Function of histaminergic retinopetal axons in rat and primate retinas

Mammalian retinas receive input from histaminergic neurons in the posterior hypothalamus. These neurons are most active during the waking state of the animal, but their role in retinal information processing is not known. To determine the function of these retinopetal axons, their targets in the rat and monkey retina were identified. Using antibodies to three histamine receptors, HR1, HR2, and HR3, the immunolabeling was analyzed by confocal and electron microscopy. These experiments showed that mammalian retinas possess histamine receptors. In macaques and baboons, diurnal species, HR3 receptors were found at the apex of ON-bipolar cell dendrites in cone pedicles and rod spherules, sclerad to the other neurotransmitter receptors that have been localized there. In addition, HR1 histamine receptors were localized to large puncta in the inner plexiform layer, a subset of ganglion cells and retinal blood vessels. In rats, a nocturnal species, the localization of histamine receptors in the retina was markedly different. Most HR1 receptors were localized to dopaminergic amacrine cells and on elements in the rod spherule. To determine how histaminergic retinopetal axons contribute to retinal information processing, responses of retinal ganglion cells to histamine were analyzed. The effects of histamine on the maintained and light-evoked activity of retinal ganglion cells were analyzed. In monkeys, histamine and the HR3 agonist, methylhistamine, increased or decreased the maintained activity of most ganglion cells, but a few did not respond. The responses of a subset of ganglion cells to light stimuli were decreased by histamine, a finding suggesting that histaminergic retinopetal axons contribute to light adaptation during the day. In rats, histamine nearly always increased the maintained activity and produced both increases and decreases in the light responses. The effects of histamine on maintained activity of ganglion cells in the rat can be partially attributed to HR1-mediated changes in the activity of dopaminergic amacrine cells, at night. Together, these experiments provide the first indication of the function of retinopetal axons in mammalian retinas. ^

Function of cardiolipin in mitochondria of Saccharomyces cerevisiae

Cardiolipin and its precursor phosphatidylglycerol, phospholipids found uniquely in membranes engaged in oxidative phosphorylation, play important roles in multimeric complexes of the energy transducing system (ETS) associated with the inner mitochondrial membrane. A combined molecular genetic and biochemical approach was used to more precisely define the role of cardiolipin in cell processes. ^ Strains of yeast Saccharomyces cerevisiae unable to synthesize cardiolipin because of the crd1Δ allele (encodes cardiolipin synthase) with different phenotypes were analyzed to determine which phenotypes are due to lack of cardiolipin. We concluded that many of the severe phenotypes ascribed to cells lacking cardiolipin, particularly when grown at 37°C, are because of the synergistic interaction of the crd1Δ mutation with the reduced expression of the PET56 gene which encodes a component essential for the formation of functional mitochondrial ribosomes. We also demonstrate that much of the reduced mitochondrial function in crd1Δ is because of reduced expression of ETS components at elevated temperature. ^ A crd1Δ mutant of S. cerevisiae has less severe physiological changes than strains lacking both phosphatidylglycerol and cardiolipin due to an increased level of phosphatidylglycerol, which might partially substitute for the cardiolipin-requiring functions. By varying the level of cardiolipin, we were able to correlate phenotypes in a dose-dependent manner with the level of cardiolipin to support more strongly an involvement of cardiolipin in a particular cellular process. There is almost complete lack of a supercomplex composed of cytochrome bc1 complex (complex III) and cytochrome c oxidase (complex IV) in extracts of cardiolipin-lacking mitochondria when compared to wild type cells and the level of supercomplex varies in proportion to the cardiolipin levels. Reduced cardiolipin levels also compromise the growth properties of yeast in a dose-dependent manner suggesting that the loss in growth efficiency is related to a role of cardiolipin that cannot be replaced by phosphatidylglycerol. An independent kinetic approach was performed to compare organization of the respiratory chain in wild-type and cardiolipin-lacking mitochondria. Cardiolipin-lacking mitochondria display kinetic properties for electron transfer between complexes III and IV via cytochrome c consistent with cytochrome c being a freely diffusible carrier, confirming complexes III and IV exist as individual complexes and not associated into a supercomplex in cardiolipin-lacking mitochondria. ^

