Electron Microscopic Analysis of a Spherical Mitochondrial Structure

Mitochondria undergo dynamic structural alterations to meet changing needs and to maintain homeostasis. We report here a novel mitochondrial structure. Conventional transmission electron microscopic examination of murine embryonic fibroblasts treated with carbonyl cyanide m-chlorophenylhydrazone (CCCP), a mitochondrial uncoupler, found that more than half of the mitochondria presented a ring-shaped or C-shaped morphology. Many of these mitochondria seemed to have engulfed various cytosolic components. Serial sections through individual mitochondria indicated that they formed a ball-like structure with an internal lumen surrounded by the membranes and containing cytosolic materials. Notably, the lumen was connected to the external cytoplasm through a small opening. Electron tomographic reconstruction of the mitochondrial spheroids demonstrated the membrane topology and confirmed the vesicular configuration of this mitochondrial structure. The outside periphery and the lumen were defined by the outer membranes, which were lined with the inner membranes. Matrix and cristae were retained but distributed unevenly with less being kept near the luminal opening. Mitochondrial spheroids seem to form in response to oxidative mitochondrial damage independently of mitophagy. The structural features of the mitochondrial spheroids thus represent a novel mitochondrial dynamics.     

Antenna-Attached Parabolic Probe for Excitation and Collection Modes in SNOM

A novel optical fiber probe with a parabola-like shape and a nano-antenna mounted on the center of its endface is proposed for simultaneous excitation and collection modes in scanning near-field optical microscopy. The working principles of the probe are demonstrated, and its optical properties are theoretically investigated and compared with the conventional tip-on-aperture probe. It shows that the probe can greatly boost both the enhancement factor for the excitation mode and the collection efficiency for the collection mode. The proposed probe is a promising tool to realize low-cost and high resolution for a wide variety of near-field measurements in biology, physics, and chemistry.     

Electron Microscopy of the Spherical Body of Oral Spirochetes In Vitro: Further Studies

The surface and inner structure of the spherical bodies (SB) produced by the human oral treponeme strain G7201, similar to Treponema macrodentium, were studied by electron microscopy. Ultrathin sectioning and scanning techniques demonstrated that in the presence of a high concentration of sucrose, the outer envelope of one or both terminal ends of this oral spirochete changed into a swollen structure, the SB. Spirochetal cells adhered firmly to the surface of the resultant body. The membrane of the SB, i.e. the outer envelope, enclosed the coiled protoplasmic cylinder and five axial fibrils which were located between the envelope and the cylinder. Large expanded protoplasmic cylinders were observed, surrounded by a partially disrupted double membrane in some SBs. A number of frizzly fibrous structures, which differed from axial fibrils in number and shape, were also observed within these SBs. Except for abnormal or partially broken cylinders, the protoplasmic cylinders tended to be located close to the inner surface of the SB membrane, resulting in a central vacant space with occasional axial fibrils. These findings suggest that the oral spirochete produces an SB by terminal expansion of the outer envelope in the presence of high concentrations of sucrose. The outer envelope of the SB, which consists of two electron-dense layers, has the property of binding spirochetal cells to its outer layer and the protoplasmic cylinder and axial fibrils to the inner layer. Some protoplasmic cylinders were also observed to be swollen in the presence of high sucrose concentrations.     

Unique Mechanisms of Excitation Energy Transfer, Electron Transfer and Photoisomerization in Biological Systems

We discuss unique mechanisms typical in the elementary processes ofbiological functions. We focus on three topics. Excitation energytransfer in the light-harvesting antenna systems of photosyntheticbacteria is unique in its structure and the energy transfer mechanism. Inthe case of LH2 of Rhodopseudomonas acidophila, the B850 intra-ringenergy transfer and the inter-ring energy transfer between B800 and B850take place by the intermediate coupling mechanism of energy transfer. Theexcitonic coherent domain shows a wave-like movement along the ring, andthis property is expected to play a significant role in the inter-ringenergy transfer between LH2's. The electron transfer in biological systemsis mostly long-range electron transfer that occurs by the electrontunneling through the protein media. There is a long-standing problem thatwhich part of protein media is used for the electron tunneling root. As aresult of our detailed analysis, we found that the global electron tunnelingroot is a little winded with a width of a few angstrom, reflecting theproperty of tertiary and secondary structures of the protein and it isaffected by the thermal fluctuation of protein structure. Photoisomerizationof rhodopsin is very unique: The cis-transphotoisomerization ofrhodopsin occurs only around the C11 = C12 bond in the counterclockwisedirection. Its molecular mechanism is resolved by our MD simulation studyusing the structure of rhodopsin which was recently obtained by the X-raycrystallographic analysis.     

