A cone formation theory of contamination in high resolution transmission electron microscopy

The formation theory of the contamination cone in high resolution transmission electron microscopy is discussed on the basis of a time dependent series of micrographs and their tilted images for evaluating the contamination process. For a high current density of an electron probe focused on the specimen, it was observed that two contaminated cones covering both upper and lower surfaces of a carbon substrate are formed as a function of the exposure time of the electron beam. From the measurement of the cross-section and height of contaminated cones, the contamination rate together with the volume rate, and time dependent shapes of various cones were analysed. The analysis was dependent on the diffusion cross-section and current density together with an average lifetime of adsorption molecules.     

Quantitative analysis of knock-on and thermal damage of biological specimens by electron irradiation in transmission electron microscopy

High-energy electrons are able to transfer momentum to nuclei, which results in displacement on to the interstitial lattice sites with a maximum transferred energy of 4 · 10⁴ eV for carbon at 100 keV. Moreover, most of the energy dissipated in energy losses is converted into heat, which results in melting and evaporation.The specimen temperature rise was calculated by the heat conduction theory and confirmed by the specimen drift due to the thermal damage. The damage can be reduced by a small area of illumination, the use of a metal-coated microgrid and small area scanning.A further displacement due to the knock-on collision and the resulting etching rate of biological specimens was measured. The damage is proportional to the current density in c cm^-2 at the specimen. The allowable maximum dose was obtained from the measurement of an etching rate with the weight loss and dry density of the specimens.It was found that the images affected by the electron irradiation, in which -H, C-H, C-N bonds break molecules in proteinaceous biological specimens are removed, and the remaining molecules are changed to stable carbon-rich molecules by deposition, polymerization and contamination. In addition, defect images were observed in high contrast, when compared with unaffected images taken with a small area scanning method.     

Ionization of molecular nitrogen by radiation from a channel surface discharge

Ionization of atmospheric-pressure nitrogen by nearly blackbody radiation from a channel surface discharge is investigated. By analyzing the data from measurements of the current of an electrostatic electron detector, the ionization rate of nitrogen and the time evolution of the electron density are determined. It is shown that the electron density reaches its maximum ～5 μs after the irradiation pulse. The results obtained indicate that the most probable mechanism for the observed nitrogen ionization is the formation of an ensemble of nitrogen molecules in metastable states and their subsequent collisional ionization, rather than direct one-photon or multiphoton ionization.     

Question 9: Quantum Self-Assembly and Photoinduced Electron Tunneling in Photosynthetic Systems of Artificial Minimal Living Cells

Natural and artificial living cells and their substructures are self-assembling, due to electron correlation interactions among biological and water molecules, which lead to attractive dispersion forces and hydrogen bonds. Dispersion forces are weak intermolecular forces that arise from the attractive force between quantum multipoles. A hydrogen bond is a special type of quantum attractive interaction that exists between an electronegative atom and a hydrogen atom bonded to another electronegative atom; and this hydrogen atom exist in two quantum states. The best method to simulate these dispersion forces and hydrogen bonds is to perform quantum mechanical non-local density functional potential calculations of artificial minimal living cells consisting of around 1,000 atoms. The cell systems studied are based on peptide nucleic acid and are 3.0–4.2 nm in diameter. The electron tunneling and associated light absorption of the most intense transitions, as calculated by the time dependent density functional theory method, differs from spectroscopic experiments by only 0.2–0.3 nm, which is within the value of experiment errors. This agreement implies that the quantum mechanically self-assembled structures of artificial minimal living cells very closely approximate realistic ones.     

