Quartz crystal microbalance use in biological studies

Design, development, and applications of quartz crystal microbalance are discussed. Two types of crystals are used. One serves as reference and other senses changes in mass. Specific application to study of bacterial spores is described

Calculation of 3D genome structures for comparison of chromosome conformation capture experiments with microscopy: An evaluation of single-cell Hi-C protocols.

Single-cell chromosome conformation capture approaches are revealing the extent of cell-to-cell variability in the organization and packaging of genomes. These single-cell methods, unlike their multi-cell counterparts, allow straightforward computation of realistic chromosome conformations that may be compared and combined with other, independent, techniques to study 3D structure. Here we discuss how single-cell Hi-C and subsequent 3D genome structure determination allows comparison with data from microscopy. We then carry out a systematic evaluation of recently published single-cell Hi-C datasets to establish a computational approach for the evaluation of single-cell Hi-C protocols. We show that the calculation of genome structures provides a useful tool for assessing the quality of single-cell Hi-C data because it requires a self-consistent network of interactions, relating to the underlying 3D conformation, with few errors, as well as sufficient longer-range cis- and trans-chromosomal contacts

K*(892)0 Production in Relativistic Heavy Ion Collisions at sqrt(s_NN) = 130 GeV

Preliminary results on the K*(892)0 -> pi + K production using the mixed-event technique are presented. The measurements are performed at mid-rapidity by the STAR detector in sqrt(s_NN) = 130 GeV Au-Au collisions at RHIC. The K*0 to negative hadron, kaon and phi ratios are obtained and compared to the measurements in e+e-, pp and pbarp at various energies.Comment: 8 pages, 3 figures, proceedings of Strange Quarks in Matter (SQM2001), Frankfurt am Main, Germany, to be published in J. Phys.

Dynamic monitoring of single cell lysis in an impedance-based microfluidic device.

A microfluidic device that is capable of trapping and sensing dynamic variations in the electrical properties of individual cells is demonstrated. The device is applied to the real-time recording of impedance measurements of mouse embryonic stem cells (mESCs) during the process of membrane lysis, with the resulting changes in the electrical properties of cells during this process being quantitatively tracked over time. It is observed that the impedance magnitude decreases dramatically after cell membrane lysis. A significant shift in the phase spectrum is also observed during the time course of this process. By fitting experimental data to physical models, the electrical parameters of cells can be extracted and parameter variations quantified during the process. In the cell lysis experiments, the equivalent conductivity of the cell membrane is found to increase significantly due to pore formation in the membrane during lysis. An increase in the specific capacitance of the membrane is also observed. On the other hand, the conductivity of the cytoplasm is observed to decrease, which may be explained the fact that excess water enters the cell through the gradual permeabilization of the membrane during lysis. Cells can be trapped in the device for periods up to several days, and their electrical response can be monitored by real-time impedance measurements in a label-free and non-invasive manner. Furthermore, due to the highly efficient single cell trapping capacity of the device, a number of cells can be trapped and held in separate wells for concurrent parallel experiments, allowing for the possibility of stepped parametric experiments and studying cell heterogeneity by combining measurements across the array.Biotechnology and Biological Sciences Research Council (Grant ID: BB/K013726/1)This is the final version of the article. It first appeared from Springer via http://dx.doi.org/10.1007/s10544-016-0081-

QCD matter within a quasi-particle model and the critical end point

We compare our quasi-particle model with recent lattice QCD results for the equation of state at finite temperature and baryo-chemical potential. The inclusion of the QCD critical end point into models is discussed. We propose a family of equations of state to be employed in hydrodynamical calculations of particle spectra at RHIC energies and compare with the differential azimuthal anisotropy of strange and charm hadrons.Comment: talk at Quark Matter 2005, August 4 - 9, 2005, Budapest, Hungar

Quantitative single-molecule microscopy reveals that CENP-A(Cnp1) deposition occurs during G2 in fission yeast

The inheritance of the histone H3 variant CENP-A in nucleosomes at centromeres following DNA replication is mediated by an epigenetic mechanism. To understand the process of epigenetic inheritance, or propagation of histones and histone variants, as nucleosomes are disassembled and reassembled in living eukaryotic cells, we have explored the feasibility of exploiting photo-activated localization microscopy (PALM). PALM of single molecules in living cells has the potential to reveal new concepts in cell biology, providing insights into stochastic variation in cellular states. However, thus far, its use has been limited to studies in bacteria or to processes occurring near the surface of eukaryotic cells. With PALM, one literally observes and 'counts' individual molecules in cells one-by-one and this allows the recording of images with a resolution higher than that determined by the diffraction of light (the so-called super-resolution microscopy). Here, we investigate the use of different fluorophores and develop procedures to count the centromere-specific histone H3 variant CENP-A(Cnp1) with single-molecule sensitivity in fission yeast (Schizosaccharomyces pombe). The results obtained are validated by and compared with ChIP-seq analyses. Using this approach, CENP-A(Cnp1) levels at fission yeast (S. pombe) centromeres were followed as they change during the cell cycle. Our measurements show that CENP-A(Cnp1) is deposited solely during the G2 phase of the cell cycle

