MEMS-based sample preparation for molecular diagnostics

Completion of the Human Genome Project is driving the rapid development of molecular diagnostics in the laboratory. To accelerate the penetration of genetic tests and other nucleic acid-based tests into clinical markets, simple, compact, automatic sample-preparation systems for molecular diagnostics must be developed. Microelectromechanical systems (MEMS) is a promising approach for the development of automated sample preparation for the clinical laboratory or point-of-care setting. This review discusses MEMS-based components that could be applied to the different stages of the sample-preparation process such as cell separation, nucleic acid purification, and nucleic acid amplification. Examples of functional component integration are given. Issues discussed include partitioning of functions between the instrument and disposable unit, methods of propulsion of fluids and particles, vapor and liquid barriers, and sample size. Although further evaluation and development are needed to provide practical solutions to some of these issues, we conclude that MEMS-based components might contribute to some components in a sample-preparation system consisting of modular instruments and disposable units, but will not provide a generic or a totally integrated solution.     

Capillary electrophoresis of DNA for molecular diagnostics

A number of applications of capillary zone electrophoresis (CZE) in sieving liquid polymers (notably linear polyacrylamides and cellulose) for the analysis of polymerase chain reaction (PCR) products of clinically relevant, diagnostic DNA, are reviewed. The fields covered are: human genetics, quantitative gene dosage, microbiology and virology, forensic medicine and therapeutic DNA (notably, antisense nucleotides). Some unique, novel developments are highlighted, such as: (i) nonisocratic CZE, i.e., temperature-programmed CZE for detection of DNA point mutations; (ii) the synthesis of novel N-substituted acrylamides, offering extreme resistance to alkaline hydrolysis coupled to high hydrophilicity. In the field of denaturing gradient gel electrophoresis (DGGE), as routinely performed in gel slabs, a novel methodology is described in CZE: double-gradient DGGE. In this technique, two gradients are simultaneously applied along the migration direction: a chemical (or thermal) denaturing gradient, for partially unwinding homo- and hetero-duplexes of DNA, and a porosity gradient, for recompacting diffuse bands melting over a broader range of denaturing conditions. It is thus demonstrated that chemical gradients, in addition to temperature gradients, can be easily implemented even in a capillary format.     

Surface-enhanced Raman scattering molecular sentinel nanoprobes for viral infection diagnostics

In this paper, we describe a surface-enhanced Raman scattering (SERS)-based detection approach, referred to as “molecular sentinel” (MS) plasmonic nanoprobes, to detect an RNA target related to viral infection. The MS method is essentially a label-free technique incorporating the SERS effect modulation scheme associated with silver nanoparticles and Raman dye-labeled DNA hairpin probes. Hybridization with target sequences opens the hairpin and spatially separates the Raman label from the silver surface thus reducing the SERS signal of the label. Herein, we have developed a MS nanoprobe to detect the human radical S-adenosyl methionine domain containing 2 (RSAD2) RNA target as a model system for method demonstration. The human RSAD2 gene has recently emerged as a novel host-response biomarker for diagnosis of respiratory infections. Our results showed that the RSAD2 MS nanoprobes exhibits high specificity and can detect as low as 1 nM target sequences. With the use of a portable Raman spectrometer and total RNA samples, we have also demonstrated for the first time the potential of the MS nanoprobe technology for detection of host-response RNA biomarkers for infectious disease diagnostics.     

Optimization of capillary array electrophoresis single-strand conformation polymorphism analysis for routine molecular diagnostics

Mutation screening is widely used for molecular diagnostics of inherited disorders. Furthermore, it is anticipated that the present and future identification of genetic risk factors for complex disorders will increase the need for high-throughput mutation screening technologies. Capillary array electrophoresis (CAE) SSCP analysis is a low-cost, automated method with a high throughput and high reproducibility. Thus, the method fulfills many of the demands to be met for application in routine molecular diagnostics. However, the need for performing the electrophoresis at three temperatures between 18 degrees C and 35 degrees C for achievement of high sensitivity is a disadvantage of the method. Using a panel of 185 mutant samples, we have analyzed the effect of sample purification, sample medium and separation matrix on the sensitivity of CAE-SSCP analysis to optimize the method for molecular diagnostic use. We observed different effects from sample purification and sample medium at different electrophoresis temperatures, probably reflecting the complex interplay between sequence composition, electrophoresis conditions and sensitivity in SSCP analysis. The effect on assay sensitivity from three different polymers was tested using a single electrophoresis temperature of 27 degrees C. The data suggest that a sensitivity of 98-99% can be obtained using a 10% long chain poly-N,N-dimethylacrylamide polymer.     

