Bead array

There are many protocols and different types of platforms available, e.g. GeneChips from Affymetrix, Illumina Bead Arrays, Arrays from Agilent, Applied Biosystems, GE Healthcare, customized spotted cDNA microarrays etc. the basic procedure for a large-scale measurement of gene expression involves the preparation of total or mRNA from the biological sample(s) under investigation (e.g. candidate tissue) and the hybridization of copied labelled RNA or cDNA to the DNA elements on the array surface (Fig. 1). 

Marquette CA, Blum LJ (2005) Beads Arraying and Beads Used in DNA Chips. 261 113-129 Mascini M, see Palchetti I (2005) 261 27-43... 

Bibikova M, Talantov D, Chudin E, et al. Quantitative gene expression profiling in formalin-fixed, paraffin-embedded tissues using universal bead arrays. Am. J. Pathol. 2004 165 1799-1807. 

Figure 5. Schematic depiction of a self-encoded bead array. A mixture of three sensor types fills the fiber tip wells randomly. The sensors are identified by their characteristic responses to a test vapor pulse. Reprinted with permission from ref. 9b. Copyright 1999 American Chemical Society.

Fig. 6 (a) Schematic illustration of a flow cytometer used in a suspension array. The sample microspheres are hydrodynamically focused in a fluidic system and read-out by two laser beams. Laser 1 excites the encoding dyes and the fluorescence is detected at two wavelengths. Laser 2 is used to quantify the analyte, (b) Scheme of randomly ordered bead array concept. Beads are pooled and adsorbed into the etched wells of an optical fiber, (c) Scheme of randomly-ordered sedimentation array. A set of encoded microspheres is added to the analyte solution. Subsequent to binding of the analyte, microparticles sediment and assemble at the transparent bottom of a sample tube generating a randomly ordered array. This array is evaluated by microscope optics and a CCD-camera. Reproduced with permission from Refs. [85] and [101]. Copyright 1999, 2008 American Chemical Society... 

Yang X, Zhao X, Zuo X, Wang K, Wen J, Zhang H (2009) Nucleic acids detection using cationic fluorescent polymer based on one-dimensional microfluidic beads array. Talanta 77 1027-1031... 

Illumina produces fiberoptic random bead arrays. Latex beads are encoded using different fluorescent dye mixtures that are either adsorbed into the particles or attached to the surfaces. Presynthesized oligonucleotides are attached to selected bead populations so that a single dye or dyerdye ratio identifies the attached oligonucleotide. Populations are mixed in bulk and then loaded onto the tips of a fiberoptic, one end of which has been acid etched to form microscopic nanowells. The nanowells are filled at random with the mixed bead population to create a BeadArray . Such bxmdles can... 

Human IFNy Cytometric Bead Array (CBA) Flex set (Becton Dickinson, CA, USA). 

Interferon production of PBMCs cultured in the presence of selected DIMS determined by ELISA for IFNa, IFNp (mean data from six healthy individuals) and by Cytometric Bead Array (Becton Dickinson) for IFNy (mean data from four healthy individuals)... 

Maier, R., et al. (2006) Application of multiplex cytometric bead array technology for the measurement of angiogenic factors in the vitreous. Mol Vis. 12, 1143-7. 

McDuffie, E., et al. (2006) Detection of cytokine protein expression in mouse lung homogenates using suspension bead array. J Inflamm (Land). 3, 15. 

Shen R, Fan JB, Campbell D et al. High-throughput SNP genotyping on universal bead arrays. Mutat Res 2005 573 70-82. 

Fig. 11.15. A multiplex bead array that can be used to capture multiple soluble analytes. In the dot plot, 15 types of beads are distinguished by their red/orange ratios they capture 15 different cytokines. For example, the beads in Region 1 capture interleukin (IL)-9 in Region 5, IL-2 in Region 9, IL-5 and in Region 13, MCP-1. The green fluorescence histograms from each region show, by their intensity, how much cytokine has been captured by each type of bead. Standard curves can relate the green fluorescence intensity to the concentration of cytokine in the sample. The experimental format illustrated in the cartoon here is patterned directly from work by RT Carson and DAA Vignali (1999).

Fig. 12.17 Inhibition of phosphorylation of p38 MAP kinase in neutrophils (a, flow cytometry) and cytokine production (c-e, flow-cytometric bead array) in whole human blood stimulated with 100 ng/mL LPS, with either DS-96 or PMB (b) Forward scatter/side scatter profile and the gating for p38 MAPK-negative and positive gates obtained on unstimulated (negative control) and LPS-stimulated (positive control) cells, respectively...

The nucleic acid immobilization chemistry involved is detailed and presented together with the bead arraying or the bead immobilization systems, respectively. 

Three different systems could be distinguished according to the organization of the beads bead arrays, composed of highly organized beads bead biochips, using beads as immobilization support without precise positioning of each bead and the beads in microfluidic networks, characterized by a possible displacement of the beads. 

One major handicap of these bead arraying systems is that usually no physical addressing of the beads in a particular trap can be achieved these are then randomly self organized in the traps. 

Currently, two methods co-exist to determine the position of the probe grafted beads on a self-assembled bead array. 

A solution to cope with this problem is to use beads with a larger diameter (230 pm) in order to permit their manipulation with a micromanipulator [10]. Each particular bead could then be placed at a precise location of the etched array. Nevertheless, at the present time, only low density bead arrays (4x3 array) could be physically addressed simultaneously, since the procedure is found to be time consuming. 

All those systems, based on beads arraying and using optical detection are characterized by a very low target detection limit with a lowest value at 1 zmole [5]. 

Immobilized bead biochips are furthermore an interesting alternative to the dramatically complex bead arrays. Indeed, different populations of DNA... 

Fig. 8 Classical optical image of the bead arrays capillary (a) and fluorescent microscope images (b)-(k) of the bead arrays after hybridization (reproduced from [31]) (with permission)...

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