Patent Publication Number: US-6667159-B1

Title: Optical fiber biosensor array comprising cell populations confined to microcavities

Description:
This is a divisional of application U.S. Ser. No. 09/033,462, filed Mar. 2, 1998; now U.S. Pat. No. 6,210,910 which application is incorporated herein by reference and to which applications priority is claimed under 35 USC §120. 
    
    
     This invention was made with government support under GM48142 awarded by the National Institutes of Health. The government may have certain rights in the invention. 
    
    
     FIELD OF THE INVENTION 
     The present invention is generally concerned with biosensors, biosensor arrays, and sensing apparatus, and sensing methods for the analysis of chemical and biological materials. More particularly, the invention is directed to biosensors, biosensor arrays, sensing apparatus and sensing methods which employ cells and mixed populations of cells for analysis of chemical and biological materials. 
     BACKGROUND OF THE INVENTION 
     It is generally recognized that important technical advances in chemistry, biology and medicine benefit from the ability to perform microanalysis of samples in minute quantities. However, making analytical measurements on minute quantities has long been a challenge due to difficulties encountered with small volume sample handling, isolation of analytes, and micro-analysis of single-cell physiology. 
     Nanoliter, picoliter, and femtoliter volume studies have been explored in a range of applications involving in vitro and in vivo cellular investigations [R. M. Wightman, et al.,  Proc. Natl. Acad. Sci. U.S.A.  88:10754(1991); R. H. Chow, et al.  Nature  356:60(1992); T. K. Chen, et al.  Anal. Chem . 66:3031(1994); S. E. Zerby, et al.,  Neurochem . 66:651(1996); P. A. Garis, et al.  J.Neurosci . 14:6084(1994); G. Chen, et al.,  J.Neurosci . 15:7747(1995)], electrochemistry [R. A. Clark, et al.,  Anal. Chem . 69(2):259(1997)], matrix-assisted laser desorption-ionization mass spectrometry [S. Jespersen, et al.,  Rapid Commun. Mass Spectrom . 8:581(1994)], micro-column liquid chromatography [I. A. Holland, et al., Anal Chem. 67:3275(1995); M. D. Oates, et al.,  Anal. Chem . 62:1573(1990)], micro-titration [M. Gratzl, et al  Anal. Chem . 65:2085(1993); C. Yi, et al.,  Anal. Chem . 66:1976(1994)], and capillary electrophoresis [M. Jansson, et al.,  J.Chromatogr . 626:310(1992); P. Beyer Hietpas, et al.  J.Liq.Chromatogr . 18:3557(1995)]. 
     Clark, et al. [ Anal. Chem . 69(2):259(1997)] has disclosed a method for fabricating picoliter microvials for electrochemical microanalysis using conventional photolithographic masking and photoresist techniques to transfer mold polystyrene microvials on silicon wafer templates. These microvials typically exhibit non-uniformity in size and shape due to the difficulty in controlling the resist etching of the molding surface and the transfer molding process. 
     Park, et al. [ Science  276:1401(1997)] has disclosed a modified lithographic method for producing arrays of nanometer-sized holes using polystyrene-polybutadiene, ordered, diblock copolymers as masks in reactive ion etching of silicon nitride. This multi-step method is capable of producing arrays of picoliter-sized holes which are typically 20 nanometers in diameter and 20 nanometers deep with a spacing of 40 nanometers. Hole densities of up to 10 11  holes/cm 2  are disclosed. The range of sizes and spacings of the holes produced by this method is limited by the size of the copolymer microdomains. Uniformity of hole size and spacing is difficult to maintain with this method due to difficulties in controlling the etching method employed to form the holes. 
     Deutsch, et al. [ Cytometry  16:214(1994)] have disclosed a porous electroplated nickel microarray comprised of micron-sized conical holes in blackened nickel plate. Hole sizes range from a 7 um upper diameter to a 3 um lower diameter with an 8 um depth. The array is used as a cell carrier for trapping individual cells while studying the responses of individual cells to changes in their microenvironment. In U.S. Pat. No. 4,772540, Deutsch, et al., have also disclosed a method for making such an array using a combined photoresist and electroplating technique. 
     Coming Costar Corp. (Acton, Ma) produces a commercial microwell array for miniaturized assays under the trademark PixWell™. These arrays are made from microformed glass plates and comprise 40 um diameter by 20 um deep tapered wells with a well density of 4356 wells/cm 2 . 
     Microwell arrays have particular utility in the study of living cells. In cell research, the measurement of responses of individual cells to changes or manipulations in their local environment is desirable. Any method or device designed for such studies must provide for the capability of maintaining cell viability, identifying the location of individual cells, and correlating response measurements with individual cells. 
     Due to the availability of viable fluorescent probes for intracellular studies, fluorescence measurements of living cells have significant utility in the study of cell functions. Thus fluorescence optical measurements are often utilized in cell studies where three generic methods of cell measurement are available, comprising bulk measurements of cell populations, dynamic measurements of cell populations or individual cells, and static measurements of individual cells. 
     The characteristics of an entire cell population as a whole can be studied with bulk measurements of sample volumes having a plurality of cells. This method is preferred where cell populations are very homogeneous. A generally recognized limitation of this method is the presence of background fluorescence which reduces the sensitivity of measurements and the inability of distinguishing differences or heterogeneity within a cell population. 
     Flow cytometry methods are often employed to reduce problems with background fluorescence which are encountered in bulk cell population measurements [M. R. Gauci, et al.,  Cytometry  25:388(1996); R. C. Boltz, et al.,  Cytometry  17:128(1994)]. In these methods, cell fluorescence emission is measured as cells are transported through an excitation light beam by a laminar flowing fluid. Flow cytometry methods may be combined with static methods for preliminary sorting and depositing of a small number of cells on a substrate for subsequent static cell measurements [U.S. Pat. No. 4,009,435 to Hogg, et al.; Kanz, et al.,  Cytometry  7:491(1986); Schildkraut, et al.,  J.Histochem Cytochem  27;289(1979)]. 
     Gauci, et al., disclose a method where cell size, shape and volume is measured by light scattering and fluorescent dyes are utilized to determine protein content and total nucleic acid content of cells. This method further provides for counting and sizing various cells at a rate of approximately 100 cells per second. 
     Flow cytometry techniques are generally limited to short duration, single measurements of individual cells. Repetitive measurements on the same cell over time are not possible with this method since typical dwell times of a cell in the excitation light beam are typically a few microseconds. In addition, the low cumulative intensity from individual cell fluorescence emissions during such short measurement times reduces the precision and limits the reliability of such measurements. 
     Regnier, et al., [ Trends in Anal.Chem . 14(4):177(1995)] discloses an invasive, electrophoretically mediated, microanalysis method for single cell analysis. The method utilizes a tapered microinjector at the injection end of a capillary electrophoresis column to pierce an individual cell membrane and withdraw a sample of cytoplasm. The method measures cell contents, one cell at a time. The method is generally limited to the detection of easily oxidized species. 
     Hogan, et al., [ Trends in Anal.Chem . 12(l):4(1993)] discloses a microcolumn separation technique which may be utilized in combination with either a conventional gas chromatograph-mass spectrometer, micro thin layer chromatography or high pressure liquid manipulation of small cellular volumes. The sensitivity of the method is limited and may require pre-selection of target compounds for detection. 
     Static methods are generally the preferred method for measurements on individual cells. Measurement methods range from observing individual cells with a conventional optical microscope to employing laser scanning microscopes with computerized image analysis systems [see L. Hart, et al.,  Anal. Quant. Cytol. Histol . 12:127(1990)]. Such methods typically require the attachment of individual cells to a substrate prior to actual measurements. Problems are typically encountered in attaching single cells or single layers of cells to substrates and in maintaining cells in a fixed location during analysis or manipulation of the cell microenvironment. Additionally, repetitive measurements on individual cells typically require physically indexing the location of individual cells and providing a mechanism for scanning each cell sequentially and returning to indexed cell locations for repeated analysis of individual cells. 
     Huang, et al., [ Trends in Anal. Chem ., 14(4)158(1995)] discloses a static electrochemical method and electrode for monitoring the biochemical environment of single cells. The method requires fabrication and manual positioning of a microelectrode reference and working electrode within the cell. The method has been used to detect insulin, nitric oxide and glucose inside single cells or external to the cells. The method is generally limited to the study of redox reactions within cells. 
     Ince, et al. [ J.Immunol. Methods  128:227(1990)] disclose a closed chamber device for the study of single cells under controlled environments. This method employs a micro-perfusion chamber which is capable of creating extreme environmental conditions for cell studies. Individual cells are held in place by two glass coverslips as various solutions are passed through the chamber. One limitation of the method is the difficulty in eliminating entrapped gas bubbles which cause a high degree of autofluorescence and thus reduces the sensitivity of measurements due to background fluorescence. 
     In an attempt to overcome the limitations encountered with conventional static methods, Deutsch, et al., [ Cytometry  16:214(1994)] and Weinreb and Deutsch, in U.S. Pat. Nos. 4,729,949, 5,272,081, 5,310,674, and 5,506,141, have disclosed an apparatus and method for repetitive optical measurements of individual cells within a cell population where the location of each cell is preserved during manipulation of the cell microenvironment. 
     A central feature of the apparatus disclosed by Deutsch, et al., is a cell carrier, comprising a two dimensional array of apertures or traps which are conical-shaped in order to trap and hold individual cells by applying suction. The cell carrier is typically fabricated by the combined electroplating-photoresist method disclosed in U.S. Pat. No. 4,772540 to Deutsch, et al. The purpose of the cell carrier is to provide a means for maintaining the cells in fixed array locations while manipulating the cell environment. Individual cells are urged into cell carrier holes by suction and the wells are subsequently illuminated with a low intensity beam of polarized light that reads back-emitted polarization and intensity. Measurements are compared when two different reagents are sequentially reacted with the cells. The method as disclosed requires two separate cell carriers for both a baseline control and analyte measurement. 
     The method and device of Deutsch, et al., have been employed by pathologists in diagnostic tests to determine the health and viability of cell samples taken from patients. The method and device have been applied to both cancer screening [Deutsch, et al.,  Cytometry  16:214(1994),  Cytometry  23:159(1996), and  European J.Cancer  32A(10):1758(1996)] and rheumatoid arthritis [Zurgil, et al.,  Isr.J.Med.Sci . 33:273(1997)] in which fluorescence polarization measurements are used to differentiate lymphocytes of malignant versus healthy cells based on changes in the internal viscosity and structuredness of the cytoplasmic matrix induced by exposure to tumor antigen and mitogens. 
     The method and device disclosed by Deutsch, et al., requires employment of a scanning table driven by three stepping motors and a computer control system for mapping, indexing and locating individual cells in the cell carrier. The use of such mechanical scanning methods introduces limitations in reproducibility and accuracy of measurements due to conventional mechanical problems encountered with backlash and reproducible positioning of individual cell locations for repeated measurements. In addition, mechanical scanning of the entire array prolongs the measurement time for each cell in the array. 
     The method disclosed by Deutsch, et al., is further limited by the use of fluorescence polarization measurements which have certain intrinsic limitations due to the significant influence of various optical system components on polarization as the fluorescence emission response is passed from the cell carrier to optical detectors. Birindelli, et al. [European J. Cancer 33(8):1333(1997)], has also identified limitations in this method due to fluctuations in electropolarisation values which require taking averages of at least three measurement scans for each condition so as to obtain reliable measurements. In addition, for cell studies, polarization measurements are generally limited to cell responses which produce sufficient changes in cytoplasm viscosity to produce a detectable change in polarization. Since not all cell responses are accompanied by detectable viscosity changes, the method is further limited to the cell activities which create such viscosity changes in the cytoplasm. 
     Zare, et al., [ Science  267:74(1995);  Biophotonics International , March-April, pl7 (1995)] discloses a biosensor system based on the response of living cells to complex biological materials fractionated by a microcolumn separation technique. Cells which were positioned on a glass cover slip were treated with a fluorescent probe and subsequently shown to be sensitive to a series of biological compounds including acetylcholine, bradykinin, and adenosine triphosphate as well as changes in intracellular calcium levels. 
     Yeung, et al. [ Acc. Chem. Res . 27:409(1994)] has reviewed a number of methods for single cell response studies and has observed a significant variation and heterogeneity within cell populations based on analyte measurements. For example, the reference discloses a capillary electrophoresis method for exposing cells to biologically reactive compounds, extracting the intracellular fluid of individual cells produced in response to such compounds, and identifying analytes from migration times in the capillary column. Other fluorescence-based assays are also disclosed. Significant cell-to-cell variations and heterogeneity in individual cell responses within a cell population were observed which differences could provide a means for discriminating between biological and chemical compounds in contact with individual cells. 
     McConnell, et al. [ Science , 257:1906(1992)], disclose a microphysiometer device known as the “Cytosensor” which uses a light addressable potentiometer sensor to measure the rate at which cells acidify their environment. This sensor acts as miniaturized pH electrode for monitoring cell responses which produce detectable changes in local pH. The disclosed device is limited to the measurement of proton excretions from cells and thus is only capable of detecting acidic cell responses to analytes. 
     U.S. Pat. No. 5,177,012 to Kim, et al., disclose a biosensor for the determination of glucose and fructose. The biosensor is produced by treating whole cells with an organic solvent and immobilizing the treated cells residue on a support to form a whole cell membrane which is applied to a pH electrode. 
     U.S. Pat. No. 5,690,894 to Pinkel, et al., discloses a biosensor which employs biological “binding partners”, materials such as nucleic acids, antibodies, proteins, lectins and other materials derived from cells, tissues, natural or genetically-engineered organisms. These agents are used in conjunction with a fiber optic array where each species of binding partners is uniquely addressed by a group of fibers within the fiber optic bundle which is coupled to an optical detector. The array was designed for screening of extensive arrays of biological binding partners. 
