Three-map absolute moiré contouring

In the shadow-moiré system, the period of the grating is varied by rotation of the grating, so the phase of the moiré pattern is changed as well. By the selection of suitable rotation angles, three images at different positions of the grating are acquired to obtain the absolute distance from the object to the grating. A theoretical analysis is presented for the method, and some experiments have been done to verify the theoretical analysis. The results show that the method is fast and the accuracy is better than 10 μm. The measurable range is directly proportional to the period of the grating and inversely proportional to the angles at which the grating is rotated.     

Development of an automated platform for high-throughput P1-phage transduction of Escherichia coli

Synthetic biology depends on the ability to rapidly produce strains with improved phenotypes but is limited by the ability to rapidly produce strain collections with directed mutations. Here, we present a system capable of overcoming this limitation through automated P1-phage transductions of Escherichia coli. By combining the Keio collection of single-gene deletion E. coli mutants with P1-phage, it is possible to generate an engineered host-strain collection consisting of every possible gene deletion mutant. This strategy was tested by transducing 355 genetic markers from the Keio collection into five different host strains, and it achieved a 98% success rate. This method offers an improved mechanism for rapidly engineering collections of microbes and provides one method for rapidly deploying a broader synthetic biology effort.     

Design of a grid service-based platform for in silico protein-ligand screenings

Grid computing offers the powerful alternative of sharing resources on a worldwide scale, across different institutions to run computationally intensive, scientific applications without the need for a centralized supercomputer. Much effort has been put into development of software that deploys legacy applications on a grid-based infrastructure and efficiently uses available resources. One field that can benefit greatly from the use of grid resources is that of drug discovery since molecular docking simulations are an integral part of the discovery process. In this paper, we present a scalable, reusable platform to choreograph large virtual screening experiments over a computational grid using the molecular docking simulation software DOCK. Software components are applied on multiple levels to create automated workflows consisting of input data delivery, job scheduling, status query, and collection of output to be displayed in a manageable fashion for further analysis. This was achieved using Opal OP to wrap the DOCK application as a grid service and PERL for data manipulation purposes, alleviating the requirement for extensive knowledge of grid infrastructure. With the platform in place, a screening of the ZINC 2,066,906 compound "drug-like" subset database against an enzyme's catalytic site was successfully performed using the MPI version of DOCK 5.4 on the PRAGMA grid testbed. The screening required 11.56 days laboratory time and utilized 200 processors over 7 clusters.     

Human pathogenic streptococcal proteomics and vaccine development

Gram-positive streptococci are non-motile, chain-forming bacteria commonly found in the normal oral and bowel flora of warm-blooded animals. Over the past decade, a proteomic approach combining 2-DE and MS has been used to systematically map the cellular, surface-associated and secreted proteins of human pathogenic streptococcal species. The public availability of complete streptococcal genomic sequences and the amalgamation of proteomic, genomic and bioinformatic technologies have recently facilitated the identification of novel streptococcal vaccine candidate antigens and therapeutic agents. The objective of this review is to examine the constituents of the streptococcal cell wall and secreted proteome, the mechanisms of transport of surface and secreted proteins, and describe the current methodologies employed for the identification of novel surface-displayed proteins and potential vaccine antigens.     

Dynamic diamond anvil cell (dDAC): a novel device for studying the dynamic-pressure properties of materials

We have developed a unique device, a dynamic diamond anvil cell (dDAC), which repetitively applies a time-dependent load/pressure profile to a sample. This capability allows studies of the kinetics of phase transitions and metastable phases at compression (strain) rates of up to 500 GPa/s (approximately 0.16 s(-1) for a metal). Our approach adapts electromechanical piezoelectric actuators to a conventional diamond anvil cell design, which enables precise specification and control of a time-dependent applied load/pressure. Existing DAC instrumentation and experimental techniques are easily adapted to the dDAC to measure the properties of a sample under the varying load/pressure conditions. This capability addresses the sparsely studied regime of dynamic phenomena between static research (diamond anvil cells and large volume presses) and dynamic shock-driven experiments (gas guns, explosive, and laser shock). We present an overview of a variety of experimental measurements that can be made with this device.     

