Fabrication of polymeric replicas of cell surfaces with nanoscale resolution

We report an approach for fabricating biomimetic surface replicas of cells with nanoscale resolution. Fixed cells serve as a template for a two-stage replica molding process. Cast from the template, the impression replica contains a reproduction of cellular topographical features indented into its surface, and cast from the impression replica, the relief replica contains a copy of these features protruding from its surface. Various polymers and cells can be utilized, and scanning electron microscopy, atomic force microscopy, and white light interferometry analyses confirm the replication of nanoscale features. These replicas are useful for investigating cellular function and for biomimetic tissue engineering.     

Cannabinoid CB1 receptor recognition of endocannabinoids via the lipid bilayer: molecular dynamics simulations of CB1 transmembrane helix 6 and anandamide in a phospholipid bilayer

The phospholipid bilayer plays a central role in the lifecycle of the endogenous cannabinoid, N-arachidonoylethanolamine (anandamide, AEA). Therefore, the orientation and location of AEA in the phospholipid bilayer with respect to key membrane associated proteins, is a central issue in understanding the mechanism of endocannabinoid signaling. In this paper, we report a test of the hypothesis that a βXXβ motif (formed by beta branching amino acids, V6.43 and I6.46) on the lipid face of the cannabinoid CB1 receptor in its inactive state may serve as an initial CB1 interaction site for AEA. Eight 6 ns NAMD2 molecular dynamics simulations of AEA were conducted in a model system composed of CB1 transmembrane helix 6 (TMH6) in a 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) bilayer. In addition, eight 6 ns NAMD2 molecular dynamics simulations of a low CB1 affinity (20:2, n−6) analog of AEA were conducted in the same model system. AEA was found to exhibit a higher incidence of V6.43/I6.46 groove insertion than did the (20:2, n−6) analog. In certain cases, AEA established a high energy of interaction with TMH6 by first associating with the V6.43/I6.46 groove and then molding itself to the lipid face of TMH6 to establish a hydrogen bonding interaction with the exposed backbone carbonyl of P6.50. Based upon these results, we propose that the formation of this hydrogen bonded AEA/TMH6 complex may be the initial step in CB1 recognition of AEA in the lipid bilayer.     

Improved cell typing by charge-state deconvolution of matrix-assisted laser desorption/ionization mass spectra

Robust, specific, and rapid identification of toxic strains of bacteria and viruses, to guide the mitigation of their adverse health effects and optimum implementation of other response actions, remains a major analytical challenge. This need has driven the development of methods for classification of microorganisms using mass spectrometry, particularly matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS), that allows high-throughput analyses with minimum sample preparation. We describe a novel approach to cell typing based on pattern recognition of MALDI mass spectra, which involves charge-state deconvolution in conjunction with a new correlation analysis procedure. The method is applicable to both prokaryotic and eukaryotic cells. Charge-state deconvolution improves the quantitative reproducibility of spectra because multiply charged ions resulting from the same biomarker attaching a different number of protons are recognized and their abundances are combined. This allows a clearer distinction of bacterial strains or of cancerous and normal liver cells. Improved class distinction provided by charge-state deconvolution was demonstrated by cluster spacing on canonical variate score charts and by correlation analyses. Deconvolution may enhance detection of early disease state or therapy progress markers in various tissues analyzed by MALDI-MS.     

Relative importance of criteria in multiobjective programming: A cone-based approach

This article develops a convex polyhedral cone-based preference modeling framework for decision making with multiple criteria which extends the classical notion of Pareto optimality and accounts for relative importance of the criteria. The decision maker’s perception of the relative importance is quantified by an allowable tradeoffs between two objectives representing the maximum allowable amount of decay of a less important objective per one unit of improvement of a more important objective. Two cone-based models of relative importance are developed. In the first model, one criterion is designated as less important while all the others are more important. In the second model, more than one criterion may be classified as less important while all the others are considered more important. Complete algebraic characterization of the models is derived and the relationship between them and the classical Pareto preference is examined. Their relevance to decision making is discussed.     

Selective Reflection of Potassium Vapor Nanolayers in a Magnetic Field

The selective reflection of laser radiation from the interface between a dielectric window and the atomic vapors confined in a nanocell of thickness L ≈ 350 nm is used to develop effective Doppler-broadening- free spectroscopy of potassium atoms. A small atomic line width and a relation between the signal intensity and the transition probability allowed us to resolve four lines of atomic transitions responsible for the D1 lines of the ³⁹K and ⁴¹K isotopes. Two groups containing four atomic transitions form in an applied magnetic field upon pumping by radiation with circular polarization σ⁺ or σ^–. Different intensities (probabilities) of transitions for the σ⁺ and σ^– excitations are detected in magnetic field B₀ ≈ A _hfs /μ_B ≈ 165 G (A _hfs is the magnetic dipole constant for the ground state and μ_B is the Bohr magneton). A substantially different situation is observed at B ? B₀, since high symmetry appears for the two groups formed by radiation with circular polarization σ⁺ or σ^–. Each group is the mirror image of the other group with respect to the frequency of the 4²S_1/2–4²P_1/2 transition, which additionally proves the occurrence of the complete Paschen–Back regime of the hyperfine structure at B ≈ 2.5 kG. A developed theoretical model well reproduces the experimental results. Possible practical applications are described. The results obtained can also be applied to the D₁ lines of ⁸⁷Rb and ²³Na.     

