Phasing coherently illuminated nanocrystals bounded by partial unit cells

With the use of highly coherent femtosecond X-ray pulses from a free-electron laser, it is possible to record protein nanocrystal diffraction patterns with far more information than is present in conventional crystallographic diffraction data. It has been suggested that diffraction phases may be retrieved from such data via iterative algorithms, without the use of a priori information and without restrictions on resolution. Here, we investigate the extension of this approach to nanocrystals with edge terminations that produce partial unit cells, and hence cannot be described by a common repeating unit cell. In this situation, the phase problem described in previous work must be reformulated. We demonstrate an approximate solution to this phase problem for crystals with random edge terminations.     

Toward structure determination using membrane-protein nanocrystals and microcrystals

Membrane proteins are very important for all living cells, being involved in respiration, photosynthesis, cellular uptake and signal transduction, amongst other vital functions. However, less than 300 unique membrane protein structures have been determined to date, often due to difficulties associated with the growth of sufficiently large and well-ordered crystals. This work has been focused on showing the first proof of concept for using membrane protein nanocrystals and microcrystals for high-resolution structure determination. Upon determining that crystals of the membrane protein Photosystem I, which is the largest and most complex membrane protein crystallized to date, exist with only 100 unit cells with sizes of less than 200 nm on an edge, work was done to develop a technique that could exploit the growth of the Photosystem I nanocrystals and microcrystals. Femtosecond X-ray protein nanocrystallography was developed for use at the first high-energy X-ray free electron laser, the LCLS at SLAC National Accelerator Laboratory, in which a liquid jet brought fully-hydrated Photosystem I nanocrystals into the interaction region of the pulsed X-ray source. Diffraction patterns were recorded from millions of individual PSI nanocrystals and data from thousands of different, randomly oriented crystallites were integrated using Monte Carlo integration of the peak intensities. The short pulses (～70fs) provided by the LCLS allowed the possibility to collect the diffraction data before the onset of radiation damage, exploiting the diffract-before-destroy principle. During the initial experiments at the AMO beamline using 6.9-? wavelength, Bragg peaks were recorded to 8.5-? resolution, and an electron-density map was determined that did not show any effects of X-ray-induced radiation damage [94]. Many additional techniques still need to be developed to explore the femtosecond nanocrystallography technique for experimental phasing and time-resolved X-ray crystallography experiments. The first proof-of-principle results for the femtosecond nanocrystallography technique indicate the incredible potential of the technique to offer a new route to the structure determination of membrane proteins.     

Direct immunofluorescence of plant microtubules based on semiconductor nanocrystals

Fluorescence microscopy in combination with multiple, simultaneous labeling of biomolecules has been a key breakthrough in cell biology. However, the spatiotemporal resolution of this approach is limited by bleaching of the fluorescence label and illegitimate cross-reference of the label. CdSe-based semiconductor nanocrystals with their excellent bleaching stability would be an alternative to overcome this limitation. We therefore explored direct immunofluorescence based on nanocrystal-conjugated antibodies using plant microtubules as model. We compared two strategies of bioconjugation, covalent coupling of antitubulin antibodies to BSA-coated nanocrystals and covalent coupling to nanocrystals that were surrounded by functionalized silica shells. Both nanoparticle-antibody conjugates were used to follow the dynamic reorganization of microtubules through the cell cycle of a tobacco cell culture in double and triple staining with FITC as conventional fluorochrome and Hoechst 33258 as marker for mitotic duplication of DNA. BSA-coated nanocrystals visualized fluorescent dots that decorated the various arrays of microtubules. The specificity of the antibody was maintained after conjugation with the nanocrystals, and the antibodies correctly represented the dynamics of cell-cycle-dependent microtubular reorganization. However, this approach did not yield a contiguous signal. In contrast, silica-shelled nanocrystals visualized contiguous microtubules in the same pattern as found for the conventional fluorochrome FITC and thus can be used as labels for direct immunofluorescence in plant cells.     