Diagnostic Potentials of Diamagnetic Measurements with Two Loops in Tokamaks

Plasma Physics Reports - The magnetic flux through the diamagnetic loop consists of two parts: one is produced by the poloidal current in the plasma and another by the external currents. Separation...     

An Internal View of the Spherical Body of Treponema macrodentium as Revealed by Scanning Electron Microscopy

The osmium-dimethyl sulfoxide-osmium method for clear visualization of intracellular structure was used to observe the detailed inner structure of the spherical bodies produced in vitro by a human oral treponeme. Scanning electron microscopy of the cracked spherical body revealed no morphological differences between the outer and inner surfaces of the spherical body membrane, and that multiple folded or somewhat linear main bodies adhere closely to the inner surface. In addition, axial flagella partially free from the main bodies spread widely within the body to make a network, and a number of blebs ranging from approximately 1 μm to 0.2 μm in diameter were located near the terminal or subterminal areas of the main bodies. The origin of the blebs and the mechanism of spherical body formation are discussed.     

Computational Modeling Reveals Dendritic Origins of GABAA-Mediated Excitation in CA1 Pyramidal Neurons

GABA is the key inhibitory neurotransmitter in the adult central nervous system, but in some circumstances can lead to a paradoxical excitation that has been causally implicated in diverse pathologies from endocrine stress responses to diseases of excitability including neuropathic pain and temporal lobe epilepsy. We undertook a computational modeling approach to determine plausible ionic mechanisms of GABA_A-dependent excitation in isolated post-synaptic CA1 hippocampal neurons because it may constitute a trigger for pathological synchronous epileptiform discharge. In particular, the interplay intracellular chloride accumulation via the GABA_A receptor and extracellular potassium accumulation via the K/Cl co-transporter KCC2 in promoting GABA_A-mediated excitation is complex. Experimentally it is difficult to determine the ionic mechanisms of depolarizing current since potassium transients are challenging to isolate pharmacologically and much GABA signaling occurs in small, difficult to measure, dendritic compartments. To address this problem and determine plausible ionic mechanisms of GABA_A-mediated excitation, we built a detailed biophysically realistic model of the CA1 pyramidal neuron that includes processes critical for ion homeostasis. Our results suggest that in dendritic compartments, but not in the somatic compartments, chloride buildup is sufficient to cause dramatic depolarization of the GABA_A reversal potential and dominating bicarbonate currents that provide a substantial current source to drive whole-cell depolarization. The model simulations predict that extracellular K⁺ transients can augment GABA_A-mediated excitation, but not cause it. Our model also suggests the potential for GABA_A-mediated excitation to promote network synchrony depending on interneuron synapse location - excitatory positive-feedback can occur when interneurons synapse onto distal dendritic compartments, while interneurons projecting to the perisomatic region will cause inhibition.     

Higher Order Plasmonic Modes Excited in Ag Triangular Nanoplates by an Electron Beam

Ag triangular nanoplates are known to generate strong plasmonic resonances when excited by both light and electron beams. Experimental electron energy-loss spectra (EELS) and maps were acquired using an aberration-corrected JEOL-ARM microscope. The corner, edge and centre modes that are often observed in such structures were also observed in these measurements. In addition, novel higher order internal modes were observed and were found to be well reproduced by theoretical calculations using boundary element method (BEM). These modes are “dark modes” so are not observed in the optical extinction spectra. They are confined surface propagating modes and are analogous to laser cavity modes.     