     While many of the prior art methods provide for the analysis of either single cells or populations of cells and some of these methods provide for monitoring cell responses to target analytes, none of the disclosed methods provides for employing large populations of monocultures or mixed populations of living cells for simultaneously monitoring the responses of individual cells to biological stimuli produced by chemical and biological analytes. Thus there is a need for a biosensor array and method which efficiently utilizes the ability of populations of living cells to respond to biologically significant compounds in a unique and detectable manner. Since the selectivity of living cells for such compounds has considerable value and utility in drug screening and analysis of complex biological fluids, a biosensor which makes use of the unique characteristics of living cell populations would offer distinct advantages in high throughput screening of combinatorial libraries where hundreds of thousands of candidate pharmaceutical compounds must be evaluated. In addition, such a sensor would be useful in monitoring bioprocesses and environmental pollution where the enhanced sensitivity of living cells to their environment can be exploited. 
     SUMMARY OF THE INVENTION 
     In general, the invention provides for a biosensor, a biosensor array, a biosensor sensing system and sensing methods for the analysis of chemical and biological materials. More particularly, the invention provides for biosensors and biosensor arrays, sensing apparatus and sensing methods which employ living cells and mixed populations of living cells for analysis of chemical and biological materials. 
     The biosensor array of the present invention comprises either a monoculture of living cells or randomly mixed populations of living cells wherein each individual cell in the array is positioned in an optically addressable microwell which is preformed to accommodate the size and shape of the individual cells. The biosensor array sensing method relies on the well known fact that individual cells, which are chemically or biologically stimulated by the presence of a biological or chemical material in the cell environment, will respond by producing a change in the cell or cellular environment which can be optically interrogated and detected within the cell itself or from an indicator compound, for example, a fluorophore, chromophore or dye, either attached to the cell, taken up in the cell, or added to the local cell environment. The biosensor of the present invention thus capitalizes on the ability of living cells to respond to biologically significant compounds. Since the selectivity of living cells for such compounds has considerable value and utility in drug screening and analysis of complex biological fluids, the biosensor of the present invention offers distinct advantages to high throughput screening of combinatorial libraries where hundreds of thousands of candidate compounds must be evaluated. 
     In a preferred embodiment, the biosensor array of the present invention is incorporated into a fiber optic array. In this embodiment, the distal end of each fiber strand in a fiber optic bundle or fiber optic array is chemically etched so as to create a cavity or microwell. A schematic diagram of the biosensor array concept of the present invention is shown in FIG.  1 . In a preferred embodiment, individual living cells of either a monoculture of cells or mixed populations of cell lines are deployed in the microwells. The microwells are formed by anisotropic etching of the cores of the individual fiber in the fiber bundle or fiber array. The microwells are formed by controlling the etching process so as to remove a centralized core portion of the individual fiber strands while leaving the surrounding cladding intact. The resultant etched cavity is dimensioned for accommodating an individual cell. By selecting a fiber optic bundle or fiber optic array whose individual fiber cores are appropriately sized and by careful control of the etching conditions, the diameter and depth of the microwells can be controlled and adjusted over any convenient dimension range so as to match the size of any desired cell type. 
     In one embodiment, the interior surfaces of the microwells may be coated with a thin film of biologically inert material such as collagen, fibronectin, polylysine, polyethylene glycol, polystyrene, or a metal such as gold, platinum or palladium. In an alternative embodiment, an indicator compound, for example, a fluorophore, a chromophore or dye, may be attached to the microwell surface for detecting cell responses to chemical or biological stimulation. 
     By incorporating a biosensor into a fiber optic array, the innovation of the biosensor of the present invention is in providing for optical coupling of individual cells located in microwells with discrete individual optical fibers in a fiber optic array or bundle. Since typical fiber optic arrays contain thousands of discrete individual fiber strands, the invention thus provides for the individual optical coupling and interrogation of thousands of cells within an array, thereby providing for a large number of independent cell response measurements for each cell population within an array. Due to both the number of cell populations available and the correspondingly large number of individual cells within each cell population, a significant innovation of the present invention is in providing for the summing and amplification of the characteristic optical response signatures of multiple independent measurements taken from cells within each cell population, thereby improving the detection limit and sensitivity of the biosensor. 
     An additional innovation of the present invention is that, by deploying a large number of cell populations within the array, and providing a large number of individual cells in each population, the discriminating capabilities of the biosensor array toward biological or chemical analytes is significantly enhanced by providing for thousands of cell responses from a large number of cell populations. This feature directly mimics the actual behavior of the human olfactory system where the combined signals from thousands of receptor cells, in each grouping of nearly a thousand different receptor cell types found in the epithelium layer, none of which are particularly sensitive in themselves, lead to a highly amplified sensory response to odors [see Kauer, et al,  Trends Neurosci . 14:79(1991). One embodiment of the present invention thus mimics the evolutionary scent amplification process found in the human olfactory system in order to significantly enhance biosensor array sensitivity to analytes by summing the low-level responses of a large number of cells in the biosensor array. By summing the responses from a number of cells at low analyte concentrations, a substantial improvement in signal-to-noise ratio can be achieved and a corresponding reduction in the detection limit of the biosensor array is obtained. 
     A unique feature of the biosensor array of the present invention is that each of the individual cells and cell populations in the array may be encoded for maintaining cell type identity and location where randomly mixed populations of cells are employed. Cells may be encoded prior to disposing them in the microwells or, alternatively, following placement in the microwells. The invention provides for either encoding randomly mixed individual cells and cell populations with a fluorophoric or chromophoric dye compound or, alternatively, using self-encoded cells which are either naturally fluorescing or genetically engineered to fluoresce. Although cell populations may be randomly mixed together, this innovative feature provides for the identity and location of each cell type to be determined via a characteristic optical response signature when the cell array is either illuminated by excitation light energy or, alternatively, subjected to biological stimuli. 
     In one embodiment, cells or cell populations may be self-encoded by selecting cell populations, such as green fluorescent protein mutants, which exhibit either chemiluminescence, bioluminescence, or whose optical response to biological stimuli yield a unique detectable fluorescence signal. Other cell populations may be employed where cells within a population yield a unique temporal optical response to stimuli. Either naturally occurring of genetically engineered cell lines may be utilized. 
     In various alternative embodiments, cells may be encoded with dye compounds which are attached to cells, taken up by cells or provided in the local cell environment. Examples of useful encoding dyes include fluorophores, chromophores, stains or a dye compounds. For example, conventional cell fluorophore probes such as fluoresceins, rhodamines, naphthalimides, phycobiliproteins, nitrobenzoxadiazole may be utilized. A particularly useful reference for selecting appropriate encoding dyes is R. P. Haugland,  Handbook of Fluorescent Probes and Research Chemicals  (6 th  ed.), Molecular Probes Inc.(Eugene, Oreg., 1996) which is herein incorporated by this reference. 
     When dye compounds are employed for encoding, cell populations within the biosensor array may be readily decoded by exciting the array with excitation light and indexing cells types within randomly dispersed populations by their response to excitation. In one embodiment, a single fluorophoric or chromophoric material or dye is used for encoding the cells. In an alternative embodiment, two or more encoding materials or dyes may be used to encode cell populations and the optical response intensity ratios for the dyes, produced by exposure to excitation light energy, are employed to encode and identify members of the cell population with the array. In an alternative embodiment, cells may be decoded by excitation light when exposed to a common analyte. In another embodiment, encoded cells may be decoded by their response to a generic cell activator using either a pH or Ca +2  indicator. 
     The innovative cell encoding feature of the present invention overcomes certain limitations of prior art devices by eliminating the need for mechanically scanning the array, mechanically indexing the location of cells, and mechanically positioning the array for measurements of individual cells within the array. The invention thus provides for rapid, simultaneous measurements of all cells and cell populations within the array without the need to mechanically scan the array to acquire a series of sequential measurements for each cell. Thus monitoring and measuring the responses of all cells in the array occurs simultaneously without a prolonged delay between the first cell measurement and last cell measurement. The ability to measure all cell responses simultaneously thus provides for the capability to monitor both short term cell response and long term cell response. This innovative feature thus enables the monitoring of rapid biologically significant cell processes and cell responses on a short time scale. In addition, the ability to simultaneously measure cell responses over a short time scale enables the measurement of individual cell and cell population response rates to changes in the biosensor array environment. This feature thus provides for additional discriminating response information which is useful for detecting biological or chemical analytes. 
     The biosensor array of the present invention can employ either naturally occurring cells and cell populations or genetically engineered cell lines. Virtually any cell type and size can be accommodated by matching the cell size to individual optical fiber optic core diameters and etching conditions. In one embodiment, NIH 3T3 mouse fibroblast cells were employed. In alternative embodiments, other cells types such as  e. coli  bacteria, staphylococcus bacteria, myoblast precursors to skeletal muscle cells, neutrophil white blood cells, lymphocyte white blood cells, erythroblast red blood cells, osteoblast bone cells, chondrocyte cartilage cells, basophil white blood cells, eosinophil white blood cells, adipocyte fat cells, invertebrate neurons ( Helix aspera ), mammalian neurons, or adrenomedullary cells, may be utilized as well. Any cell type or mixtures of cell population types may also be employed providing the microwell can accommodate the individual cell size. 
     The optical responses of individual cells and cell populations to chemical or biological stimuli are typically interrogated and detected by coupling individual cells with appropriate indicators which may be either fluorophores, chromophores, stains or a dye compounds. For example, conventional cell fluorophore probes such as fluoresceins, rhodamines, naphthalimides, phycobiliproteins, nitrobenzoxadiazole may be utilized. Alternatively, permeant or impermeant cell membrane potential indicators, ion indicators, reactive oxygen indicators and pH indicators may be employed. A particularly useful reference for selecting appropriate indicators is R. P. Haugland,  Handbook of Fluorescent Probes and Research Chemicals  (6 th  ed.), Molecular Probes Inc.(Eugene, Oreg., 1996) which is herein incorporated by this reference. Any suitable indicator or combinations of indicators may be utilized provided the indicator does not compromise cell response. In a variety of alternative embodiments, indicators may be either incorporated directly into the cell, for example by attachment to the cell membrane, by absorption or injection into the cell cytoplasm, or added to the cell external environment, such as a fluid contained within the microwells. In an alternative embodiment, indicators may be attached to the surface of the microwells. 
     In summary, the biosensor array and sensing method of the present invention offers many distinct advantages in overcoming the limitations of prior art devices. The sensor arrays are easily fabricated from commercially available optical imaging fibers to yield a cost effective, high density, precisely formed, biosensor array without requiring any sophisticated machining or forming process. Since optical imaging fibers and fiber optic arrays are available in a wide variety of core diameters, most cell types and sizes may be accommodated in by the device and method of the present invention. In addition, cells can be readily dispersed into the microwell array in random fashion with no need for physical indexing or scanning to locate individual cells or cell populations due to the innovative cell encoding technique. Sensing methods and sensing systems which employ the biosensor and sensor array of the present invention avoids many of the limitations in manipulating cells encountered with prior art devices. Once cells are placed within the microwells of the array, conventional imaging systems and methods which employ an imaging camera and conventional optics, can monitor the response of thousands of cells simultaneously, eliminating requirements for mechanical scanning mechanisms. Analysis of measurement data is further facilitated by implementing commercially available imaging software to process images of the biosensor array using pattern recognition techniques combined with neural network and other statistical methods. 
     The biosensor array and sensing method of the present invention may be employed for a number of useful analytical applications where individual cells, which are chemically or biologically stimulated by the presence of a biological or chemical material in the local cell environment, will respond to their environment by producing an optically detectable response either due to the presence of an appropriate indicator or due to the characteristic optical response of particular cell types which exhibit either natural or genetically-engineered chemiluminescence or bioluminescence. The biosensor array and method of the present invention thus capitalizes on the ability of living cells to respond to biologically significant compounds. Since the selectivity of living cells for such compounds has considerable value and utility in drug screening and analysis of complex biological fluids, the biosensor of the present invention offers distinct advantages to high throughput screening of combinatorial libraries where hundreds of thousands of candidate compounds must be evaluated. 
    
