Patent Publication Number: US-9410115-B2

Title: Portable sample disruptor apparatus, kits, and methods

Description:
CROSS-REFERENCE TO RELATED APPLICATIONS 
     This application is a continuation of U.S. application Ser. No. 13/419,178, filed Mar. 13, 2012, which claims priority to U.S. Provisional Patent Application No. 61/452,464, filed Mar. 14, 2011. The entire contents of each of the above-referenced applications are incorporated herein by reference in their entirety. 
    
    
     BACKGROUND 
     1. Field of the Invention 
     The present invention relates generally to sample disruption (e.g., for cell lysis). More particularly, but not by way of limitation, the present invention relates to portable or in-field sample disruption. 
     2. Background Information 
     Degradation and contamination of biological samples have been obstacles to scientific study, and may be particularly problematic in highly sensitive molecular-analysis techniques. For example, reliability of techniques such as single molecule sequencing and quantitative polymerase chain reaction (PCR) generally depends upon high-quality, unadulterated, biological samples. In a laboratory setting sterile equipment and careful technique can prevent contamination of samples. Likewise, cryogenic freezing and/or limiting exposure to high temperature may be utilized to attempt to maintain the integrity of samples. For collection of biological samples in the field, such as in forensics and environmental science, use of cryogenic freezing is generally too impractical to be employed. 
     SUMMARY 
     The present disclosure includes embodiments of apparatuses, kits, and methods. 
     Embodiments of the present apparatuses comprise: a body defining a chamber having a first end and a second end configured to permit a container (e.g., vial) to be inserted into the chamber, the body configured to be coupled to a device having a piston such that the volume of the chamber can be varied by reciprocating the piston between a retracted position and an extended position; and a cap configured to be coupled to the body such that the cap covers the second end of the chamber; where if the body is coupled to the device, the piston can be reciprocated to vibrate a container (e.g., vial) disposed in the chamber. 
     Some embodiments of the present apparatuses further comprise: a resilient member coupled to at least one of the cap and the body such that if a container (e.g., vial) is vibrated in the chamber, the resilient member is compressed when the piston is in the extended position. In some embodiments, the body comprises threads, and the cap comprises threads corresponding to the threads of the body for coupling the cap to the body. In some embodiments, the cap comprises a retractable protrusion biased in a bias direction that is toward at least a portion of the body when the cap is coupled to the body; the body comprises a plurality of indents; and the apparatus is configured such that if coupled to the body the cap is rotatable to adjust the length of the chamber between innermost and outermost positions of the cap at which the retractable protrusion of the cap will extend into one of the plurality of indents of the body to resist rotation of the cap relative to the body. In some embodiments, the cap includes a shoulder configured such that if a container (e.g., vial) is disposed in the chamber and the cap is coupled to the body, the shoulder will limit lateral movement of the container (e.g., vial). In some embodiments, the cap includes one or more openings configured to permit fluid communication through the cap if the cap is coupled to the body. 
     In some embodiments, the body is configured to fit within a rectangular volume of 12 cubic inches. In some embodiments, the body and cap are configured to be coupled together such that the body and cap fit within a rectangular volume of 16 cubic inches. Some embodiments of the present apparatuses further comprise a device having a piston; where the body is coupled to the such that the volume of the chamber can be varied by reciprocating the piston between a retracted position and an extended position. In some embodiments, the device is battery powered. In some embodiments, the device is an auto-hammer. 
     Some embodiments of the present kits comprise; an embodiment of the present apparatuses, and a battery charger. Some embodiments further comprise: one or more containers (e.g., vials) each sized to be vibrated in the chamber of the body. Some embodiments further comprise: at least one component selected from the group consisting of: earplugs, lysis beads, lysis solutions, an instruction manual, and a battery. 
     Some embodiments of the present methods comprise: providing an embodiment of the present apparatuses (e.g., comprising a body and a cap, the body defining a chamber having a first end and a second end, and the cap configured to be coupled to the body such that the cap covers the second end of the chamber); and coupling the body to a device having a piston (e.g., such that: the volume of the chamber can be varied by reciprocating the piston between a retracted position and an extended position; and/or the piston can be reciprocated to vibrate a container (e.g., vial) disposed in the chamber). 
