SYSTEMS AND METHODS FOR DETERMINING PRESENCE AND/OR CHARACTERISTICS OF TARGET ANALYTES IN A SAMPLE

Abstract

A cartridge for providing a target analyte for detection is described. One such exemplar cartridge includes a base portion including: (1) a receiving area disposed at or near a center region of the base portion; (2) multiple reaction wells disposed outside the center region or radially disposed at or near a perimeter of the base portion; and (3) multiple connecting tracks that substantially linearly extend from a region at or proximate to the receiving area to the multiple reaction wells and designed to convey a sample including the target analyte from the receiving area to the multiple reaction wells, each of which are configured to transform the sample to a detectable sample.

Systems and methods of reacting and detecting the sample including the target analyte are also described.

Claims

1. A reaction chamber for thermally activating multiple samples including a target analyte, said reaction chamber comprising: a cartridge stage having defined therein an opening for receiving a cartridge that has disposed thereon multiple reaction wells, each configured to hold said sample including said target analyte; and a reaction heating block disposed inside a housing that is proximate to said cartridge stage and having defined therein a heating block aperture that includes an inner heating surface having a curved profile that conforms to a curved profile of an outer surface of a side portion of said multiple reaction wells, such that upon direct contact of said inner heating surface with said outer surface of said side portion of said multiple reaction wells, said reaction heating block effectively thermally activates said multiple samples including said target analyte contained inside said multiple reaction wells.

2. The reaction chamber for thermally activating multiple samples including a target analyte of claim 1, wherein each of said opening and said reaction heating block is of a non-linear shape.

3. The reaction chamber for thermally activating multiple samples including a target analyte of claim 3, wherein each of said opening and said reaction heating block is circular.

4. The reaction chamber for thermally activating multiple samples including a target analyte of claim 1, further comprising multiple alignment ribs disposed inside a housing that is designed to receive said reaction heating block, wherein said reaction heating block, disposed inside said housing, includes an outer heating surface such that said multiple alignment ribs are disposed around said reaction heating block and contact said outer heating surface to secure and prevent displacement of said reaction heating block.

5. The reaction chamber for thermally activating multiple samples including a target analyte of claim 1, further comprising a rigid, optically transparent film disposed adjacent to said reaction heating block and designed to mechanically support said cartridge under compression.

6. The reaction chamber for thermally activating multiple samples including a target analyte of claim 1, wherein during an operative state of said reaction heating block, said cartridge is secured on said cartridge stage such that said curved profile of said inner heating surface conforms to said curved profile of said outer surface of said side portion of said multiple reaction wells to effectively thermally activate multiple samples including said target analyte contained inside said multiple reaction wells.

7. The reaction chamber for thermally activating multiple samples including a target analyte of claim 6, further comprising a compression module that during an operative state of said reaction chamber, compresses a cap portion of said cartridge, that is secured within said opening, to prevent escape of vapor from said multiple reaction wells and/or to prevent cross-contamination between said multiple reaction wells.

8. An optical detection assembly for detecting at least one property of multiple samples including a target analyte, said optical detection assembly comprising: a cartridge stage having defined therein an opening for receiving a cartridge that has defined therein multiple reaction wells, each configured to hold said sample including said target analytes; multiple, non-linearly arranged, excitation light sources adjacent to said cartridge stage and designed to emit an incident light beam; multiple, non-linearly arranged, photodetectors disposed adjacent to said cartridge stage and designed to detect a transmitted light beam; and wherein position of each of said multiple excitation light sources longitudinally aligns with position of a corresponding one of said multiple photodetectors, such that during an operative state of said multiple photodetectors, an incident light beam, generated at one of said multiple excitation light sources, extends longitudinally to strike and be transmitted through said sample including said target analyte in said multiple reaction wells and generate said transmitted light beam, at least one property of which is measured by said corresponding one of said multiple photodetectors.

9. The optical detection assembly for detecting at least one property of multiple samples including a target analyte of claim 8, wherein at least one said property of said transmitted light beam is intensity or fluorescence.

10. The optical detection assembly for detecting at least one property of multiple samples including a target analyte of claim 8, wherein said multiple excitation light sources are arranged in a circular configuration and in corresponding fashion, said multiple photodetectors are arranged in said circular configuration.

11. The optical detection assembly for detecting at least one property of multiple samples including a target analyte of claim 8, wherein said multiple excitation light sources emit light at wavelengths having a peak intensity that ranges from about 430 nm to about 510 nm.

12. The optical detection assembly for detecting at least one property of multiple samples including a target analyte of claim 8, wherein said multiple excitation light sources are at least one member selected from a group comprising light emitting diodes, lasers, and excited gas lamps.

13. The optical detection assembly for detecting at least one property of multiple samples including a target analyte of claim 8, wherein said multiple photodetectors are at least one member chosen from a group comprising photodiodes, photoresistors, and complementary metal oxide sensors (CMOS).

14. The optical detection assembly for detecting at least one property of multiple samples including a target analyte of claim 8, further comprising: an excitation filter disposed between said multiple excitation light sources and said multiple reaction wells, wherein said excitation filter blocks wavelengths greater than a band of excitation wavelengths and allows said band of excitation wavelengths to pass through, such that in an operative state of said excitation filter, said excitation wavelengths enter said multiple reaction wells; and an emission filter disposed between said multiple reaction wells and said multiple photodetectors, wherein said emission filter blocks wavelengths less than said band of excitation wavelengths and allows wavelengths greater than said band of excitation wavelengths to pass through said emission filter to produce multiple emission signals, such that in an operative state of said emission filter, said multiple emission signals are detected by said multiple photodetectors.

15. The optical detection assembly for detecting at least one property of multiple samples including a target analyte of claim 14, wherein said emission filter and/or said excitation filter is comprised of a glass or polymer substrate having a coating that provides for pass-through of desired wavelengths.

16. The optical detection assembly for detecting at least one property of multiple samples including a target analyte of claim 14, further comprising at least one member selected from a group comprising: multiple excitation light source alignment keys disposed adjacent to and around said multiple excitation light sources for aligning said multiple excitation light sources with said multiple reaction wells and said multiple photodetectors, and wherein said multiple excitation light source alignment keys are made from an opaque polymer that is not auto fluorescent or excitable by light transmitted by said multiple excitation light sources; a compression module for sealing said reaction wells, disposed between said excitation filter and said cartridge, wherein said compression module includes multiple light channels that align with said multiple excitation light sources and said multiple reaction wells and that provide a path for passage of said band of excitation wavelengths and wavelengths greater than said band of excitation wavelengths to enter said multiple reaction wells; an aperture cover disposed between said multiple reaction wells and said emission filter, wherein said aperture cover has defined therein multiple crosstalk preventing apertures that align with said multiple excitation light sources, said multiple reaction wells, and said multiple photodetectors, for preventing crosstalk between transmitted light from said multiple reaction wells, and wherein said aperture cover is made of an opaque material; and a photodetector base, aligned adjacent to and around said multiple photodetectors, having defined therein multiple base apertures that are configured to align said multiple photodetectors with said multiple reaction wells and said multiple excitation light sources, and wherein said photodetector base is made from an opaque polymer that is not auto fluorescent or excitable by light transmitted by said multiple excitation light sources.

17. The optical detection assembly for detecting at least one property of multiple samples including a target analyte of claim 16, wherein said photodetector base is of a non-linear shape and has, non-linearly arranged, multiple base apertures defined therein, and position of each of said base apertures longitudinally align with position of a corresponding one of said multiple excitation light sources such that said transmitted beam of light propagating into one of said base apertures strikes said corresponding one of said multiple photodetectors.

