Arrays of hope

A large study by the MAQC consortium has established that different DNA microarray platforms can generate reproducible lists of differentially expressed genes. Now scientists are grappling with the challenges of moving the technology toward the clinic.     

Coherence Converting Plasmonic Hole Arrays

Simulations are presented that demonstrate that the global state of spatial coherence of an optical wavefield can be altered on transmission through an array of subwavelength-sized holes in a metal plate that supports surface plasmons. It is found that the state of coherence of the emergent field strongly depends on the separation between the holes and their scattering strength. Our findings suggest that subwavelength hole arrays on a metal film can be potentially employed as a plasmon-assisted coherence converting device, useful in modifying the directionality, spectrum, and polarization of the transmitted wave.     

基于微电极阵列的微生物电融合

利用自主研制的梳状交叉微电极阵列细胞电融合芯片系统,研究微生物电融合。在酶解浓度1．5％、酶解温度33℃、酶解时间3h、酶解pH值6．0、0．8mol／L山梨醇的渗透压条件下,获得生成率和再生率分别为95．2％和8．9％的微生物细胞原生质体。在脉冲峰值电压50V、持续时间80μs、8个脉冲、间隔1s的电融合条件下,该原生质体通过电融合获得一株菌株其乳化性能从62％提高到85％。     

Protein-Mediated Chromosome Pairing of Repetitive Arrays

Chromosomally integrated arrays of lacO and tetO operator sites visualized by LacI and TetR repressor proteins fused with GFP (green fluorescent protein) (or other fluorescent proteins) are widely used to monitor the behavior of chromosomal loci in various systems. However, insertion of such arrays and expression of the corresponding proteins is known to perturb genomic architecture. In several cases, juxtaposition of such arrays located on different chromosomes has been inferred to reflect pairing of the corresponding loci. Here, we report that a version of TetR-GFP mutated to disrupt GFP dimerization (TetR-A206KGFP or “TetR-kGFP”) abolishes pairing of tetO arrays in vivo and brings spatial proximity of chromosomal loci marked with those arrays back to the wild-type level. These data argue that pairing of arrays is caused by GFP dimerization and thus presents an example of protein-assisted interaction in chromosomes. Arrays marked with another protein, TetR-tdTomato, which has a propensity to form intramolecular dimers instead of intermolecular dimers, also display reduced level of pairing, supporting this idea. TetR-kGFP provides an improved system for studying chromosomal loci with a low pairing background.     

Deciphering Enzyme Function Using Peptide Arrays

Enzymes are key molecules in signal-transduction pathways. However, only a small fraction of more than 500 human kinases, 300 human proteases and 200 human phosphatases is characterised so far. Peptide microarray based technologies for extremely efficient profiling of enzyme substrate specificity emerged in the last years. This technology reduces set-up time for HTS assays and allows the identification of downstream targets. Moreover, peptide microarrays enable optimisation of enzyme substrates. Focus of this review is on assay principles for measuring activities of kinases, phosphatases or proteases and on substrate identification/optimisation for kinases. Additionally, several examples for reliable identification of substrates for lysine methyl-transferases, histone deacetylases and SUMO-transferases are given. Finally, use of high-density peptide microarrays for the simultaneous profiling of kinase activities in complex biological samples like cell lysates or lysates of complete organisms is described. All published examples of peptide arrays used for enzyme profiling are summarised comprehensively.     

Chromatin Heterogeneity Within Multicopy Transgene Arrays

Transgenic Research -     

Muscle-like Arrays in a Fibroblast Line

SEVERAL investigators have speculated that the basis for all cellular contractile activity resides in a common molecular mechanism involving an interaction between actin and myosin^1–4. Thin filaments resembling the actin filaments of muscle have indeed been widely observed^3–5 and the recent demonstrations of heavy meromyosin binding to thin filaments^4–6 suggest that these ubiquitous filaments are, in fact, actin. Although muscle-like thick filaments have not been observed in non-muscle cells, myosin thick filaments have been reconstituted from blood platelet preparations¹. To our knowledge, however, no one has presented evidence for the natural occurrence of ordered arrays of thick and thin filaments in non-muscle cells.     

Protein Arrays in Functional Genome Research

Whole-genome analyses become more and more necessary for pharmaceutical research. DNA chip hybridizations are an important tool for monitoring gene expression profiles during diseases or medical treatment. However, drug target identification and validation as well as an increasing number of antibodies and other polypeptides tested as potential drugs produce an increasing demand for genome-wide functional assays. Protein arrays are an important step into this direction. Peptide arrays and protein expression libraries are useful for the identification of antibodies and for epitope mapping. Antibody arrays allow protein quantification, protein binding studies, and protein phosphorylation assays. Tissue micro-arrays give a detailed information about the localization of macromolecules. More complex interactions can be addressed in cells spotted in array format. Finally, microfluidics chips enable us to describe the communication between cells in a tissue. In this review, possibilities, limitations and chances of different protein array techniques are discussed.     

Phosphokinase Antibody Arrays on Dendron-Coated Surface

Monitoring protein phosphorylation at the cellular level is important to understand the intracellular signaling. Among the phosphoproteomics methods, phosphokinase antibody arrays have emerged as preferred tools to measure well-characterized phosphorylation in the intracellular signaling. Here, we present a dendron-coated phosphokinase antibody array (DPA) in which the antibodies are immobilized on a dendron-coated glass slide. Self-assembly of conically shaped dendrons well-controlled in size and structure resulted in precisely controlled lateral spacing between the immobilized phosphosite-specific antibodies, leading to minimized steric hindrance and improved antigen-antibody binding kinetics. These features increased sensitivity, selectivity, and reproducibility in measured amounts of protein phosphorylation. To demonstrate the utility of the DPA, we generated the phosphorylation profiles of brain tissue samples obtained from Alzheimer''s disease (AD) model mice. The analysis of the profiles revealed signaling pathways deregulated during the course of AD progression.     

