Applications of protein microarray technology

Protein microarrays, an emerging class of proteomic technologies, are quickly becoming essential tools for large-scale and high throughput biochemistry and molecular biology. Recent progress has been made in all the key steps of protein microarray fabrication and application, such as the large-scale cloning of expression-ready prokaryotic and eukaryotic ORFs, high throughput protein purification, surface chemistry, protein delivery systems, and detection methods. Two classes of protein microarrays are currently available: analytical and functional protein microarrays. In the case of analytical protein microarrays, well-characterized molecules with specific activity, such as antibodies, peptide-MHC complexes, or lectins, are used as immobilized probes. These arrays have become one of the most powerful multiplexed detection platforms. Functional protein microarrays are being increasingly applied to many areas of biological discovery, including drug target identification/validation and studies of protein interaction, biochemical activity, and immune responses. Great progress has been achieved in both classes of protein microarrays in terms of sensitivity and specificity, and new protein microarray technologies are continuing to emerge. Finally, protein microarrays have found novel applications in both scientific research and clinical diagnostics.     

Surface free energy and microarray deposition technology

Microarray techniques use a combinatorial approach to assess complex biochemical interactions. The fundamental goal is simultaneous, large-scale experimentation analogous to the automation achieved in the semiconductor industry. However, microarray deposition inherently involves liquids contacting solid substrates. Liquid droplet shapes are determined by surface and interfacial tension forces, and flows during drying. This article looks at how surface free energy and wetting considerations may influence the accuracy and reliability of spotted microarray experiments.     

Recent developments in protein microarray technology

The sequencing of the human genome and the advent of DNA chips and sophisticated bioinformatics platforms have enabled molecular biologists to take a more global view of biological systems and to analyze naturally occurring genetic variation. Microarrays of antibodies can measure the concentrations of many proteins quickly and simultaneously. Microarrays of genomically encoded proteins allow scientists to screen entire genomes for proteins that interact with particular factors, catalyze particular reactions, or act as substrates for protein-modifying enzymes or as targets of autoimmune responses. The new protein microarray platforms will prove invaluable to basic biological research, and will dramatically accelerate the pace of discovery of drug targets and diagnostic biomarkers.     

Optimization of aptamer microarray technology for multiple protein targets

Aptamer-based microarrays for the quantitation of multiple protein analytes have been developed. A multiplex aptamer microarray was generated by printing two RNA aptamers (anti-lysozyme and anti-ricin) and two DNA aptamers (anti-IgE and anti-thrombin) on to either streptavidin (SA) or neutravidin (NA)-coated glass slides. However, substantial optimization was required in order to ensure the simultaneous function of the aptamer:analyte pairs. The effects of protein labeling, assay buffer, surface coating, and immobilization chemistry and orientation were investigated. A single buffer (PBS buffer containing 5 mM MgCl₂ and 0.1% Tween 20) was found to work well with all the aptamers, even though this was not the buffer originally used in their selection, while neutravidin-coated slides yielded a lower detection limit, wider detection range, and more uniform background than streptavidin-coated slides. Incubation with Cy3-labeled proteins yielded sensitive, target-specific, and dose-dependent responses to each protein. Target protein concentrations as low as 72 pg/mL (5 pM, lysozyme), 15 ng/mL (0.5 nM, ricin), 1.9 ng/mL (0.01 nM, IgE), and 170 ng/mL (5 nM, thrombin) could be detected. These results show that aptamer arrays can potentially be used with numerous proteins in parallel, furthering the notion that aptamer arrays may be useful in proteomics.     

Feature-size limitations of microarray technology - a critical review

The appeal of microarray technology is the possibility of large-scale parallel determination of a variety of variables simultaneously. Hence, microarray technologies attract the interest of both the scientific and business worlds alike. High-throughput screening has been the major focus of the utilization of microarray technologies in recent years, and has provided the strong driving force for developments in this field. DNA chip and biochip technologies have been developed as a consequence of worldwide activity in genome research. This review focuses on microarray-based analysis and emphasizes some of its principal constraints, especially detection limits.     

Advances in cancer tissue microarray technology: Towards improved understanding and diagnostics

Over the past few years, tissue microarray (TMA) technology has been established as a standard method for assessing the expression of proteins or genes across large sets of tissue specimens. It is being adopted increasingly among leading research institutions around the world and utilized in cancer research in parallel with the cDNA microarray technology. This article summarizes various aspects of cancer understanding and diagnostics in which TMA has had great impact. Although tremendous advances continue to be made to facilitate imaging and archiving of TMA specimens, automatic evaluation and quantitative analysis of TMA still remains an important challenge for modern investigators.     