18. A reaction chamber for thermally activating multiple samples containing a target analyte, said reaction chamber comprising: a reaction assembly including: a cartridge stage having defined therein an opening for receiving a cartridge that has disposed thereon multiple reaction wells, each configured to hold sample containing a target analyte; a reaction heating block disposed adjacent to said cartridge stage and having defined therein a heating block aperture that includes an inner heating surface having a curved profile designed to conform to a curved profile of an outer surface of a side portion of said multiple reaction wells, such that upon direct contact of said inner heating surface with said outer surface of said side portion of said multiple reaction wells, said reaction heating block effectively thermally activates said analyte contained inside multiple reaction wells; and an optical detection assembly including: multiple, non-linearly arranged, excitation light sources adjacent to said cartridge stage and designed to emit an incident light beam; multiple, non-linearly arranged, photodetectors, disposed adjacent to said cartridge stage and designed to detect a transmitted light beam; and wherein positions of each of said multiple excitation light sources, a corresponding one of said multiple reaction wells, and said corresponding one of said multiple photodetectors longitudinally align with each other, such that during an operative state of said reaction chamber, multiple incident light beams, generated at one of said multiple excitation light sources, each extend longitudinally to strike and be transmitted through said corresponding one of said multiple reaction wells and generate said transmitted light beam, at least one property of which is measured by said corresponding one of said multiple photodetectors.

19. The reaction chamber for thermally activating multiple samples containing said target analyte of claim 18, wherein said reaction assembly and said optical detection assembly extend in an overlapping longitudinal space.

20. The reaction chamber for thermally activating multiple samples containing said target analyte of claim 18, further comprising a compression module for compressing a cap portion of said cartridge and having defined therein multiple light channels, each of which provides an optical path to a light beam generated at one of said multiple excitation light sources such that during an operative state of said reaction chamber, said incident light beam is transmitted through a corresponding one of said light channels to strike said corresponding one of said multiple reaction wells.

Description

BRIEF DESCRIPTIONS OF THE DRAWINGS

[0064] FIG. 1 shows a perspective view of a portable, hand-held target analyte data collecting device, a cartridge card assembly, and a lysing tube, all of which represent one embodiment of the respective arrangements, and that may be used to analyze sample including a target analyte.

[0065] FIG. 2 shows a perspective view of the portable, hand-held target analyte data collecting device of FIG. 1.

[0066] FIG. 3 shows a perspective view of the lysing tube shown in FIG. 1.

[0067] FIG. 4A shows a side-sectional view of the portable, hand-held target analyte data collecting device shown in FIG. 1 and that shows certain salient components/features of a lysing chamber.

[0068] FIG. 4B shows a side-sectional view of the portable, hand-held target analyte data collecting device shown in FIG. 1 having installed therein the lysing tube shown in FIGS. 1 and 3.

[0069] FIG. 5 shows a perspective view of the cartridge card assembly shown in FIG. 1.

[0070] FIG. 6A shows a side view of a base portion, without the cap portion, of the cartridge shown in FIGS. 1 and 5.

[0071] FIG. 6B shows a top perspective view of the base portion shown in FIG. 6A to show salient components/features inside the base portion.

[0072] FIG. 7A shows a top perspective view of the cap portion shown in FIG. 7A to show salient components/features inside the cap portion.

[0073] FIG. 7B shows a bottom view of the cap portion of FIG. 7A.

[0074] FIG. 8 shows a perspective, side-sectional view of an assembled cap portion and base portion, wherein the cap portion shown in FIG. 7B is secured above the base portion shown in FIG. 6B.

[0075] FIG. 9A shows a top view of a non-linear shaped reaction chamber heating block, according to one embodiment of the present arrangements.

[0076] FIG. 9B shows a side-sectional view of the heating block shown in FIG. 9A.

[0077] FIG. 10A shows a perspective, side-sectional view of the cartridge card assembly shown in FIG. 1 and of the core assembly portion, according to one embodiment of the present arrangements and that is a part of the portable, hand-held target analyte data collecting device of FIG. 1.

[0078] FIG. 10B shows a perspective, side-sectional view of the cartridge card assembly disposed inside the core assembly portion shown in FIG. 10A.

[0079] FIG. 11A shows a side-sectional view of the salient components/features of an optical detection assembly, according to one embodiment of the present arrangements and that is part of the core assembly portion shown in FIG. 10A.

[0080] FIG. 11B shows an exploded view of the salient components/features of the optical detection assembly shown in FIG. 11A.

[0081] FIG. 12 shows a side-sectional view of the integration of the salient components/features of the optical detection assembly of FIG. 11A and of the reaction assembly that are both part of the core assembly portion shown in FIG. 10A.

[0082] FIG. 13 shows certain salient steps of a method, according one embodiment of the present teachings for detecting a presence and/or a characteristic of a target analyte.

[0083] FIG. 14 shows certain salient steps of a method, according to one embodiment of the present teachings, for determining presence and/or a characteristic of a target analyte in a sample.

[0084] FIG. 15 shows certain salient steps of a collection method, according to one embodiment of the present teachings, for collecting target analyte data.

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS

[0085] In the following description, numerous specific details are set forth in order to provide a thorough understanding of the present arrangements and teachings. It will be apparent, however, to one skilled in the art that the present teachings may be practiced without limitation to some or all of these specific details. In other instances, well-known method steps have not been described in detail in order to not unnecessarily obscure the present arrangements and teachings.

[0086] The systems and methods of the present inventions provide a simple, integrated method and a portable, hand-held device for performing an analyte test that determines presence and/or characteristics of one or more target analytes in a sample.

[0087] FIG. 1 shows a target data analyte detection arrangement 100 for collecting target analyte data, according to one embodiment of the present teachings. Target analyte data collecting arrangement 100 includes a target analyte data collecting device 102, a lysing tube assembly 104 and a cartridge card assembly 106. Target analyte data collecting device 102 has a length that ranges from about 215 mm to about 235 mm, and is, preferably about 226 mm, has a width that ranges from about 80 mm to about 95 mm, and is, preferably about 88 mm, and has a thickness (or height) that ranges from about 50 mm to about 65 mm, and is, preferably, about 57 mm. The weight of target analyte data collecting device 102 ranges from about 1.5 pounds to about 2.5 pounds and is, preferably, about 2 lbs.

[0088] As will be explained in connection with FIGS. 3, 4A, and 4B, the lysing tube assembly (substantially similar to lysing tube assembly 104 of FIG. 1) facilitates lysing, in a lysing chamber (explained in FIGS. 4A and 4B), of a sample including a target analyte to produce a lysed sample. Further, in connection with FIGS. 5, 6A-6B, 7A-7B and 8, it is explained that the lysed sample is transferred to the cartridge, or cartridge assembly (substantially similar to cartridge assembly 1031 of FIG. 1), which facilitates thermal activation or thermal processing, in the presence of certain buffer, reagents, and/or probes, the lysed sample (containing the target analyte) to produce a detectable sample. This thermal activation is carried out using a reaction assembly (describe in connection with FIGS. 10A and 10B). An optical detection assembly (described in connection with FIGS. 11A and 11B) detects the target analyte in the detectable sample. In certain embodiments of the preferred arrangements, the same reaction chamber (as explained in connection with FIG. 12) is configured to both thermally activate to produce the detectable sample and detect the target analyte in the detectable sample. Further, the results relating to the target analyzed detection are displayed on a user interface of the device for collecting target analyte data.

[0089] FIG. 2 shows a target analyte data collecting device 202, which is substantially similar to target analyte data collecting device 102 of FIG. 1 and includes handle portion 208 and a core assembly portion 295, which, in turn, includes a lysing chamber 209 and a reaction chamber 210. A user interface 211 is provided on a top or loading surface of handle region 208. The top or loading surface at core assembly portion 295 has defined therein a lysing chamber inlet 212 that provides access to a lysing chamber door 213 with a raised lip that is designed to receive a lysing tube (e.g., lysing tube 104 of FIG. 1) when lysing chamber door 213 is open. FIGS. 4A and 4B show additional structural details that may be found inside lysing chamber 209.