Determination of chemical identity and occupancy from experimental density maps

Three basic electronic properties of molecules, electron density (ED), charge density (CD), and electrostatic potentials (ESP), are dependent on both atomic mobility and occupancy of components in the molecules. Small protein subunits may bind large macromolecular complexes with a reduced occupancy or an increased atomic mobility or both due to affinity‐based functional regulation, and so may substrates, products, cofactors, ions or solvent molecule to the active sites of enzymes. A quantitative theory is presented in this study that describes the dependence of atomic functions on atomic B‐factor in Fourier transforms of the corresponding maps. An application of this theory is described to an experimental ED map at 1.73‐Å resolution, and to an experimental CD map at 2.2‐Å resolution. All the three density functions are linearly proportional to occupancy when the structure factor F(000) term of Fourier transforms of experimental density maps is included. Upon application of this theory to both experimental CD and ESP maps recently reported for photosystem II‐light harvesting complex II supercomplex at 3.2‐Å resolution, the occupancy of two extrinsic protein subunits PsbQ and PsbP is determined to be 20.4 ± 0.2%, and the negative mean ESP value of vitreous ice displaced by the supercomplex on electron scattering path is estimated to be 3% of the mean ESP value of protein α‐helices.     

Optimizing cell arrays for accurate functional genomics

ABSTRACT: BACKGROUND: Cellular responses emerge from a complex network of dynamic biochemical reactions. In order to investigate them is necessary to develop methods that allow perturbing a high number of gene products in a flexible and fast way. Cell arrays (CA) enable such experiments on microscope slides via reverse transfection of cellular colonies growing on spotted genetic material. In contrast to multi-well plates, CA are susceptible to contamination among neighboring spots hindering accurate quantification in cell-based screening projects. Here we have developed a quality control protocol for quantifying and minimizing contamination in CA. RESULTS: We imaged checkered CA that express two distinct fluorescent proteins and segmented images into single cells to quantify the transfection efficiency and interspot contamination. Compared with standard procedures, we measured a 3-fold reduction of contaminants when arrays containing HeLa cells were washed shortly after cell seeding. We proved that nucleic acid uptake during cell seeding rather than migration among neighboring spots was the major source of contamination. Arrays of MCF7 cells developed without the washing step showed 7-fold lower percentage of contaminant cells, demonstrating that contamination is dependent on specific cell properties. CONCLUSIONS: Previously published methodological works have focused on achieving high transfection rate in densely packed CA. Here, we focused in an equally important parameter: The interspot contamination. The presented quality control is essential for estimating the rate of contamination, a major source of false positives and negatives in current microscopy based functional genomics screenings. We have demonstrate that a washing step after seeding enhances CA quality for HeLA but is not necessary for MCF7. The described method provides a way to find optimal seeding protocols for cell lines intended to be used for the first time in CA.     

The 7.5-A electron density and spectroscopic properties of a novel low-light B800 LH2 from Rhodopseudomonas palustris.

A novel low-light (LL) adapted light-harvesting complex II has been isolated from Rhodopseudomonas palustris. Previous work has identified a LL B800-850 complex with a heterogeneous peptide composition and reduced absorption at 850 nm. The work presented here shows the 850 nm absorption to be contamination from a high-light B800-850 complex and that the true LL light-harvesting complex II is a novel B800 complex composed of eight alpha beta(d) peptide pairs that exhibits unique absorption and circular dichroism near infrared spectra. Biochemical analysis shows there to be four bacteriochlorophyll molecules per alpha beta peptide rather than the usual three. The electron density of the complex at 7.5 A resolution shows it to be an octamer with exact 8-fold rotational symmetry. A number of bacteriochlorophyll geometries have been investigated by simulation of the circular dichroism and absorption spectra and compared, for consistency, with the electron density. Modeling of the spectra suggests that the B850 bacteriochlorophylls may be arranged in a radial direction rather than the usual tangential arrangement found in B800-850 complexes.     