Modeling Techniques for the High-Resolution Interpretation of Cryo-Electron Microscopy Reconstructions

Essential biological processes are governed by organized, dynamic interactions between multiple biomolecular systems. Complexes are thus formed to enable the biological function and get dissembled as the process is completed. Examples of such processes include the translation of the messenger RNA into protein by the ribosome, the folding of proteins by chaperonins or the entry of viruses in host cells. Understanding these fundamental processes by characterizing the molecular mechanisms that enable then, would allow the (better) design of therapies and drugs. Such molecular mechanisms may be revealed trough the structural elucidation of the biomolecular assemblies at the core of these processes. Various experimental techniques may be applied to investigate the molecular architecture of biomolecular assemblies. High-resolution techniques, such as X-ray crystallography, may solve the atomic structure of the system, but are typically constrained to biomolecules of reduced flexibility and dimensions. In particular, X-ray crystallography requires the sample to form a three dimensional (3D) crystal lattice which is technically di‑cult, if not impossible, to obtain, especially for large, dynamic systems. Often these techniques solve the structure of the different constituent components within the assembly, but encounter difficulties when investigating the entire system. On the other hand, imaging techniques, such as cryo-electron microscopy (cryo-EM), are able to depict large systems in near-native environment, without requiring the formation of crystals. The structures solved by cryo-EM cover a wide range of resolutions, from very low level of detail where only the overall shape of the system is visible, to high-resolution that approach, but not yet reach, atomic level of detail. In this dissertation, several modeling methods are introduced to either integrate cryo-EM datasets with structural data from X-ray crystallography, or to directly interpret the cryo-EM reconstruction. Such computational techniques were developed with the goal of creating an atomic model for the cryo-EM data. The low-resolution reconstructions lack the level of detail to permit a direct atomic interpretation, i.e. one cannot reliably locate the atoms or amino-acid residues within the structure obtained by cryo-EM. Thereby one needs to consider additional information, for example, structural data from other sources such as X-ray crystallography, in order to enable such a high-resolution interpretation. Modeling techniques are thus developed to integrate the structural data from the different biophysical sources, examples including the work described in the manuscript I and II of this dissertation. At intermediate and high-resolution, cryo-EM reconstructions depict consistent 3D folds such as tubular features which in general correspond to alpha-helices. Such features can be annotated and later on used to build the atomic model of the system, see manuscript III as alternative. Three manuscripts are presented as part of the PhD dissertation, each introducing a computational technique that facilitates the interpretation of cryo-EM reconstructions. The first manuscript is an application paper that describes a heuristics to generate the atomic model for the protein envelope of the Rift Valley fever virus. The second manuscript introduces the evolutionary tabu search strategies to enable the integration of multiple component atomic structures with the cryo-EM map of their assembly. Finally, the third manuscript develops further the latter technique and apply it to annotate consistent 3D patterns in intermediate-resolution cryo-EM reconstructions. The first manuscript, titled An assembly model for Rift Valley fever virus, was submitted for publication in the Journal of Molecular Biology. The cryo-EM structure of the Rift Valley fever virus was previously solved at 27Å-resolution by Dr. Freiberg and collaborators. Such reconstruction shows the overall shape of the virus envelope, yet the reduced level of detail prevents the direct atomic interpretation. High-resolution structures are not yet available for the