     Some embodiments of the present methods comprise: providing an embodiment of the present apparatuses (comprising a body and a cap, the body defining a chamber having a first end and a second end, and the cap configured to be coupled to the body such that the cap covers the second end of the chamber, where the body is coupled to a device having a piston such that the volume of the chamber can be varied by reciprocating the piston between a retracted position and an extended position); disposing a container (e.g., vial) in the chamber; coupling the cap to the body; and activating the device to vibrate the container (e.g., vial). In some embodiments, the device is held such that the cap is above at least a portion of the device while the device is activated. In some embodiments, the container (e.g., vial) includes a body portion and a lid portion, and the container (e.g., vial) is disposed in the chamber such that at least part of the lid portion of the container (e.g., vial) is disposed between the cap and the body portion of the container (e.g., vial). In some embodiments, the device is activated for at least 30 seconds. Some embodiments further comprise: disposing a sample in the vial prior to disposing the vial in the chamber. 
     Some embodiments of the present methods comprise: mechanically disrupting a cell sample disposed in a container such that nucleic acid is released from cells in the sample; where mechanically disrupting includes activating a battery-powered device of an apparatus (e.g., one of the present apparatuses) to cause reciprocation of a piston to vibrate the container. 
     In some embodiments of the present methods, the container contains a sample (e.g., a cell sample). In some embodiments, the container contains a plurality of beads. In some embodiments, the beads comprise ceramic. In some embodiments, the container contains a lysis solution. In some embodiments, the lysis solution comprises an organic lysis solution. In some embodiments, the sample (e.g., cell sample) comprises soil, fecal matter, or biological tissue. In some embodiments, the container comprises a storage tube. 
     In any embodiment of the present disclosure, the term “substantially” may be substituted with “within [a percentage] of” what is specified, where the percentage includes 5, 10, and/or 15 percent. 
     Any embodiment of any of the present systems and/or methods can consist of or consist essentially of—rather than comprise/include/contain/have—any of the described steps, elements, and/or features. Thus, in any of the claims, the term “consisting of” or “consisting essentially of” can be substituted for any of the open-ended linking verbs recited above, in order to change the scope of a given claim from what it would otherwise be using the open-ended linking verb. 
     Details associated with the embodiments described above and others are presented below. 
    
    
     
       BRIEF DESCRIPTION OF THE DRAWINGS 
       The following drawings illustrate by way of example and not limitation. For the sake of brevity and clarity, every feature of a given structure is not always labeled in every figure in which that structure appears. Identical reference numbers do not necessarily indicate an identical structure. Rather, the same reference number may be used to indicate a similar feature or a feature with similar functionality, as may non-identical reference numbers. 
         FIG. 1  depicts is a perspective view of one of the present portable sample-disruption apparatuses coupled to an auto-hammer. 
         FIG. 2  depicts a perspective view of a body of the apparatus of  FIG. 1 . 
         FIG. 3  depicts a perspective view of the cap of the apparatus of  FIG. 1 . 
         FIG. 4  depicts an enlarged perspective view of the cap of  FIG. 3  coupled to the body of  FIG. 2 . 
         FIG. 5  depicts a perspective exploded view of the apparatus of  FIG. 1 . 
         FIG. 6  depicts an enlarged perspective view of a portion of the auto-hammer of  FIG. 1 . 
         FIGS. 7A-7D  depict various enlarged views of the apparatus of  FIG. 1 . 
         FIG. 8  depicts a perspective view of one of the present kits. 
         FIG. 9  depicts various dimensioned views of one embodiment of the body of  FIG. 2 . 
         FIG. 10  depicts various dimensioned views of one embodiment of the cap of  FIG. 3 . 
     
    
    
     DESCRIPTION OF ILLUSTRATIVE EMBODIMENTS 
     The term “coupled” is defined as connected, although not necessarily directly, and not necessarily mechanically; two items that are “coupled” may be integral with each other. The terms “a” and “an” are defined as one or more unless this disclosure explicitly requires otherwise. The terms “substantially,” “approximately,” and “about” are defined as largely but not necessarily wholly what is specified, as understood by a person of ordinary skill in the art. 
