Nuclear Pore Complex Number and Distribution throughout the Saccharomyces cerevisiae Cell Cycle by Three-Dimensional Reconstruction from Electron Micrographs of Nuclear Envelopes

The number of nuclear pore complexes (NPCs) in individual nuclei of the yeast Saccharomyces cerevisiae was determined by computer-aided reconstruction of entire nuclei from electron micrographs of serially sectioned cells. Nuclei of 32 haploid cells at various points in the cell cycle were modeled and found to contain between 65 and 182 NPCs. Morphological markers, such as cell shape and nuclear shape, were used to determine the cell cycle stage of the cell being examined. NPC number was correlated with cell cycle stage to reveal that the number of NPCs increases steadily, beginning in G1-phase, suggesting that NPC assembly occurs continuously throughout the cell cycle. However, the accumulation of nuclear envelope observed during the cell cycle, indicated by nuclear surface area, is not continuous at the same rate, such that the density of NPCs per unit area of nuclear envelope peaks in apparent S-phase cells. Analysis of the nuclear envelope reconstructions also revealed no preferred NPC-to-NPC distance. However, NPCs were found in large clusters over regions of the nuclear envelope. Interestingly, clusters of NPCs were most pronounced in early mitotic nuclei and were found to be associated with the spindle pole bodies, but the functional significance of this association is unknown.

Three-dimensional modeling of and ligand docking to vitamin D receptor ligand binding domain

The ligand binding domain of the human vitamin D receptor (VDR) was modeled based on the crystal structure of the retinoic acid receptor. The ligand binding pocket of our VDR model is spacious at the helix 11 site and confined at the β-turn site. The ligand 1α,25-dihydroxyvitamin D3 was assumed to be anchored in the ligand binding pocket with its side chain heading to helix 11 (site 2) and the A-ring toward the β-turn (site 1). Three residues forming hydrogen bonds with the functionally important 1α- and 25-hydroxyl groups of 1α,25-dihydroxyvitamin D3 were identified and confirmed by mutational analysis: the 1α-hydroxyl group is forming pincer-type hydrogen bonds with S237 and R274 and the 25-hydroxyl group is interacting with H397. Docking potential for various ligands to the VDR model was examined, and the results are in good agreement with our previous three-dimensional structure-function theory.

Photoactive yellow protein: A structural prototype for the three-dimensional fold of the PAS domain superfamily

PAS domains are found in diverse proteins throughout all three kingdoms of life, where they apparently function in sensing and signal transduction. Although a wealth of useful sequence and functional information has become recently available, these data have not been integrated into a three-dimensional (3D) framework. The very early evolutionary development and diverse functions of PAS domains have made sequence analysis and modeling of this protein superfamily challenging. Limited sequence similarities between the ∼50-residue PAS repeats and one region of the bacterial blue-light photosensor photoactive yellow protein (PYP), for which ground-state and light-activated crystallographic structures have been determined to high resolution, originally were identified in sequence searches using consensus sequence probes from PAS-containing proteins. Here, we found that by changing a few residues particular to PYP function, the modified PYP sequence probe also could select PAS protein sequences. By mapping a typical ∼150-residue PAS domain sequence onto the entire crystallographic structure of PYP, we show that the PAS sequence similarities and differences are consistent with a shared 3D fold (the PAS/PYP module) with obvious potential for a ligand-binding cavity. Thus, PYP appears to prototypically exhibit all the major structural and functional features characteristic of the PAS domain superfamily: the shared PAS/PYP modular domain fold of ∼125–150 residues, a sensor function often linked to ligand or cofactor (chromophore) binding, and signal transduction capability governed by heterodimeric assembly (to the downstream partner of PYP). This 3D PAS/PYP module provides a structural model to guide experimental testing of hypotheses regarding ligand-binding, dimerization, and signal transduction.

Characterizations of diverse residue clusters in protein three-dimensional structures.

