Biochips

Chip-on-foil devices for DNA analysis based on inkjet-printed silver electrodes

For a rapid on-site diagnosis of pathogens, low-cost chip-based devices are of great interest. Here, we report the successful fabrication of inkjet printed silver electrodes on polymer foils as disposable chips for molecular DNA analytics. In order to manufacture these electrode structures, silver nanoparticle inks were inkjet printed onto planar polypropylene substrates. Due to the low thermal stability of the foils, substrate preserving sintering techniques, including low temperature thermal sintering and low pressure argon plasma sintering, were implemented. Thus, sufficient electrical conductance of the printed structures at processing temperatures ≤100 °C was achieved. To test the applicability of the manufactured chips, specific capture DNA was immobilized within the gaps of the conductive electrode paths and hybridized in the next step with biotin-labeled target DNA. Subsequently, an enzymatically generated silver nanoparticle deposition was induced that bridges the electrode gap. This enabled both conductance measurement and gray value analysis as a fast, simple and robust electrical and optical read-out system. The proof-of-principle experiments successfully demonstrated the applicability of these convenient chip-on-foil devices for nucleic acid based pathogen detection.

Laboratory diagnosis of tuberculosis in resource-poor countries: challenges and opportunities

With an estimated 9.4 million new cases globally, tuberculosis (TB) continues to be a major public health concern. Eighty percent of all cases worldwide occur in 22 high-burden, mainly resource-poor settings. This devastating impact of tuberculosis on vulnerable populations is also driven by its deadly synergy with HIV. Therefore, building capacity and enhancing universal access to rapid and accurate laboratory diagnostics are necessary to control TB and HIV-TB coinfections in resource-limited countries. The present review describes several new and established methods as well as the issues and challenges associated with implementing quality tuberculosis laboratory services in such countries. Recently, the WHO has endorsed some of these novel methods, and they have been made available at discounted prices for procurement by the public health sector of high-burden countries. In addition, international and national laboratory partners and donors are currently evaluating other new diagnostics that will allow further and more rapid testing in point-of-care settings. While some techniques are simple, others have complex requirements, and therefore, it is important to carefully determine how to link these new tests and incorporate them within a country's national diagnostic algorithm. Finally, the successful implementation of these methods is dependent on key partnerships in the international laboratory community and ensuring that adequate quality assurance programs are inherent in each country's laboratory network.

Effects of different ingredients of zedoary on gene expression of HSC-T6 cells

AIM: To investigate the effects of four different ingredients of zedoary (Curcuma aromatica oil, Curcumol, β-elemence, and Curcumin) on the gene expressions of hepatic stellate cells (HSCs), and to explore the molecular mechanism of zedoary against hepatic fibrosis at gene network level.

METHODS: We detected the mRNA sequences of 50 liver fibrosis-related genes in GenBank and designed oligonucleotide probes. We synthesized oligonucleotides with PE8909 DNA synthesizing instrument, and carried out oligonucleotide microarray with OGR-04 dropping instrument and aldehyded glass chip. Cultured HSC-T6 cells were treated with different concentrations of Colchicine, Curcuma aromatica oil, Curcumol, β-elemence, and Curcumin. According to the experiment of cell toxicity, we took the appropriate concentrations of medicines that resulted in over 50% of cell survival as experiment concentrations. We collected the cells at 1, 6, 12, and 24 h, and extracted total RNA with TRIzol reagent, then labeled cDNAs with Cy3-dUTP and Cy5-dUTP. These labeled cDNAs were hybridized to an oligonucleotide microarray which was washed several times and scanned by scanner GenePix 4000B. Different gene expressions of HSC-T6 cells were analyzed by ImaGene 4.2 software.

RESULTS: After HSC-T6 cells were cultured in a medium containing 6.25 μg/mL Colchicine for 12 h, expression of TIMP-1 decreased 2.2-folds. After HSC-T6 cells were cultured in a medium containing 78.125 μg/mL of Curcuma aromatica oil for 24 h, the expression of TIMP-2 and IL-6 decreased 2.3- and 2.2-folds, respectively. Moreover, after HSC-T6 cells were cultured in a medium containing 1.5625 μg/mL of Curcumol for 12 h, the expression of TGFβ1 and P450a decreased 2.3- and 2.1-folds, respectively.

CONCLUSION: Our results may show the possible molecular mechanism of Curcuma aromatica oil and Curcumol against hepatic fibrosis.

Real time analysis of intact organelles using surface plasmon resonance

Membrane proteins remain refractory to standard protein chip analysis. They are typically expressed at low densities in distinct subcellular compartments, their biological activity can depend on assembly into macromolecular complexes in a specific lipid environment. We report here a real-time, label-free method to analyze membrane proteins inserted in isolated native synaptic vesicles. Using surface plasmon resonance-based biomolecular interaction analysis (Biacore), organelle capture from minute quantities of 10,000 g brain supernatant (1-10 microg) was monitored. Immunological and morphological characterization indicated that pure intact synaptic vesicles were immobilized on sensor chips. Vesicle chips were stable for days, allowing repetitive use with multiple analytes. This method provides an efficient way in which to characterize organelle membrane components in their native context. Organelle chips allow a broad range of measurements, including interactions of exogenous ligands with the organelle surface (kinetics, Kd), and protein profiling.