Cherenkov Excitation of Spatial Waves by a Straight Nonrelativistic Electron Beam in a Plasma Waveguide

The problem of the excitation of plasma waves by a thin-walled annular electron beam in a waveguide filled entirely with a plasma is analyzed in the quasistatic approximation. The instability growth rates are derived and are studied as functions of the waveguide parameters. The evolution of different seed perturbations in the nonlinear stage of the instability is investigated.     

Interaction of Inward and Outward Cylindrical and Spherical Solitary Rings in Quantum Electron Ion Dust Plasmas

Plasma Physics Reports - Wave–wave interaction, specifically solitary ring interaction in nonplanar geometry is an important source of information to study the nature and the characteristics...     

Spherical Parasporal Inclusions of the Lepidoptera-Specific and Coleoptera-Specific Bacillus thuringiensis Strains: A Comparative Electron Microscopic Study

Four Lepidoptera-specific Bacillus thuringiensis strains that belong to the four H serogroups (serovars sumiyoshiensis, fukuokaensis, darmstadiensis, and japonensis) and a Coleoptera (Scarabaeidae)-specific strain belonging to serovar japonensis were examined for comparative ultrastructure of spherical parasporal inclusions. The prominent feature of the inclusions of the Lepidoptera-specific strains was the existence of thick, highly electron-dense envelopes surrounding a homogeneous protein matrix. The envelopes were 15.0–66.7 nm thick and consisted of 5–12 layers of membrane. This is also the case with inclusions of a Coleoptera-specific strain. The ultrastructure of inclusions from the five strains was in marked contrast to that of the bipyramidal parasporal inclusions produced by a Lepidoptera-specific serovar sotto strain. Received: 26 July 1999 / Accepted: 30 August 1999     

Bayesian Weighing of Electron Cryo-Microscopy Data for Integrative Structural Modeling

1. Download high-res image (283KB)
2. Download full-size image

     

Modeling of Electron Hole Transport within a Small Ribosomal Subunit

Russian Journal of Bioorganic Chemistry - Synchronized operation of various parts of the ribosome during protein synthesis implies the presence of a coordinating pathway, however, this is still...     

Excitation and Optimization Modeling of Surface Plasmon Polaritons in a Concentric Circular Metallic Grating Film

Interaction behavior between surface plasmon polaritons (SPPs) and Hankel-distributed diffracted waves (DWs) on a silver concentric circular grating film is studied using a rigorous coupled-wave technique for circular structure. It is shown that the numerical technique reveals the excitation characteristics of SPPs in the circular metal grating as well as provides an accurate calculation of SPP intensities for further optimization designs. Results show that the SPPs can be excited by various DWs through the control of wavelength and angle of the incident light. The most efficient excitation of SPPs from this circular metal grating structure can be obtained from the +1^st-order DW under a normal incidence with wavelength close to the grating period, and the optimal thickness and duty cycle of the grating are found to be 370 and 0.5 nm, respectively. It is shown that the optimized intensity of SPPs excited from circular metal grating can be higher than that from strip metal grating by over one order of magnitude.     

Modeling the Biodegradation Kinetics of Perchlorate in the Presence of Oxygen and Nitrate as Competing Electron Acceptors

A mathematical model was developed to describe the biodegradation kinetics of perchlorate in the presence of nitrate and oxygen as competing electron acceptors. The rate of perchlorate degradation is described as a function of the electron donor (acetate) degradation rate, the concentration of the alternate electron acceptors, and rates of biomass growth and decay. The kinetics of biomass growth are described using a modified Monod model, and inhibition factors are incorporated to describe the influence of oxygen and nitrate on perchlorate degradation. In order to develop input parameters for the model, a series of batch biodegradation studies were performed using Azospira suillum JPLRND, a perchlorate-degrading strain isolated from groundwater. This strain is capable of utilizing oxygen, nitrate, or perchlorate as terminal electron acceptors. The maximum specific growth rate (μ_max) and half-saturation constant (K _S ^don) for the bacterium when utilizing either perchlorate or nitrate were similar; 0.16 per h and 158 mg acetate/L, respectively. However, these parameters were different when the strain was growing on oxygen. In this case, μ_max and K _S ^don were 0.22 per h and 119 mg acetate/L, respectively. The batch experiments also revealed that nitrate inhibits perchlorate biodegradation by this strain. This finding was incorporated into the model by applying an inhibition coefficient (K _i ^nit) value of 25 mg nitrate/L. Combined with appropriate groundwater transport models, this model can be used to predict perchlorate biodegradation during in situ remediation efforts.     