     The terms “comprise” (and any form of comprise, such as “comprises” and “comprising”), “have” (and any form of have, such as “has” and “having”), “include” (and any form of include, such as “includes” and “including”) and “contain” (and any form of contain, such as “contains” and “containing”) are open-ended linking verbs. As a result, a method that “comprises,” “has,” “includes” or “contains” one or more steps possesses those one or more steps, but is not limited to possessing only those one or more steps. Likewise, a watering system that “comprises,” “has,” “includes” or “contains” one or more elements possesses those one or more elements, but is not limited to possessing only those elements. For example, in a watering system that comprises one or more surfaces and a platform, the watering system includes the specified elements but is not limited to having only those elements. For example, such a watering system could also include a drainage structure. 
     Further, a device or structure that is configured in a certain way is configured in at least that way, but it can also be configured in other ways than those specifically described. 
     At least some embodiments of the present apparatuses, kits, and methods relate to portable apparatuses (e.g., battery-powered and/or compact apparatuses) for disrupting cell samples (e.g., for cell lysis). Samples obtained in the field may be difficult to transport to a lab for analysis in such a way that degradation of the sample is prevented or reduced. At least some embodiments of the present apparatuses, kits, and methods permit (i) rapid processing of a sample into a stabilizing buffer that can prevent or reduce sample degradation; (ii) rapid processing in a way that avoids or reduces the likelihood of contamination (which is generally difficult to achieve outside of the laboratory setting); and/or (iii) rapid processing with an apparatus that is easily transportable and efficient to operate in the field. 
     Referring now to the drawings, and more particularly to  FIGS. 1-10 , shown therein and designated by the reference numeral  10  is one embodiment of the present portable sample-disruption apparatuses. In the embodiment shown, apparatus  10  comprises a body  14 , and a cap  18  configured to be coupled to body  14 . Body  14  and/or cap  18  may comprise any suitable material, such as, for example, one or more polymers (e.g., polyamide (also known as NYLON), polyoxymethylene (POM) (also known as acetal or DELRIN), acrylonitrile butadiene styrene (ABS), polyvinyl chloride (PVC)), and/or one or more metals (e.g., aluminum, stainless steel, titanium, alloys, and the like). Body  14  and cap  18  may comprise the same material(s) and/or may comprise different materials. For example, in one embodiment, body  14  comprises polyoxymethylene or acetal, and cap  18  comprises ABS. 
     As also shown, body  14  is configured to be coupled to device  22  having a piston  26  configured to reciprocate between a retracted position (innermost position in direction  30 ) and an extended position (outermost position in direction  34 ). Device  22  may, for example, be an auto-hammer (e.g., such as is available from Sears Brands LLC under the CRAFTSMAN brand, U.S.A. under the name “Craftsman 11818 Nextec 12-volt Lithium-Ion Cordless Hammerhead Auto Hammer”). In the embodiment shown, device  22  is battery powered, and comprises a removable battery (e.g., battery pack)  38 . In other embodiments, battery pack  38  may not be removable. In the embodiment shown, device  22  also includes a trigger  42  configured to be depressed to activate device  22  and thereby reciprocate piston  26 . In the embodiment shown, device  22  is configured such that activation of device  22  will not translate to reciprocation of piston  26  unless some force is applied to piston  22  in direction  30  (e.g., to engage the piston with the internal drive mechanism (not shown) of device  22  to cause the piston to be drive in direction  34  and/or direction  30 ). In other embodiments, piston  26  may reciprocate whenever device  22  is activated (e.g., regardless of whether pressure is applied to piston  26  in direction  30 ). As used in this disclosure, “reciprocate” includes alternating motion of piston  26  in directions  30  and  34 , and does not require that the piston is driven in both directions (e.g., the piston may be driven in direction  34  and simply recoil in direction  30 ), nor that the piston travels at the same speed in both of directions  30  and  34  (e.g., in a sinusoidal fashion). 