Protein A tangential flow affinity membrane cartridge for extracorporeal immunoadsorption therapy.

Tangential flow affinity membrane cartridge (TFAMC) is a new model of immunoadsorption therapy for hemoperfusion. Recombinant Protein A was immobilized on the membrane cartridge through Schiff base formation for extracorporeal IgG and immune complex removal from blood. Flow characteristics, immunoadsorption capacity and biocompatibility of protein A TFAMC were studied. The results showed that the pressure drop increased with the increasing flow rate of water, plasma and blood, demonstrating reliable strength of membrane at high flow rate. The adsorption capacities of protein A TFAMC for IgG from human plasma and blood were measured. The cartridge with 139 mg protein A immobilized on the matrix (6 mg protein A/g dry matrix) adsorbed 553 mg IgG (23.8 mg IgG/g dry matrix) from human plasma and 499.4 mg IgG (21.5 mg IgG/g dry matrix) from human blood, respectively. The circulation time had a major influence on IgG adsorption capacity, but the flow rate had little influence. Experiments in vitro and in vivo confirmed that protein A TFAMC mainly adsorbed IgG and little of other plasma proteins, and that blood cell damage was negligible. The extracorporeal circulation system is safe and reliable.     

A microarray enzyme-linked immunosorbent assay for autoimmune diagnostics

In order to quantify autoantibodies in the sera of patients with autoimmune disease, we have created a microarray-based immunoassay that allows the simultaneous analysis of 18 known autoantigens. The microarrays contain serial dilutions of the various antigens, thereby allowing accurate determination of autoantibody titer using minimal amounts of serum. The assay is very sensitive and highly specific: as little as 40 fg of a known protein standard can be detected with little or no cross-reactivity to nonspecific proteins. The signal intensities observed from serial dilutions of immobilized antigen correlate well with serial dilutions of autoimmune sera. Miniaturized and highly parallelized immunoassays like these will reduce costs by decreasing reagent consumption and improve efficiency by greatly increasing the number of assays that can be performed with a single serum sample. This system will significantly facilitate and accelerate the diagnostics of autoimmune diseases and can be adapted easily to any other kind of immunoassay.     

Lasers for plasma diagnostics,time resolved measurement and molecular fluorometry in analytical science

In chemical measurement and characterization, lasers are playing a unique role in improving sensitivity, enhancing spatial and spectral resolution, and enabling time resolution on the fastest time scales that are chemically significant. Furthermore, lasers have permitted entirely new classes of measurements to be undertaken that would not be possible without the high radiant power, directionality, and coherence of a laser beam. In this paper, a number of these capabilities are illustrated with examples from the authors' laboratory. Prominent among these examples is the use of a high-power pulsed laser for producing scattering and fluorescence from species in an inductively coupled plasma (ICP). With the appropriate laser and photometric equipment, such measurements enable the determination of time-resolved and spatially resolved values for electron concentration, electron energy distribution, gas-kinetic temperature, and the concentrations of important sample and intrinsic species that the plasma contains. Another example shows how either a continuous wave (CW) or repetitively pulsed laser can be coupled with relatively simple electronic instrumentation to permit measurements to be obtained on a sub-nanosecond time scale. Interestingly, a recent development might obviate the need for a sophisticated laser in such schemes. Lastly, a relatively simple experimental configuration can be used to determine as few as 10⁶ molecules in a real sample. In this arrangement, a single aliquot of the sample is dispensed in a volume as small as 6 nL. This aliquot, in droplet from, then constitutes the sample cell itself. As the droplet falls through the focused laser beam, its contents can be determined with extraordinarily high sensitivity. Methods to improve even this detection capability will be outlined.     