Refining a relativistic,hydrodynamic solver: Admitting ultra-relativistic flows

We have undertaken the simulation of hydrodynamic flows with bulk Lorentz factors in the range 10²–10⁶. We discuss the application of an existing relativistic, hydrodynamic primitive variable recovery algorithm to a study of pulsar winds, and, in particular, the refinement made to admit such ultra-relativistic flows. We show that an iterative quartic root finder breaks down for Lorentz factors above 10² and employ an analytic root finder as a solution. We find that the former, which is known to be robust for Lorentz factors up to at least 50, offers a 24% speed advantage. We demonstrate the existence of a simple diagnostic allowing for a hybrid primitives recovery algorithm that includes an automatic, real-time toggle between the iterative and analytical methods. We further determine the accuracy of the iterative and hybrid algorithms for a comprehensive selection of input parameters and demonstrate the latter’s capability to elucidate the internal structure of ultra-relativistic plasmas. In particular, we discuss simulations showing that the interaction of a light, ultra-relativistic pulsar wind with a slow, dense ambient medium can give rise to asymmetry reminiscent of the Guitar nebula leading to the formation of a relativistic backflow harboring a series of internal shockwaves. The shockwaves provide thermalized energy that is available for the continued inflation of the PWN bubble. In turn, the bubble enhances the asymmetry, thereby providing positive feedback to the backflow.     

Multi-species simple exclusion processes

A motility mechanism based on a simple exclusion process, where the movement of discrete agents on a lattice is either unbiased (symmetric) or biased (asymmetric) is considered. Estimates of diffusivities from tracking data do not describe the population-level response of the system. This mismatch between the individual-level and population-level behaviour can be resolved by averaging the individual-level mechanism in terms of an expected site occupancy. New insight into simple exclusion processes is obtained by representing the system as a series of interacting subpopulations. This formalism leads to a system of nonlinear advection-diffusion equations which can be interpreted in terms of the agent fluxes. These interactions have consequences for both agent-based modelling and continuum modelling in cell biology, such as tracking subpopulations of cells within a total cell population.     

Validation of an adapted MRI pulse sequence for quantification of fatty infiltration in muscle

Purpose

The long-term goal of our research is to develop a patient-specific biomechanical model of the supraspinatus muscle and tendon for analyzing the effects of fatty infiltration and pennation angle changes. One input of the model will be the amount and distribution of fat within the muscle. Therefore, the objective of this project was to adapt and validate a novel magnetic resonance imaging pulse sequence for quantifying the extent of fatty infiltration for the supraspinatus muscle.

Methods

Samples of incremental combinations of muscle and fat from a cow were prepared and scanned with our quantitative MR technique. The MR results were compared to actual fat measurements taken using a Soxtec extraction analyzer.

Results

The MR fat quantification results closely match those values determined by Soxtec analysis (R²=.98, root mean square deviation=4.9).

Conclusions

Our MR fat quantification protocol can be used to accurately quantify fatty infiltration in skeletal muscle. This ability to evaluate skeletal muscle tissue noninvasively will improve the efficacy of evaluation of fatty degeneration in assessing tissue quality preoperatively. This can be important in surgical planning of any musculoskeletal repairs, particularly rotator cuff tears.     

First observation of the Greisen-Zatsepin-Kuzmin suppression

The High Resolution Fly's Eye (HiRes) experiment has observed the Greisen-Zatsepin-Kuzmin suppression (called the GZK cutoff) with a statistical significance of five standard deviations. HiRes' measurement of the flux of ultrahigh energy cosmic rays shows a sharp suppression at an energy of 6 x 10(19) eV, consistent with the expected cutoff energy. We observe the ankle of the cosmic-ray energy spectrum as well, at an energy of 4 x 10(18) eV. We describe the experiment, data collection, and analysis and estimate the systematic uncertainties. The results are presented and the calculation of the statistical significance of our observation is described.     

Evaporative isotope enrichment as a constraint on reach water balance along a dryland river

Deuterium and oxygen-18 enrichment in river water during its transit across dryland region is found to occur systematically along evaporation lines with slopes of close to 4 in (2)H-(18)O space, largely consistent with trends predicted by the Craig-Gordon model for an open-water dominated evaporating system. This, in combination with reach balance assessments and derived runoff ratios, strongly suggests that the enrichment signal and its variability in the Barwon-Darling river, Southeastern Australia is acquired during the process of evaporation from the river channel itself, as enhanced by the presence of abundant weirs, dams and other storages, rather than reflecting inherited enrichment signals from soil water evaporation in the watershed. Using a steady-state isotope mass balance analysis based on monthly (18)O and (2)H, we use the isotopic evolution of river water to re-construct a perspective of net exchange between the river and its contributing area along eight reaches of the river during a drought period from July 2002 to December 2003, including the duration of a minor flow event. The resulting scenario, which uses a combination of climatological averages and available real-time meteorological data, should be viewed as a preliminary test of the application rather than as a definitive inventory of reach water balance. As expected for a flood-driven dryland system, considerable temporal variability in exchange is predicted. While requiring additional real-time isotopic data for operational use, the method demonstrates potential as a non-invasive tool for detecting and quantifying water diversions, one that can be easily incorporated within existing water quality monitoring activities.