[0090] In connection with core assembly portion 205, reaction chamber 210 includes a cartridge slot opening switch 214 when placed in an “on” position provides a cartridge card assembly (e.g., cartridge card assembly 106 of FIG. 1) access through cartridge inlet 215 inside reaction chamber 210. According to one embodiment of the present teachings, a sufficient external force, e.g., a user's push, applied to the cartridge secures the cartridge near a cartridge stage (not shown to simplify illustration) inside reaction chamber 210. A cartridge card opening or slot 215, preferably, provides access to optical detection and reaction enabling components disposed inside reaction chamber 210. To this end, FIGS. 10A-10B, 11A-11B, and 12 show such components in detail.

[0091] Before the cartridge is inserted inside reaction chamber 210, however, contents inside lysing tube assembly 304 of FIG. 3 are transferred to the cartridge. According to this figure, lysing tube assembly 304 has a lysing tube cap 321 and a lysing tube 320. In one embodiment of the present arrangements, lysing tube assembly 304 includes a securing mechanism that secures lysing tube cap 321 to lysing tube 320.

[0092] A lysing tube 320 loaded with a sample including a target analyte is sealed using lysing tube cap 321 and placed inside lysing chamber 409, which is shown in FIG. 4A. FIG. 4A shows a core assembly portion 495 includes lysing chamber 409 and reaction chamber 410. A separation wall 476 preferably separates lysing chamber 409 and reaction chamber 410.

[0093] Lysing chamber 409 includes a lysing chamber housing 428 that preferably houses an insulation 427 for surrounding a heating block 425. A heater input 426, which is disposed adjacent to and is coupled to lysing heating block 425, preferably surrounds heating block 425 to provide thermal energy for application of a thermal regimen. Additional structural details that allow securing lysing tube assembly 404 inside heating block 425 include a lysing chamber door 413 that slides open to provides access to lysing tube assembly 404 and an o-ring that holds in place lysing tube assembly 404 inside heating block 425. FIG. 4B shows a lysing tube assembly 404′, which is substantially similar to lysing tube assembly 404, in an inserted state or position inside a heating block of lysing chamber 409.

[0094] When lysing tube assembly 404 is secured inside heating block 425, using an energy source (e.g., a battery provided in the target analyte data collecting device), a lysing heating block 425 is energized to lyse the sample contained inside the lysing tube assembly to produce a lysed sample. A temperature sensor 429 is provided to measure temperature at or near heater input 426, which approximates the temperature of the sample inside lysing tube assembly 404.

[0095] This temperature is conveyed to a printed circuit board that determines the duration of the heat treatment, according to a first thermomechanical regimen, to produce the lysed sample. Application of a thermal regimen to lyse samples in lysing chamber 409 may be automated such that an untrained user may implement the thermal regimen via a user interface.

[0096] Lysing tube 420 may be preloaded with a desired buffer and/or reagent prior to placement in lysing chamber 409. In certain embodiments of the present arrangements, such preloaded buffer and/or reagent is lyophilized and/or freeze-dried inside lysing tube 420.

[0097] In alternate embodiments of the present arrangements, sample-preparation techniques (i.e., for downstream processing in a reaction chamber) other than lysing are performed in chamber 409. In such manner, lysing chamber 409 may alternatively be considered a sample-preparation chamber. Indeed, the systems of the present arrangement contemplate performing any sample preparation that facilitates extraction of a target analyte from a sample and/or deactivation of one or more compounds in a sample that are inhibitory downstream detection using an assay for a target analyte (e.g., nucleic acid amplification or an enzyme-linked immunosorbent assay indicated by a fluorescent probe).

[0098] FIG. 5 shows a cartridge card assembly 506, according to one preferred embodiment of the present arrangements. Cartridge card assembly 506 is substantially similar to its counterpart described above with reference FIG. 1 (i.e., cartridge card assembly 106 of system 100). Cartridge card assembly 506 includes a rectangular card 530 with a cartridge assembly 531 disposed at or near a first end. Preferably, cartridge assembly 531 is secured within a card opening defined within rectangular card 530. As shown in FIG. 5, rectangular card 530 is configured in a longer, rectangular shape such that a user may handle cartridge card assembly 506 on the end opposite to cartridge assembly 531 (e.g., for insertion into a target analyte data collecting device such as device 102 of FIG. 1). Space on rectangular card 530 may also be used to implement a barcode to track reaction data and results by a target analyte data collecting device configured to implement cartridge card assembly 506, which may also be configured with a barcode reader for such purpose.

[0099] Cartridge assembly 531 on cartridge card assembly 506 includes a base portion 532 (described in further detail below with reference to FIGS. 6A-6B) with a cap portion 533 (described in further detail below with reference to FIGS. 7A-7B) secured thereon, preferably by press fitting cap portion 533 onto base portion 532 to engage complementary regions and features. Preferably, base portion 532 is attached to a card opening defined within rectangular card 530. In this preferred embodiment, rectangular card 530 has defined thereon a card opening and includes multiple card attaching features disposed on base portion 532 such that multiple card attaching features connect base portion 532 to said rectangular card 530.

[0100] In certain other embodiments of the present arrangements, however, a rectangular card 530 is not used, and cartridge assembly 531, unattached to any card feature, is used to facilitate detection of presence and/or characteristics of a target analyte by systems disclosed herein. The systems and methods disclosed herein contemplate any means of delivering a cartridge for further data collecting and analysis by the target analyte data collecting devices disclosed herein.

[0101] FIGS. 6A and 6B shows features of a base portion 632 that allows the cartridge assembly (e.g., cartridge assembly 531 of FIG. 5) to both serve as a receptacle for reactions and withstand the compression forces that may be encountered during the reactions. Before reaction, and if required, compression, is carried out inside or on the cartridge assembly, a cap portion (e.g., cap portion 533 of FIG. 5) is secured on a base portion (e.g., base portion 532 of FIG. 5) to complete the cartridge assembly (which also may be thought of simply as a “cartridge”). To this end, FIG. 6A shows a base portion 632, which is substantially similar to base portion 532 of FIG. 5, includes multiple securing features 644 that are designed to secure therewithin an edge of the cap portion, such that the cap portion is effectively secured to base portion 632. Further, an orientation key 634 extends from an edge of base portion 632 and away from a center region of base portion 632. In an operative state of the cartridge, orientation key 634 functions in conjunction with an orientation lock disposed on or near cartridge stage (e.g. orientation lock 1073 of FIG. 10A) and is designed to place the cartridge in a desired orientation to allow heating of said sample and/or detection of said target analyte.

[0102] To facilitate reactions inside an assembled cartridge, base portion 632 includes multiple reaction well housings 636. The structural details inside each of reaction well housings 636 are shown in FIG. 6B.

[0103] According to this figure, base portion 632 includes, at or near a center region, a supporting feature 641 having disposed thereon a receiving area 639 and multiple channel dividers 642 that are radially disposed around receiving area 639. In this configuration, multiple channel entry regions 698 are defined between multiple channel dividers 642 for receiving the sample received at receiving area 639. Multiple connecting tracks 640 substantially linearly extend from receiving area 639 or a region proximate thereto (such as multiple channel entry regions 698) to multiple reaction wells 637. As a result, multiple connecting tracks 640 are designed to convey a sample including said target analyte from receiving area 639 to multiple reaction wells 637. As explained later, each of multiple reaction wells 637 are configured to transform said sample to a detectable sample.

[0104] A base portion flow path for the sample is defined from receiving area 639 to each of multiple reaction wells 637 and includes passing through one of multiple channel entry regions 698 and one of multiple connecting tracks 640.

[0105] To withstand compression forces, each of connecting tracks 640 includes a second compression resisting region 638 and each of multiple reaction well housings 636 includes a first compression resisting region 697. As shown in FIG. 6B, first compression resisting region 697 and second compression resisting region 638 surround reaction well 637. As will be explained in further detail below with reference to FIG. 8, when cartridge assemblies of the present arrangements are in use, reaction well 637, first compression resisting region 697, and second compression resisting region 638 align with corresponding regions on a cap portion (e.g., cap portion 733, described below with reference to FIGS. 7A-7B) to facilitate sealing of reaction well 637 during reactions, including optical detection reaction.