Phenomenon of Quantum Entanglement in a System Composed of Two Minimal Protocells

The quantum mechanical self-assembly of two separate photoactive supramolecular systems with different photosynthetic centers was investigated by means of density functional theory methods. Quantum entangled energy transitions from one subsystem to the other and the assembly of logically controlled artificial minimal protocells were modeled. The systems studied were based on different photoactive sensitizer molecules covalently bonded to a non-canonical oxo-guanine::cytosine supramolecule with the precursor of a fatty acid (pFA) molecule attached via Van der Waals forces, all surrounded by water molecules. The electron correlation interactions responsible for the weak hydrogen and Van der Waals chemical bonds increased due to the addition of polar water solvent molecules. The distances between the separated sensitizer, nucleotide, pFA, and water molecules are comparable to Van der Waals and hydrogen bonding radii. As a result, the overall system becomes compressed, resulting in photo-excited electron tunneling from the sensitizer (bis(4-diphenylamine-2-phenyl)-squarine or 1,4-bis(N,N-dimethylamino)naphthalene) to the pFA molecules. Absorption spectra as well as electron transfer trajectories associated with the different excited states were calculated using time dependent density functional theory methods. The results allow separation of the quantum entangled photosynthetic transitions within the same minimal protocell and with the neighboring minimal protocell. The transferred electron is used to cleave a “waste” organic molecule resulting in the formation of the desired product. A two variable, quantum entangled AND logic gate was proposed, consisting of two input photoactive sensitizer molecules and one output (pFA molecule). It is proposed that a similar process might be applied for the destruction of tumor cancer cells or to yield building blocks in artificial cells.     

Complex formation between the copper protein, azurin and the cytochrome c peroxidase of Pseudomonas aeruginosa.

Reduced azurin reacts with the resting, oxidized cytochrome c peroxidase of Pseudomonas aeruginosa to yield time courses observed at 420 nm, which consist of the sum of two exponential processes. Each process exhibits a hyperbolic dependence of the observed rate constant on the reduced azurin concentration. The fraction of the total optical density change which each process contributes is found to be dependent on the reduced azurin concentration. This pattern of reactivity is maintained at pH values between 5.5 and 8.0. The data has been analyzed in terms of a complex formation between the two proteins followed by an intramolecular electron exchange reaction. This analysis yields values for the binding constants at each pH value. The intramolecular exchange reaction is independent of pH, whilst the pH dependence of the binding reaction suggests the involvement of a histidine residue in this process.     

31P- and 1H-NMR investigations of the effect of n-alcohols on the hydrolysis by phospholipase A2 of phospholipid vesicular membranes

31P- and 1H-NMR spectroscopy of small, unilamellar egg yolk phosphatidylcholine (PC) vesicles in the presence of the lanthanide ion Dy3+ have been used to study the effect of various n-alcohols on the permeability induced by the action of the enzyme phospholipase A2 (PLA2). The method allows the monitoring of the number of PC and lysoPC molecules in the outer and inner monolayers. The results indicate that the initial rate of hydrolysis of PC by PLA2 is increased by all the n-alcohols but in a chain-length dependent manner and that the maximum rate occurs at n = 8 (octan-1-ol). The subsequent rate is dependent upon the rate of transbilayer lipid exchange (flip-flop) of PC molecules from the inner to the outer monolayer. The vesicles only become permeable to the Dy3+ ions when lysoPC is mobilised in the flip-flop process of exchange of lipid molecules between the two monolayers. The n-alcohols affect both the time taken to initiate flip-flop of inner monolayer PC and the subsequent rate of permeability to Dy3+. The n-alcohols are seen to affect all the above rates in an identical chain-length dependent manner, indicating a common cause for all observations which we identify as the degree of clustering of the n-alcohol molecules in the bilayer. The results are discussed in terms of the chain-length dependent mechanism of n-alcohol interactions with the membrane and the mechanism by which the vesicles become permeable to Dy3+ ions.     