Development and Characterisation of Ursolic Acid Nanocrystals Without Stabiliser Having Improved Dissolution Rate and In Vitro Anticancer Activity

Ursolic acid (UA), which is a natural pentacyclic triterpenoid, has the potential to be developed as an anticancer drug, whereas its poor aqueous solubility and dissolution rate limit its clinical application. The aim of the present study was to develop UA nanocrystals to enhance its aqueous dispersibility, dissolution rate and anticancer activity. Following the investigation on the effects of stabiliser, the ratio of organic phase to aqueous solution and drug concentration, the UA nanocrystals without stabiliser were successfully prepared by anti-solvent precipitation approach. The nanocrystals maintained similar crystallinity with particle size, polydispersion index and zeta potential values of 188.0 ± 4.4 nm, 0.154 ± 0.022, and −25.0 ± 5.9 mV, respectively. Compared with the raw material, the UA nanocrystals showed good aqueous dispensability and a higher dissolution rate, and they could be completely dissolved in 0.5% SDS solution within 120 min. Moreover, the suspension of UA nanocrystals was physically stable after storage at 4°C for 7 weeks. By inducing G₂/M phase cell cycle arrest, the UA nanocrystals significantly induced stronger cell growth inhibition activity against MCF-7 cells compared with free drug in vitro, although the uptake of free UA was approximately twice higher than that of the UA nanocrystals. The UA nanocrystals may be used as a potential delivery formulation for intravenous injection with enhanced dissolution velocity and anticancer activity.Key words: anticancer, dissolution, MCF-7, nanocrystals, ursolic acid     

Recherche de cas médicaux multimodaux à l’aide d’arbres de décision

In this article, we present a Case-based Reasoning system for the retrieval of patient files similar to a case placed as query. We focus on patient files made up of several images with contextual information (such as the patient age, sex and medical history). Indeed, medical experts generally need varied sources of information (which might be incomplete) to diagnose a pathology. Consequently, we derive a retrieval framework from decision trees, which are well suited to process heterogeneous and incomplete information. To be integrated in the system, images are indexed by their digital content. The method is evaluated on a classified diabetic retinopathy database. On this database, results are promising: the retrieval sensitivity reaches 79.5% for a window of five cases, which is almost twice as good as the retrieval of single images alone.     

Potential accuracy of genetic evaluation for calving difficulty with incomplete data on calving difficulty and/or birth weight using a bivariate threshold-linear animal model

The purpose of this study was to evaluate the potential loss of accuracy in direct and maternal predicted breeding values (PBV) for calving difficulty (CD) with different levels of missing records of CD and/or birth weight (BW), using a bivariate threshold-linear animal model. Data obtained from the American Gelbvieh Association included 84,420 first-parity records with both CD and BW available. The final pedigree file included 178,858 animals. The model included fixed calf-sex-dam-age, random herd-year-season, and animal direct and maternal effects. Different levels of missing observations for CD and BW were obtained by randomly deleting 0, 25, 50, 75, and 100% of records for both traits in various combinations. Correlation estimates between PBV for CD obtained with complete and incomplete data were used to measure the changes in PBV for different levels of missing records. Reported correlations are means of three replicates. The results suggest that the information on direct and maternal PBV provided by CD records is more reliable than the information provided by BW records. The difference was especially large when a high proportion of CD records were missing. Correlations above 0.96 and 0.95 for direct and maternal PBV, respectively, when missing 25% or 0% of the CD or BW records suggest that small changes would be predicted with a low proportion incomplete data. For genetic prediction of popular sires (with > 100 pogeny), a higher proportion of missing records could be tolerated. The results suggest that the bivariate threshold-linear animal model is useful for routine genetic evaluation of CD with incomplete field data.     

Normal Human Telomeres Are Not Late Replicating

Telomeres in yeast are late replicating. Genes placed next to telomeres in yeast can be repressed (telomere positional effects), leading to the hypothesis that telomeres may be heterochromatic and may control the expression of subtelomeric genes. In addition, yeast telomeres are processed to have a transient long overhang at the end of S phase. The applicability of the yeast data to human biology was examined by determining the timing of telomere replication and processing in normal human diploid fibroblasts. Telomeres were purified from synchronized cells that had been labeled with 5-bromodeoxyuridine (BrdU) at hourly intervals, and the fraction of labeled telomeres was analyzed by retrieval with anti-BrdU antibodies. We determined that normal human telomeres replicate throughout S phase rather than being very late replicating. Furthermore, the overall timing of replication was unaffected by telomere length in young versus old cells or cells whose telomeres had been elongated following transfection with the catalytic subunit of telomerase. Finally, the asymmetry in the length of the G-rich overhang in daughter telomeres produced by leading versus lagging strand synthesis was shown to be established within 1 h of telomere replication, indicating there is no significant delay between synthesis and the processing events that contribute to the establishment of asymmetric overhangs. Therefore, the timings of replication and processing of human telomeres are very different from those of yeast.     