Laser diagnostics of elementary processes in molecular beam scattering on surfaces

We survey the main aspects of the laser techniques to study the elementary processes that take place in the scattering of molecules from crystallographic surfaces. We discuss the salient features of the accommodation of the translational, rotational and vibrational degrees of freedom of the scattered molecules and we summarize the main results of a recent comparative study of molecular beam scattering on graphite and diamond.     

Current applications and future trends of molecular diagnostics in clinical bacteriology

Molecular diagnostics of infectious diseases, in particular, nucleic-acid-based methods, are the fastest growing field in clinical laboratory diagnostics. These applications are stepwise replacing or complementing culture-based, biochemical, and immunological assays in microbiology laboratories. The first-generation nucleic acid assays were monoparametric such as conventional tests, determining only a single parameter. Improvements and new approaches in technology now open the possibility for the development of multiparameter assays using microarrays, multiplex nucleic acid amplification techniques, or mass spectrometry, while the introduction of closed-tube systems has resulted in rapid microbial diagnostics with a subsequently reduced contamination risk. Whereas the first assays were focused on the detection and identification of microbial pathogens, these new technologies paved the way for the parallel determination of multiple antibiotic resistance determinants or to perform microbial epidemiology and surveillance on a genetic level.     

Packing structure and self-heating in capillary electrochromatography

The origin of bubble formation during operation of capillary electrochromatography (CEC) has been an issue of debate. Ohmic heating resulted from current passed through a packed column was proposed as the primary cause. However, this explanation has been questioned on the ground that the current measured in CEC is much lower than that measured with open-tubular separation systems where no bubble formation occurs. To resolve this issue, we carried out a theoretical study correlating self-heating of the electrolyte with packing structure of the column. We used a bundle of capillary tubes, a bundle of two types of capillary tubes and two bundles of capillary tubes connected serially to model, respectively, the flow channels in the column of non-porous particles, in the column of porous particles and in the column of various packing densities. The results from this study indicate that, for columns of homogeneous packing density, the heat output is indeed smaller than that in open-tubular columns of the same dimensions. In this case, the self-heating cannot be a key factor responsible for the bubble formation in CEC. However, for columns of heterogeneous packing density, a large excess of heat release may be produced in column sections of high packing density and, in turn, over-heating in such sections may become the primary cause for the formation of bubbles. It follows from this study that preparation of columns of homogeneous packing structure is essential to obtain reproducible and bubble-free CEC systems.     

Optical tweezers for medical diagnostics

Laser trapping by optical tweezers makes possible the spectroscopic analysis of single cells. Use of optical tweezers in conjunction with Raman spectroscopy has allowed cells to be identified as either healthy or cancerous. This combined technique is known as laser tweezers Raman spectroscopy (LTRS), or Raman tweezers. The Raman spectra of cells are complex, since the technique probes nucleic acids, proteins, and lipids; but statistical analysis of these spectra makes possible differentiation of different classes of cells. In this article the recent development of LTRS is described along with two illustrative examples for potential application in cancer diagnostics. Techniques to expand the uses of LTRS and to improve the speed of LTRS are also suggested.     

The use of electrostatic probes for plasma diagnostics—A review

The use of electrostatic, or Langmuir, probes for plasma diagnostics is reviewed. The emphasis is on experimental implementation and current techniques, and particular attention is paid to sources of error in theoretical interpretation as well as to experimental problems that can occur in complex, reactive plasmas.     

Activation energy of self-heating process Studied by DSC

In order to identify the kinetic process of self-heating in DSC experiment for Ti+3Al→TiAl₃ reaction, two approaches, linear-fitting approach developed from Semenov"s theory of spontaneous ignition and variation of Friedman method, were carried out with cylindrical Ti-75 at% Al samples. Following these approaches, two identical activation energies are obtained as 169±15 kJ mol^-1 and 170±5 kJ mol^-1, respectively. Compared with the activation energies of reactions and interdiffusions between Ti and Al, the possible rate-controlling process of self-heating in DSC experiment for Ti+3Al→TiAl₃ reaction is the interdiffusion between Ti and Al through TiAl₃-layer. This revised version was published online in August 2006 with corrections to the Cover Date.     