    
     The above and other features of the invention, including various novel details of construction and methods, and other advantages, will now be more particularly described with reference to the accompanying drawings and claims. It will be understood to one skilled in the art that the particular apparatus and method embodying the invention are shown by way of illustration and not as a limitation of the invention. The principles and features of the invention may be employed in various and numerous embodiments without departing from the scope of the invention. 
     BRIEF DESCRIPTION OF THE DRAWINGS 
     The invention is pointed out with particularity in the appended claims. Other features and benefits of the invention can be more clearly understood with reference to the specification and the accompanying drawings in which: 
     FIG. 1 is a schematic diagram of the biosensor array concept of an optical sensor array of cultured cells. A polished optical imaging fiber is chemically etched to produce an array of micron-sized wells at the distal face of the fiber. Cells suspended in media above the array of wells settle into the wells and adhere to the well bottom. The wells are etched such that each well accommodates one cell. Differences in core diameters and etch times can accommodate a wide variety of cell types and sizes; 
     FIGS. 2 a-b  are atomic force microscope photomicrographs of a microwell array used in a biosensor array of the present invention Atomic Force Micrograph (AFM) images of an (A) 75 μm×75 μm 2-D array and a (B) 25 μm×25 μm 3-D array of etched microwells. An array of micron-sized wells is formed at the distal tip of an optical imaging fiber by a wet-etch process that takes advantage of differences in core and clad etch rates; 
     FIG. 3 is a schematic diagram of the method for depositing cells in microwells used for a biosensor array of the present inventions. Cells are deposited into wells at the distal face of an optical imaging fiber. Cells are trypsinized using aseptic technique to remove them from the cell culture dish and suspended in growth media. A portion of the cell suspension is concentrated using centrifugation and added to a 1.5 mm diameter capillary tube. The etched face of the fiber id inserted into the tube and secured in place with a thin strip of laboratory film. The tube/fiber set-up is then incubated in the vertical position for 12-15 hours for cell adhesion to occur; 
     FIG. 4 is an SEM photomicrograph of a single NIH 3T3 mouse fibroblast cell in an etched microwell. Each well has a diameter of 7 μm, depth of 5 μm, and a volume of ˜145 fL; 
     FIG. 5 is a schematic representation of the response of cells adhered in wells to the acetoxymethyl (AM) ester form of the fluorscein derivative, bis-carboxyethyl bis-carboxy fluorscein (BCECF). The array of cells (A) is incubated in a solution of BCECF-AM (B) and then rinsed thoroughly. The non-fluorescent BCECF-AM passively enters the cell. Once inside the cell, the lypophillic blocking groups are cleaved by the non-specific esteraces resulting in an increase in fluorescent intensity (C); 
     FIG. 6 is a characteristic fluorescence image pattern identifying the location of a cells which test positively for cell viability in a biosensor array of the present invention. Fluorescently labeled (551ex, 567em) NIH 3T3 mouse fibroblast cells were deposited in wells at the distal face of an optical imaging fiber. The location of the adhered cells is pin-pointed by exciting at a wavelength compatible with the cell label. The fifteen cells within the designated region of interest form a characteristic pattern which will act as a locational template for fluorescence measurements at the excitation wavelength of BCECF (505ex, 535em); 
     FIG. 7 shows the temporal response of the combined fluorescence intensity of the viable cell population identified in FIG.  6 . An array of adhered cells in wells was immersed in a 0.001 mM solution of BCECF-AM, prepared in serum-free media, for 1 minute. The cell array was removed and rinsed thoroughly with serum-free media to remove any residual dye. Fluorescent images (lex 505 nm, lem 535 nm) were acquired every 30 seconds using a 1.0 second acquisition time. The locational template generated by the fluorescent cell label was transferred to the measurement images in order to locate wells which contain cells. The flourescent intensity response of the cells shows a gradual increase as the lypophillic groups are cleaved from the BCECF-AM dye within the cell. The fluorescent intensity response of the wells which do not contain cells is negligible; 
     FIG. 8 is a fluorescence optical image of an encoded cell population within a biosensor array of the present inventions. Fluorescently labeled (lex 490 nm, lem 502 mn) NIH 3T3 mouse fibroblast cells were cultured in wells etched at the distal face of a 1 mm diameter optical imaging fiber. Excess cells (those not accommodated by a well) were wiped away with a cotton swab wet with growth media. The cells were then excited through the fiber. Cell packing densities can be obtained on the order of ˜10%; 
     FIG. 9 is a schematic block diagram of the measurement system used for optical measurements of the microwell sensor array. The system ( 100 ) may include an image processing computer ( 180 ), frame transfer CCD camera ( 170 ), emission filter ( 160 ), magnification changer ( 165 ), reflected light fluorescence attachment (with 3 position cube slider) ( 130 ), microscope nosepiece ( 140 ), X-Y micropositioner ( 150 ), imaging fiber ( 200 ), Z-translation stage ( 152 ), ND filter slide ( 122 ), excitation filter ( 120 ), condensing lens ( 112 ) and 75 watt Xe lamp ( 110 ). The emission filter ( 160 ) and excitation filter ( 120 ) may include computer controlled shutter and filter wheel; 
     FIG. 10 is a plot of average BCECF fluorescence for nine biosensor array cells over time; and 
     FIGS. 11 a-b  compares the viability of cells inserted in microwells both with and without a pretreatment for filling the microwells with culture media. 
    