Terahertz Dipole Nanoantenna Arrays: Resonance Characteristics

Resonant dipole nanoantennas promise to considerably improve the capabilities of terahertz spectroscopy, offering the possibility of increasing its sensitivity through local field enhancement, while in principle allowing unprecedented spatial resolutions, well below the diffraction limit. Here, we investigate the resonance properties of ordered arrays of terahertz dipole nanoantennas, both experimentally and through numerical simulations. We demonstrate the tunability of this type of structures, in a range (～1–2 THz) that is particularly interesting and accessible by means of standard zinc telluride sources. We additionally study the near-field resonance properties of the arrays, finding that the resonance shift observed between near-field and far-field spectra is predominantly ascribable to ohmic damping.     

Design and Use of Multiplexed Chemostat Arrays

Chemostats are continuous culture systems in which cells are grown in a tightly controlled, chemically constant environment where culture density is constrained by limiting specific nutrients.^1,2 Data from chemostats are highly reproducible for the measurement of quantitative phenotypes as they provide a constant growth rate and environment at steady state. For these reasons, chemostats have become useful tools for fine-scale characterization of physiology through analysis of gene expression^3-6 and other characteristics of cultures at steady-state equilibrium.⁷ Long-term experiments in chemostats can highlight specific trajectories that microbial populations adopt during adaptive evolution in a controlled environment. In fact, chemostats have been used for experimental evolution since their invention.⁸ A common result in evolution experiments is for each biological replicate to acquire a unique repertoire of mutations.^9-13 This diversity suggests that there is much left to be discovered by performing evolution experiments with far greater throughput. We present here the design and operation of a relatively simple, low cost array of miniature chemostats—or ministats—and validate their use in determination of physiology and in evolution experiments with yeast. This approach entails growth of tens of chemostats run off a single multiplexed peristaltic pump. The cultures are maintained at a 20 ml working volume, which is practical for a variety of applications. It is our hope that increasing throughput, decreasing expense, and providing detailed building and operation instructions may also motivate research and industrial application of this design as a general platform for functionally characterizing large numbers of strains, species, and growth parameters, as well as genetic or drug libraries.     

Study of Implosion of Combined Nested Arrays

New experimental data on the implosion of plasma of nested kapron?tungsten arrays are obtained at the Angara-5-1 facility. The mode of plasma implosion is implemented in which a shock wave region forms in the space between the inner and outer arrays where a transition from the super-Alfvénic (V _r > V _A ) to sub-Alfvénic (V _r < V _A ) plasma flow takes place. Specific features of the formation and decay of the shock region are studied using laser shadow imaging and X-ray frame photography. The plasma density in the transition region is estimated. By comparing the experimental data with the results of simulations of quasi-steady implosion of a nested array with allowance for extended plasma production, the physical conditions are determined at which the implosion mode with the formation the shock region takes place. Stable compression of the plasma of the inner array was observed during the implosion of combined nested arrays with a fiber outer array and tungsten inner array. Suppression of magnetic Rayleigh-Taylor instability during the compression of the inner array plasma results in the formation of a compact radiating Z-pinch and generation of a soft X-ray pulse with a peak power of 4 TW and duration of about 5 ns.     

Sealable Femtoliter Chamber Arrays for Cell-free Biology

Cell-free systems provide a flexible platform for probing specific networks of biological reactions isolated from the complex resource sharing (e.g., global gene expression, cell division) encountered within living cells. However, such systems, used in conventional macro-scale bulk reactors, often fail to exhibit the dynamic behaviors and efficiencies characteristic of their living micro-scale counterparts. Understanding the impact of internal cell structure and scale on reaction dynamics is crucial to understanding complex gene networks. Here we report a microfabricated device that confines cell-free reactions in cellular scale volumes while allowing flexible characterization of the enclosed molecular system. This multilayered poly(dimethylsiloxane) (PDMS) device contains femtoliter-scale reaction chambers on an elastomeric membrane which can be actuated (open and closed). When actuated, the chambers confine Cell-Free Protein Synthesis (CFPS) reactions expressing a fluorescent protein, allowing for the visualization of the reaction kinetics over time using time-lapse fluorescent microscopy. Here we demonstrate how this device may be used to measure the noise structure of CFPS reactions in a manner that is directly analogous to those used to characterize cellular systems, thereby enabling the use of noise biology techniques used in cellular systems to characterize CFPS gene circuits and their interactions with the cell-free environment.     

Cellulose-bound Peptide Arrays: Preparation and Applications

Spatial organization of metabolic enzymes may represent a general cellular mechanism to regulate metabolic flux. One recent example of this type of cellular phenomenon is the purinosome, a newly discovered multi-enzyme metabolic assembly that includes all of the enzymes within the de novo purine biosynthetic pathway. Our understanding of the components and regulation of purinosomes has significantly grown in recent years. This paper reviews the purine de novo biosynthesis pathway and its regulation, and presents the evidence supporting the purinosome assembly and disassembly processes under the control of G-protein-coupled receptor (GPCR) signaling. This paper also discusses the implications of purinosome and GPCR regulation in drug discovery.