     In the embodiment shown, apparatus  10  is configured as a portable, hand-held device, that can be used for vigorous cell disruption outside of a laboratory setting (e.g., in remote locations and in various weather conditions). For example, apparatus  10  can be used as described in more detail below to disrupt cells in and/or from samples (e.g., of yeast, bacteria, plant, soil, fecal, animal tissue, and the like). Likewise, in the embodiment shown, apparatus  10  is configured for use in nearly any location (e.g., if battery  38  is sufficiently charged), and in various weather conditions, for rapid processing of sample collections (e.g., to preserve and improve stability of processed samples). In the embodiment shown, apparatus  10  is configured to receive a container  46  (e.g., a  2 -milliliter (mL) vial or “tube”) within body  14  for disruption of a sample disposed in the container, as described in more detail below. Containers such as 2-mL vials are known, and are available with “skirted” or pointed bottoms. In some embodiments of the present apparatuses and methods, vials with skirted bottoms are used or included. In some embodiments, the container comprises a storage tube. In the embodiment shown, trigger  42  can be depressed for any desired length of time for disruption of a sample, permitting customization and individual control over the duration of sample disruption. In some embodiments, device  22  includes a timer (e.g., a timer circuit) configured to enable activation of device  22  for pre-set durations (e.g., 30, 45, 60, 90, 120, and/or 180 seconds). 
     In the embodiment shown, body  14  defines a chamber  100  having a first end  104  and a second end  108 . In the embodiment shown, second end  108  of chamber  100  is configured to permit a vial  46  to be inserted into chamber  100 . Body  14  is configured to be coupled to (and is shown coupled to) device  22 . For example, in the embodiment shown, device  22  includes a coupling portion  50  to which body  14  is configured to correspond and be coupled (e.g., via screws  112 ). In the embodiment shown, body  14  includes flange portions  116  extending from opposite lateral sides of the body, and including holes  120  positioned to align with matching holes in attachment portion  50  of device  22 . Other embodiments may include only a single flange portion (e.g., extending around the entire perimeter of the body). In the embodiment shown, screws  112  comprise machine screws with 10-32 threads having a length of approximately 0.75 inches, such as, for example, machine screws configured to be driven by an Allen or star wrench or bit. Other embodiments may include any suitable fasteners that couple body  14  to device  22  such that apparatus  10  can function as described in this disclosure. In the embodiment shown, cap  18  is configured to be coupled to body  14  such that cap  18  covers second end  108  of chamber  100 . Apparatus  10  is configured such that, if body  14  is coupled to device  22 , as shown, piston  26  can be reciprocated (e.g., by depressing trigger  42 ) to vibrate a vial  46  that is disposed in chamber  100  (e.g., with cap  18  coupled to body  14  to cover second end  108  and retain the vial in the chamber). 
     In the embodiment shown, body  14  comprises threads  124 , and cap  18  comprises threads  128  corresponding to threads  124  for coupling the cap to the body. In the embodiment shown, cap  18  is configured such that if coupled to body  14 , cap  18  is rotatable to adjust the distance between piston  26  and cap  18  (e.g., to accommodate vials of different lengths). In the embodiment shown, cap comprises a retractable protrusion  132  biased in a bias direction  136  (that is toward at least a portion of body and/or first end  104  of cavity  100 ) when the cap is coupled to the body. Retractable protrusion  132  need not be entirely retractable (e.g., may not be capable of retracting below bottom surface  140  of cap  18 ) and/or may be entirely retractable (e.g., may be capable of retracting below bottom surface  140 ). In the embodiment shown, bias direction  136  is substantially parallel to the central longitudinal axis of cavity  100 . In other embodiments, bias direction may be non-parallel to the central longitudinal axis of cavity  100 . In the embodiment shown, retractable protrusion  132  comprises a ball catch in which a ball is biased in bias direction  136  by a spring (not shown), such that the ball catch extends beyond surface  140  in the absence of a force compressing the biasing spring. 