entire virus nor for the two different component glycoproteins that form its envelope. However, homology models may be generated for these glycoproteins based on similar structures that are available at atomic resolutions. The manuscript presents the steps required to identify an atomic model of the entire virus envelope, based on the low-resolution cryo-EM map of the envelope and the homology models of the two glycoproteins. Starting with the results of the exhaustive search to place the two glycoproteins, the model is built iterative by running multiple multi-body refinements to hierarchically generate models for the different regions of the envelope. The generated atomic model is supported by prior knowledge regarding virus biology and contains valuable information about the molecular architecture of the system. It provides the basis for further investigations seeking to reveal different processes in which the virus is involved such as assembly or fusion. The second manuscript was recently published in the of Journal of Structural Biology (doi:10.1016/j.jsb.2009.12.028) under the title Evolutionary tabu search strategies for the simultaneous registration of multiple atomic structures in cryo-EM reconstructions. This manuscript introduces the evolutionary tabu search strategies applied to enable a multi-body registration. This technique is a hybrid approach that combines a genetic algorithm with a tabu search strategy to promote the proper exploration of the high-dimensional search space. Similar to the Rift Valley fever virus, it is common that the structure of a large multi-component assembly is available at low-resolution from cryo-EM, while high-resolution structures are solved for the different components but lack for the entire system. Evolutionary tabu search strategies enable the building of an atomic model for the entire system by considering simultaneously the different components. Such registration indirectly introduces spatial constrains as all components need to be placed within the assembly, enabling the proper docked in the low-resolution map of the entire assembly. Along with the method description, the manuscript covers the validation, presenting the benefit of the technique in both synthetic and experimental test cases. Such approach successfully docked multiple components up to resolutions of 40Å. The third manuscript is entitled Evolutionary Bidirectional Expansion for the Annotation of Alpha Helices in Electron Cryo-Microscopy Reconstructions and was submitted for publication in the Journal of Structural Biology. The modeling approach described in this manuscript applies the evolutionary tabu search strategies in combination with the bidirectional expansion to annotate secondary structure elements in intermediate resolution cryo-EM reconstructions. In particular, secondary structure elements such as alpha helices show consistent patterns in cryo-EM data, and are visible as rod-like patterns of high density. The evolutionary tabu search strategy is applied to identify the placement of the different alpha helices, while the bidirectional expansion characterizes their length and curvature. The manuscript presents the validation of the approach at resolutions ranging between 6 and 14Å, a level of detail where alpha helices are visible. Up to resolution of 12 Å, the method measures sensitivities between 70-100% as estimated in experimental test cases, i.e. 70-100% of the alpha-helices were correctly predicted in an automatic manner in the experimental data. The three manuscripts presented in this PhD dissertation cover different computation methods for the integration and interpretation of cryo-EM reconstructions. The methods were developed in the molecular modeling software Sculptor (http://sculptor.biomachina.org) and are available for the scientific community interested in the multi-resolution modeling of cryo-EM data. The work spans a wide range of resolution covering multi-body refinement and registration at low-resolution along with annotation of consistent patterns at high-resolution. Such methods are essential for the modeling of cryo-EM data, and may be applied in other fields where similar spatial problems are encountered, such as medical imaging.