We present new methods for identifying and analyzing statistically significant residue clusters that occur in three-dimensional (3D) protein structures. Residue clusters of different kinds occur in many contexts. They often feature the active site (e.g., in substrate binding), the interface between polypeptide units of protein complexes, regions of protein-protein and protein-nucleic acid interactions, or regions of metal ion coordination. The methods are illustrated with 3D clusters centering on four themes. (i) Acidic or histidine-acidic clusters associated with metal ions. (ii) Cysteine clusters including coordination of metals such as zinc or iron-sulfur structures, cysteine knots prominent in growth factors, multiple sets of buried disulfide pairings that putatively nucleate the hydrophobic core, or cysteine clusters of mostly exposed disulfide bridges. (iii) Iron-sulfur proteins and charge clusters. (iv) 3D environments of multiple histidine residues. Study of diverse 3D residue clusters offers a new perspective on protein structure and function. The algorithms can aid in rapid identification of distinctive sites, suggest correlations among protein structures, and serve as a tool in the analysis of new structures.

Three-dimensional planar object tracking with sub-pixel accuracy

Subpixel techniques are commonly used to increase the spatial resolution in tracking tasks. Object tracking with targets of known shape permits obtaining information about object position and orientation in the three-dimensional space. A proper selection of the target shape allows us to determine its position inside a plane and its angular and azimuthal orientation under certain limits. Our proposal is demonstrated both numerical and experimentally and provides an increase the accuracy of more than one order of magnitude compared to the nominal resolution of the sensor. The experiment has been performed with a high-speed camera, which simultaneously provides high spatial and temporal resolution, so it may be interesting for some applications where this kind of targets can be attached, such as vibration monitoring and structural analysis.

Three-dimensional solitons in coupled atomic-molecular Bose-Einstein condensates

We present a theoretical analysis of three-dimensional (3D) matter-wave solitons and their stability properties in coupled atomic and molecular Bose-Einstein condensates (BECs). The soliton solutions to the mean-field equations are obtained in an approximate analytical form by means of a variational approach. We investigate soliton stability within the parameter space described by the atom-molecule conversion coupling, the atom-atom s-wave scattering, and the bare formation energy of the molecular species. In terms of ordinary optics, this is analogous to the process of sub- or second-harmonic generation in a quadratic nonlinear medium modified by a cubic nonlinearity, together with a phase mismatch term between the fields. While the possibility of formation of multidimensional spatiotemporal solitons in pure quadratic media has been theoretically demonstrated previously, here we extend this prediction to matter-wave interactions in BEC systems where higher-order nonlinear processes due to interparticle collisions are unavoidable and may not be neglected. The stability of the solitons predicted for repulsive atom-atom interactions is investigated by direct numerical simulations of the equations of motion in a full 3D lattice. Our analysis also leads to a possible technique for demonstrating the ground state of the Schrodinger-Newton and related equations that describe Bose-Einstein condensates with nonlocal interparticle forces.

Theoretical investigation of convective instability in inclined and fluid-saturated three-dimensional fault zones.

The convective instability of pore-fluid flow in inclined and fluid-saturated three-dimensional fault zones has been theoretically investigated in this paper. Due to the consideration of the inclined three-dimensional fault zone with any values of the inclined angle, it is impossible to use the conventional linear stability analysis method for deriving the critical condition (i.e., the critical Rayleigh number) which can be used to investigate the convective instability of the pore-fluid flow in an inclined three-dimensional fault zone system. To overcome this mathematical difficulty, a combination of the variable separation method and the integration elimination method has been used to derive the characteristic equation, which depends on the Rayleigh number and the inclined angle of the inclined three-dimensional fault zone. Using this characteristic equation, the critical Rayleigh number of the system can be numerically found as a function of the inclined angle of the three-dimensional fault zone. For a vertically oriented three-dimensional fault zone system, the critical Rayleigh number of the system can be explicitly derived from the characteristic equation. Comparison of the resulting critical Rayleigh number of the system with that previously derived in a vertically oriented three-dimensional fault zone has demonstrated that the characteristic equation of the Rayleigh number is correct and useful for investigating the convective instability of pore-fluid flow in the inclined three-dimensional fault zone system. The related numerical results from this investigation have indicated that: (1) the convective pore-fluid flow may take place in the inclined three-dimensional fault zone; (2) if the height of the fault zone is used as the characteristic length of the system, a decrease in the inclined angle of the inclined fault zone stabilizes the three-dimensional fundamental convective flow in the inclined three-dimensional fault zone system; (3) if the thickness of the stratum is used as the characteristic length of the system, a decrease in the inclined angle of the inclined fault zone destabilizes the three-dimensional fundamental convective flow in the inclined three-dimensional fault zone system; and that (4) the shape of the inclined three-dimensional fault zone may affect the convective instability of pore-fluid flow in the system. (C) 2004 Published by Elsevier B.V.