    
     DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS 
     A. Fabrication of Microwell Arrays 
     An array of micrometer-sized wells is created at the distal face of an optical imaging fiber by a selective etching process which takes advantage of the difference in etch rates between core and cladding materials. This process has been previously disclosed by Pantano, et al.,  Chem. Mater . 8:2832 (1996), and Walt, et al., in U.S. patent application Ser. No. 08/818,199. The etch reaction time and conditions are adjusted to achieve desired control over the resultant microwell size and volume. Microwells are thus sized to accommodate a single cell of any desired cell type. 
     The sensor array design can accommodate a variety of cell sizes and configurations utilizing either commercially available optical fibers and fiber optic arrays or custom made fibers or fiber arrays. The major requirement in selecting candidate fibers or fiber optic arrays for fabricating sensors is that the individual fibers have etchable cores. 
     In one embodiment, the interior surfaces of the microwells may be coated with a thin film of passivation layer of biologically compatible material such as collagen, fibronectin, polylysine, polyethylene glycol, polystyrene, or a metal such as gold, platinum or palladium. In an alternative embodiment, an indicator compound, for example, a fluorophore, a chromophore or dye, may be attached to the microwell surface for detecting cell responses to chemical or biological stimulation. 
     The method of fabricating microwells can be adapted to any fiber size so as to accommodate a wide range of cell sizes for incorporation into appropriately sized microwells. For example, optical fibers having core diameters ranging from 1.6 to 100 um are commercially available from either Galileo Electro-Optics Corp. (Sturbridge, Mass.) or Edmund Scientific (Barrington, N.J.). In addition, larger sizes are available by custom order. Thus, appropriately sized fibers can be utilized to study such diverse cell sizes as  E. coli , with a typical cell dimension of 0.7 to 1.5 um, and mammalian neurons, with a cell dimension of up to 150 um. 
     In one embodiment, a fiber optic array, having a 1 mm outer diameter and 7 um individual fiber core diameters, available from Galileo Electro-Optics Corp. (Sturbridge, Mass.), was utilized. One end of the fiber optic array was polished using a series of aluminum oxide lapping films 12, 9, 3, 1, 0.3 um available from Mark V Lab (East Granby, Conn.). The fibers were then sonicated for approximately 1 minute to remove any residue from the polishing procedure. The etching procedure was performed by submerging the distal face of the fiber at a right angle in 700 uL of a buffered hydrofluoric acid solution, comprising 100 uL hydrofluoric acid (50%), 0.2 g ammonium fluoride, and 600 uL of deionized water, for approximately 65 seconds. The fiber was then rinsed with deionized water and sonicated for 1 minute to remove any salts that may have been formed during the etching procedure. In this embodiment, the etch reaction time was tailored such that the well size was 7 microns in diameter, 3 microns in depth, and approximately 90 fL in volume. Both scanning electron microscopy (SEM) and atomic force microscopy (AFM) may be utilized to characterize etched microwells. In FIG. 2 a , a typical microwell array formed by the etching procedure is shown in an AMF photomicrograph (Digital Instruments Nanoscope III9, Santa Barbara, Calif.). In FIG. 2, an oblique view of the microwell array is provided. As shown in these figures, the microwells formed by this process are extremely uniform due to the uniform characteristic structure of the fiber optic array. 
     B. Selection of Cell Types 
     Virtually any cell type and size can be accommodated in fabricating the sensor of the present invention by matching the cell size to individual optical fiber optic core diameters. In one embodiment, NIH 3T3 mouse fibroblast cells were employed. These cells are typically 15-20 um in size. Other cells types such as  E. coli  bacteria, 1×3 um, staphylococcus bacteria, approximately 1 um, myoblast precursors to skeletal muscle cells, 15-20 um, neutrophil white blood cells, 10 um, lymphocyte white blood cells, 10 um, erythroblast red blood cells, 5 um, osteoblast bone cells, 15-20 um, chondrocyte cartilage cells, 15-20 um, basophil white blood cells, 10 um, eosinophil white blood cells, 10 um, adipocyte fat cells, 20 um, invertebrate neurons ( Helix aspera ), 125 um, mammalian neurons, 4-140 um, or adrenomedullary cells, 13-16 um, melanocytes, 20 um, epithelial cells, 20 um, or endothelial cells, 15-20 um, may be utilized as well. In addition, any naturally occurring or genetically engineered plant, for example green fluorescent protein mutants, mammalian, invertebrate or other cell line may be employed as well as mixtures of cell lines. A particularly useful source of cell lines may be found in  ATCC Cell Lines and Hybridomas  (8 th  ed., 1994),  Bacteria and Bacteriophages  (19 th  ed., 1996), Yeast (1995),  Mycology and Botany  (19 th  ed., 1996), and  Protists: Algae and Protozoa  (18 th  ed., 1993), available from American Type Culture Co. (Rockville, Md.), all of which are herein incorporated by reference. 
     C. Dispersion of Cells in Microwells 
     Once the microwell size is tailored to accommodate specific cell sizes, the next step in creating an array of cells is to randomly disperse cells into the microwells. FIG. 3 is a schematic diagram showing the method for dispersing and depositing cells in the microwell array. Cell populations are conventionally cultured with growth media which matches cell needs. Culture media is formulated according to either recipes provided by cell line providers, journal articles or reference texts. A particularly useful reference for media preparation is  ATCC Quality Control Methods for Cell Lines  (2 nd  ed.), American Type Culture Co. (Rockville, Md.) which is herein incorporated by reference. After culturing, cells are typically trypsinized using aseptic techniques to remove them from the cell culture dish and suspend them in growth media. 
     In one embodiment, NIH 3T3 mouse fibroblast cells, available from American Type Culture Collection (Rockville, Md.) were utilized. The cells were randomly dispersed into the wells by removing the adhered cells from the culture dish with a proteolytic enzyme, such as Trypsin-EDTA (0.05% Trypsin, 0.53 mM EDTA.4Na), available from; Gibco BRL (Grand Island, N.Y., using aseptic techniques and placing the cells into a single-cell suspension in growth media, such as Dulbecco&#39;s Modified Eagle Medium with 1% PenicillinStreptomycin, 1% L-Glutamine-200 mM, and 10% fetal calf serum, available from Gibco BRL. 
     To disperse cells into the wells, approximately 1.5 ml of the cell suspension was concentrated by centrifugation at 2000 RPM for 3.5 minutes. The supernatant is drawn off and the centrifuge tube was tapped to resuspend the cells. The cell suspension was then added to a 1.5 mm diameter capillary tube. Prior to adding cells to the microwell array, the end of the fiber optic array which contains the microwells was sonicated under vacuum in cell media for approximately 15 minutes to flush and fill the microwells with media. The microwell end of the fiber was then inserted into the capillary tube and secured in place with a thin strip of laboratory film. The capillary tube/fiber set-up was then incubated in the vertical position for 1-2 hours allowing the suspended cells to settle into the wells and adhere to the well bottom. The length of time required to fill the microwells is dependent only on the amount of time required for the cells to adhere to the microwell bottom. Excess cells which were not accommodated by a well were wiped away with a cotton swab wet with growth media. FIG. 4 is an SEM photomicrograph of a single cell dispersed in an etched microwell. 
     Once they are positioned within the microwells, cells with typically attach to microwell surfaces within 1-2 hours by protein contact. Cell culture media in the microwells may be periodically replenished by exposing the distal surface of the fiber optic array to fresh media and allowing nutrients to diffuse into the microwell cavities. Typically, cells will divide every twelve to fifteen hours. While the size of the microwells tends to confine individual cells, the array will accommodate limited cell splitting over time. Microwell volume will restrict cell splitting due to the well know cell phenomenon of contact inhibition when cells are touching. 
     D. Establishing Cell Viability 
     In one embodiment, the cell viability in the wells was investigated using a pH indicator, 2′-7′-bis-(2carboxyethyl)-5-(and-6-)-carboxyfluorescein (BCECF-AM) which has an excitation wavelength of 505 nm and an emission wavelength of 535 nm and is available from Molecular Probes (Eugene, Oreg.). The acetoxymethyl (AM) ester form of BCECF is non-fluorescent in solution. The BCECF-AM is cell membrame permeant and passively enters the cell where, once inside the cell, the lipophilic blocking groups are cleaved by non-specific esterases resulting in an increase in fluorescent intensity. This increase in fluorescent intensity is indicative of the cell viability. FIG. 5 is a schematic representation of one embodiment of a method used for establishing cell viability in a sensor array. 
     For viability tests, an array of encoded cells previously dispersed in microwells was immersed in a 1 uM solution of BCECF-AM for 1 minute. The cell array was removed and rinsed thoroughly to remove any residual dye. Fluorescent images of cell responses were acquired every 30 seconds using a 1.0 second acquisition time to monitor the increase in fluorescent intensity due to the pH of healthy cells. Prior to viability measurements, a cell location template was generated through excitation of the encoded cells, using the encoding method described herein, and the locations of individual cells was superimposed on viability measurement images in order to identify the location of healthy cells within the array. A fluorescence image of the encoded cells is shown in FIG.  6 . In FIG. 7, the fluorescent intensity response of the cells indicates a gradual increase as the lipophilic groups are cleaved from the BCECF-AM dye within the cell. The fluorescent intensity response of the wells which do not contain cells was negligible. 
     In a alternative embodiment, BCECF-Dextran, available from Molecular Probes, was used for cell viability measurements. A 0.1 uM solution of the dye was added to cell media contained within array microwells. BCECF requires excitation at two wavelengths, 490 nm and 440 nm, and the ratio of the emitted light intensity at 530 nm for each wavelength is proportional to pH. This dye is conjugated with a large Dextran group to prevent entry into the cell through the cell membrane. Thus, BCECF-Dextran can monitor decreases in pH within the external cell environment due to cell metabolism. FIG. 10 shows the average response of nine cells over time where the pH of the cell environment gradually decreases due to cell metabolism. 
     In another embodiment a commercial cell viability assay, LIVE/DEAD® from Molecular Probes (Eugene, Oreg.), was employed. This assay provides a two-color fluorescence cell viability assay based on intracellular esterase activity and plasma membrane integrity. Live cells are distinguished by the enzymatic conversion of the cell-permeant non-fluorescent calcein AM to fluorescent calcein, with an excitation wavelength at 495 nm and an emission wavelength at 515 nm. Dead cells are distinguished by binding ethidium homodimer (EthD-1), with an excitation wavelength at 495 nm and an emission wavelength at 635 nm, to nucleic acids which is accompanied by a 40-fold increase in fluorescent intensity. EthD-1 is excluded by the intact plasma membranes of living cells. Background fluorescence levels are inherently low with this assay technique because the dyes are virtually non-fluorescent before interacting with cells. 
     In a typical procedure, a working solution of 2 uM calcein AM and 4 uM EthD-1 was prepared in serium-free medium. An array of NIH 3T3 mouse fibroblast cells was cultured at the distal face of a microwell array. The proximal face of the imaging fiber was focused on the imaging system. The cell array at the distal face of the imaging fiber was placed in serium-free medium without dye. The cell array was excited at 495 nm and emission values from a population of 25 cells were acquired for 300 ms at 515 nm (Live) and 635 nm (Dead). These values serve as background reading for these measurements. The cell array was then placed in the dye solution and the cell array was excited at 495 nm and emission values from 25 cells were acquired for 300 ms at 515 nm (Live) and 635 nm (Dead) every minute for 30 minutes. All measurements were performed at room temperature. Average fluorescent intensity for the live and dead cell wavelengths are plotted versus time after subtracting the background fluorescence measurement at each emission wavelength. 
     This assay was used to evaluate pretreatment methods for filling the microwells of a biosensor arrray with culture media prior to inserting cells. By comparing the viability of cells placed in microwells after various treatments, it was determined that, in a preferred embodiment, sonicating the mircrowell array under vacuum for 15 minutes prior to insertion of cells improves viability by ensuring that the microwells are filled with culture media. In FIG. 11 a , the average fluorescent intensity for dead cells and live cells is plotted with time where no pretreatment was utilized. In FIG. 11 b , results are plotted for a pretreated microwell array. Comparison of the two figures demonstrates the advantage of prefilling the microwells with culture media prior to cell insertion. In this example, when the microwell array was not sonicated prior to adding the cells the cells displayed immediate cell death. In this example, when the microwells were sonicated under vacuum to fill the arrays with culture media, the cells remained viable for approximately 20 minutes. 
     E. Encoding Cell Populations 
     A unique feature of the biosensor array of the present invention is that cells within each cell population are individually encoded for maintaining cell identity within the array when randomly mixed populations of cells are employed. Cells may be encoded with a single fluorophore or chromophore dye or ratios of such dyes. Alternatively, cells may be encoded by either injecting a non-toxic fluorescing compound into the cell cytoplasm or by employing natural or genetically-engineered cells lines which exhibit chemiluminescence or bioluminescence, such as green fluorescent protein mutants. Although a plurality of cell populations may be randomly mixed in the biosensor array, the identity and location of each cell type is determined via a characteristic optical response signature when the array is illuminated by excitation light energy. Cells may be encoded prior to disposing them in the microwells or, alternatively, following placement in the microwells. . In one embodiment, a single fluorophoric or chromophoric material or dye is used for encoding the cells. In an alternative embodiment, two or more encoding materials or dyes may be used to encode cell populations and the ratio of the optical response light intensity from each material or dye, produced by exposure to excitation light energy, is used to identify the positions of individual cells within the cell population and locate them in the array. In various alternative embodiments, cells may be encoded with dye compounds which are attached to cells, taken up by cells or provided in the local cell environment. 
     A wide variety of fluorophores, chromophores, stains or a dye compounds may be used for encoding cells. Encoding dyes may be permeant or impermeant to the cell membrane. Impermeant dyes may be conjugated with acetoxymethyl ester to allow take up is by cells. In one embodiment, conventional conjugate or reactive cell membrane stains, cell tracers, or cell probes such as fluoresceins, rhodamines, eosins naphthalimides, phycobiliproteins, nitrobenzoxadiazole may be utilized. In other embodiments, cyanine dyes, such as SYTO® (Molecular Probes), amine-reactive dyes, thiol-reactive dyes, lipopilic dyes, and DNA intercalators, such as acridine orange, may be employed. In one embodiment, fluorogenic or chromogenic enzyme substrates may be taken up by the cells, processesed by intracellular enzymes, such as glycosidases, phosphatases, luciferase, or chloramphenicol acetyltransferase, and provide encoding for cell populations. In an alternative embodiment, cell organelle dye probes may be employed for encoding. In one embodiment, cell membrane probes such as carbocyanines and lipophilicaminostyrls may be utilized for encoding. 
     By way of example, Tables 1 and 2 provide a partial listing of a various types of dyes and their corresponding excitation and emission wavelengths which have utility for encoding cell populations in sensor arrays of the present invention. In addition, a particularly useful reference for selecting other types of encoding dyes is R. P. Haugland,  Handbook of Fluorescent Probes and Research Chemicals  (6 th  ed.), Molecular Probes Inc.(Eugene, Oreg., 1996). 
     Cell encoding eliminates the need for mechanically scanning the array, mechanically indexing the location of cells, and mechanically positioning the array for measurements of individual cells. In addition, by encoding all cells within the array, simultaneous measurements of the entire array are possible since the responses of individual cells are readily associated with a specific cell population type because each cell is encoded. Encoding of cells thus provides for rapid, simultaneous measurements of all cells and cell populations within the array without the need to mechanically scan the array to acquire a series of sequential measurements for each cell. Since monitoring and measuring the responses of all cells in the array occurs simultaneously, without a prolonged delay between the first cell measurement and last cell measurement, the biosensor array of the present invention provides the capability to monitor both short term and long term cell responses to biological stimuli. The biosensor array of the present invention thus has the unique ability for measuring both cell responses and response rates to analytes. This feature provides 
     