A new model of thermal inactivation and its application to clonogenic survival data for WiDr human colonic adenocarcinoma cells

Based on the analysis of clonogenic survival data for human colonic adenocarcinoma cells (WiDr) after a single heating, a new model is proposed to describe cell survival after hyperthermia quantitatively. The effects of heat are explained as heat-induced cell damage assuming a first-order (single-hit) and a second-order (cumulative damage) process. Thus cell survival at a specified temperature can be described by the linear-quadratic (LQ) model. The proposed model is based on an alternative definition of the (single) thermal dose, given as the (normalized) product of heating time and a specified nonlinear function of the increase in temperature (relative to a threshold temperature) to be interpreted as the thermal dose rate. In further analogy to the modeling of the effects of low-dose-rate radiation, an inherent capacity of the cells to repair sublethal damage is assumed, and these effects are quantified by the usual g factor measuring incomplete repair effects. The model defines thermal dose-response and isoeffect dose relationships, enabling a direct (i. e. single-step) analysis of the available thermal response data. Additionally, the analysis of our data based on heating times in the range from 0 to 360 min and temperatures from 41 to 46 degrees C and covering a broad spectrum of different densities of cells seeded for colony formation did not yield any evidence of the existence of a breaking point usually derived from Arrhenius plots based on the single-hit, multitarget model and the Arrhenius equation. The model includes no specific assumptions describing the development of thermotolerance, which can be assumed to be negligible under our experimental conditions. The proposed thermal dose-response model correlates satisfactorily with the in vitro survival data for WiDr adenocarcinoma cells.     

Response of mouse spermatogonial stem cells to X-ray induction of heritable reciprocal translocations

Although heritable translocations are an important endpoint for the assessment of genetic risk from radiation, there has been a serious information gap with regard to thier induction in spermatogonical stem cells, the most important cell stage in males for risk considerations. This led to uncertainty in estimating the magnitude of risk per unit exposure. Further, the relationship between the frequency of r eciprocal exchanges scored by cytological analysis of the exposed male's meiocytes and the frequency of those transmitted to first-generation offspring needed to be re-examined. In order to fill in these gaps, two radiation studies, i.e., dose response and dose fractionation, were conducted on spermatogonial stem cells in which heritable and cytologically detected translocations were scored.The present data are by far the most extensive, to date, for heritable translocation induction in spermatogonial stem cells. The linearity of the rising portion of the dose-effect curve and the additivity of effects observed in the fractionation study allow a direct estimation of the number of transmissible translocations expected per unit exposure. Thus,t he expected increase in heritable translocations per rad of acute X-rays in 3.89 × 10^?5 per gamete. The data also show a lack of consistensy between cytologically and genetically scored translocations.     

Basolateral cycling mediated by a lumenal domain targeting determinant

All identified basolateral sorting signals of integral membrane proteins are cytoplasmically disposed, suggesting that basolateral targeting is mediated exclusively by direct interaction with vesicle coat components. Here, we report that GPP130, a cis-Golgi protein that undergoes endosome-to-Golgi retrieval using the late endosome-bypass pathway in nonpolarized cells, cycles via the basolateral membrane in polarized MDCK cells. Significantly, the membrane-proximal lumenal domain of GPP130, which mediates GPP130 localization and trafficking in nonpolarized cells, was both necessary and sufficient for basolateral cycling in MDCK cells. The use of lumenal determinants for both basolateral cycling and endosome-to-Golgi retrieval suggests that a novel receptor-mediated mechanism operates at both the trans-Golgi network and distal sites to sort GPP130 along the late-endosome-bypass retrieval pathway in polarized cells.     

Thermodynamic models for water-protein sorption hysteresis

Sorption isotherms of water by proteins show hysteresis that appears to be due to interactions at the molecular level. Four thermodynamically consistent models for this irreversible process are presented. Hysteresis could be the result of slow, incomplete conformational changes occurring upon addition and removal of water. Conformational hysteresis would occur if a number of different conformations, each corresponding to a local free energy minimum, could be present at each pressure of water vapor. Hysteresis might result from an incomplete process of intermolecular phase annealing. Finally, hysteresis might be due to incomplete phase change if two different protein phases are present. Experimental tests for these models are presented. Further study should lead to more insight into the effects of the presence of water on protein conformation and dynamics.     