[0106] The open geometry of base portion 632 (i.e., before a cap portion is secured thereon to form a cartridge assembly) provides the advantage of pre-loading reaction materials, such as buffers, reagents and probes for a desired reaction (e.g., an amplification reaction) into each of multiple reaction wells 637. By way of example, a reaction material that includes at least one of buffer, reagent and probe, is preloaded into each of multiple reaction wells 637 by removing, using securing features 644, the cap portion and then lyophilizing and/or freeze drying the reaction materials. In this example, a cap portion (e.g. cap portion 732 of FIGS. 7A and 7B) is secured, preferably by press-fitting using securing features 644, onto a preloaded base portion 632 to form a preloaded cartridge assembly, which is readily stored, or transported for later use, for example, in the field. This provides the advantage of such pre-loading steps being performed by trained technicians away from the field such that reactions may be carried out by untrained users in the field. This provides the further advantage of being able to store such reagents, buffers, and/or probes at room temperature, whereas conventional systems may require storage of such reagents, buffers, and/or probes in refrigerators or freezers.

[0107] FIGS. 7A and 7B shows a cap portion 733 that includes provisions for effectively carrying both reactions and receiving compression forces. In connection with facilitating reaction, cap portion 733 has defined therein multiple vents 749, which are described in detail in connection with FIG. 8.

[0108] Cap portion 733 includes multiple connecting track covers 757 that are disposed adjacent to multiple connecting tracks 640 shown in FIG. 6B. In this configuration, each of multiple connecting track covers 757 cover each of multiple connecting tracks 640 and each of multiple connecting track covers 757 includes a second compression region 755. This portion of second compression region 755 corresponds to or is adjacent to second compression resisting region 638 shown in FIG. 6B in the cartridge assembly.

[0109] Multiple reaction well housing covers 750, in complementary fashion, are disposed adjacent to cover multiple reaction well housings 636. Each of multiple reaction well housing covers 750 include a first compression region 754 and second compression region 755 and a reaction well cover 756. In an assembled configuration of the cartridge, multiple first compression regions 754 are adjacent to and combine with multiple first compression resisting regions 697 shown in FIG. 6B, portions of multiple second compression regions 755 are adjacent to and integrate with portions of multiple second compression resisting region 638 shown in FIG. 6B and multiple reaction well covers 756 are adjacent to and combine with multiple reaction wells 637 to effectively seal the bottom portion such that during reaction, vapors of the reactional materials and/or target analyte do not escape.

[0110] FIG. 8 specifically shows that first compression region 754 and first compression resisting regions 697 combine to form a first seal (i.e. at a location 1 on a cartridge assembly 831) and second compression region 755 and second compression resisting regions 638 combine to form a second seal (i.e., at a location 2 on cartridge assembly 831). Seals at location 1 and location 2 are configured to effectively seal a reaction well during a detection reaction.

[0111] According to FIG. 8, cartridge assembly 831 of the present arrangements is substantially similar to it counterpart in FIG. 5 (i.e., cartridge assembly 531). Base portion 832, reaction well 837, first compression resisting region 897, second compression resisting region 838, receiving area 839, channel entry region 898, securing feature 844, and connecting track 840, are substantially similar to their counter parts described above with reference to FIGS. 6A-6B (i.e., base portion 632, reaction well 637, first compression resisting region 697, second compression resisting region 638, receiving area 639, channel entry region 698, securing feature 644, and connecting track 640). Further, cap portion 833, vents 849, gasket 852, inlet port 853, first compressing region 854, second compressing region 855, reaction well cover 856, and third compressing region 859, are substantially similar to their counterparts described above with reference to FIGS. 7A-7C (i.e., cap portion 733, vents 749, gasket 752, inlet port 753, first compressing region 754, second compressing region 755, reaction well cover 756, and third compressing region 759.

[0112] Complementary features aligned in cartridge assembly 831 serve multiple purposes in connection with facilitating reactions and undergoing compression, during the reactions. As explained above, seals at locations 1 and 2 in FIG. 8 effectively seal reaction well 837 from receiving additional amounts of sample (including the target analyte) when the sample already present inside reaction well 837 is undergoing a reaction according to a thermomechanical regimen. Specifically, the seal at location 1 will effectively block a respective vent 849, and the seal at location 2 will effectively block a reaction well entrance 862.

[0113] In connection with effective flow of sample (including the target analyte) to facilitate a reaction, complementary features on base portion 832 and cap portion 833 align to define a channel 861 that extends from a channel entry region 898 (e.g., defined by channel dividers, such as channel dividers 642 of FIG. 6 B) to reaction well 837 (i.e., through reaction well entrance 862). To this end, as shown in FIG. 8, inlet port 853 aligns with receiving area 839 (i.e., for supply of fluid through channel entry region 898), connecting track 840 (which includes second compression resisting region 838) aligns with connecting track cover 857 (which includes a bottom end of second compression resisting region 855) to define an enclosed channel 861 that has a cross-sectional area.

[0114] Enclosed channels 861 include sidewalls that extend from channel entry region 898 to reaction well entrance 862. In certain embodiments of the present arrangements, portions of sidewalls are defined by undercuts in cap portion 833. These portions of the sidewalls may be received into base portion 832 by complementary aligning recesses cut into base portion 832. In other embodiments of the present arrangements, portions of the sidewalls extend from base portion 832, and complementary recesses may be cut into cap portion 833.

[0115] Regardless of the manner of forming channels and fabricating sidewalls, sidewalls, if they are used, are preferably raised, from a base of their respective connecting tracks, by a height ranging from about 0.2 mm to about 3.0 mm. Further, in one preferred embodiment, channels 861 of the present arrangements have a cross-sectional area that ranges from about 0.6 mm.sup.2 to about 1.0 mm.sup.2 and linearly extend by a distance that ranges from about 2 mm to about 12 mm.

[0116] FIG. 8 also shows a third compression region 859 disposed on inlet port 853 that may be blocked with compressive force applied to third compression region 859 and/or to gasket 852. Regardless of whether the compression force is applied to third compression region 859 or on or near gasket 852 (which may also be thought of as a third compression region), the compression force in this case serves to block inlet port 853 from ambient conditions. In such embodiments, receiving 839 and/or adjacent features (not shown in FIG. 8 to simplify illustration), which are assembled adjacent to inlet port 853, include a supporting feature (e.g., supporting feature 641 of FIG. 6A) that serves as a third compression resisting region. In these embodiments, where compressive force is applied at or near third compression region 859, a seal at location 3 is created that effective seals off inlet port 853 from ambient conditions. In another embodiment, one dimension of said inlet port ranges from about 1 mm to about 5 mm and to the extent inlet port 853 is circular in shape, it has an inlet port diameter that ranges from about 3.5 mm to about 3.8 mm.

[0117] In a non-compressed state of cartridge assembly 831, vents 897 may be considered “open” such that they are configured to regulate fluid flow through channel 861 and provide for relatively equal distribution of sample (including the target analyte) and/or mixture (e.g., lysate) in reaction wells 837.

[0118] First, open vents 897 provide and escape path for air that is being displaced by fluid and/or mixture during filling of reaction wells 837. Second, vents 897 are configured at a cross-sectional area that is large enough to accommodate air flow but small enough to effectively restrict fluid flow therethrough. Accordingly, a vent 749 may configured at a height in well 837 such that when fluid reaches vent 849, resistive forces caused by the fluid covering vents 849 prevent or substantially reduce filling of fluid in that reaction well. Thus, if one reaction well fills faster, resistance created by contact of the fluid with vent 849 will prevent or substantially inhibit further fluid flow into that reaction well, filling of other reaction wells will continue until similar resistive forces caused by blocking of vents 849 restrict fluid flow into those reaction wells. According to preferred embodiments of the present arrangements, vents 849 are configured to provide a relatively even distribution of fluid or mixture (e.g., lysate) that is delivered through inlet port 853.

