Band-selective hetero- and homonuclear cross-polarization using trains of shaped pulses

Summary The performance of solution cross-polarization using trains of shaped pulses on two channels is investigated by computer simulation and experiment. It is determined that a Waltz modulation pattern of Gaussian pulses of individual flip angles of 225°, issued to two coupled spins simulatneously, yields excellent coherence transfer with good phasing behavior. Simulations and experimental verification were carried out for both heteronuclear cross-polarization between two restricted areas (e.g. ¹H–¹³C) and for homonuclear cross-polarization between two spectral regions (e.g. ¹³CO–¹³C). It is shown that shaped cross-polarization behaves as pure heteronuclear cross-polarization when the two radiofrequency (rf) fields are far apart, while it behaves in some aspects analogous to homonuclear cross-polarization when the two rf fields approach each other. The novel coherence-transfer sequence, referred to as cosine-modulated shaped Waltz (CSW), was implemented in a 3D (H)C(CCO)NH experiment using an 18-kDa isotopically labeled protein.     

Metastable equilibrium with random local fluctuations: Simulations of dynamic receptor pattern generation in a fluid mosaic membrane

The generation of receptors in the animal cell's membrane was simulated by a model consisting of units in four possible states within a hexagonal area (playboard) ofn units of a triangular network. The state of each unit was determined by the previous state or itself and of its six nearest neighbours, as regulated by a set of transition rules, which kept the mean relative frequency (m.r.f.) of each state constant. The transition rules were applied to the system exactlyn times, regardedless whether this involved selection of a unit on 0, 1, 2 or more occasions (programme random selection with repeat; RS-R). Comparison to previous results obtained by other ways of application of the rules has shown that the RS-R programme accounted for the highest m.r.f. of quiet (Q) units and Q clusters (sub-patterns), and also for the longest survival of Q configurations through several generations. Functioning of the model under the RS-R programme simulates an integrated system in metastable equilibrium with random local fluctuations, such as the cytoplasmic membrane is imagined to be in standardized environmental conditions. The formation-persistence-disintegration cycle of the sub-patterns is believed to simulate the dynamic generation of transitory receptor configurations in the cell membrane.     

Attenuation of photobleaching in two-photon excitation fluorescence from green fluorescent protein with shaped excitation pulses

The two-photon excitation fluorescence (TPEF) process of an enhanced green fluorescent protein (EGFP) for fluorescence signals was adaptively controlled by the phase-modulation of femtosecond pulses. After the iteration of pulse shaping, a twofold increase in the ratio of the fluorescence signal to the laser peak power was achieved. Compared with conventional pulses optimized for peak power, phase-optimized laser pulses reduced the bleaching rate of EGFP by a factor of 4 while maintaining the same intensity of the fluorescence signal. Our method will provide a powerful solution to various problems confronting researchers, such as the photobleaching of dyes in two-photon excitation microscopy.     

Rapid generation of random mutant libraries

A simple and efficient method utilizing in vivo recombination to create recombinant libraries incorporating the products of PCR amplification is described. This will be especially useful for generating large pools of randomly mutagenized clones after error-prone PCR mutagenesis. Here we investigate various parameters to optimize this approach and we demonstrate that as little as 1 pmole of PCR fragment can generate a library with greater than 104 clones in a single transformation without ligation.     

Cell membrane permeability during the cell generation cycle in Chinese hamster ovary cells

Summary Changes in the permeability of the cell membrane in cultured Chinese hamster ovary cells at different stages of the cell cycle were investigated. These were followed by measuring the intracellular retention of fluorescein molecules produced by the enzymatic hydrolysis of fluoresceindiacetate in the cytoplasm of CHO cells. Rate constants for the permeation of fluorescein have been calculated.     