缺失数据和贝叶斯系统发育分析精确度之探索

The effect of missing data on phylogenetic methods is a potentially important issue in our attempts to reconstruct the Tree of Life. If missing data are truly problematic, then it may be unwise to include species in an analysis that lack data for some characters (incomplete taxa) or to include characters that lack data for some species. Given the difficulty of obtaining data from all characters for all taxa (e.g., fossils), missing data might seriously impede efforts to reconstruct a comprehensive phylogeny that includes all species. Fortunately, recent simulations and empirical analyses suggest that missing data cells are not themselves problematic, and that incomplete taxa can be accurately placed as long as the overall number of characters in the analysis is large. However, these studies have so far only been conducted on parsimony, likelihood, and neighbor-joining methods. Although Bayesian phylogenetic methods have become widely used in recent years, the effects of missing data on Bayesian analysis have not been adequately studied. Here, we conduct simulations to test whether Bayesian analyses can accurately place incomplete taxa despite extensive missing data. In agreement with previous studies of other methods, we find that Bayesian analyses can accurately reconstruct the position of highly incomplete taxa (i.e., 95% missing data), as long as the overall number of characters in the analysis is large. These results suggest that highly incomplete taxa can be safely included in many Bayesian phylogenetic analyses.     

Cytotoxic effects of dexamethasone restricted to noncycling,early G1-phase cells of L1210 leukemia

The cytostatic and cytolytic effects of dexamethasone were studied as functions of cell cycle position in mouse L1210 leukemia cells. To this end, the cells were separated according to size by sedimentation at unit gravity in a specially designed sedimentation chamber. The fractions were analyzed by radioautography and flow cytophotometry. The size-distributions obtained by 1g sedimentation coincided with cell-cycle age distribution. With increasing fraction number, samples highly enriched in G1, S, and G2/M cells, respectively were obtained: the smallest cells being in early G1 and the largest in mitosis. In the presence of dexamethasone (10^?6-10^?5 M), growth slowed down after a few cell cycles and the cells accumulated in early G1 phase. Lytic cell kill by continued exposure to the drug was confined to the fractions containing the small, early G1-phase cells. These fractions were also enriched in noncycling cells that were not labeled by prolonged exposure to ³H-thymidine. After removal of dexamethasone, the cells in S and G2/M phase completed cell cycle traverse but were retarded again in the G1 and early S phase of the next division cycle. The data suggest a memory effect for previous drug exposure. It is concluded that the cytostatic and cytolytic effects of dexamethasone are separate, though not unrelated events. Cytolysis is confined to the noncycling cells that in untreated populations can exit from the dividing compartment during a transitional phase of about 60 minutes subsequent to mitotic division. The cytostatic effects potentiate cytolysis by accumulating the cells in the early G1 phase and thus increasing the probability of their transit to the G0 compartment, sensitive for drug-mediated cytolysis.     

Interaction of syntaxins with the amiloride-sensitive epithelial sodium channel.

Amiloride-sensitive sodium channels mediate sodium entry across the apical membrane of epithelial cells in variety of tissues. The rate of Na(+) entry is controlled by the regulation of the epithelial sodium channel (ENaC) complex. Insertion/retrieval of the ENaC complex into the apical membrane as well as direct kinetic effects at the single channel level are recognized mechanisms of regulation. Recent data suggest that the syntaxin family of targeting proteins interact with and functionally regulate a number of ion channels and pumps. To evaluate the role of these proteins in regulating ENaC activity, we co-expressed rat ENaC cRNA (alpha, beta, gamma subunits) with syntaxin 1A or 3 cRNAs in Xenopus oocytes. Basal ENaC currents were inhibited by syntaxin 1A and stimulated by syntaxin 3. Both syntaxin 1A and syntaxin 3 could be co-immunoprecipitated with ENaC subunit proteins, suggesting physical interaction. Interestingly, immunofluorescence data suggest that with either syntaxin isoform the ENaC-associated epifluorescence on the oocyte surface is enhanced. These data indicate that (i) both syntaxin isoforms increase the net externalization of the ENaC channel complex, (ii) that the functional regulation is isoform specific, and (iii) suggest that ENaC may be regulated through mechanisms involving protein-protein interactions.     

X-ray diffraction from membrane protein nanocrystals

Membrane proteins constitute >30% of the proteins in an average cell, and yet the number of currently known structures of unique membrane proteins is <300. To develop new concepts for membrane protein structure determination, we have explored the serial nanocrystallography method, in which fully hydrated protein nanocrystals are delivered to an x-ray beam within a liquid jet at room temperature. As a model system, we have collected x-ray powder diffraction data from the integral membrane protein Photosystem I, which consists of 36 subunits and 381 cofactors. Data were collected from crystals ranging in size from 100 nm to 2 μm. The results demonstrate that there are membrane protein crystals that contain <100 unit cells (200 total molecules) and that 3D crystals of membrane proteins, which contain <200 molecules, may be suitable for structural investigation. Serial nanocrystallography overcomes the problem of x-ray damage, which is currently one of the major limitations for x-ray structure determination of small crystals. By combining serial nanocrystallography with x-ray free-electron laser sources in the future, it may be possible to produce molecular-resolution electron-density maps using membrane protein crystals that contain only a few hundred or thousand unit cells.     