[0119] In other words, a vent 849 is configured to have a cross-sectional area that facilitates air flow, but significantly inhibits or blocks fluid flow. Preferably, vent 849 has a cross-sectional area that is a value that is between about 0.01 mm.sup.2 and about 0.25 mm.sup.2 to accomplish this. Further, as shown in FIG. 7B, vents may incorporate various angles (e.g., a t-shaped configuration) to use angles to further implement resistive force preventing fluid flow therethrough.

[0120] According to one embodiment of the present arrangements, each of reaction wells 837 has a volume that ranges from about 5 microliters to about 100 microliters and has a diameter that ranges from about 1 mm to about 4 mm. Although FIGS. 6A, 6B and 8 show arranged in a circular configuration on a generally circular base portion 832, the present teachings are not so limited and reactions wells 837 may be arranged in a non-linear configuration on a base portion that is of a non-linear shape.

[0121] According to one embodiment of the present arrangements, cap portion 833 is comprised of optically transparent material (which allows for interrogation of optical signals from within a reaction chamber). By way of example, cap portion 833 is comprised of at least one member chosen from a group comprising silicone rubber, polydimethylsiloxane, and a thermoplastic elastomer. Preferably, cap portion 833 comprises a relatively flexible, elastomeric material.

[0122] According to another embodiment of the present arrangements, base portion 832 is comprised of material that is optically transparent (which allows for interrogation of optical signals from within a reaction chamber), as well as relatively rigid, such that base portion 832 can maintain high dimensional tolerance (i.e., during compression). According to one embodiments of the present arrangements, base portion 832 is comprised of polypropylene or cyclic olefin copolymer. Use of such materials not only facilitates press fitting of cap portion 833, which is preferably relatively flexible, into base portion 832, which is relatively rigid, but also allows for compression, if required during the reactions that render the sample including the target analyte detectable.

[0123] FIG. 9A shows a reaction heating block 964, according to one embodiment of the present arrangements. Reaction heating block 964 has defined therein a heating block aperture 971.

[0124] As shown in FIG. 9A, reaction heating block 964 has a circular shape with a corresponding circular heating block aperture 971 defined therein. Preferably, heating block aperture 971 is configured to secure a cartridge assembly (e.g., cartridge assembly 831 of FIG. 8). Reaction chamber heating block and/or heating block aperture 971 may be of a non-linear shape.

[0125] A heating element 967 is shown connected to an outer surface of reaction heating block 964. A temperature sensor may also be coupled to reaction heating block 964. Preferably, a script running on a computer element (e.g., a printed circuit board) is communicatively coupled to the temperature sensor and heating element 967 in a closed-feedback loop to control temperature conditions during thermally activating steps (including isothermal heat treatment) carried out inside the reaction chambers of the present arrangements. Such precise control of reaction chamber temperatures, including maintaining isothermal conditions, may be facilitated by use of one or more components that facilitate temperature control (e.g., a heating element, a thermistor, and/or a temperature sensor).

[0126] FIG. 9B shows the same reaction hearting block as shown in FIG. 9A, except the FIG. 9B clearly shows features and/or components that are clearly visible from a side view. By way of example, FIG. 9B shows an inner heating surface 965. Inner heating surface 965 may be thought of as a surface that heats a portion of the outer surface of each of the multiple reaction wells (e.g., reaction wells 837 of FIG. 8) during the reaction carried out in the reaction chamber of the present arrangements.

[0127] Preferably, inner heating surface 965 has a curved profile that conforms to a curved profile of an outer surface of a side portion of multiple reaction wells. As a result, upon direct contact of inner heating surface 965 with the outer surface of the side portion of the multiple reaction wells, reaction heating block 964 effectively thermally activates samples including target analyte contained inside one or more reaction wells. Stated another way, during an operative state of reaction heating block 964, a cartridge is secured within heating block aperture 971 such that a curved profile of inner heating surface 965 conforms to a curved profile of an outer surface of a side portion of multiple reaction wells to effectively thermally activate multiple samples including target analyte contained inside reaction wells. In other embodiments of the present arrangements, however, the inner heating surface 965 need not necessarily conform to a curved profile of an outer surface of a side portion of multiple reaction wells. Further, the outer surface of reaction wells, which contacts the inner heating surface, need not necessarily have a curved profile.

[0128] Preferably, reaction heating block 964 has a diameter that ranges from about 10 mm to about 50 mm, a diameter of heating block aperture 971 ranges from about 3 mm to about 48 mm, and a height of reaction heating block 964 has a value that ranges from about 1 mm to about 20 mm.

[0129] In preferred embodiments of the present arrangements, inner heating surface 965 of reaction heating block 964 is configured to slope or taper slight inward to facilitate securing of a corresponding cartridge assembly therein. According to such embodiments, an inner diameter (i.e., diameter of aperture 971) at a top end of reaction heating block 964 is preferably about 5%-15% larger than an inner diameter at a bottom end of reaction heating block 964. According to one preferred embodiment of the present arrangements, reaction heating block 964 has an inner diameter of between about 23 mm to about 29 mm at a top end, and an inner diameter of about between 20 mm to about 25 mm at a bottom end.

[0130] Though not shown in FIGS. 9A and 9B, heating block 964 may be secured within a reaction chamber by one or more alignment ribs disposed inside a housing. According to one embodiment of the present arrangements, one or more alignment ribs are disposed around reaction heating block 964 and effectively contact an outer heating surface of reaction heating block 964 to secure and prevent its displacement during thermal processing of samples containing target analytes. The present teachings recognize, however, contact of such alignment ribs with heating block 964 may act as “heat sinks” that draw heat away from reaction heating block 964 during thermal processing of samples containing target analytes. To this end, the present teachings recognize that the number of such contact points and the surface area of contact between heating block 964 and support elements should be minimized. Preferably, alignment ribs, as well as certain other components disposed near reaction heating block 964 or a lysing heating block (e.g., lysing heating block 425 of FIG. 4A) are comprised of insulative, temperature resistance material such as polyether ether ketone, polyoxymethylene, polyphenylene sulfide, polysulfone, polyethersulfone, and/or nylon.

[0131] FIG. 10A shows a cartridge card assembly 1006 prior to its insertion into a reaction chamber 1010, according to one embodiment of the present arrangements. Cartridge card assembly 1006 is substantially similar to its counterpart in FIG. 1 (i.e., cartridge card assembly 106) and includes a cartridge assembly 1031 (which is substantially similar to its counterpart in FIG. 8, i.e., cartridge card assembly 831) secured therein.

[0132] Reaction chamber 1010 includes a cartridge card assembly opening or slot 1015 substantially similar to cartridge card assembly opening 215 of FIG. 2 and includes a retractable cartridge door 1016 that expands and retracts to provide access to an assembly of optical elements disposed inside reaction chamber 1010. A compression module 1074, in accordance with one embodiment of the present arrangements, is shown connected at a bottom end of cartridge door 1016. Reaction chamber 1010 also includes a reaction heating block 1064 with an inner heating surface 1065, which are substantially similar to their counterparts in FIG. 9A (i.e., reaction heating block 1064 and inner heating surface 965). FIG. 10A also shows a cartridge support film 1059 secured at a bottom end of reaction heating block 1064 and an orientation lock 1073 disposed at a top end of reaction heating block 1064. Reaction heating block 1064 is shown disposed adjacent to a cartridge stage 1070.

[0133] In FIG. 10A, reaction chamber 1010 is shown in an open state, exposing salient features and/or components. In this figure, cartridge door 1016 is in a raised position such that cartridge card opening 1015 is open and capable and receiving cartridge card assembly 1006 for placement in reaction heating block 1064.

[0134] FIG. 10B shows a reaction chamber 1010′, according to one embodiment of the present arrangements, with a cartridge card assembly 1006′ inserted therein. A cartridge card assembly 1006′, a cartridge assembly 1031′, a reaction chamber 1010′, a cartridge card assembly opening 1015′, retractable optical detection assembly components 1016′, a compression module 1074′, a reaction heating block 1064′, a cartridge support film 1059′, an orientation lock 1073′, and a cartridge stage 1070, are substantially similar to their counterparts in FIG. 10A (i.e., cartridge card assembly 1006, a cartridge assembly 1031, reaction chamber 1010, cartridge card assembly opening 1015, retractable optical detection assembly components 1016, compression module 1074, reaction heating block 1064, cartridge support film 1059, orientation lock 1073, and cartridge stage 1070).