       
         
           
               
             
               
                 TABLE 1 
               
               
                   
               
             
            
               
                 1. Plasma Membrane Stains 
               
            
           
           
               
               
               
            
               
                 PKH22 
                 green fluorochrome 
                 551 ex/567 em 
               
               
                 PHK67 
                 green fluorochrome 
                 490 ex/502 em 
               
               
                 PKH26 
                 red fluorochrome 
                 551 ex/567 em 
               
            
           
           
               
            
               
                 lipophilic carbocyanines 
               
            
           
           
               
               
            
               
                   
                 DiI — orange fluorescence 
               
               
                   
                 DiO — green fluorescence 
               
               
                   
                 DiD — red fluorescence 
               
               
                   
                 FM 1-43 — green fluorescence 510 ex/626 em 
               
               
                   
                 FM 4-64 — red fluorescence 515 ex/640 em 
               
               
                   
                 RH 414 — orange fluorescence 532 ex/716 em 
               
            
           
           
               
            
               
                 lipophilic dextrans 
               
            
           
           
               
               
            
               
                   
                 tetramethylrhodamine dextrans (10,000 MW) 470 ex/500 em 
               
               
                   
                 fluorescein dextran (10,000 MW) 495 ex/530 em 
               
            
           
           
               
            
               
                 2. Tracker Probes 
               
               
                 Blue  7-amino-4-chloromethyl coumarin 354 ex/466 em 
               
               
                 4-chloromethyl-6,8-difluoro-7-hydroxy coumarin 371 ex/464 em 
               
               
                 4-chloromethyl-7-hydroxy coumarin 372 ex/470 em 
               
               
                 Green  5-chloromethyl fluorescein diacetate 492 ex/516 em 
               
               
                 8-chloromethyl BODIPY 522 ex/528 em 
               
               
                 Yellow-Green 
               
               
                 5-chloromethyleosin diacetate 524 ex/544 em 
               
               
                 Orange 
               
               
                 5-(and 6)-(((4-chloromethyl)benzoyl)amino) tetramethylrhodamine 
               
               
                 540 ex/566 em 
               
               
                 3. Amine-Reactive Probes 
               
               
                 fluorescein isothiocyanate 494 ex/519 em 
               
               
                 carboxyfluorescein succinimidyl esters 504 ex/529 em 
               
               
                 carboxyeosin succinimidyl esters 492 ex/517 em 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 2 
               
             
            
               
                   
               
               
                 Molecular Probes 
               
               
                 organelle-selective probes 
               
            
           
           
               
               
               
               
            
               
                 Blue Fluorescent and 
                   
                 Yellow and 
                   
               
               
                 Nonfluorescent Probes 
                 Green Fluorescent Probes 
                 Orange Fluorescent Probes 
                 Red Fluorescent Probes 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 Cat # 
                 Probe 
                 Cat # 
                 Probe 
                 Cat # 
                 Probe 
                 Cat # 
                 Probe 
               
               
                   
               
            
           
           
               
            
               
                 Probes for Mitochondria — see Section 12.2 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 L-6868 
                 Lucigenin† 
                 A-1372 
                 Nonyl acridine orange 
                 D-288 
                 4-Di-1-ASP (DASPMI) 
                 M-7512 
                 MitoTracker Red 
               
               
                   
                   
                   
                   
                   
                   
                   
                 CMXRos* 
               
               
                   
                   
                 D-273 
                 DiOC 6 (3) 
                 D-308 
                 2-Di-1-ASP (DASPMI) 
                 T-3168 
                 JC-1‡ 
               
               
                   
                   
                 D-303 
                 DiOC 3 (5) 
                 D-426 
                 DASPEI 
               
               
                   
                   
                 D-378 
                 DiOC 7 (3) 
                 M-7510 
                 MitoTracker Orange 
               
               
                   
                   
                   
                 (for plant mitochondria) 
                   
                 CMTMRos* 
               
               
                   
                   
                 M-7502 
                 MitoFluor Green 
                 R-634 
                 Rhodamine 6G 
               
               
                   
                   
                 M-7514 
                 MitoTracker Green FM* 
                 R-648 
                 Rhodamine B, hexyl ester 
               
               
                   
                   
                 R-302 
                 Rhodamine 123 
                 T-639 
                 Tetramethylrosamine 
               
               
                   
                   
                 S-7529 
                 SYTO 18 yeast 
                 T-668 
                 Tetramethylrhodamine, 
               
               
                   
                   
                   
                 mitochondrial strain 
                   
                 methyl ester 
               
               
                   
                   
                 T-3168 
                 JC-1‡ 
                 T-669 
                 Tetramethyl:hodamine, 
               
               
                   
                   
                   
                   
                   
                 ethyl ester 
               
            
           
           
               
            
               
                 Probes for Mitochondria (Probes Requiring Intracellular Oxidation) — see Section 12.2 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                   
                 D-632 
                 Dihydrorhodamine 123 
                 D-633 
                 Dihydrorhodamine 6G 
                 M-7513 
                 MitoTracker Red 
               
               
                   
                   
                   
                   
                   
                   
                   
                 CM-H 2 XRos* 
               
               
                   
                   
                   
                   
                 D-638 
                 Dihydrotetramethyl- 
               
               
                   
                   
                   
                   
                   
                 rosamine 
               
               
                   
                   
                   
                   
                 M-7511 
                 MitoTracker Orange 
               
               
                   
                   
                   
                   
                   
                 CM-H 2 TMRos* 
               
            
           
           
               
            
               
                 Probes for Acidic Organelles, Inducing Lyscsomes — see Section 12.3 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 D-1552 
                 DAMP§ 
                 L-7526 
                 LysoTracker Green 
                 D-113 
                 Dansyl cadaverine 
                 L-7528 
                 LysoTracker Red 
               
               
                   
                   
                   
                 DND-26 
                   
                   
                   
                 DND-99 
               
               
                 H-7599 
                 Hydroxystilbamidine¶ 
                 L-7542 
                 LysoTracker Green Br 2   
                 L-7527 
                 LysoTracker Yellow 
               
               
                   
                   
                   
                   
                   
                 DND-68 
               
               
                 L-7525 
                 LysoTracker Blue 
               
               
                   
                 DND-22¶ 
               
               
                 L-7537 
                 LysoTracker biotin§ 
               
               
                 L-7538 
                 LysoTracker biotin/DNP§ 
               
            
           
           
               
            
               
                 Probes for Acidic Organelles, Including Tysosomes (pH-Sensitive Probes) — see Section 12.3 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 L-7532 
                 LysoSensor Blue 
                 L-7534 
                 LysoSensor Green 
                 A-1301 
                 Acridine orange 
                 N-3246 
                 Neutral red 
               
               
                   
                 DND-192¶ 
                   
                 DND 153 
               
               
                 L-7533 
                 LysoSensor Blue 
                 L-7535 
                 LysoSensor Green 
                 L-7545 
                 LysoSensor Yellow/Blue 
               
               
                   
                 DND-167¶ 
                   
                 DND-189 
                   
                 DND-160‡ 
               
               
                 L-7545 
                 LysoSensor Yellow/Blue 
               
               
                   
                 DND-160‡ 
               
            
           
           
               
            
               
                 Probes for Endoplasmic Reticulum — see Section 12.4 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                   
                   
                 B-7447 
                 BODIPY FL brefeldin A 
                 B-7449 
                 BODIPY 558/568 
                   
                   
               
               
                   
                   
                   
                   
                   
                 brefeldin A 
               
               
                   
                   
                 D-272 
                 DiOC 3 (3) 
                 D-282 
                 DiIC 18 (3) 
               
               
                   
                   
                 D-273 
                 DiOC 6 (3) 
                 D-384 
                 DiIC 16 (3) 
               
               
                   
                   
                   
                   
                 R-648 
                 Rhodamine B, hexyl ester 
               
               
                   
                   
                   
                   
                 R-634 
                 Rhodamine 6G 
               
               
                   
                   
                   
                   
                 T-668 
                 Tetramethylrhodamine, 
               
               
                   
                   
                   
                   
                   
                 methyl ester 
               
               
                   
                   
                   
                   
                 T-669 
                 Tetramethylrhodantine, 
               
               
                   
                   
                   
                   
                   
                 ethyl ester 
               
            
           
           
               
            
               
                 Probes for Goigi Apparatus — See Section 12.4 
               
            
           
           
               
               
               
               
               
               
               
               
            
               
                 B-7450 
                 Brefeldin A 
                 B-7417 
                 BODIPY FL brefeldin A 
                 B-7449 
                 BODIPY 558/568 
                 D-3521 
                 BODIPY FL C 5     −     
               
               
                   
                   
                   
                   
                   
                 brefeldin A 
                   
                 ceramide‡ 
               
               
                   
                   
                 D-3521 
                 BODIPY FL C 5     −   ceramide‡ 
                   
                   
                 D-7540 
                 BODIPY TR ceramide‡ 
               
               
                   
                   
                 D-3522 
                 BODIPY FL C 3     −     
                   
                   
                 D-7546 
                 BODIPY FL Br 2 C 5     −     
               
               
                   
                   
                   
                 sphingomyclin 
                   
                   
                   
                 ceramide‡ 
               
               
                   
                   
                 D-7546 
                 BODIPY FL Br 2 C 5     −     
               
               
                   
                   
                   
                 ceramide‡ 
               
               
                   
                   
                 N-1154 
                 NBD C 6 ceramide 
               
               
                   
                   
                 N-3524 
                 NBD C 6     −   splangomyelin 
               
               
                   
               
               
                 *Aldehyde-fixable probe.  
               
               
                 †Chemiluminescent probe.  
               
               
                 ‡Dual emission spectrum.  
               
               
                 §Nonfluorescent probe.  
               
               
                 ¶Blue fluorescent probe.  
               