Kinetics and safety analysis of sulfide mineral self-heating

Thermal methods of analysis such as DSC and TGA provide a powerful methodology for the study of solid reactions. This paper proposes an improved thermal analysis methodology for thermal stability and safety investigation of complex solid-state reactions. The proposed methodology is based on differential iso-conversional approach and involves peak separation and individual peak analysis for kinetic analysis and safety prediction. The proposed thermal analysis method was coupled with Mineral Libration Analysis (MLA) to investigate self-heating of sulfide mineral ores. The influence of sample’s mineralogy on thermal degradation was examined and discussed. The information gained from the advanced kinetic analysis of DSC/TGA measurements were up-scaled for TMR and SADT determination. The described thermal analysis method provides not only an understanding of sulfide mineral self-heating, but also aids the design of effective mitigation measures for their adverse environmental and safety effects.     

A fully automated catecholamines analyzer based on cartridge extraction and HPLC separation

Summary A fully automated analyzer is described for the HPLC analysis of catecholamines. Firstly urinary and plasma catecholamines are reacted with diphenylboronic acid giving a complex without requiring a pH-meter step. This complex is strongly retained on a C 18 cartridge and elution with acetic acid solutions shows recoveries higher than 90 %. The catecholamines are eluted also by the mobile phase employed for the HPLC’ analysis. An intelligent autosampler makes the complex and fills a loop with all the solvents necessary for the sample cleanup. It then inverts the flow and pumps the sample and the solvents throught the cartridge. In the elution step the disposable extraction cartridge is positioned on stream with the HPLC analytical column by an automatic sampler. The separation is performed by ion-pair reversed-phase high-performance liquid chromatography, with sodium dodecyl sulphate as pairing ion, a short analytical column and electrochemical detection. The HPLC analysis time is 3 min and the total sample turnover time is 8 min. The recoveries and the precision of the analyzer are given together with correlation with manual HPLC.     

A fluorescent nitrate sensing system using a reaction cartridge and titanium trichloride

A simple and highly sensitive cartridge type nitrate sensing system was developed using titanium trichloride (TiCl(3)) in hydrochloric acid to reduce nitrate to ammonium ion. The system primarily consisted of a nitrate reduction section using titanium trichloride and an ammonia detection section. The nitrate was reduced in a simply made cartridge equipped with filter units and the resulting ammonium ion solution was directly introduced into a flow injection system, where it was neutralized to ammonia and allowed to react with o-phthalaldehyde (OPA). The isoindole thus formed was detected by virtue of its fluorescence, allowing quantitation of the nitrate in the initial sample. Our sensing system has a detection limit of 0.01 mg l(-1) and a dynamic linear range from 0.05 to 2.5 mg l(-1) with response times of less than 5 min for the entire procedure. The system had a relative standard deviation (RSD) of less than 2.56% after more than 30 consecutive measurements of 0.5 mg l(-1) NO(3)(-). The system is unaffected by FeCl(3), Na(2)SO(4) and NaCl at concentrations of 200 mg l(-1) or by biological oxygen demand (BOD) values as high as 110 mg O l(-1). The effects of reaction time and titanium trichloride concentration were also investigated. Furthermore, several river water samples were examined.     

A molecular spring for vision

Light absorption by the visual pigment rhodopsin leads to vision via a complex signal transduction pathway that is initiated by the ultrafast and highly efficient photoreaction of its chromophore, the retinal protonated Schiff base (RPSB). Here, we investigate this reaction in real time by means of unrestrained molecular dynamics simulations of the protein in a membrane mimetic environment, treating the chromophore at the density functional theory level. We demonstrate that a highly strained all-trans RPSB is formed starting from the 11-cis configuration (dark state) within approximately 100 fs by a minor rearrangement of the nuclei under preservation of the saltbridge with Glu113 and virtually no deformation of the binding pocket. Hence, the initial step of vision can be understood as the compression of a molecular spring by a minor change of the nuclear coordinates. This spring can then release its strain by altering the protein environment.