[0135] FIG. 10B shows a cartridge card opening 1015 in a closed position with cartridge assembly 1031′ secured on a cartridge stage opening such that the base portion is contacting reaction heating block 1064′. FIG. 10B may be thought of as depicting the state of reaction chamber 1010′ during thermal processing of samples containing target analyte (e.g., lysate) in cartridge 1031′.

[0136] Cartridge support film 1059′ disposed adjacent to the reaction heating block is designed to mechanically support cartridge 1031 under compression. To facilitate compression, reaction chamber 1010′ may include a compression module such as compression module 1074′ of FIG. 10B that, during an operative state of the reaction chamber, compresses a cap portion of cartridge assembly 1031′ against a complementary base portion, which contacts inner heating surface of reaction heating block 1064′. The cap portion when secured to a base portion is configured to prevent escape of vapor from the multiple reaction wells and/or to prevent cross-contamination between the different multiple reaction wells. Moreover, placing the cap portion under compressive force further facilitates preventing escape of vapor and cross-contamination between the different reaction wells.

[0137] FIG. 11A shows an optical detection assembly 1180 with a cartridge assembly 1131 secured therein, according to one embodiment of the present arrangements. FIG. 11A includes a printed circuit board 1191, an excitation light source 1182, an alignment key 1190, an excitation filter 1183, a compression module 1174 with light channels 1181 disposed therein, detection wells 1137, a cartridge support film 1159, an aperture cover 1185, an emission filter 1189, photodetectors 1186, and a photodetector plate 1187. Cartridge assembly 1131 includes a cap portion 1133 and a base portion 1132 having reaction wells 1137 disposed therein.

[0138] As shown in FIG. 11A, cartridge assembly 1131 may be thought of as being in a compressed state such that compression module 1174 delivers compressive force to cap portion 1133 and that force is also received by base portion 1132.

[0139] Printed circuit board 1191 is a uniquely placed printed circuit board capable of driving the optical detection methods described herein.

[0140] Excitation light source 1182 is an excitation light source that produces light at a peak intensity centered at an excitation wavelength of any probe (e.g., fluorophore) used to detect presence and/or characteristics one or more target analytes in a reaction well. Preferably, a peak intensity of excitation light source 1183 is adjusted based on choice of probe and/or fluorophore used for optical detection of analytes and analyte characteristics in reaction wells. According to one embodiment of the present arrangement, a peak intensity of excitation light source 1182 is centered at a wavelengths of about 480 nm.

[0141] According to one embodiment of the present arrangements, an excitation light source is at least one member chosen from a group comprising light emitting diode, laser, and gas lamp.

[0142] Alignment key 1190 is a structural element configured to receive and to facilitate alignment of excitation light source 1183 with other features of optical detection assembly 1180 and/or a reaction well that are disposed within optical detection assembly 1180 (e.g., reaction well 1137).

[0143] Alignment key 1190 is preferably comprised of an opaque polymer that is not auto-fluorescent or excitable by light delivered by photodetectors 1182 during optical detection.

[0144] Excitation filter 1183 preferably blocks all wavelengths from excitation light source 1182 that would overlap from an emission signal from a probe and/or fluorophore. According to one embodiment of the present arrangements, excitation filter 1183 is a short pass filter that blocks all wavelengths above about 500 nm.

[0145] Compression module 1174 is a component used to compress cartridge assembly 1131 and seal reaction wells 1137 during the reactions of the present teachings that are susceptible to optical detection. According to the embodiment of FIG. 11A, compression module 1174 also includes one or more light channels 1184 disposed therein to facilitate transfer of light that passes through excitation filter to reach reaction wells 1137. Preferably, light channels 1184 are longitudinally aligned with excitation light sources 1182.

[0146] As shown in FIG. 11A, a cartridge assembly 1131 having a base portion 1132 with a cap portion 1132 secured thereon is shown disposed under light channels 1184. Preferably, light channels 1184 are longitudinally aligned with reaction wells 1137 disposed inside cartridge assembly 1131.

[0147] As shown in FIG. 11A, compression module 1174 presses against and into cartridge assembly 1131. To this end, cartridge assembly 1131 may be thought as being in a compressed state.

[0148] As shown in FIG. 11A, cartridge assembly 1131 is shown supported by cartridge support film 1159, which is disposed on aperture cover 1185. Cartridge support film 1159 and/or aperture cover 1185 provide mechanical stability for cartridge assembly 1131 when maintained in a compressed state during the optical detection reactions of the present invention. Aperture cover 1185 may have defined therein small apertures that longitudinally align with the bottom of each of reaction wells 1137. These small holes are configured to prevent crosstalk between light that passes through each of reaction wells 1137.

[0149] Cartridge support film 1159 (which is substantially similar to its counterpart in FIG. 10A, i.e., cartridge support film 1059), is comprised of optically transparent material that does not absorb light in the range of common organic fluorescent dyes associated with probes and/or fluorophores for optical detection. Preferably, cartridge support film 1159 is of sufficient rigidity to support cartridge 1131 during compression. According to one embodiments of the present arrangements, cartridge support film 1159 is comprised of cyclic olefin polymer.

[0150] Aperture cover 1185 is preferably comprised of material that is opaque, even when in the form of a film or thin sheet, such as stainless steel.

[0151] The present teachings recognize that when filtered excitation light (e.g., incident light generated by excitation light source 1182 that has been filtered by excitation filter 1183) reaches a probe and/or fluorophore in a reaction well, the probe and/or fluorophore is excited such that, as a response, it will emit light at a relatively higher wavelength (i.e., a wavelength that is similar to or greater than wavelengths that were blocked by excitation filter 1183). To this end, optical detection assembly 1180 implements emission filter 1189 beneath aperture cover 1185 to allow passthrough of light wavelengths emitted by a probe and/or fluorophore and to filter out excitation wavelengths from advancing. Light that passes through emission filter 1189 may be thought of as an emission signal. In one preferred embodiment of the present arrangements, emission filter is a 510 nm long pass filter.

[0152] Excitation filter 1183 and/or emission filter 1187 are preferably comprised of a glass or polymer substrate having a coating or dye that provides sufficient pass-through properties to facilitate detection of presence or characteristics of one or more target analytes.

[0153] Photodetectors 1186 are configured to receive an emission signal that propagates from emission filter 1189 and to convert the emission signal (i.e., an optical signal) to an electrical signal that is coupled to various computer elements (e.g. a printed circuit board) for further processing and interpretation of optical detection reactions carried out in reaction wells 1137, including detection of one or more target analytes. Preferably, photodetectors 1186 are longitudinally aligned with reaction wells 1137. Photodetectors 1186 may be at least one member chosen from a group comprising photodiode, photoresistor, and CMOS sensor.

[0154] Photodetector plate 1187 rests beneath and/or supports photodetectors 1186. Photodetector plate 1187 is preferably configured to longitudinally align photodetectors 1186 with reaction wells 1187 and/or to prevent cross-talk of emission signals.

[0155] FIG. 11B shows an exploded view of the components shown in FIG. 11A. An optical detection assembly 1180′, a printed circuit board 1191′, an excitation light source 1182′, an alignment key 1190′, an excitation filter 1183′, a compression module 1174′ with light channels 1181′ disposed therein, a cartridge cap portion 1133′, a cartridge base portion 1132′, detection wells 1137′, a cartridge support film 1159′, an aperture cover 1185′, an emission filter 1189′, photodetectors 1186′, and a photodetector plate 1187′, are substantially similar to their counterparts in FIG. 11A (i.e., optical detection assembly 1180, printed circuit board 1191, an excitation light source 1182, alignment key 1190, excitation filter 1183, compression module 1174 with light channels 1181 disposed therein, cartridge cap portion 1133, cartridge base portion 1132, detection wells 1137, cartridge support film 1159, aperture cover 1185, emission filter 1189, photodetectors 1186, and photodetector plate 1187).