DNA microarray technology used for studying foodborne pathogens and microbial habitats: minireview

Microarray analysis is an emerging technology that has the potential to become a leading trend in bacterial identification in food and feed improvement. The technology uses fluorescent-labeled probes amplified from bacterial samples that are then hybridized to thousands of DNA sequences immobilized on chemically modified glass slides. The whole gene or open reading frame(s) is represented by a polymerase chain reaction fragment of double-strand DNA, approximately 1000 base pair (bp) or 20-70 bp single-strand oligonucleotides. The technology can be used to identity bacteria and to study gene expression in complex microbial populations, such as those found in food and gastrointestinal tracts. Data generated by microarray analysis can be potentially used to improve the safety of our food supply as well as ensure the efficiency of animal feed conversion to human food, e.g., in meat and milk production by ruminants. This minireview addresses the use of microarray technology in bacterial identification and gene expression in different microbial systems and in habitats containing mixed populations of bacteria.     

Clicking together Alkynes and Tetracyanoethylene

The [2+2] cycloaddition – retro-electrocyclization (CA-RE) reaction allows ready synthesis of redox-active donor-acceptor chromophores from an electron-rich alkyne and electron-poor olefins like tetracyanoethylene (TCNE). The detailed mechanism of the reaction has been subject of both computational and experimental studies. While several studies point towards a stepwise mechanism via a zwitterionic intermediate for the first step, the cycloaddition, the reaction follows neither simple second-order nor first-order kinetics. Recent studies have shown that the kinetics can be understood if an autocatalytic step is introduced in the mechanism, in which complex formation with the donor-substituted tetracyanobutadiene (TCBD) product possibly facilitates nucleophilic attack of the alkyne onto TCNE, generating the zwitterionic intermediate of the CA step. This Concept highlights the convenient use of the “click-like” CA-RE reaction to obtain elaborate donor-acceptor chromophores and the recent mechanistic results.     

Localization of electrons and excitations

Electrons, electron holes, or excitations in finite or infinite ‘multimer systems’ may be localized or delocalized. In the theory of Hush, localization depends on the ratio Δ/λ (Δ/2 = coupling; λ = reorganization energy). The latter theory has been extended to the infinite system [S. Larsson, A. Klimkāns, Mol. Cryst. Liq. Cryst. 355 (2000) 217]. The metal/insulator transition often takes place abruptly as a function of Δ/λ. It is argued that localization in a system with un-filled bands cannot be determined on the basis of Mott–Hubbard U alone, but depends on the number of accessible valence states, reorganization energy λ and coupling Δ (=2t). In fact U = 0 does not necessarily imply delocalization. The analysis here shows that there are many different situations for an insulator to metal transition. Charge transfer in doped NiO is characterized by Ni²⁺ − Ni³⁺ exchange while charge transfer in pure NiO is characterized by a disproportionation 2Ni²⁺ → Ni⁺ + Ni³⁺. In spite of the great differences between these two cases, U has been applied without discrimination to both. The relevant localization parameters appear to be Δ and λ in the first case, with only two oxidation states, and U, Δ and λ in the second case with three oxidation states. The analysis is extended to insulator-metal transitions, giant magnetic resistance (GMR) and high T_c superconductivity (SC). λ and Δ can be determined quite accurately in quantum mechanical calculations involving only one and two monomers, respectively.     

Polyamines and corresponding aminoacids measured together

Summary A two-column switching technique plus gradient elution have been developed to separate polyamines (putrescine, spermine and spermidine) and related aminoacids (aspartic, glutamic, glycine, taurine and gaba) as isoindole derivatives. The system uses two columns (CN and C18) arranged in series, via a valve which allows the effluent to be switched from the primary column to the secondary column or directly to the detector.     

Structure and electrons in mayenite electrides

One major goal in materials chemistry is to find inexpensive compounds with improved capabilities. Stable inorganic electrides, derived from nanoporous mayenite [Ca12Al14O32]O, are a new family that has very interesting properties such as electronic conductivity combined with transparency. However, an intriguing fundamental problem is to understand the structures of these cubic materials and to characterize their free-electron loadings. Here we report an accurate structural study for three members of the series [Ca12Al14O32]O(1-delta)e(2delta) (delta = 0, 0.15, and 0.45), from single-crystal low-temperature synchrotron X-ray diffraction. The complex structural disorder imposed by the presence of the oxide anions into the mayenite cages has been unravelled. Furthermore, the final electron density map for delta = 0.45 black mayenite has shown electron density localized into the center of the cages, which is the first experimental proof of their electride nature. The reported structural findings challenge theorists to improve predictive models in this new family of materials.     

Reflection of electrons and photons from solids bombarded by 0.1 - to 100-MeV electrons

Electron and photon reflection ratios (in number and energy) for absorbers bombarded by electrons have been computed with the ITS Monte Carlo system version 3. Electrons of energies from 0.1 to 100 MeV have been assumed normally incident on an effectively semi-infinite absorber. The absorbers considered are elemental solids of atomic numbers from 4 to 92. The data on the electron reflection ratios agree rather well with the experimental data collected from literature except some discrepancies when the number-reflection ratio is small. For photons, the number-reflection ratio increases with increasing energy, but the energy-reflection ratio shows a maximum around 10 MeV. Empirical equations for the electron reflection ratios and the photon energy-reflection ratio are given (for electrons, graphs only).