            
           
         
       
     
     additional discriminating response information which is useful for detecting biological or chemical analytes of interest. 
     While a number of encoding dyes and methods are available, in one embodiment, external fluorescent cell membrane labels, PKH67 with an excitation wavelength of 490 nm and an emission wavelength of 502 nm, and PKH26 with an excitation wavelength of 551 nm and an emission wavelength of 567 nm, were utilized. PKH26 and PKH67 are part of a family of dyes manufactured by Zynaxis Cell Science (Malvern, Pa.), sold under the trademark Zyn-Linker® (Phanos Technologies Inc.), produced by the method of U.S. Pat. No. 5,665,328 to Hogan, et al., and available from Sigma (St.Louis, Mo.). In this embodiment, both dyes were applied to suspended fibroblast cells to encode the cells prior to placement in the sensor array. Encoded cells were placed in microwells filled with growth media. The encoded cells were then illuminated with excitation light transmitted through the fiber optic array and the resulting fluorescent emission response of cells was collected through the same fiber and passed to the detection system. FIG. 6 shows a typical fluorescence optical image of a PKH26 encoded cell population in a biosensor array of the present invention. FIG. 8 shows a typical fluorescence image of a PKH67 encoded cell population in a biosensor array. Note that only those microwells containing encoded cells yields a fluorescent signal upon excitation at the encoding dye wavelength. 
     In a typical encoding procedure, external or internal encoding labels are applied to suspended cell populations prior to placement in the sensor array. In one embodiment, an external label is applied to the cell by first washing the suspended cells with serum-free media and then centrifuging the cells into a loose pellet at 2000 RPM for 5 minutes. The supernatant is drawn off and the centrifuge tube is tapped to resuspend the cells. Approximately 1 mL of Diluent C, available as dye kit from Sigma, was added to the cells and the tube was inverted to mix. Immediately prior to encoding, a solution of 4×10 −6  M Diluent C dye was prepared. The suspended cells are added to the dye solution, mixed by pipetting the cell/dye solution, and incubated for 5 minutes. To stop the encoding reaction, 2 mL of fetal calf serum was added to the cells, incubated for 1 minute, and then diluted by adding 4 mL growth media. The cells are then centrifuged at 2000 RPM for 10 minutes to remove the cells from the staining solution. The supernatant was drawn off and the cells are transferred to a new tube. Finally, the cells are subjected to a minimum of three washings by adding 10 mL growth media, centrifuging, and resuspending the cells. 
     To demonstrate the encoding method with PKH26 and PKH67 dyes, encoded NIH 3T3 mouse fibroblast cells were dispersed in microwells in sensor array and the location of encoded cells within the array was determined by excitation of the cells at a wavelength of 551 nm. Upon excitation, the encoded cells form a characteristic, detectable fluorescence pattern within the sensor array where the pattern provides a locational template for cell viability measurements using BCECF and an excitation wavelength of 505 nm. The excitation and emission wavelengths of the PKH26 encoding label and the BCECF-AM dye are sufficiently separated so that there is no interference between the two dyes. FIG. 6 is a characteristic fluorescence image pattern identifying the location of PKH26 encoded cells in the biosensor array. A similar procedure was followed for encoding the mouse fibroblast cells with PKH67 where a corresponding characteristic fluorescence image pattern is shown in FIG.  8 . 
     In addition to encoding individual cell populations with a single unique dye, each cell population within the array may be encoded with unique dye ratios which yield a characteristic fluorescent intensity ratio in a distinct wavelength range. A range of dye ratios may be employed with two or more dye combination for producing a series of encoding ratios useful for a identifying a large number of cell populations. The fluorescent intensity ratio, produced by a specific dye ratio which is used for encoding a cell population, can be distinguished by taking the mean intensity minus the background intensity at each emission wavelength and then dividing the two values to obtain the range for that particular ratio. 
     In one embodiment, two separate populations of NIH 3T3 mouse fibroblast cells were encoded by labeling cell membranes with either a 1:5 or a 5:1 ratio of PHK67 and PHK26 dyes. Each cell population comprised approximately 125 encoded cells. The cell populations were illuminated at 490 nm and 551 nm excitation wavelengths and emitted fluorescent intensity ratios were measured at 502 nm and 567 nm. Measurements of the average intensity ratio for each dye ratio were made over a two day period. The initial average intensity ratio for the 1:5 PKH67/PKH26 ratio was 0.0863 and the ratio for the 5:1 dye ratio was 0.7014. The final average intensity ratio for the 1:5 ratio was 0.2655 and for the 5:1 ratio it was 0.9090 indicating that the ratios are reasonably stable, even where cell splitting has occurred, and that dye ratio encoded cell populations remain distinguishable with time. Thus, dye ratios can provide a useful alternative encoding mechanism for identifying and locating cell populations which are randomly dispersed on a biosensor array of the present invention. 
     F. Indicator Dyes 
     The optical responses of individual cells and cell populations to chemical or biological stimuli are typically interrogated and detected by coupling individual cells with appropriate indicators which may be either fluorophores, chromophores, stains or a dye compounds. Any suitable indicator or combinations of indicators may be utilized provided the indicator does not compromise cell response. 
     For example, conventional cell fluorophore probes such as fluoresceins, rhodamines, naphthalimides, phycobiliproteins, nitrobenzoxadiazole may be utilized. Alternatively, permeant or impermeant cell membrane potential indicators, ion indicators, reactive oxygen indicators and pH indicators may be employed. By way of example a number of indicators which would have particular utility for the biosensor array of the present invention are listed in Tables 3 through 8 together with their characteristic excitation and emission wavelengths. A particularly useful reference for selecting appropriate indicators is R. P. Haugland,  Handbook of Fluorescent Probes and Research Chemicals  (6 th  ed.), Molecular Probes Inc.(Eugene, Oreg., 1996). 
     
       
         
           
               
             
               
                 TABLE 23.1 
               
             
            
               
                   
               
               
                 Molecular Probes&#39; pH indicator, in order of 
               
               
                 decreasing pK 2 . 
               
            
           
           
               
               
               
               
            
               
                   
                 Parent Fluorophore 
                 pH Range 
                 Typical Measurement 
               
               
                   
                   
               
               
                   
                 SNAFL indicators 
                 7.2-8.2 
                 Excitation ratio 490/540 nm 
               
               
                   
                   
                   
                 emission ratio 540/630 nm 
               
               
                   
                 SNARF indicators 
                 7.0-8.0 
                 Emission ratio 580/640 nm 
               
               
                   
                 HPTS (pyranine) 
                 7.0-8.0 
                 Excitation ratio 450/405 nm 
               
               
                   
                 BCECF 
                 6.5-7.5 
                 Excitation ratio 490/440 nm 
               
               
                   
                 Fluoresceins and 
                 6.0-7.2 
                 Excitation ratio 490/450 nm 
               
               
                   
                 carboxyfluoresceins 
               
               
                   
                 Oregon Green dyes 
                 4.2-5.7 
                 Excitation ratio 510/450 nm 
               
               
                   
                   
                   
                 excitation ratio 490/440 nm 
               
               
                   
                 Rhodols (including 
                 4.0-6.0 
                 Excitation ratio 514/488 nm 
               
               
                   
                 NERF dyes) 
                   
                 excitation 500/450 nm 
               
               
                   
                 LysoSensor probes 
                 3.5-8.0* 
                 Excitation ratio 340/380 nm 
               
               
                   
                   
               
               
                   
                 *Depends on pK 2  of selected probe; see Table 23.2 for pk 2  of each LysoSensor probe. †Applies to L-7545 only. Other LysoSensor probes allow single excitation and emission measurements only; see Table 23.3 for wavelengths.  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 23.2 
               
             
            
               
                   
               
               
                 Summary of the pH response of our LysoSensor probes. 
               
            
           
           
               
               
               
               
               
            
               
                   
                 LysoSensor 
                 Abs/Em* 
                   
                 Useful pH 
               
               
                 Cat # 
                 Probe 
                 (nm) 
                 pK 2 † 
                 Range† 
               
               
                   
               
               
                 L-7532 
                 LysoSensor 
                 374/424 
                 7.5 
                 6.5-8.0 
               
               
                   
                 Blue DND-192 
               
               
                 L-7533 
                 LysoSensor 
                 373/425 
                 5.1 
                 4.5-6.0 
               
               
                   
                 Blue DND-167 
               
               
                 L-7534 
                 LysoSensor Green 
                 442/505 
                 7.5 
                 6.5-8.0 
               
               
                   
                 DND-153 
               
               
                 L-7535 
                 LysoSensor Green 
                 443/505 
                 5.2 
                 4.5-6.0 
               
               
                   
                 DND-189 
               
               
                 L-7545 
                 LysoSensor 
                 384/540‡ 
                 4.2 
                 3.0-5.0 
               
               
                   
                 Yellow/Blue 
                 329/440§ 
               
               
                   
                 DND-160 
               
               
                   
               
               
                 *Absorption (Abs) and fluorescence emission (Em) maxima, at pH 5; values may vary somewhat in cellular environments. †All pK 2  values were determined in vitro; values different in cells. ‡at pH 3; §at pH 7.  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 23.4 
               
             
            
               
                   
               
               
                 Reactive pH indicator dyes. 
               
            
           
           
               
               
            
               
                 pH Indicator 
                 Preferred Reactive Form 
               
               
                   
               
               
                 BCECF 
                 BCECF (B-1151, see Section 23.2)* 
               
               
                 Carboxyfluorescein 
                 5-(and-6)-carboxyfluorescein, 
               
               
                   
                 succinimidyl ester (C-1311, see Section 1.3) 
               
               
                 CI-NERF 
                 CI-NERF (C-6831, see Section 23.3)* 
               
               
                 Dichlorofluorescein 
                 2′,7′-dichlorofluorescein-5-isothiocyanate 
               
               
                   
                 (D-6078, see Section 1.5) 
               
               
                 Dimetylfluorescein 
                 5-(and-6)-carboxy-4′,5′-dimethylfluorescein 
               
               
                   
                 (C-366, see Section 23.2)* 
               
               
                 DM-NERF 
                 DM-NERF (D-6830, see Section 23.3)* 
               
               
                 Naphthofluorescein 
                 5-(and-6)-carboxynaphthofluorescein, 
               
               
                   
                 succinimidyl ester (C-653) 
               
               
                 Oregon Green 488 
                 Oregon Green 488 carboxylic acid, 
               
               
                   
                 succinimidyl ester (O-6147, O-6149) 
               
               
                 Oregon Green 500 
                 Oregon Green 500 carboxylic acid, 
               
               
                   
                 succinimidyl ester (O-6136) 
               
               
                 Oregon Green 514 
                 Oregon Green 514 carboxylic acid, 
               
               
                   
                 succinimidyl ester (O-6139) 
               
               
                 Rhodol Green 
                 Rhodol Green carboxylic acid, 
               
               
                   
                 succinimidyl ester (R-6108) 
               
               
                 SNAFL-1 
                 5-(and-6)-carboxy SNAFL-1, 
               
               
                   
                 succinimidyl ester (C-3061) 
               
               
                 SNAFL-2 
                 5-(and-6)-carboxy SNAFL-2, 
               
               
                   
                 succinimidyl ester (C-3062) 
               
               
                 SNARF-1 
                 5-(and-6)-carboxy SNARF-1 
               
               
                   
                 (C-1270, see Section 23.2)* 
               
               
                   
               
               
                 *Carboxylic acids require activation with EDAC/NHSS before reaction with amines (see Section 1.1).  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 4 
               
             
            
               
                   
               
               
                 Molecular Probes pH indicator dextrans, in order of decreasing pK 2   
               
            
           
           
               
               
               
               
               
            
               
                 Dye 
                 Cat # 
                 pK 2 * 
                 Measurement Wavelengths 
                 Application Notes 
               
               
                   
               
               
                 SNAFL 
                 D-3301, D-3302 
                 ˜7.8 
                 Excitation ratio 490/540 nm 
                 Acidic form has the higher quantum yield (see FIG. 23.7) 
               
               
                   
                   
                   
                 detected at 580 nm 
                 Fluorescence increases in acidic organelles. 
               