[0156] FIG. 12 shows certain components of a core assembly portion 1295 of an exemplar target analyte data collecting device, according to one embodiment of the present arrangements. FIG. 12 includes a lysing chamber region 1209 with lysing tube assembly 1204 disposed therein, an o-ring 1224, a lysing heating block 1225, a heating element 1226, and an insulation 1227, which are substantially similar to their counterparts in FIG. 4A, i.e., lysing chamber region 409, lysing tube assembly 404, o-ring 424, lysing heating block 425, heating element 426, and insulation 427. FIG. 12 also shows a separation 1276 separating lysing chamber region 1209 from a reaction chamber region 1210. Reaction chamber region 1210 includes a cartridge card opening 1215, a cartridge state 1270, a reaction heating block 1264, with an inner heating surface 1265 disposed therein, a cartridge stage 1270, an orientation lock 1273, and a cartridge support film 1159, which are substantially similar to their counterparts in FIG. 10A, i.e., separation 1076, reaction chamber region 1010, cartridge card opening 1015, cartridge stage 1070, reaction heating block 1264, and inner heating surface 1065). FIG. 12 also shows certain optical detection assembly components integrated with reaction chamber components, including a printed circuit board 1291, excitation light sources 1282, an alignment key 1290, an excitation filter 1283, a compression module 1274, an emission filter 1289, photodetectors 1286, a photodetector plate 1287, which are substantially similar to their counterparts in FIG. 11A (i.e., printed circuit board 1191, excitation light sources 1182, alignment key 1190, excitation filter 1183, compression module 1174, emission filter 1189, photodetectors 1186, and photodetector plate 1187).

[0157] In the arrangement shown in FIG. 12, the reaction assembly and the optical detection assembly extend in an overlapping longitudinal space. FIG. 12 also conveys that the reaction assembly may be arranged such that it is disposed within certain components of the optical detection assembly. This saving of real estate on the target analyte data collecting device allows for the device to provide functionalities that allow for on-site testing and real time results.

[0158] FIGS. 13-15 describe various methods according to the present teachings. It is not necessary to use the structural details described herein (i.e., details described in connection with FIGS. 1-13) to practice these methods. However, using the structural details described herein to carry out the present methods, as they are described in FIGS. 13-15, represents preferred embodiments of the present teachings.

[0159] FIG. 13 is a flowchart of a method of detecting a presence and/or a characteristic of a target analyte 1300, according to one embodiment of the present teachings. Method 1300, preferably, begins with a step 1302 of obtaining a cartridge (e.g., cartridge 531 shown in FIG. 5) including a base portion (e.g., base portion 532 shown in FIG. 5) and a cap portion (e.g., cap portion 533 shown in FIG. 5). In this step, the cap portion includes an inlet port (e.g., inlet port 753 shown in FIG. 7B) and the base portion including multiple reaction wells (e.g., multiple reaction wells 637 shown in FIG. 6B).

[0160] Next a step 1304 includes introducing the sample containing the target analyte into the inlet port to form a loaded cartridge. Then, method 1300 proceeds to a step 1306, which includes placing the loaded cartridge in a reaction chamber (e.g., reaction chamber 1010 shown in FIGS. 10A and 10B). Inside the reaction chamber, a next step 1308 is carried out. This step includes compressing the loaded cartridge to form a compressed cartridge such that the multiple reaction wells are sealed from the ambient conditions to form sealed multiple reaction wells. In one embodiment of the present teachings, a compression module (e.g., compression module 1174 shown in FIG. 11A) is used to implement step 1308. Method 1300 then performs a step 1310, which includes commence heat treatment of the sample containing the target analyte in the sealed multiple reaction wells such that no amount to a substantially reduced amount of evaporation of the sample escapes the sealed multiple reaction wells. Step 1310 also transforms the sample including the target analyte into a detectable sample.

[0161] In certain preferred implementations of the present teachings, method 1300 further includes a step of equally distributing, which is carried out as part of step 1304, the sample containing the target analyte inside the multiple wells. Method 1300 may further include orienting, prior to performing step 1308, the cartridge using an orientation key (e.g., orientation key 634 shown in FIGS. 6A-6C) disposed on the cartridge. In this step, the orientation key serves as a point of reference that positions each of the multiple reaction wells at a predefined location. In one implementation, the commencing step of the present teachings includes contacting a reaction heating block with the multiple reaction wells. Further, as a result of the orientation step, the multiple reactions wells are in the proper position to undergo heating and/or detecting as described herein.

[0162] Method 1300 further, preferably, includes preloading one or more reaction material in the multiple reaction wells to form a pre-loaded cartridge. In this step of preloading, one or more of the reaction materials is at least one member chosen from a group comprising reagent, buffer, and probe. Method 1300 may further include, after the step of preloading, a step of lyophilizing the reaction materials in the multiple reaction wells. The steps of preloading and lyophilizing are preferably carried out prior to obtaining step 1302. As a result, method of detecting a presence and/or a characteristic of a target analyte 1300, if desired may be carried out on-site and real-time results may be obtained. In this embodiment of the present teachings, the need for going to a laboratory is obviated because all the necessary reaction materials for method 1300 are preloaded in the cartridge.

[0163] In another aspect, the present teachings provide other methods for determining presence and/or a characteristic of a target analyte in a sample. One such method 1400 is described in FIG. 14 and, preferably, begins with a step 1402, which includes collecting a sample including a target analyte. Next, a step 1404 involves placing the sample in a lysing tube (e.g., lysing tube 104 shown in FIG. 1). Then, in a step 1406, the lysing tube is introduced into the lysing chamber (e.g., lysing chamber 409 shown in FIG. 4A). At this stage of method 1400, lysing tube is prepared for undergoing lysing. To this end, a step 1408 includes heat treating, using a heating block, the lysing tube to produce a lysed sample. The present teachings recognize that steps 1402, 1404, 1406 and 1408 are optional and are carried out in certain preferred embodiments of the present teachings.

[0164] According to one preferred embodiment of the present teachings, heat treating in step 1408 maintaining a temperature of the lysing chamber at about 95° C. for about 2 minutes and then at about 65° C. for about 5 minutes. Similar heat treating steps may also be carried out in a reaction chamber in heat treatment performed (e.g., in step 1414, described below).

[0165] Regardless of whether steps 1402 to 1408, are implemented, method 1400 includes a step 1410 that includes obtaining a cartridge including multiple reaction wells having contained therein the sample including the target analyte. Step 1410 is substantially similar to step 1302 of FIG. 13. Then, in an optional step 1412, the lysed sample is transferred from the lysing tube (e.g., lysing chamber 409 shown in FIG. 4A) to the cartridge (e.g., cartridge 531 shown in FIG. 5). This transferring step of the present teachings may be carried out using at least one member chosen from a group comprising syringe, pipette, eye dropper, capillary tube, paper strip, and dipstick.

[0166] Next, a step 1414 includes securing, inside a reaction chamber (reaction chamber 1010 shown in FIG. 10A), the cartridge disposed on a cartridge stage (e.g., cartridge stage 1070 shown in FIG. 10A). In this step, the cartridge stage has defined therein an opening (e.g., opening 1015 shown in FIG. 10A) such that a cap portion (e.g., cap portion 733 shown in FIG. 7B) is disposed above the opening and the base portion (e.g., base portion 632 shown in FIG. 6B) is disposed below the opening. In this step, the reaction chamber includes a nonlinear-shaped heating block (e.g., circular shaped reaction heating block 964 shown in FIGS. 9A and 9B and reaction heating block 1064 shown in FIG. 10A) disposed inside a housing disposed below the opening. Further, the heating block has defined therein a heating block aperture (e.g., heating block aperture 971 shown in FIGS. 9A and 9B) that includes an inner heating surface (e.g., inner heating surface 965 shown in FIG. 9B) having a curved profile designed to conform to a curved profile of an outer surface of a side portion of the multiple reaction wells. Securing step 1414 may further include establishing direct contact of the inner heating surface with the outer surface of the side portion of the multiple reaction wells (e.g., reaction well 637 shown in FIG. 6B) or multiple reaction housings (e.g., reaction housing 636 shown in FIG. 6A).