Second-harmonic generation imaging of membrane potential with retinal analogues

Second-harmonic generation (SHG) by membrane-incorporated probes is a nonlinear optical signal that is voltage-sensitive and the basis of a sensitive method for imaging membrane potential. The voltage dependence of SHG by four different probes, three retinoids (all-trans retinal), and two new retinal analogs, 3-methyl-7-(4′-dimethylamino-phenyl)-2,4,6-heptatrienal (AR-3) and 3,7-dimethyl-9-(4′-dimethylamino-phenyl)-2,4,6,8-nonatetraenal (AR-4), and a styryl dye (FM4-64), were compared in HEK-293 cells. Results were analyzed by fitting data with an expression based on an electrooptic mechanism for SHG, which depends on the complex-valued first- and second-order nonlinear electric susceptibilities (χ₂ and χ₃) of the probe. This gave values for the voltage sensitivity at the cell's resting potential, the voltage where the SHG is minimal, and the amplitude of the signal at that voltage for each of the four compounds. These measures show that χ₂ and χ₃ are complex numbers for all compounds except all-trans retinal, consistent with the proximities of excitation and/or emission wavelengths to molecular resonances. Estimates of probe orientation and location in the membrane electric field show that, for the far-from-resonance case, the shot noise-limited signal/noise ratio depends on the location of the probe in the membrane, and on χ₃ but not on χ₂.     

DNA-based random number generation in security circuitry

DNA-based circuit design is an area of research in which traditional silicon-based technologies are replaced by naturally occurring phenomena taken from biochemistry and molecular biology. This research focuses on further developing DNA-based methodologies to mimic digital data manipulation. While exhibiting fundamental principles, this work was done in conjunction with the vision that DNA-based circuitry, when the technology matures, will form the basis for a tamper-proof security module, revolutionizing the meaning and concept of tamper-proofing and possibly preventing it altogether based on accurate scientific observations. A paramount part of such a solution would be self-generation of random numbers. A novel prototype schema employs solid phase synthesis of oligonucleotides for random construction of DNA sequences; temporary storage and retrieval is achieved through plasmid vectors. A discussion of how to evaluate sequence randomness is included, as well as how these techniques are applied to a simulation of the random number generation circuitry. Simulation results show generated sequences successfully pass three selected NIST random number generation tests specified for security applications.     

Cell culture of infantile digital fibromatosis

Two cell cultures were obtained from excised tumors of two cases of infantile digital fibromatosis (IDF). The cells had eosinophilic cytoplasmic inclusion bodies characteristic of IDF. Although the rate of cells bearing the inclusion bodies was high at the earlier passage levels, it was reduced to zero by the 15th passage of one of the cultures, but the cells of the other culture continued to produce the inclusion bodies even at the 30th passage. Chromosome analysis revealed both cultures to have tetraploid cells in approximately 8 to 12% in late passage levels. No viruslike particles were found in electron microscopy. No tumors developed when the cells were inoculated into athymic, nude mice subcutaneously. These cell cultures will be valuable for characterizing the eosinophilic inclusion bodies and determining the origin of the tumors.     

Permeabilization of cell membrane by programmed form of electrical pulses

The role of the shape of electric pulses of cell permeabilization and lysis was studied using the newly developed DPS electroporator. The effects of bipolar pulses, steep rising and falling edges in the pulses, delays between pulses, and shapes of DC signals between the edges on the lysis of bovine oocytes and the permeabilization of their cell membranes were investigated. Comparing the permeabilization rates with the lysis rates revealed a number of correlations, which make it possible to optimize the pulse shapes for achieving maximum permeabilization rates while keeping the lysis rates low. The optimization of pulse shape is essential for improving the procedure of electroporation in mammalian cloning technology.     

Prospore membrane formation: how budding yeast gets shaped in meiosis

During meiosis in Saccharomyces cerevisiae four daughter cells, called spores, are generated within the boundaries of the mother cell. This cell differentiation process requires de novo synthesis of prospore membranes (PSMs), which are the precursors of the spore plasma membranes. Assembly of these membranes is initiated at the spindle pole bodies (SPBs) during meiosis II. At this stage of the cell cycle, 4 SPBs are present. Two different meiosis-specific structures are known to be required for PSM formation. At the SPBs, specialized attachments, called the meiotic plaques, provide the required functionality necessary for the recruitment and assembly of the membranes. During subsequent membrane elongation, a second structure becomes important. This proteinaceous assembly forms a coat, called the leading edge protein coat (LEP coat), which covers the boundaries of the membranes. Assembly of the coat occurs at sites next to the SPBs, whereas its disassembly is concomitant to the closure of the membranes. This mini review discusses our current understanding of how the meiotic plaque and the LEP coat might function during biogenesis of the prospore membrane.     