A two-stage model for the SIR outbreak: accounting for the discrete and stochastic nature of the epidemic at the initial contamination stage

The evolution of an infectious disease outbreak in an isolated population is split into two stages: a stochastic Markov process describing the initial contamination and a linked deterministic dynamical system with random initial conditions for the continued development of the outbreak. The initial contamination stage is well approximated by the randomized SI (susceptible/infected) model. We obtain the probability density function for the early behavior of the epidemic. This provides an appropriate distribution for the initial conditions with which to describe the subsequent deterministic evolution of the system. We apply the method of matching asymptotic expansions to link the two stages. This allows us to estimate the standard deviation of the number of infectives in the developed outbreak, and the statistical characteristics of the outbreak time. The potential trajectories caused by the stochastic nature of the contamination stage show greatest divergence at the initial and fade-out stages and coincide most tightly just after the peak of the epidemic. The time to the peak of the outbreak is not strongly dependent on the initial trajectory.     

Positive detection of mycoplasma contamination by the whole-mount preparation of cell cultures for transmission electron microscopy.

Low-level mycoplasma contamination of cell cultures is difficult to recognize with presently available techniques. This report describes the adaptation of the whole-mount technique, usually used for scanning microscopy, for transmission electron microscopy. The differentiation between microvilli and the equal-sized filamentous mycoplasma is based on the differential density obtained by the use of the method described. This method allows positive identification of mycoplasma and reduces the preparation time and the time necessary for scanning the preparation.     

Echinococcus granulosus: lethal effect of low voltage direct electric current on hydatid cyst protoscoleces

We have studied a small scale method for killing hydatid cyst protoscoleces using low voltage direct electric current. After collecting hydatid cysts from infected organs of slaughtered animals, protoscoleces were cultured in four different media: hydatid cyst fluid, RPMI, normal saline, and Tris buffer, respectively. Protoscoleces from each of the above media were then transferred to an electrolysis device through which different electric current densities were applied. For measuring the survival rate of protoscoleces, flame cell movement and eosin staining was used. The results show that the survival rate of protoscoleces in hydatid fluid was dependent on the electric current density and the time of the applied current. Current densities of 62.5 mA/cm2 (11 V), 53.71 mA/cm2 (10 V), and 18.18 mA/cm2 (5 V) after 1, 2, and 3 min, respectively, killed all the parasites in the hydatid fluid. However, a current density of 7 mA/cm2 (9 V) in RPMI medium after 3 min was most effective.     

Displacement of apolipophorin III from the surface of low density lipophorin by human apolipoprotein A-I

A hybrid low density lipophorin particle (LDLp) was prepared by incubation with human apolipoprotein (apo) A-I in vitro. ApoA-I associated with LDLp in a concentration dependent, saturable manner which was accompanied by dissociation of apolipophorin III (apoLp-III). The apoA-I hybrid LDLp had the same lipid composition, density and morphology as native LDLp indicating that displacement of apoLp-III by apoA-I did not affect its structural properties. The molar ratio of apoLp-I:apoLp-II:apoLp-III was maximally reduced from 1:1:16 to 1:1:2 in native versus hybrid LDLp with the latter particle binding 7 molecules of apoA-I. The inability of apoA-I to displace the remaining 2 apoLp-III supports the concept that these apoLp-III molecules are not equivalent to the other fourteen. Native and hybrid LDLp particles were both metabolized to high density lipophorin in vivo. The displacement reaction represents a novel method for the production of apolipoprotein hybrids of LDLp and the results indicate that apoA-I has an inherently higher affinity for lipid surfaces than apoLp-III.     

Cell surface expression of H2 antigens on primary sensory neurons in response to acute but not latent herpes simplex virus infection in vivo.

CD8(+) T lymphocytes and class I major histocompatibility complex (MHC-I) molecules profoundly influence the severity of neuronal herpes simplex virus (HSV) infection in experimentally infected mice. Paradoxically, neurons are classically regarded as MHC-I deficient. However, it is shown here that H2-encoded heavy chains (alphaCs) and their associated light chain, beta2 microglobulin, are present on the surfaces of primary sensory neurons recovered from sensory ganglia within 1 to 2 weeks of HSV infection. During this time, some neurons are found to be tightly associated with T cells in vivo. Prior data showed that termination of productive HSV infection in the peripheral nervous system is not dependent on cell-mediated lysis of infected neurons. Consistent with these data, immunogold electron microscopy showed that the density of cell surface H2 on neurons is an order of magnitude lower than on satellite glia, which is predicted to favor a noncytolytic CD8 cell response.     