[0167] As shown in FIG. 14, method 1400 then proceeds a step 1416, which includes thermally activating, using the reaction heat block disposed inside the reaction chamber, the sample including the target analyte to render the sample detectable. By way of example, thermally activating step 1416 is carried out under isothermal conditions.

[0168] The analyte, preferably, includes at least one member selected from a group comprising DNA, RNA, and protein. Further, the step of thermally activating may include amplifying the analyte. The analyte may be a severe acute respiratory syndrome coronavirus 2 (Covid-19). In one implementation, the step of thermally activating of the present teachings may include applying one or more different types of energy that is chosen from a group comprising thermal energy, mechanical energy, magnetic energy, electric energy, acoustic energy, radiation energy, and fluidic energy.

[0169] Method 1400, similar to method 1300 of FIG. 13, may further still include a step of preloading the cartridge with any one reaction material chosen from a group comprising reagent, buffer and probe to form a preloaded cartridge and to facilitate detection of the analyte. As explained in connection with FIG. 13, after the step of preloading, a step of lyophilizing may be carried out. The steps of preloading and lyophilizing are, preferably, carried out prior to the step of collecting.

[0170] Method 1400 may also involve detecting the analyte. To this end, method 1400 may perform a step 1418 of energizing, using an energy source (e.g., a battery installed inside device 100 shown in FIG. 1), non-linearly arranged, multiple excitation light sources (e.g., light sources 1182 shown in FIG. 11A) to generate multiple incident light beams. Next, a step 1420 includes transmitting each of the multiple incident light beams through a corresponding one of the multiple reaction wells (e.g., reaction wells 1137 shown in FIG. 11A) to generate multiple emission light beams. Then, a step 1422 includes detecting, using multiple photodetectors (e.g., photodetectors 1186 of FIG. 11A) energized using the energy source, each of the multiple emitted light beams at a corresponding one of the multiple photodetectors. In this step, each of the multiple excitation light sources corresponds to one of the multiple incident light beams, one of the multiple reaction wells, one of the multiple emission light beams, and one of the multiple photodetectors. In one embodiment of the present teachings, energizing step 1418 does not energize a cooling mechanism on device 100 of FIG. 1 to effect isothermal reactions either in the lysing chamber or in the reaction chamber.

[0171] The step of detection may be in carried out according many different implementations. In one implementation of the present teachings, the detecting step includes detecting an emission signal generated by a probe. By way of example, the step of detecting an emission signal includes translating the emission signal, using an algorithm, to produce a result that is displayed at a user interface (e.g., user interface 211 shown in FIG. 2). As another example, the step of detecting the emission signal includes detecting a signature that is at least one member selected from a group comprising optical signature, electrochemical signature, magnetic signature, and mechanical signature.

[0172] The step of detecting may include detecting presence of the analyte in a biomolecule sample. In this embodiment, the above-mentioned step of the obtaining includes collecting a sample from of at least one member chosen from a group comprising virus, microbe, bacteria, water, food, beverage, soil, plant, oil, animal tissue, animal byproduct, air, filter of air or water, and item that has contacted food.

[0173] FIG. 15 shows a flowchart for a method of collecting target analyte data 1500, according to one embodiment of the present teachings. Method 1500, preferably, begins with a step 1502 that includes energizing, using an energy source, a reaction heating block, a lysing heating block, multiple excitation light sources and multiple photodetectors. Then, a step 1504 includes introducing a sample containing a target analyte inside a lysing chamber (which includes the lysing heating block).

[0174] Method 1500 then proceeds to a step 1506, which includes lysing, using the lysing heating blocked disposed inside the lysing chamber, the sample to produce a lysed sample. By way of example, lysing heating block 425 shown in FIG. 4A includes a receiving surface (which is designed to receive lysing tube 404 shown in FIG. 4A) having a shape that conforms to the shape of the outer surface of lysing tube 104. As a result, the lysing heating block effectively lyses the sample to produce a lysed sample.

[0175] Next, a step 1508 includes thermally activating, using the reaction heating block disposed inside a reaction chamber (e.g., circular shaped reaction heating block 964 shown in FIGS. 9A and 9B and reaction heating block 1064 shown in FIG. 10A), the lysed sample to produce a detectable sample in which the target analyte is rendered detectable. After thermal activation is performed to obtain a detectable sample, a step 1510 is performed. Step 1510 includes detecting, using the multiple excitation light sources and the multiple photodetectors disposed inside the reaction chamber, the detectable sample to determine presence and/or a characteristic of the target analyte in the sample.

[0176] Method 1500 may further include a step of transferring the lysed sample to the reaction chamber containing the reaction heating block. The steps of lysing and/or the thermally activating, preferably, include applying one or more different types of energy that is chosen from a group comprising thermal energy, mechanical energy, magnetic energy, electric energy, acoustic energy, radiation energy, and fluidic energy. The step of detecting includes detecting an optical signal generated by a probe and determines an amount of the target analyte present in the sample.

[0177] The systems and methods of the present arrangements and teachings recognize the need for sample testing that may be carried in the field by non-experts in a manner that provides quick and accurate results, and in particular, determining presence and/or characteristics of one or more target analytes in a sample. By way of example, such sample testing may include but is not limited to, quantitative PCR analysis of target DNA in biosamples for purposes of species identification. The systems and methods of the present teachings, however, are not intended to be limited to biosamples testing, nor are they confined to amplification reactions or isothermal reactions, and instead contemplate testing of any sample containing one or more target analytes that are capable of being tested according to the systems and arrangements of the present inventions, using any method known to those of skill in the art. By way of non-limiting example, a sample to be tested for the presence and/or characteristics of one or more target analytes according to the systems and methods of the present inventions may include a food, a beverage, a soil sample, a plant sample, an oil sample, a sample of animal tissue, a sample from an animal byproduct, an air sample, a sample from a filter of air or water, a virus sample, a microbe sample, a bacteria sample, and a water sample, an oil sample, a dairy sample, a wine sample, or a sample that has contacted food, beverages, water, plants, or animals.

[0178] Likewise, such diagnostic testing using the devices of the present invention may include, but are not limited to, heavy metal testing, immunoassays and enzyme linked immunosorbent assays, hormone tests, lipid panels, and antibiotic tests. Unlike conventional systems, which carry out such testing in laboratory settings, the present inventions relate to systems and methods that allow for carrying out such testing in the field, via a single, hand-held device that integrates a sample preparation chamber and a reaction/detection chamber and that includes components (e.g., a user interface and computer) that serve to facilitate ease of use by a non-user. Further, the systems and methods of the present teachings implement a novel system that provides for closed-feedback control of temperature in the sample-preparation chamber and/or the reaction/detection chamber.

[0179] It is also noteworthy that because certain reactions in a lysing chamber and/or a reaction may be automated via connection of each chamber to various components, such as a heater (e.g., a resistive heater), a cooler (e.g., a thermoelectric cooler), a temperature sensor, a computer, and/or user interface, a non-expert user in the field may carry out these steps so long as the user is capable of simply collecting and/or introducing a collected sample into the system, and transferring a treated or processed sample from a sample-processing (e.g., lysing) chamber to a reaction. Such features facilitate ease of use such that a non-expert end-user may practice the present teachings and produce results in the field.

[0180] Although illustrative embodiments of the present arrangements and teachings have been shown and described, other modifications, changes, and substitutions are intended. Accordingly, it is appropriate that the appended claims be construed broadly and in a manner consistent with the scope of the disclosure, as set forth in the following claims.