Heavy Quark Diffusion and Lattice Correlators

We study charmonia correlators at finite temperature. We analyze to what extent heavy quarkonia correlators are sensitive to the effect of heavy quark transport and whether it is possible to constrain the heavy quark diffusion constant by lattice calculations. Preliminary lattice calculations of quarkonia correlators performed on anisotropic lattices show that they are sensitive to the effect of heavy quark transport, but much detailed calculations are required to constrain the value of the heavy quark diffusion constant.Comment: Based on talks presented on Lattice 2005, Extreme QCD 2005 and Quark Matter 2005, 5 pages, 4 Figure

Estimation of non-linear site response in a deep Alpine valley

We simulate non-linear behaviour of soils during strong ground motion in the Rhône valley in southern Switzerland. Previous studies of the site response using weak ground motion, ambient noise and linear 3-D FD simulations suggest that the 2-D structure of the basin will lead to amplification factors of up to 12 in the frequency band between 0.5 and 10 Hz. To estimate the importance of non-linear soil behaviour during strong ground motion in the Rhône valley we simulate the response of a superficial soft layer with a fully non-linear 1-D finite difference code. The non-linear wave propagator is based on an effective stress constitutive soil model capable of predicting pore pressure evolution due to shear. We determine the required dilatancy parameters from laboratory analysis of soil samples using cyclic triaxial tests. In order to include the effect of the strong 2-D structure in our non-linear analysis synthetic seismograms are convolved with the transfer function of the basin and then propagated through a 1-D non-linear layer. We find that reduced amplification due to soil non-linearity can be expected at rock accelerations above 0.5 ms−2, and that de-amplification occurs at ground motion levels of approximately 2 ms−2. Nevertheless, the spectral accelerations simulated for the valley centre are still exceeding the design spectra at about 0.5 Hz for magnitudes above 6.0, which reflects the strong amplification of ground motion by the deep 2-D resonance of the basin. For frequencies above 1 Hz the design spectra are generally in agreement with the strongest simulated accelerations. We evaluate the occurrence of soil failure using the 5 per cent strain criterion as a function of hypocentral distance and magnitude. Results confirm observations of liquefaction reported after the 1855 Mw 6.4 earthquake of Visp, and they suggest that soil liquefaction may occur at distances beyond those predicted by empirical relations in the valley. Near the basin edge, however, the simulated liquefaction occurrence agrees with the empirical relations. These results suggest that the response of the whole structure needs to be simulated in order to estimate the non-linear seismic response of complex basins like the Rhône valle

Time dependence of Bragg forward scattering and self-seeding of hard x-ray free-electron lasers

Free-electron lasers (FELs) can now generate temporally short, high power x-ray pulses of unprecedented brightness, even though their longitudinal coherence is relatively poor. The longitudinal coherence can be potentially improved by employing narrow bandwidth x-ray crystal optics, in which case one must also understand how the crystal affects the field profile in time and space. We frame the dynamical theory of x-ray diffraction as a set of coupled waves in order to derive analytic expressions for the spatiotemporal response of Bragg scattering from temporally short incident pulses. We compute the profiles of both the reflected and forward scattered x-ray pulses, showing that the time delay of the wave $\tau$ is linked to its transverse spatial shift $\Delta x$ through the simple relationship $\Delta x = c\tau \cot\theta$, where $\theta$ is the grazing angle of incidence to the diffracting planes. Finally, we apply our findings to obtain an analytic description of Bragg forward scattering relevant to monochromatically seed hard x-ray FELs.Comment: 11 pages, 6 figure

Human NK Cell Subset Functions Are Differentially Affected by Adipokines

Background: Obesity is a risk factor for various types of infectious diseases and cancer. The increase in adipose tissue causes alterations in both adipogenesis and the production of adipocyte-secreted proteins (adipokines). Since natural killer (NK) cells are the host’s primary defense against virus-infected and tumor cells, we investigated how adipocyte-conditioned medium (ACM) affects functions of two distinct human NK cell subsets. Methods: Isolated human peripheral blood mononuclear cells (PBMCs) were cultured with various concentrations of human and murine ACM harvested on two different days during adipogenesis and analyzed by fluorescent-activated cell sorting (FACS). Results: FACS analyses showed that the expression of tumor necrosis factor-related apoptosis-inducing ligand (TRAIL), granzyme A (GzmA) and interferon (IFN)-γ in NK cells was regulated in a subset-specific manner. ACM treatment altered IFN-γ expression in CD56dim NK cells. The production of GzmA in CD56bright NK cells was differentially affected by the distinct adipokine compositions harvested at different states of adipogenesis. Comparison of the treatment with either human or murine ACM revealed that adipokine-induced effects on NK cell expression of the leptin receptor (Ob-R), TRAIL and IFN-γ were species-specific. Conclusion: Considering the growing prevalence of obesity and the various disorders related to it, the present study provides further insights into the roles human NK cell subsets play in the obesity-associated state of chronic low-grade inflammation