Intercellular adhesion and membrane polarity in rat hepatocytes: Localization of cell -CAM 105 and other domain-specific membrane proteins {\it in situ\/} and {\it in vitro\/} by electron microscopy

Cell-CAM 105 has been identified as a cell adhesion molecule (CAM) based on the ability of monospecific and monovalent anti-cell-CAM 105 antibodies to inhibit the reaggregation of rat hepatocytes. Although one would expect to find CAMs concentrated in the lateral membrane domain where adhesive interactions predominate, immunofluorescence analysis of rat liver frozen sections revealed that cell-CAM 105 was present exclusively in the bile canalicular (BC) domain of the hepatocyte. To more precisely define the in situ localization of cell-CAM 105, immunoperoxidase and electron microscopy were used to analyze intact and mechanically dissociated fixed liver tissue. Results indicate that although cell-CAM 105 is apparently restricted to the BC domain in situ, it can be detected in the pericanalicular region of the lateral membranes when accessibility to lateral membranes is provided by mechanical dissociation. In contrast, when hepatocytes were labeled following incubation in vitro under conditions used during adhesion assays, cell-CAM 105 had redistributed to all areas of the plasma membrane. Immunofluorescence analysis of primary hepatocyte cultures revealed that cell-CAM 105 and two other BC proteins were localized in discrete domains reminscent of BC while cell-CAM 105 was also present in regions of intercellular contact. These results indicate that the distribution of cell-CAM 105 under the experimental conditions used for cell adhesion assays differs from that in situ and raises the possibility that its adhesive function may be modulated by its cell surface distribution. The implications of these and other findings are discussed with regard to a model for BC formation.^ Analysis of molecular events involved in BC formation would be accelerated if an in vitro model system were available. Although BC formation in culture has previously been observed, repolarization of cell-CAM 105 and two other domain-specific membrane proteins was incomplete. Since DMSO had been used by Isom et al. to maintain liver-specific gene expression in vitro, the effect of this differentiation system on the polarity of these membrane proteins was examined. Based on findings presented here, DMSO apparently prolongs the expression and facilitates polarization of hepatocyte membrane proteins in vitro. ^

ESPINA: a tool for the automated segmentation and counting of synapses in large stacks of electron microscopy images

The synapses in the cerebral cortex can be classified into two main types, Gray’s type I and type II, which correspond to asymmetric (mostly glutamatergic excitatory) and symmetric (inhibitory GABAergic) synapses, respectively. Hence, the quantification and identification of their different types and the proportions in which they are found, is extraordinarily important in terms of brain function. The ideal approach to calculate the number of synapses per unit volume is to analyze 3D samples reconstructed from serial sections. However, obtaining serial sections by transmission electron microscopy is an extremely time consuming and technically demanding task. Using focused ion beam/scanning electron microscope microscopy, we recently showed that virtually all synapses can be accurately identified as asymmetric or symmetric synapses when they are visualized, reconstructed, and quantified from large 3D tissue samples obtained in an automated manner. Nevertheless, the analysis, segmentation, and quantification of synapses is still a labor intensive procedure. Thus, novel solutions are currently necessary to deal with the large volume of data that is being generated by automated 3D electron microscopy. Accordingly, we have developed ESPINA, a software tool that performs the automated segmentation and counting of synapses in a reconstructed 3D volume of the cerebral cortex, and that greatly facilitates and accelerates these processes.

Luminescence from two-dimensional electron gases in InAlN/GaN heterostructures with different In content

The luminescence properties of InxAl1−xN/GaN heterostructures are investigated systematically as a function of the In content (x = 0.067 − 0.208). The recombination between electrons confined in the two-dimensional electron gas and free holes in the GaN template is identified and analyzed. We find a systematic shift of the recombination with increasing In content from about 80 meV to only few meV below the GaN exciton emission. These results are compared with model calculations and can be attributed to the changing band profile and originating from the polarization gradient between InAlN and GaN.

Piezoelectric and electroacoustic properties of Ti-doped AlN thin films as a function of Ti content

In this work we present the assessment of the structural and piezoelectric properties of Al(0.5-x)TixN0.5 compounds (titanium content menor que6% atomic), which are expected to possess improved properties than conventional AlN films, such as larger piezoelectric activity, thermal stability of frequency and temperature resistance. Al:Ti:N films were deposited from a twin concentric target of Al and Ti by reactive AC sputtering, which provided films with a radial gradient of the Ti concentration. The properties of the films were investigated as a function of their composition, which was measured by electron dispersive energy dispersive X-ray spectroscopy and Rutherford backscattering spectrometry. The microstructure and morphology of the films were assessed by X-ray diffraction and infrared reflectance. Their electroacoustic properties and dielectric constant were derived from the frequency response of BAW test resonators. Al:Ti:N films properties appear to be strongly dependent on the Ti content, which modifies the AlN wurtzite crystal structure leading to greater dielectric constant, lower sound velocities, lower electromechanical factor and moderately improved temperature coefficient of the resonant frequency.