Using two dimensional sectional distributions to infer three dimensional volumetric distributions - Validation using tomography

The critical process parameter for mineral separation is the degree of mineral liberation achieved by comminution. The degree of liberation provides an upper limit of efficiency for any physical separation process. The standard approach to measuring mineral liberation uses mineralogical analysis based two-dimensional sections of particles which may be acquired using a scanning electron microscope and back-scatter electron analysis or from an analysis of an image acquired using an optical microscope. Over the last 100 years, mathematical techniques have been developed to use this two dimensional information to infer three-dimensional information about the particles. For mineral processing, a particle that contains more than one mineral (a composite particle) may appear to be liberated (contain only one mineral) when analysed using only its revealed particle section. The mathematical techniques used to interpret three-dimensional information belong, to a branch of mathematics called stereology. However methods to obtain the full mineral liberation distribution of particles from particle sections are relatively new. To verify these adjustment methods, we require an experimental method which can accurately measure both sectional and three dimensional properties. Micro Cone Beam Tomography provides such a method for suitable particles and hence, provides a way to validate methods used to convert two-dimensional measurements to three dimensional estimates. For this study ore particles from a well-characterised sample were subjected to conventional mineralogical analysis (using particle sections) to estimate three-dimensional properties of the particles. A subset of these particles was analysed using a micro-cone beam tomograph. This paper presents a comparison of the three-dimensional properties predicted from measured two-dimensional sections with the measured three-dimensional properties.

Assessment of cell viability in a three-dimensional enzymatically cross-linked collagen scaffold

Microbial transglutaminase (mTGase) is an enzyme that introduces a covalent bond between peptide bound glutamine and lysine residues. Proteins cross-linked in this manner are often more resistant to proteolytic degradation and show increased tensile strength. This study evaluates the effects of mTGase mediated cross-linking of collagen on the cellular morphology, behaviour and viability of murine 3T3 fibroblasts following their seeding into collagen scaffolds. Additionally, cell mediated scaffold contraction, porosity and level of cross-linking of the scaffold has been analysed using image analysis software, scanning electron microscopy (SEM), colorimetric assays, and Fourier transform infrared spectroscopy (FTIR). We demonstrate that the biocompatibility and cellular morphology, when comparing cultures of fibroblasts integrated in mTGase cross-linked collagen scaffolds with the native collagen counterparts, remained unaffected. It has been also elicited that the structural characteristics of collagen have been preserved while introducing enzymatically resistant covalent bonds.