Modeling of Alternative Pathways of Electron Transport to Photosystem I in Isolated Thylakoids

Kinetics of dark decay of absorbance changes at 830 nm (₈₃₀) was examined in thylakoids isolated from leaves of pea seedlings at various concentrations of exogenous NADPH or NADH. Absorbance changes were induced by far-red light to avoid electron donation from photosystem II. In the presence of either biological reductant, the kinetics of ₈₃₀ decay reflecting dark reduction of 700⁺, the primary electron donor of photosystem I, was fitted by a single exponential term. The rate of 700⁺ reduction increased with the rise in the concentration of both NADPH and NADH. The values of K _M and V _max for 700⁺ reduction estimated from concentration dependences were 105 ± 21 M and 0.32/s for NADPH or 21 ± 8 M and 0.12/s for NADH. The rate of P700⁺ reduction by either NADPH or NADH significantly increased in the presence of rotenone, a specific inhibitor of chloroplast reductase. The value of V _max was changed only in the presence of rotenone, whereas K _m was practically unaffected. Unlike the chloroplasts of intact leaves, the only enzyme mediating the input of reducing equivalents from NADPH or NADH to the electron transport chain was concluded to be present in thylakoids.     

Surface Erosion of Metals under the Effect of Plasma Flows Typical of Transient Processes in Tokamaks

Plasma Physics Reports - It is shown theoretically that under the effect of plasma flows typical of transient processes in tokamaks not only can Kelvin–Helmholtz instability develop and waves...     

Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens

Geobacter species are of great interest for environmental and biotechnology applications as they can carry out direct electron transfer to insoluble metals or other microorganisms and have the ability to assimilate inorganic carbon. Here, we report on the capability and key enabling metabolic machinery of Geobacter metallireducens GS-15 to carry out CO₂ fixation and direct electron transfer to iron. An updated metabolic reconstruction was generated, growth screens on targeted conditions of interest were performed, and constraint-based analysis was utilized to characterize and evaluate critical pathways and reactions in G. metallireducens. The novel capability of G. metallireducens to grow autotrophically with formate and Fe(III) was predicted and subsequently validated in vivo. Additionally, the energetic cost of transferring electrons to an external electron acceptor was determined through analysis of growth experiments carried out using three different electron acceptors (Fe(III), nitrate, and fumarate) by systematically isolating and examining different parts of the electron transport chain. The updated reconstruction will serve as a knowledgebase for understanding and engineering Geobacter and similar species.     

Modes of Action of ADP-Ribosylated Elongation Factor 2 in Inhibiting the Polypeptide Elongation Cycle: A Modeling Study

Despite the fact that ADP-ribosylation of eukaryotic elongation factor 2 (EF2) leads to inhibition of protein synthesis, the mechanism by which ADP-ribosylated EF2 (ADPR•EF2) causes this inhibition remains controversial. Here, we applied modeling approaches to investigate the consequences of various modes of ADPR•EF2 inhibitory actions on the two coupled processes, the polypeptide chain elongation and ADP-ribosylation of EF2. Modeling of experimental data indicates that ADPR•EF2 fully blocks the late-phase translocation of tRNAs; but the impairment in the translocation upstream process, mainly the GTP-dependent factor binding with the pretranslocation ribosome and/or the guanine nucleotide exchange in EF2, is responsible for the overall inhibition kinetics. The reduced ADPR•EF2-ribosome association spares the ribosome to bind and shield native EF2 against toxin attack, thereby deferring the inhibition of protein synthesis inhibition and inactivation of EF2. Minimum association with the ribosome also keeps ADPR•EF2 in an accessible state for toxins to catalyze the reverse reaction when nicotinamide becomes available. Our work underscores the importance of unveiling the interactions between ADPR•EF2 and the ribosome, and argues against that toxins inhibit protein synthesis through converting native EF2 to a competitive inhibitor to actively disable the ribosome.