Comparison of the indentation and elasticity of E. coli and its spheroplasts by AFM

Atomic force microscopy (AFM) provides a unique opportunity to study live individual bacteria at the nanometer scale. In addition to providing accurate morphological information, AFM can be exploited to investigate membrane protein localization and molecular interactions on the surface of living cells. A prerequisite for these studies is the development of robust procedures for sample preparation. While such procedures are established for intact bacteria, they are only beginning to emerge for bacterial spheroplasts. Spheroplasts are useful research models for studying mechanosensitive ion channels, membrane transport, lipopolysaccharide translocation, solute uptake, and the effects of antimicrobial agents on membranes. Furthermore, given the similarities between spheroplasts and cell wall-deficient (CWD) forms of pathogenic bacteria, spheroplast research could be relevant in biomedical research. In this paper, a new technique for immobilizing spheroplasts on mica pretreated with aminopropyltriethoxysilane (APTES) and glutaraldehyde is described. Using this mounting technique, the indentation and cell elasticity of glutaraldehyde-fixed and untreated spheroplasts of E. coli in liquid were measured. These values are compared to those of intact E. coli. Untreated spheroplasts were found to be much softer than the intact cells and the silicon nitride cantilevers used in this study.     

Continuous planar phospholipid bilayer supported on porous silicon thin film reflector

Reconstituting artificial membranes for in vitro studies of cell barrier mechanisms and properties is of major interest in biology. Here, artificial membranes supported on porous silicon photonic crystal reflectors are prepared and investigated. The materials are of interest for label-free probing of supported membrane events such as protein binding, molecular recognition, and transport. The porous silicon substrates are prepared as multilayered films consisting of a periodically varying porosity, with pore dimensions of a few nanometers in size. Planar phospholipid bilayers are deposited on the topmost surface of the oxidized hydrophilic mesoporous silicon films. Atomic force microscopy provides evidence of continuous bilayer deposition at the surface, and optical measurements indicate that the lipids do not significantly infiltrate the porous region. The presence of the supported bilayer does not obstruct the optical spectrum from the porous silicon layer, suggesting that the composite structures can act as effective optical biosensors.     

Anomalous high-frequency oscillations in a field emission tube and their significance in pulsed field emission

Relaxation oscillations occur when a capacitor is inserted in series with a field emission tube, a DC high-voltage power supply, and a ballast resistor. The waveform of these oscillations is highly reproducible with a dominant frequency of 200 MHz and a decay time of 20 ns. The peak current as high as 320 mA has been observed although the tungsten emitter is only rated for 10 microA. We have shown that these oscillations are due to a displacement current, charging of the anode-tip capacitance, and are not of a field emission origin. We conclude that the effects of displacement current should be considered in measurements of field emission with microsecond pulses, where high-current densities can be observed.     

NodeTrix: a hybrid visualization of social networks

The need to visualize large social networks is growing as hardware capabilities make analyzing large networks feasible and many new data sets become available. Unfortunately, the visualizations in existing systems do not satisfactorily resolve the basic dilemma of being readable both for the global structure of the network and also for detailed analysis of local communities. To address this problem, we present NodeTrix, a hybrid representation for networks that combines the advantages of two traditional representations: node-link diagrams are used to show the global structure of a network, while arbitrary portions of the network can be shown as adjacency matrices to better support the analysis of communities. A key contribution is a set of interaction techniques. These allow analysts to create a NodeTrix visualization by dragging selections to and from node-link and matrix forms, and to flexibly manipulate the NodeTrix representation to explore the dataset and create meaningful summary visualizations of their findings. Finally, we present a case study applying NodeTrix to the analysis of the InfoVis 2004 coauthorship dataset to illustrate the capabilities of NodeTrix as both an exploration tool and an effective means of communicating results.