               
                   
                   
                   
                 Emission ratio 540/630 nm 
               
               
                   
                   
                   
                 excited at 514 nm 
               
               
                 SNARF 
                 D-3303, D-3304 
                 ˜7.5 
                 Emission ratio 580/640 nm 
                 Best conjugate for ratiometric emission measurement, with 
               
               
                   
                   
                   
                 excited at 514 or 488 nm 
                 spectra similar to carboxy SNARF-1 (see FIG. 23.6) 
               
               
                 HPTS 
                 D-7179 
                 ˜7.0 
                 Excitation ratio 470/380 nm 
                 Spectra of dextran conjugate are significantly shifted 
               
               
                   
                   
                   
                 detected at 530 nm 
                 (˜20 nm) relative to free dye 
               
               
                 BCECF 
                 D-1878, D-1879, 
                 ˜7.0 
                 Excitation ratio 490/440 nm 
                 Best conjugate for ratiometric excitation measurements, 
               
               
                   
                 D1880 
                   
                 detected at 530 nm 
                 with spectra similar to BCECF (see FIG. 23.3) 
               
               
                 Fluorescein 
                 D-1821, D-1823, 
                 ˜6.4 
                 Excitation ratio 490/450 nm 
                 Fluorescence is strongly quenched upon uptake into acidic 
               
               
                   
                 D-1844, D-1899, 
                   
                 detected at 520 nm 
                 organelles (see FIG. 23.2B) 
               
               
                   
                 D-3305 
               
               
                 Fluorescein and 
                 D-1950, D-1951 
                 ˜6.4 
                 Excitation ratio 495/555 nm 
                 Conjugate incorporating both pH-sensitive and 
               
               
                 tetramethylrhodamine 
                   
                   
                 detected at 580 nm† 
                 pH-insensitive fluorescent dyes (see FIG. 23.14) 
               
               
                 Rhodol Green 
                 D-7148, D-7150 
                 ˜5.6 
                 Excitation ratio 500/450 nm 
                 High photostability 
               
               
                   
                   
                   
                 detected at 530 nm 
                 Most useful below pH 6 (see FIG. 23.15) 
               
               
                 DM-NERF 
                 D-3319, D-3320 
                 ˜5.4 
                 Excitation ratio 510/450 nm 
                 Useful at a higher pH than CI-NERF dextrans 
               
               
                   
                   
                   
                 detected at 540 nm 
                 (see FIG. 23.12) 
               
               
                 Oregon Green 488 
                 D-7170, D-7172 
                 ˜4.7 
                 Excitation ratio 490/440 nm 
                 Good photostability 
               
               
                   
                   
                   
                 detected at 520 nm 
                 Optimum pH sensitivity range between of DM-NERF 
               
               
                   
                   
                   
                   
                 and CI-NERF 
               
               
                 Oregon Green 514 
                 D-7174, D-7176 
                 ˜4.7 
                 Excitation ratio 510/450 nm 
                 Excellent photostability 
               
               
                   
                   
                   
                 detected at 530 nm 
                 Optimum pH sensitivity range between that of DM-NERF 
               
               
                   
                   
                   
                   
                 and CI-NERF (see FIG. 23.11) 
               
               
                 CI-NERF 
                 D-3324, D-3325 
                 ˜3.8 
                 Excitation ratio 510/450 nm 
                 Useful at a lower pH than DM-NERF dextrans 
               
               
                   
                   
                   
                 detected at 540 nm 
                 (see FIG. 23.12) 
               
               
                   
               
               
                 *pK 2  values are those determined for the free dyes. Actual values for dextran conjugates may differ by up to +/− 0.3 pH units and may vary between production lots.  
               
               
                 †Ratiometric emission measurements at 520/580 nm with excitation at 495 nm) are also possible in principle; however, the response may be complicated by fluorescence resonance energy transfer.  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 5 
               
             
            
               
                   
               
               
                 Summary of fluorescent Ca 2+  Indicators available from Molecular Probes 
               
            
           
           
               
               
               
               
               
               
               
            
               
                   
                   
                   
                   
                   
                 K d   
                   
               
               
                 Ca 2+  Indicator 
                 Salt* 
                 AM Ester† 
                 Dextran‡ 
                 Mode§ 
                 (nM)¶ 
                 Notes 
               
               
                   
               
               
                 Bis-fura 
                 B-6810 
                   
                   
                 Ex 340/380 
                 370 
                 1 
               
               
                 BTC 
                 B-6790 
                 B-6791 
                   
                 Ex 400/480 
                 7000 
                 2 
               
               
                 Calcium Green-1 
                 C-3010 
                 C-3011, C-3012 
                 C-6765, C-3713, 
                 Em 530 
                 190 
                 3,4 
               
               
                   
                   
                   
                 C-3714, C-6766 
               
               
                 Calcium Green-2 
                 C-3730 
                 C-3732 
                   
                 Em 535 
                 550 
                 3,5 
               
               
                 Calcium Green-5N 
                 C-3737 
                 C-3739 
                   
                 Em 530 
                 14,000 
                 3 
               
               
                 Calcium Orange 
                 C-3013 
                 C-3015 
                   
                 Em 575 
                 185 
                 2 
               
               
                 Calcium Orange-5N 
                 C-6770 
                 C-6771 
                   
                 Em 580 
                 20,000 
                 2 
               
               
                 Calcium Crimson 
                 C-3016 
                 C-3018 
                 C-6824, C-6825 
                 Em 615 
                 185 
                 2 
               
               
                 Fluo-3 
                 F-1240, F-3715 
                 F-1241, F-1242 
                   
                 Em 525 
                 390 
                 3,4 
               
               
                 Fura 2 
                 F-1200, F-6799 
                 F-1201, F-1221, F-1225 
                 F-6764, F-3029, 
                 Ex 340/380 
                 145 
                 2 
               
               
                   
                   
                   
                 F-3030 
               
               
                 Fura Red 
                 F-3019 
                 F-3020, F-3021 
                   
                 Ex 420/480 
                 140 
                 2,6,7 
               
               
                 Indo-1 
                 I-1202 
                 I-1203, I-1223, I-1226 
                 I-3032, I-3033 
                 Em 405/485 
                 230 
                 2 
               
               
                 Mag-fura-2 
                 M-1290 
                 M-1291, M-1292 
                   
                 Ex 340/380 
                 25,000 
                 2 
               
               
                 Mag-fura-5 
                 M-3103 
                 M-3105 
                   
                 Ex 340/380 
                 28,000 
                 2 
               
               
                 Mag-indo-1 
                 M-1293 
                 M-1295 
                 M-6907, M-6908 
                 Em 405/485 
                 35,000 
                 2,8 
               
               
                 Magnesium Green 
                 M-3733 
                 M-3735 
                   
                 Em 530 
                 6000 
                 3 
               
               
                 Oregon Green 488 BAPTA-1 
                 O-6806 
                 O-6807 
                 O-6798, O-6797 
                 Em 520 
                 170 
                 3 
               
               
                 Oregon Green 488 BAPTA-2 
                 O-6808 
                 O-6809 
                   
                 Em 520 
                 580 
                 3,9 
               
               
                 Oregon Green 488 BAPTA-5N 
                 O-6812 
                 O-6813 
                   
                 Em 520 
                 20,000 
                 3 
               
               
                 Quin-2 
                 Q-1287 
                 Q-1288, Q-1289 
                   
                 Em 495 
                 60 
                 2,10 
               
               
                 Rhod-2 
                 R-1243 
                 R-1244, R-1245 
                   
                 Em 570 
                 570 
                 2 
               
               
                 Texas Red-Calcium Green 
                   
                   
                 C-6800 
                 Em 535/615 
                 370 
                 11 
               
               
                   
               
               
                 *Catalog number for cell-impermeant salt.  
               
               
                 †Catalog number for cell-permeant AM ester.  
               
               
                 ‡Catalog number for dextran conjugate.  
               
               
                 §Measurement wavelengths (in nm), where Ex = Fluorescence excitation and Em = Fluorescence emission. Indicators for which a pair of wavelengths are listed have dual-wavelength ratio-measurement capability.  
               
               
                 ¶Ca 2+  dissociation constant; measured at Molecular Probes in vitro at 22° C. in 100 mM KCl, 10 mM MOPS pH 7.2, unless otherwise noted. K d  values depend on temperature, ionic strength, p and other factors, and are usually higher in vivo. Because indicator dextrans are intrinsically polydisperse and have variable degrees of substitution, lot-specific K d  values are printed on al in most cases.  
               
               
                 1. Similar Ca 2+ -dependent fluorescence response to fura-2 but ˜75% greater molar absorptivity;  
               
               
                 2. AM ester form is fluorescent (a major potential source of error in Ca 2+  measurements  
               
               
                 3. AM ester form is nonfluorescent;  
               
               
                 4. Calcium Green-1 is more fluorescent than fluo-3 in both Ca 2+ -bound and Ca 2+ -free forms. Magnitude of Ca 2+ -dependent fluorescence increase a greater for fluo-3;  
               
               
                 5. Larger Ca 2+ -dependent fluorescence increase than Calcium Green-1;  
               
               
                 6. Can also be used in combination with fluo-3 for dual-wavelength ratio measurements, Ex = 488 nm, Em = 530/670 nm [Cytometry 17,135 (1994); Cell Calcium 14,359 (1993)];  
               
               
                 7. Mag-Fura Red has similar spectral properties, with K d  for Ca 2+  — 17 μM;  
               
               
                 8. K d  determine 100 mM KCl, 40 mM HEPES, pH 7.0 at 22° C. [Biochem Biophys Res Comm 177,184 (1991)];  
               
               
                 9. Larger Ca 2+ -dependent fluorescence increase than Oregon Green 488 BAPTA-1;  
               
               
                 10. K d  determined in 120 mM KCl, 20 mM NaCl, pH 7.05 at 37° C. [Meth Enzymol 172,230 (1989)];  
               
               
                 11. This indicator consists of Ca 2+ -sensitive Calcium Green-1 and Ca 2+ -insensitive Texas Red dyes linked to the same dextran.  
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 6 
               
               
                   
               
             
            
               
                 O 2  Indicators 
               
               
                 1,3-Diphenylisobenzofuran - singled oxygen in membranes and in cells 
               
            
           
           
               
               
            
               
                 Ab - 409 
                 Em - 470 
               
            
           
           
               
               
               
            
               
                 rubrene 9,10-diphenylanthracene 
                 Ab - 391 
                 Em - 405 
               
            
           
           
               
            
               
                 trans-1-(2′-Methoxyvinyl)pyrene - piconicle detection 
               
            
           
           
               
               
            
               
                 Ab - 352 
                 Em - 401 
               
            
           
           
               
            
               
                 Nitrite Indicators 
               
            
           
           
               
               
            
               
                 2,3-diaminonaphthalene 
                 10 nM-10 μM detection 
               
            
           
           
               
               
            
               
                 Ab - 340 
                 Em - 377 
               
            
           
           
               
            
               
                 NO Indicators 
               
            
           
           
               
               
               
            
               
                 luminol 
                 Ab - 355 
                 Em - 411 
               
            
           
