or groups of patterns. In practice, this discovery process should avoid redundancies with existing knowledge about class structures or groupings, and reveal novel, previously unknown aspects of the data. In order to deal with this problem, we present an extension of the information bottleneck framework, called coordinated conditional information bottleneck, which takes negative relevance information into account by maximizing a conditional mutual information score subject to constraints. Algorithmically, one can apply an alternating optimization scheme that can be used in conjunction with different types of numeric and non-numeric attributes. We discuss extensions of the technique to the tasks of semi-supervised classification and enumeration of successive non-redundant clusterings. We present experimental results for applications in text mining and computer vision.     

Erfolgsfaktoren bei der Einführung von Wissensmanagementsystemen in die Praxis

Neben der Gestaltung technischer Systeme zur Unterstützung des Wissensmanagements ist die Ausgestaltung organisatorischer Ma?nahmen gleichbedeutend wichtig.