Three-dimensional modeling of the human eye based on magnetic resonance imaging

PURPOSE. A methodology for noninvasively characterizing the three-dimensional (3-D) shape of the complete human eye is not currently available for research into ocular diseases that have a structural substrate, such as myopia. A novel application of a magnetic resonance imaging (MRI) acquisition and analysis technique is presented that, for the first time, allows the 3-D shape of the eye to be investigated fully. METHODS. The technique involves the acquisition of a T2-weighted MRI, which is optimized to reveal the fluid-filled chambers of the eye. Automatic segmentation and meshing algorithms generate a 3-D surface model, which can be shaded with morphologic parameters such as distance from the posterior corneal pole and deviation from sphericity. Full details of the method are illustrated with data from 14 eyes of seven individuals. The spatial accuracy of the calculated models is demonstrated by comparing the MRI-derived axial lengths with values measured in the same eyes using interferometry. RESULTS. The color-coded eye models showed substantial variation in the absolute size of the 14 eyes. Variations in the sphericity of the eyes were also evident, with some appearing approximately spherical whereas others were clearly oblate and one was slightly prolate. Nasal-temporal asymmetries were noted in some subjects. CONCLUSIONS. The MRI acquisition and analysis technique allows a novel way of examining 3-D ocular shape. The ability to stratify and analyze eye shape, ocular volume, and sphericity will further extend the understanding of which specific biometric parameters predispose emmetropic children subsequently to develop myopia. Copyright © Association for Research in Vision and Ophthalmology.

The influence of cutting tool geometry upon aspects of chip flow and tool wear:a theoretical, three dimensional examination of the cutting geometry and the shape of the twist drill

This work is undertaken in the attempt to understand the processes at work at the cutting edge of the twist drill. Extensive drill life testing performed by the University has reinforced a survey of previously published information. This work demonstrated that there are two specific aspects of drilling which have not previously been explained comprehensively. The first concerns the interrelating of process data between differing drilling situations, There is no method currently available which allows the cutting geometry of drilling to be defined numerically so that such comparisons, where made, are purely subjective. Section one examines this problem by taking as an example a 4.5mm drill suitable for use with aluminium. This drill is examined using a prototype solid modelling program to explore how the required numerical information may be generated. The second aspect is the analysis of drill stiffness. What aspects of drill stiffness provide the very great difference in performance between short flute length, medium flute length and long flute length drills? These differences exist between drills of identical point geometry and the practical superiority of short drills has been known to shop floor drilling operatives since drilling was first introduced. This problem has been dismissed repeatedly as over complicated but section two provides a first approximation and shows that at least for smaller drills of 4. 5mm the effects are highly significant. Once the cutting action of the twist drill is defined geometrically there is a huge body of machinability data that becomes applicable to the drilling process. Work remains to interpret the very high inclination angles of the drill cutting process in terms of cutting forces and tool wear but aspects of drill design may already be looked at in new ways with the prospect of a more analytical approach rather than the present mix of experience and trial and error. Other problems are specific to the twist drill, such as the behaviour of the chips in the flute. It is now possible to predict the initial direction of chip flow leaving the drill cutting edge. For the future the parameters of further chip behaviour may also be explored within this geometric model.

Three-dimensional nitrogen-doped graphene supported molybdenum disulfide nanoparticles as an advanced catalyst for hydrogen evolution reaction

An efficient three-dimensional (3D) hybrid material of nitrogen-doped graphene sheets (N-RGO) supporting molybdenum disulfide (MoS2) nanoparticles with high-performance electrocatalytic activity for hydrogen evolution reaction (HER) is fabricated by using a facile hydrothermal route. Comprehensive microscopic and spectroscopic characterizations confirm the resulting hybrid material possesses a 3D crumpled few-layered graphene network structure decorated with MoS2 nanoparticles. Electrochemical characterization analysis reveals that the resulting hybrid material exhibits efficient electrocatalytic activity toward HER under acidic conditions with a low onset potential of 112 mV and a small Tafel slope of 44 mV per decade. The enhanced mechanism of electrocatalytic activity has been investigated in detail by controlling the elemental composition, electrical conductance and surface morphology of the 3D hybrid as well as Density Functional Theory (DFT) calculations. This demonstrates that the abundance of exposed active sulfur edge sites in the MoS2 and nitrogen active functional moieties in N-RGO are synergistically responsible for the catalytic activity, whilst the distinguished and coherent interface in MoS 2 /N-RGO facilitates the electron transfer during electrocatalysis. Our study gives insights into the physical/chemical mechanism of enhanced HER performance in MoS2/N-RGO hybrids and illustrates how to design and construct a 3D hybrid to maximize the catalytic efficiency.