Unraveling Charge Separation and Transport Mechanisms in Aqueous‐Processed Polymer/CdTe Nanocrystal Hybrid Solar Cells

Recently great progress has been achieved in highly effective hybrid solar cells fabricated using aqueous materials. The state‐of‐the‐art energy conversion efficiency has been close to 5% with high photocurrent. However, charge separation and transport mechanism in the aqueous‐processed hybrid solar cells are rarely reported and are usually assumed to be similar to oil‐phase processed systems; that is, self‐assembly polymers are mainly responsible for charge separation and carrier transport. To date, this assumption has prohibited further improvement of the conversion efficiency in aqueous‐processed hybrid systems by adopting any appropriate technique routes. Here, ultrafast carrier dynamics in these hybrid solar cells consisting of poly(p‐phenylenevinylene) (PPV)‐based aqueous polymers and water‐solution CdTe nanocrystals (NCs) are investigated in detail. Self‐charge separation in grown CdTe NC partly capped CdS shell layers after anneal treatment is unambiguously identified. Different from their oil‐soluble counterparts, these core/shell nanocrystals do not have the restrictions of quantum confinement and surface ligands, form effective charge transport networks, and play a dominant role in the charge separation and carrier transport processes. These findings provide a greater understanding on the fundamental photophysics in aqueous‐processed hybrid systems.     

Seeded Synthesis of CdSe/CdS Rod and Tetrapod Nanocrystals

We demonstrate a method for the synthesis of multicomponent nanostructures consisting of CdS and CdSe with rod and tetrapod morphologies. A seeded synthesis strategy is used in which spherical seeds of CdSe are prepared first using a hot-injection technique. By controlling the crystal structure of the seed to be either wurtzite or zinc-blende, the subsequent hot-injection growth of CdS off of the seed results in either a rod-shaped or tetrapod-shaped nanocrystal, respectively. The phase and morphology of the synthesized nanocrystals are confirmed using X-ray diffraction and transmission electron microscopy, demonstrating that the nanocrystals are phase-pure and have a consistent morphology. The extinction coefficient and quantum yield of the synthesized nanocrystals are calculated using UV-Vis absorption spectroscopy and photoluminescence spectroscopy. The rods and tetrapods exhibit extinction coefficients and quantum yields that are higher than that of the bare seeds. This synthesis demonstrates the precise arrangement of materials that can be achieved at the nanoscale by using a seeded synthetic approach.     

Physiologically based calculation of steady-state evoked potentials and cortical wave velocities

Steady-state evoked potentials (SSEPs) elicited by sinusoidal stimuli are predicted from a physiologically-based model, including bielectrode and volume conduction effects. Comparison with visual SSEPs yields constraints on phase and latency of the retinothalamic transfer function that are consistent with experiment. Predictions of phase velocities measured as SSEPs cross the cortex are consistent with low values measured for slow waves in sleep, while resonant behavior induced by corticothalamic loops, especially near the alpha peak, contributes to wide scatter in waking-state phase velocity measurements comparable to effects from volume conduction. The common use of bielectrode derivations to compensate for volume conduction effects is examined and shown to be incomplete, tending to lead to underestimates of phase velocity, especially at low frequencies and near the alpha peak, due to incorrect elimination of true long-wavelength contributions to the SSEP.     

Synchronization of neural activity is a promising mechanism of memory information processing in networks of columns

Synchronization of the oscillatory discharge of cortical neurons could be a part of the mechanism that is involved in cortical information processing. On the assumption that the basic functional unit is the column composed of local excitatory and inhibitory cells and generating oscillatory neural activity, a network model that attains associative memory function is proposed. The synchronization of oscillation in the model is studied analytically using a sublattice analysis. In particular, the retrieval of a single memory pattern can be studied in the system, which can be derived from the original network model of interacting columns and is formally equivalent to a system of an isolated column. The network model simulated numerically shows a remarkable performance in which retrieval is achieved simultaneously for more than one memory pattern. The manifestations of this simultaneous retrieval in the network dynamics are successive transitions of the network state from a synchronized oscillation for a memory pattern to that for another memory pattern.