Dynamics of cannibalism in equal‐aged cohorts of Spodoptera frugiperda

1. Antagonistic interactions in herbivorous insects are often density‐dependent, so rates are predicted to vary dynamically over time as density changes. Fatal intraspecific interactions, especially cannibalism, occur between equal‐aged larvae in young first‐ and second‐instar Spodoptera frugiperda (J.E. Smith). 2. A cannibalism experiment was conducted, starting with seven different densities of neonate S. frugiperda larvae, each replicated 50 times. Larvae were examined daily for the duration of the first and second instars (7 days). Seven‐day mortality was density‐dependent. 3. A stochastic mathematical model was developed in which per‐capita mortality from antagonistic interactions among equal‐aged larvae varies dynamically as density changes. A maximum likelihood method was developed to estimate the conditional per‐capita mortality rate from antagonistic interactions given an intraspecific encounter. An alternative model with mean‐mortality from antagonistic interactions that depends only on the initial larval density was also developed. 4. The models were fitted to the experimental data, and compared using log‐likelihood. The dynamic model fitted the cannibalism data significantly better than the time‐averaged mortality model for all starting densities for the experimental data, implying that density‐dependent mortality varied dynamically over time even within short 7‐day periods. 5. The conditional per‐capita mortality rate from antagonistic interactions was also density‐dependent, possibly because encounters became more aggregated at higher density, or because the probability that a larva died from the interaction was higher at higher density, or both.     

Separation of mitochondria from microbodies of Pisum sativum (L. cv. Alaska) cotyledons

A method is described for separating mitochondria from microbodies in cotyledon preparations of Pisum sativum L. cv. Alaska. Pure and intact mitochondria were obtained on a continuous: discontinuous sucrose density gradient as shown by marke-enzyme assay and electron microscopy. Manipulation of sucrose-gradient construction to widen the distance between organelles provided a quick method for the separation of the mitochondria from the microbodies. The shorter time of exposure of mitochondria to centrifugation and osmotic stress produces mitochondria free of contamination.     

Microwave generation by a superluminal source at limiting current densities

It is well known that high-power directed wideband electromagnetic radiation in the microwave range can be generated by a superluminal pulse of the electron emission current. The operation of a simple emitting element driven by a superluminal current pulse and consisting of an accelerating diode with a photocathode and a source of ionizing radiation that initiates electron emission from the cathode is considered. It is shown that the parameters of an elementary superluminal source obey scaling relations that are determined by the growth rate of the electron emission current from the photocathode and the parameters of the accelerating diode. The limiting anode current density and the limiting values of the characteristics of electromagnetic radiation achievable in such a system are determined. The effect of the finite dimensions of the accelerating system on the parameters of the emitter is investigated, and the spatiotemporal characteristics of the generated electromagnetic fields are obtained.     

Optical characteristics and parameters of gas-discharge plasma in a mixture of mercury dibromide vapor with neon

Results are presented from studies of the optical characteristics and parameters of plasma of a dielectric barrier discharge in a mixture of mercury dibromide vapor with neon—the working medium of a non-coaxial exciplex gas-discharge emitter. The electron energy distribution function, the transport characteristics, the specific power losses for electron processes, the electron density and temperature, and the rate constants for the processes of elastic and inelastic electron scattering by the working mixture components are determined as functions of the reduced electric field. The rate constant of the process leading to the formation of exciplex mercury monobromide molecules is found to be 1.6 × 10^?14 m³/s for a reduced electric field of E/N = 15 Td, at which the maximum emission intensity in the blue-green spectral region (λ_max = 502 nm) was observed in this experiment.