     In the embodiment shown, body  14  comprises a plurality of indents  144 . More particularly, in the embodiment shown, body  14  includes a flange  148  around at least a portion of a perimeter of the body, and indents  144  are disposed on flange  148  at equiangular intervals around the body. In this embodiment, apparatus  10  is configured such that if coupled to body  14 , cap  18  is rotatable to adjust the length of the chamber between innermost and outermost positions of the cap at which retractable protrusion  132  will extend into one of indents  144  to resist rotation of the cap relative to the body. For example, the outermost position of the cap is the position of the cap at which the portion of protrusion  132  extending into one of the indents  144  is sufficient to resist rotation of the cap relative to the body, and the innermost position of the cap is the position at which the cap is prevented (e.g., by surface  140  and flange  148 , protrusion  132  and flange  148 , and/or by a vial  46  in cavity  100 ) from being rotated or any closer to the body (e.g., flange  148 ). 
     In the embodiment shown, cap  18  includes a shoulder  152  (in the interior of the cap) configured such that if a vial  46  is disposed in chamber  100  and cap  18  is coupled to body  14 , shoulder  152  will limit lateral movement of the vial (e.g., will maintain sufficient alignment between the vial and piston  26 ). Similarly, in the embodiment shown, device  3  includes a shoulder  156  (that extends around and beyond piston  26 ) configured such that if a vial  46  is disposed in chamber  100  and cap  18  is coupled to body  14 , shoulder  152  will limit lateral movement of the vial (e.g., will maintain sufficient alignment between the vial and piston  26 ). In other embodiments, shoulder  156  may be included in body  100  (e.g., may be defined by body  14 ), such as, for example, between first end  104  and second end  108  of cavity  100  (e.g., at or near first end  104 ). As shown, shoulder  152  defines a central portion  160  within the perimeter of shoulder  152 . The distance between central portion  160  and bottom surface  140  is greater than the distance between shoulder  152  and bottom surface  140 , such that in use, a vial  46  extends within the perimeter of shoulder  152 . 
     In the embodiment shown, cap  18  also includes one or more openings  164  configured to permit fluid communication through the cap if the cap is coupled to the body. For example, as noted above, reciprocation of piston  26  varies the volume of chamber  100  such that when the piston is extended, the pressure in chamber  100  could increase beyond an acceptable level. Openings  164  are configured to permit pressure in the chamber to equalize to pressure outside the chamber. In the embodiment shown, cap  18  includes a central opening  164  in central portion  160  (within the perimeter of shoulder  152 ), and four peripheral openings outside the perimeter of shoulder  152 . Other embodiments may include openings  164  in any suitable number or configuration. 
     In the embodiment shown, apparatus  10  further comprises a resilient member  168  coupled to at least one of cap  18  and body  14  such that if a vial  46  is vibrated in chamber  100  (with cap  18  coupled to body  14 ), resilient member  168  is compressed when piston  26  is in the extended position. For example, in the embodiment shown, resilient member  168  comprises a resilient washer (e.g., comprising rubber, polyurethane, or any other suitably resilient material) disposed in central portion  160 . In some embodiments, resilient member  168  is a rubber washer having an outer diameter of ½ inch, an inner diameter of 3/16 inch, and an uncompressed (relaxed) thickness of 1/16 inch. 
     As noted above, in the embodiment shown, apparatus  10  is configured to be portable and compact. For example, in the embodiment shown, body  14  is configured to fit within a rectangular volume of 12 cubic inches (e.g., a rectangular box with dimensions of 2 inches by 2 inches by 3 inches), or smaller (e.g., 10 cubic inches, 8 cubic inches, or less). By way of another example, in the embodiment shown, body  14  and cap  18  are configured to be coupled together such that body  14  and cap  18  fit within a rectangular volume of 16 cubic inches, or smaller (e.g., 12 cubic inches, 10 cubic inches, or less). 