Electron temperature versus laser intensity times wavelength squared: a comparison of theory and experiments

The peak temperature in the corona of plasma ejected by a laser-irradiated slab is discussed in terms of a one-electron-temperature model. Both heat-flux saturation and pulse rise-time effects are considered;the intensity in the rising half of the pulse is approximated by a linear function of time, I(t) = Iot/r. The temperature is found to be proportional to (IQX2)273 and a function of I0X4/r. Above a certain value of I0X4/T, the plasma presents two characteristic temperatures (at saturation and at the critical surface) which can be identified with experimentally observed cold- and hot-electron temperatures. The results are compared with extensive experimental data available for both nd and CO2 lasers, I0(W'cnf2) X2 (/um) starting around 1012. The agreement is good if substantial flux inhibition is assumed (flux-limit factor f = 0.03), and fails for I0X2 above 1O1S. Results for both ablation pressure and mass ablation rate are also given.

Nonlocal electron heat relaxation in a plasma shock at arbitrary ionization number

A recently obtained nonlocal expression for the electron heat flux valid for arbitrary ionization numbers Z is used to study the structure of a plane shock wave in a fully ionized plasma. Nonlocal effects are only important in the foot of the electronic preheating region, where the electron temperature gradient is the steepest. The results are quantified as a function of a characteristic Knudsen number of that region. This work also generalizes to arbitrary values of Z previous results on plasma shock wave structure.

Bare-tether cathodic contact through thermoionic emission by low work-function materials

A new material, C12A7 : electride, which might present a work function as low as 0.6 eV and moderately high temperature stability, was recently proposed as coating for floating bare tethers. Arising from heating under space operation, current is emitted by thermionic emission along a thus coated cathodic segment. A preliminary study on the space-charge-limited (SCL) double layer in front of the cathodic segment is presented using Langmuir’s SCL electron current between cylindrical electrodes and orbital-motion-limited ion-collection sheath. A detailed calculation of current and bias profiles along the entire tether length is carried out with ohmic effects and the transition from SCL to full Richardson-Dushman emission included. Analysis shows that in the simplest drag mode, under typical orbital and tether conditions, thermionic emission leads to a short cathodic section and may eliminate the need for an active cathodic device and its corresponding gas feed requirements and power subsystem, which results in a truly “propellant-less” tether system for such basic applications as de-orbiting low earth orbit satellites.

Role of surface trap states on two-dimensional electron gas density in InAlN/AlN/GaN heterostructures

In order to clarify the effect of charged dislocations and surface donor states on the transport mechanisms in polar AlInN/AlN/GaN heterostructures, we have studied the current-voltage characteristics of Schottky junctions fabricated on AlInN/AlN/GaN heterostructures. The reverse-bias leakage current behaviour has been interpreted with a Poole-Frenkel emission of electrons from trap states near the metal-semiconductor junction to dislocation induced states. The variation of the Schottky barrier height as a function of the AlN layer thickness has been measured and discussed, considering the role of the surface states in the formation of the two dimensional electron gas at AlN/GaN interface.

Mechanical behavior of tungsten-vanadium-lanthana alloys as function of temperature

The mechanical behavior of three tungsten (W) alloys with vanadium (V) and lanthana (La2O3) additions (W–4%V, W–1%La2O3, W–4%V–1%La2O3) processed by hot isostatic pressing (HIP) have been compared with pure-W to analyze the influence of the dopants. Mechanical characterization was performed by three point bending (TPB) tests in an oxidizing air atmosphere and temperature range between 77 (immersion tests in liquid nitrogen) and 1273 K, through which the fracture toughness, flexural strength, and yield strength as function of temperature were obtained. Results show that the V and La2O3 additions improve the mechanical properties and oxidation behavior, respectively. Furthermore, a synergistic effect of both dopants results in an extraordinary increase of the flexure strength, fracture toughness and resistance to oxidation compared to pure-W, especially at higher temperatures. In addition, a new experimental method was developed to obtain a very small notch tip radius (around 5–7 μm) and much more similar to a crack through the use of a new machined notch. The fracture toughness results were lower than those obtained with traditional machining of the notch, which can be explained with electron microscopy, observations of deformation in the rear part of the notch tip. Finally, scanning electron microscopy (SEM) examination of the microstructure and fracture surfaces was used to determine and analyze the relationship between the macroscopic mechanical properties and the micromechanisms of failure involved, depending on the temperature and the dispersion of the alloy.