Microfluidic technologies in clinical diagnostics

BACKGROUND

Laboratory instrumentation and analytical devices are becoming smaller, simpler, and smarter. This trend to miniaturization extends to fluid handling and fluid analysis. However, fluid behavior undergoes significant changes as geometric scale decreases. The laminar flow behavior of fluids in microfluidic devices must be accommodated in the design and development of clinical and bio-clinical miniaturized systems.

CONCLUSION

The scale of chemical and clinical analysis systems will continue to decrease. The capability to manufacture smaller fluidic devices and to quantitatively monitor smaller volumes of liquids bring this process of miniaturization into the domain of laminar flow. New and enabling technologies are being developed using the unique diffusion-based characteristics of the laminar flow domain for sample preparation and analysis. These new analytical systems will have a significant impact on the future of clinical diagnostics.

Solution and chip arrays in protein profiling

The industrialization of proteomics demands reproducible, robust and high-throughput profiling technologies that current two-dimensional gel electrophoresis cannot achieve. New technologies in protein arrays, either on chips or with self-encoded elements in solution, hold much promise for interrogating the diverse and immense proteome.

A sensitive fluorescence monitor for the detection of activated Ras: total chemical synthesis of site-specifically labeled Ras binding domain of c-Raf1 immobilized on a surface

BACKGROUND

The Ras.GDP-Ras.GTP cycle plays a central role in eukaryotic signaling cascades. Mutations in Ras which stabilize activated Ras.GTP lead to a continuous stimulation of downstream effectors and ultimately to cell proliferation. Ras mutants which increase the steady-state concentration of Ras.GTP are involved in about 30% of all human cancers. It is therefore of great interest to develop a biosensor which is sensitive to Ras.GTP but not to Ras.GDP.

RESULTS

The Ras binding domain (RBD) of c-Raf1 was synthesized from two unprotected peptide segments by native chemical ligation. Two fluorescent amino acids with structures based on the nitrobenz-2-oxa-1,3-diazole and coumaryl chromophores were incorporated at a site which is close to the RBD/Ras.GTP binding surface. Additionally, a C-terminal tag consisting of His6 was introduced. The Kd values for binding of the site-specifically modified proteins to Ras.GTP are comparable to that of wild-type RBD. Immobilization of C-terminal His6 tag-modified fluorescent RBD onto Ni-NTA-coated surfaces allowed the detection of Ras.GTP in the 100 nM range. Likewise, Ras.GTP/Q61L (an oncogenic mutant of Ras with very low intrinsic GTP hydrolysis activity) can also be detected in this assay system. Ras.GDP does not bind to the immobilized RBD, thus allowing discrimination between inactive and activated Ras.

CONCLUSIONS

The site-specific incorporation of a fluorescent group at a strategic position in a Ras effector protein allows the detection of activated Ras with high sensitivity. This example illustrates the fact that the chemical synthesis of proteins or protein domains makes it possible to incorporate any kind of natural or unnatural amino acid at the position of choice, thereby enabling the facile preparation of specific biosensors, enhanced detection systems for drug screening, or the synthesis of activated proteins, e.g. phosphorylated proteins involved in signaling pathways, as defined molecular species.

Biochips: an evolving clinical technology

The first biochips are already in use. They are computer-chip look-alikes intended to speedily, reliably, and inexpensively perform the sequential procedures that compose a medical test. Current applications lie chiefly in the analysis of genes. The devices may soon facilitate screening of potential drugs. Clinically, the immediate goal is to enable biochips to serve point-of-care diagnosis.

Expression profiling: DNA arrays in many guises

DNA arrays have become the preferred method for large-scale expression measurement. Such data are needed in view of the large amounts of sequence data available: expression levels in a number of different tissues or situations provide a first step toward functional characterisation of new entities revealed by DNA sequencing. Although the basic principle of measurement is in all cases based on hybridisation of a mixed probe derived from tissue RNA to large sets of DNA fragments representing many genes, a number of different forms of implementation of this principle are at hand. They are briefly described and compared, emphasizing the important issue of sensitivity and sample requirements and the accessibility of the methods to academic scientists. When these factors are taken into account, it appears that, contrary to a largely prevalent impression, the "best" approach is not necessarily always provided by the widely advertised glass microarrays or oligonucleotide chips.

'Genomics': buzzword or reality?

'Genomics' has become a widely used term, covering a range of approaches that make use of the newly acquired wealth of genome data (both on man and on a number of model organisms) to gain new insights and accelerate research. This review attempts to present a clear and balanced view of developments in this field, to describe the four major approaches that contribute to genomics (bioinformatics, genetic analysis of extended populations, large-scale expression studies, functional approaches), and to indicate applications in basic and pharmaceutical research.