Three-dimensional capture, representation, and manipulation of Cuneiform tablets

This paper presents the digital imaging results of a collaborative research project working toward the generation of an on-line interactive digital image database of signs from ancient cuneiform tablets. An important aim of this project is the application of forensic analysis to the cuneiform symbols to identify scribal hands. Cuneiform tablets are amongst the earliest records of written communication, and could be considered as one of the original information technologies; an accessible, portable and robust medium for communication across distance and time. The earliest examples are up to 5,000 years old, and the writing technique remained in use for some 3,000 years. Unfortunately, only a small fraction of these tablets can be made available for display in museums and much important academic work has yet to be performed on the very large numbers of tablets to which there is necessarily restricted access. Our paper will describe the challenges encountered in the 2D image capture of a sample set of tablets held in the British Museum, explaining the motivation for attempting 3D imaging and the results of initial experiments scanning the smaller, more densely inscribed cuneiform tablets. We will also discuss the tractability of 3D digital capture, representation and manipulation, and investigate the requirements for scaleable data compression and transmission methods. Additional information can be found on the project website: www.cuneiform.net

Three-dimensional gas-liquid simulation of an airlift bubble column reactor

Basic hydrodynamic parameters of an airlift reactor with internal loop were estimated experimentally and simulated using commercially available CFD software from Fluent. Circulation velocity in a 32-dm(3)-airlift reactor was measured using the magnetic tracer method, meanwhile the gas hold-up was obtained by analysis of the pressure drop using the method of inverted U-tube manometers. Comparison of simulated (in two and three dimensions) and experimental data was performed at different superficial gas velocities in the riser.

Next generation high density three-dimensional magnetic recording systems

This work is the first work using patterned soft underlayers in multilevel three-dimensional vertical magnetic data storage systems. The motivation stems from an exponentially growing information stockpile, and a corresponding need for more efficient storage devices with higher density. The world information stockpile currently exceeds 150EB (ExaByte=1x1018Bytes); most of which is in analog form. Among the storage technologies (semiconductor, optical and magnetic), magnetic hard disk drives are posed to occupy a big role in personal, network as well as corporate storage. However; this mode suffers from a limit known as the Superparamagnetic limit; which limits achievable areal density due to fundamental quantum mechanical stability requirements. There are many viable techniques considered to defer superparamagnetism into the 100's of Gbit/in2 such as: patterned media, Heat-Assisted Magnetic Recording (HAMR), Self Organized Magnetic Arrays (SOMA), antiferromagnetically coupled structures (AFC), and perpendicular magnetic recording. Nonetheless, these techniques utilize a single magnetic layer; and can thusly be viewed as two-dimensional in nature. In this work a novel three-dimensional vertical magnetic recording approach is proposed. This approach utilizes the entire thickness of a magnetic multilayer structure to store information; with potential areal density well into the Tbit/in2 regime. ^ There are several possible implementations for 3D magnetic recording; each presenting its own set of requirements, merits and challenges. The issues and considerations pertaining to the development of such systems will be examined, and analyzed using empirical and numerical analysis techniques. Two novel key approaches are proposed and developed: (1) Patterned soft underlayer (SUL) which allows for enhanced recording of thicker media, (2) A combinatorial approach for 3D media development that facilitates concurrent investigation of various film parameters on a predefined performance metric. A case study is presented using combinatorial overcoats of Tantalum and Zirconium Oxides for corrosion protection in magnetic media. ^ Feasibility of 3D recording is demonstrated, and an emphasis on 3D media development is emphasized as a key prerequisite. Patterned SUL shows significant enhancement over conventional "un-patterned" SUL, and shows that geometry can be used as a design tool to achieve favorable field distribution where magnetic storage and magnetic phenomena are involved. ^