     Some embodiments of the present methods comprise: coupling one of the present apparatuses (e.g.,  10 , comprising body  14  and cap  18 , the body defining a chamber having a first end and a second end, and the cap configured to be coupled to the body such that the cap covers the second end of the chamber) to a device (e.g.,  22 ) having a piston (e.g.,  26 ), such that the volume of the chamber (e.g.,  100 ) can be varied by reciprocating the piston between a retracted position and an extended position; and the piston can be reciprocated to vibrate a vial disposed in the chamber. For example, in one embodiment, a device  22  is modified by creating or enlarging holes in connection portion  50  (to correspond to holes  120  and screws  112 ). Holes that are created or enlarged in device  22  may be pre-threaded, or may be threaded by insertion of screws  112  (e.g., if screws  112  are self-tapping). 
     Some embodiments of the present methods comprise: mechanically disrupting a cell sample disposed in a container (e.g.,  46 ) such that nucleic acid is released from cells in the sample; where mechanically disrupting includes activating a battery-powered device (e.g.,  22 ) of an apparatus (e.g.,  10 ) to cause reciprocation of a piston (e.g.,  26 ) to vibrate the container. 
     Some embodiments of the present methods comprise: providing an embodiment of the present apparatuses (e.g.,  10 , with body  14  coupled to a device such as, for example, device  22 ); disposing a vial (e.g.,  46 ) in the chamber of the apparatus; coupling the cap (e.g.,  18 ) to the body (e.g.,  14 ); and activating the device (e.g.,  22 ) to vibrate the vial. In some embodiments, the device (and/or the apparatus) is held such that the cap (e.g.,  18 ) is above at least a portion of the device while the device is activated. For example, the device can be held such that the body and cap are oriented vertically with the cap above the body (and such that the vial in the chamber is also oriented vertically). As illustrated, vials  46  each can include a body portion  212  and a lid portion  216 . In some embodiments of the present methods, the vial is disposed in chamber  100  such that at least part of lid portion  216  of the vial is disposed between the cap and the body portion of the vial (e.g., such that lid portion  216  is adjacent cap  18 , and/or within shoulder  152  in central portion  160  of the cap). 
     In some embodiments of the present methods, the vial can contain: a sample (e.g. a soil sample), a plurality of beads (e.g., lysis beads), and/or a lysis solution (e.g., an organic lysis solution). In some embodiments of the present methods, the device is activated for at least 30 seconds (e.g., any of the durations mentioned above). Some embodiments of the present methods comprise disposing a sample in the vial prior to disposing the vial in the chamber. For example, samples (e.g., cell samples) can comprise soil, fecal matter, or biological tissue (fungal/bacterial, tissue &amp; insect, plant/seed, and the like). Various test kits for DNA and RNA testing and sample preparation from Zymo Research Corporation. 
       FIG. 10  depicts on embodiment of the present kits  200 . In the embodiment shown, kit  200  comprises an apparatus  10  with device  2 , and a battery charger  204  configured to charge battery  38 . In some embodiments, the present kits may also comprise one or more (e.g., two) vials  46 , each sized to be vibrated in chamber  100  of body  14 . In some embodiments, kit  200  further comprises at least one component selected from the group consisting of: earplugs (not shown), lysis beads and/or lysis solutions (e.g., lysis solutions and/or ceramic lysis beads, such as, for example, those available from Zymo Research Corporation, California, U.S.A.), an instruction manual, and a battery  38  (e.g., an extra or second battery). In some embodiments, kit  200  can also include a converters  208  configured to convert available power (e.g., AC power) in various locations (e.g., international locations with varying standards for power delivery). In some embodiments, vials  46  may contain lysis beads (not shown), such as, for example, a plurality of 2 millimeter beads and/or a plurality of 0.5 millimeter beads (e.g., 5 2 mm beads and 5-0.5 mm beads). 
     The various illustrative embodiments of devices, systems, and methods described herein are not intended to be limited to the particular forms disclosed. Rather, they include all modifications and alternatives falling within the scope of the claims. For example, the caps of the present apparatuses can be configured to be coupled to the bodies of the present apparatuses by any suitable structure (e.g., interlocking tabs and grooves). 
     The claims are not intended to include, and should not be interpreted to include, means-plus- or step-plus-function limitations, unless such a limitation is explicitly recited in a given claim using the phrase(s) “means for” or “step for,” respectively.