           
               
            
               
                 dihydrorhodamine - NO reacts w/ superoxide or hydrogen peroxide 
               
               
                 to produce peroxynitrite anion which oxidizes the dye 
               
            
           
           
               
               
            
               
                 Ab - 289 
                 Em - none 
               
            
           
           
               
            
               
                 Ca 2+  Indicators 
               
            
           
           
               
               
               
            
               
                 Bis-fura 
                 340/380 
                   
               
               
                 Calcium Green 
                 Em 530 
                 visible light 
               
               
                   
                   
                 excitation 
               
            
           
           
               
               
               
               
               
            
               
                  Fura 2 
                  340/380 
                  UV excitable 
                   
                   
               
               
                   
                   
                   
                    
                  ratiometric Ca 2+   
               
               
                  Indo 1 
                  405/485 
                  UV excitable 
                   
                  indicator 
               
            
           
           
               
               
               
               
            
               
                  Fluo-3 
                  Em 525 
                   
                   
               
               
                   
                   
                    
                  visible light 
               
               
                  Rhod-2 
                  Em 570 
                   
                  excitation 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
             
               
                 TABLE 7 
               
               
                   
               
             
            
               
                 Mg 2+  Indicators 
               
            
           
           
               
               
               
               
            
               
                 Mag-Fura-2 
                 340/380 
                   
                   
               
               
                 Mag-Fura-5 
                 340/380 
               
               
                 Mag-Indo-1 
                 405/485 
                    
                  UV excitable 
               
               
                 Magnesium Green 
                 475/Em 530 
               
               
                 Magnesium Orange 
                 545 ex 
               
            
           
           
               
            
               
                 Zn 2+  Indicators 
               
            
           
           
               
               
            
               
                 Newport Green 
                 506/535 
               
            
           
           
               
               
            
               
                 TSQ 
                 N-(6-methoxy-8-quinolyl)-p-toluenesulfonamide 
               
               
                   
                 334/385 
               
               
                   
                 used to localize Zn 2+  pools in the CNS. 
               
            
           
           
               
            
               
                 Cu +  Indicators 
               
            
           
           
               
               
            
               
                 Phen Green 
                 492/517 
               
            
           
           
               
            
               
                 also detects Fe 2+ , Mg 2+ , Pb 2+ , Cd 2+ , Ni 2+  at 
               
               
                 submicromolar concentrations 
               
               
                 Na +  Indicators 
               
            
           
           
               
               
               
            
               
                 SBFI 
                 Ab 339/Em 505 
                 UV ex 
               
               
                 SBFO 
                 354/515 
               
            
           
           
               
               
               
            
               
                 Sodium Green 
                 506/535 
                 visible light ex. - employs cronn ethers 
               
            
           
           
               
            
               
                 K +  Indicators 
               
            
           
           
               
               
            
               
                 PBFI 
                 Ab 336/Em 557 
               
            
           
           
               
            
               
                 Cl −  Indicators 
               
            
           
           
               
               
               
            
               
                 SPQ 
                 344/443 
                 follow Cl −  transport w/ ms time resolution 
               
               
                 MQAE 
                 350/460 
                 high fluorescence quantum yield 
               
               
                   
               
            
           
         
       
     
     
       
         
           
               
               
               
             
               
                 TABLE 8 
               
               
                   
               
             
            
               
                  Fl OxyBurst Green 
                   
                 detects 
               
               
                   
                    
                 oxidative burst that occurs 
               
               
                  Fl OxyBurst Orange 550/574 
                   
                 in phagoracuoles 
               
            
           
           
               
               
            
               
                 Dichlorodihydrofluorescein Diacetate 
                 monitors oxidative activity 
               
               
                 (H 2 DCFDA) 
                 cell permeant 
               
               
                 em 504/529 ex 
               
            
           
           
               
               
            
               
                 Dihydrorhodamine 123 
                 investigates reactive oxygen intermediates 
               
               
                 em 507/529 ex 
                 produced by phagocytes. 
               
            
           
           
               
            
               
                 Fura Red ™ - calcium indicator - calcium fluexes 
               
               
                 Dihydroethidium - respiratory burst in phagocytes. 
               
               
                 em 518/605 ex 
               
               
                 Aequorin - Bioluminescent Ca 2+  indicator 
               
               
                 em 430/465 ex 
               
               
                   
               
            
           
         
       
     
     In one embodiment, indicators may be incorporated directly into the cell by attachment to the cell membrane, by absorption into the cell cytoplasm by membrane permeant indicators, or by microinjection into the cell cytoplasm. In an alternative embodiment, ultrafine fluorescing microspheres, such as Molecular Probes FluoSpheres™, are ingested by the cells and are employed as indicators. In another environment, indicators are added to the culture media fluid contained within the microwells. In an alternative embodiment, indicators may be attached to the surface of the microwells by a conventional silanization treatment for bonding the indicator to the glass surface. In one embodiment, natural or genetically engineered cell lines which exhibit chemiluminescence, bioluminesence, or color changes when stimulated are used alone without need for a separate indicator since they produce intrinsic optical responses. Examples of such cells include green fluorescent protein mutants of human melanocytes. In other embodiments, cells which express fluorescing enzymes are employed with a reagent which enables an optical response. For example when luciferase is expressed by a cell in the presence of luciferen, the cell produces a fluorescence response when biologically stimulated. 
     In alternative embodiments, multiple indicators may be employed within a cell array, to within a cell population, or within individual cells so as to provide for simultaneous monitoring of cell responses to a variety of different chemical or biological materials. Where two or more indicators are utilized, dyes with spectral separation of narrow spectral bandwidths are particularly useful, for example Molecular Probes BODIPY™ dyes. 
     G. Optical Measurements 
     The instrumentation used for fluorescence measurements is a modified Olympus (Lake Success, N.Y.) epifluorescence microscope which was converted from a vertical to a horizontal configuration. A schematic diagram of the measurement system  100  is shown in FIG.  9 . White light from a 75 W xenon lamp  110  is collimated by a condensing lens  112 , passed through an excitation filter  120 , reflected by a dichroic mirror  130 , and focused onto the proximal end  210  of an imaging fiber  200  with a microscope objective  140 . A neutral density filter  122  may be employed for adjustment of excitation light intensity. The imaging fiber  200  is precisely positioned by an x-y micropositioner  150 , available from Spindler and Hoyer (Milford, Mass.), and a microscope z-translation stage  152 . Excitation light is transmitted through the fiber  200  to the biosensor array  300  at the distal fiber end  212 . The emitted fluorescence light from the biosensor array is returned through the fiber  200 , through the dichroic mirror  130 , filtered through an emission filter  160 , and detected by a PXL™ Photometrics (Tuscon, Ariz.) charge coupled device (CCD) camera  170 . A magnification lens  165  may be employed if necessary. Data is processed on an Apple Power Macintosh 440 (Sunnyvale, Calif.) desktop computer  180  using IPLab 3.0 image processing software, commercially available from Signal Analytics (Vienna, Va.). While a bench-top measurement system was utilized for these measurements, in one embodiment, a compact portable measurement system may be assembled from conventional optical and electronic components. 
     H. Biosensor Array Applications 
     The biosensor, biosensor array, sensing apparatus and sensing method of the present invention can be applied to a large variety of conventional assays for screening and detection purposes. The biosensor may be configured for virtually any assay and offers a distinct advantage for high throughput screening where a plurality of encoded cell populations, which have utility in particular assays or are genetically engineered cell to provide unique responses to analytes, may be employed in a single sensor array for conducting a large number of assays simultaneously on a small sample. The biosensor array thus provides both for tremendous efficiencies in screening large combinatorial libraries and allows conduction of a large number of assays on extremely small sample volumes, such as biologically important molecules synthesized on micron sized beads. The biosensor of the present invention can be applied to virtually any analyte measurements where there is a detectable cell response to the analyte due to biological stimulation. 
     The biosensor array and method of the present invention utilizes the unique ability of living cell populations to respond to biologically significant compounds in a characteristic and detectable manner. Since the selectivity of living cells for such compounds has considerable value and utility in drug screening and analysis of complex biological fluids, a biosensor which makes use of the unique characteristics of living cell populations offers distinct advantages in high throughput screening of combinatorial libraries where hundreds of thousands of candidate pharmaceutical compounds must be evaluated. In addition, such a biosensor and sensing method can be utilized for either off-line monitoring of bioprocesses or in situ monitoring of environmental pollutants where the enhanced sensitivity of living cells to their local environment can be exploited. 
     While the examples below provide a variety of specific assays which may be useful in configuring and employing the biosensor array and method of the present invention, they are not intended to limit either the scope of applications envisioned or the broad range of sensing methods which can be employed with a plurality of cell populations with the biosensor of the present invention. 
     In one embodiment, the biosensor array can be employed for remotely monitoring redox states of individual cells or cell populations in bioprocesses. For example, NADH dependent fluorescence can be measured in bacteria, fungi, plant or animal cells. NAD(P)/NAD(P)H can be measured to monitor changes from aerobic to anaerobic metabolism in fermentation processes using the method disclosed by Luong, et al., in  Practical Fluorescence , G. Guilbault ed., Marcel Dekker (New York, 1990). 
     Alternatively, the biosensor array may be employed for in situ monitoring of cellular processes in response to environmental contaminants by incorporating the method disclosed by Hughes, et al.,  Analytica Chimica Acta  307:393(1995) to provide for distinguishable cell population responses within an array. In this method, micron-sized spheres, impregnated with a fluorophore and modified on the surface with a fluorogenic enzyme probe, are ingested by cells and enzymatic activity occurs at the sphere surface, producing a detectable fluorescent signal. 
     In yet another embodiment, the biosensor array can be employed with genetically engineered bioluminescent bacteria for in situ monitoring and optical sensing of metallic compounds. For example, cell population responses to antimonite and arsenite may be utilized by incorporating the method disclosed in Ramanathan, et al.,  Anal Chem . 69:3380(1997) into cell populations within the biosensor array. With this method, cell plasmid regulates the expression of bacterial luciferase depending on the metal concentration. 
     In another embodiment, the cell populations within the biosensor array can be encoded with ATP dependent luminescent proteins, for example firefly luciferase, which are injected into rat hepatocytes for pathological studies according to the method disclosed by Koop, et al.,  Biochem. J . 295:165(1993). These cells exhibit a decrease in cytoplasmic ATP when exposed to pathological insults and changes in fluorescence directly relate to the extent of metabolic poisoning in the cell. 
     In one embodiment, the cell populations within the biosensor array can be encoded with green fluorescent protein [see T. Gura,  Science  276:1989(1997); Niswender, et al.,  J. Microscopy  180(2):109(1995); Cubitt, et al.,  TIBS  20:448(1995); Miyawaki, et al.,  Nature  388:882(1997)]. Several genetically-engineered mutants of GFP are available which have distinguishable fluorescence emission wavelengths. These proteins have additional utility as fluorescing indicators of gene expression and Ca +  levels within cells. 
     In an additional embodiment, the biosensor array can be used in measurements of cell proliferation by in situ monitoring of calcium levels and calcium oscillations in single cells using fluorescent markers, such as aequorin or fura-2, according to the method disclosed by Cobbold, et al.,  Cell Biology  1:311(1990). 
     While this invention has been particularly shown and described with references to preferred embodiments thereof, it will be understood by those skilled in the art that various changes in form and details may be made therein without departing from the spirit and scope of the invention as defined by the appended claims.