Direct Vlasov simulations of electron-attracting cylindrical Langmuir probes in flowing plasmas

Current collection by positively polarized cylindrical Langmuir probes immersed in flowing plasmas is analyzed using a non-stationary direct Vlasov-Poisson code. A detailed description of plasma density spatial structure as a function of the probe-to-plasma relative velocity U is presented. Within the considered parametric domain, the well-known electron density maximum close to the probe is weakly affected by U. However, in the probe wake side, the electron density minimum becomes deeper as U increases and a rarified plasma region appears. Sheath radius is larger at the wake than at the front side. Electron and ion distribution functions show specific features that are the signature of probe motion. In particular, the ion distribution function at the probe front side exhibits a filament with positive radial velocity. It corresponds to a population of rammed ions that were reflected by the electric field close to the positively biased probe. Numerical simulations reveal that two populations of trapped electrons exist: one orbiting around the probe and the other with trajectories confined at the probe front side. The latter helps to neutralize the reflected ions, thus explaining a paradox in past probe theory.

Mechanical characterisation of tungsten-1wt.% yttrium oxide as a function of temperature and atmosphere

This study evaluates the mechanical behaviour of an Y2O3-dispersed tungsten (W) alloy and compares it to a pure W reference material. Both materials were processed via mechanical alloying (MA) and subsequent hot isostatic pressing (HIP). We performed non-standard three-point bending (TPB) tests in both an oxidising atmosphere and vacuum across a temperature range from 77 K, obtained via immersion in liquid nitrogen, to 1473 K to determine the mechanical strength, yield strength and fracture toughness. This research aims to evaluate how the mechanical behaviour of the alloy is affected by oxides formed within the material at high temperatures, primarily from 873 K, when the materials undergo a massive thermal degradation. The results indicate that the alloy is brittle to a high temperature (1473 K) under both atmospheres and that the mechanical properties degrade significantly above 873 K. We also used Vickers microhardness tests and the dynamic modulus by impulse excitation technique (IET) to determine the elastic modulus at room temperature. Moreover, we performed nanoindentation tests to determine the effect of size on the hardness and elastic modulus; however, no significant differences were found. Additionally, we calculated the relative density of the samples to assess the porosity of the alloy. Finally, we analysed the microstructure and fracture surfaces of the tested materials via field emission scanning electron microscopy (FE-SEM) and transmission electron microscopy (TEM). In this way, the relationship between the macroscopic mechanical properties and micromechanisms of failure could be determined based on the temperature and oxides formed

Mechanical behavior and deformation micromechanisms of polypropylene nonwoven fabrics as a function of temperature and strain rate

The mechanical behavior and the deformation and failure micromechanisms of a thermally-bonded polypropylene nonwoven fabric were studied as a function of temperature and strain rate. Mechanical tests were carried out from 248 K (below the glass transition temperature) up to 383 K at strain rates in the range ≈10−3 s−1 to 10−1 s−1. In addition, individual fibers extracted from the nonwoven fabric were tested under the same conditions. Micromechanisms of deformation and failure at the fiber level were ascertained by means of mechanical tests within the scanning electron microscope while the strain distribution at the macroscopic level upon loading was determined by means of digital image correlation. It was found that the nonwoven behavior was mainly controlled by the properties of the fibers and of the interfiber bonds. Fiber properties determined the nonlinear behavior before the peak load while the interfiber bonds controlled the localization of damage after the peak load. The influence of these properties on the strength, ductility and energy absorbed during deformation is discussed from the experimental observations.