Modeling the membrane potential generation of bacteriorhodopsin

The archaeon Halobacterium salinarum can grow phototrophically with only light as its energy source. It uses the retinal containing and light-driven proton pump bacteriorhodopsin to enhance the membrane potential which drives the ATP synthase. Therefore, a model of the membrane potential generation of bacteriorhodopsin is of central importance to the development of a mathematical model of the bioenergetics of H. salinarum. To measure the current produced by bacteriorhodopsin at different light intensities and clamped voltages, we expressed the gene in Xenopus laevis oocytes. We present current-voltage measurements and a mathematical model of the current-voltage relationship of bacteriorhodopsin and its generation of the membrane potential. The model consists of three intermediate states, the BR, L, and M states, and comparisons between model predictions and experimental data show that the L to M reaction must be inhibited by the membrane potential. The model is not able to fit the current-voltage measurements when only the M to BR phase is membrane potential dependent, while it is able to do so when either only the L to M reaction or both reactions (L to M and M to BR) are membrane potential dependent. We also show that a decay term is necessary for modeling the rate of change of the membrane potential.     

Nanosecond electric pulses cause mitochondrial membrane permeabilization in Jurkat cells

Nanosecond, high‐voltage electric pulses (nsEP) induce permeabilization of the plasma membrane and the membranes of cell organelles, leading to various responses in cells including cytochrome c release from mitochondria and caspase activation associated with apoptosis. We report here evidence for nsEP‐induced permeabilization of mitochondrial membranes in living cells. Using three different methods with fluorescence indicators—rhodamine 123 (R123), tetramethyl rhodamine ethyl ester (TMRE), and cobalt‐quenched calcein—we have shown that multiple nsEP (five pulses or more, 4 ns duration, 10 MV/m, 1 kHz repetition rate) cause an increase of the inner mitochondrial membrane permeability and an associated loss of mitochondrial membrane potential. These effects could be a consequence of nsEP permeabilization of the inner mitochondrial membrane or the activation of mitochondrial membrane permeability transition pores. Plasma membrane permeabilization (YO‐PRO‐1 influx) was detected in addition to mitochondrial membrane permeabilization. Bioelectromagnetics 33:257–264, 2012. © 2011 Wiley Periodicals, Inc.     

Simulate the diffusion of hydrated ions by nanofiltration membrane process with random walk

We propose a new diffusion model describing the diffusion behaviours of hydrated ions in the process of nanofiltration (NF) based on the random walk (RW) theory when the NF membrane is uncharged or low charged. In this model, the hydration of ions and their deformation capacity are considered. The structure of the membrane is idealised into a lozenge shape and the diameter of membrane pore is defined as gapsize. A computer program named RW system in chemistry is developed to simulate based on this model. Six familiar ions Li⁺, Na⁺, Mg²⁺, Al³⁺, K⁺ and Ca²⁺ are investigated. Their characteristics are calculated by Gaussian 03, Pople, Inc., Wallingford, CT. The diffusivities of hydrated ions are calculated and discussed. The results show that the hydration of ions cannot be ignored in NF process when the membrane pore size is near the dimensions of the hydrated ions.     

Optimizing the generation of random amplified polymorphic DNAs in chrysanthemum

Many conditions of the RAPD reaction procedure may influence the result. This paper presents rapid detection of influential factors with a fractional factorial experiment. A more extensive study of these factors is also presented. Polymerase brand, thermal cycler brand, annealing temperature, and primer, are important factors in obtaining good DNA yields and optimal fragment patterns. Each primer has its optimal annealing temperature, and this is not correlated with the GC content of the primer. Optimal species-primer combinations have to be found by trial and error.     

A massively connected subthalamic nucleus leads to the generation of widespread pulses.

A composite model of the subthalamic nucleus is developed from physiological and anatomical considerations. First, study of a geometric model of the anatomical arrangements of projection neurons within the nucleus indicates that they form a massively connected network. Second, given the excitatory nature of these neurons, their threshold and peak firing rates, a simple model of neuron responses reveals that large regions of this highly interconnected nucleus can respond to excitatory input in the form of a wide-spread uniform pulse. Such widespread pulses of activity may act as a braking signal that resets the major basal ganglia output nuclei.