U.S. patent application number 14/047436 was filed with the patent office on 2014-10-16 for mixing cartridges, mixing stations, and related kits, systems, and methods.
This patent application is currently assigned to IBIS BIOSCIENCES, INC.. The applicant listed for this patent is Rex O. Bare, Jared J. Drader, Jose R. Gutierrez, Steven A. Hofstadler, Robert D. Miller, Jeffrey C. Smith. Invention is credited to Rex O. Bare, Jared J. Drader, Jose R. Gutierrez, Steven A. Hofstadler, Robert D. Miller, Jeffrey C. Smith.
Application Number | 20140307520 14/047436 |
Document ID | / |
Family ID | 41508816 |
Filed Date | 2014-10-16 |
United States Patent
Application |
20140307520 |
Kind Code |
A1 |
Hofstadler; Steven A. ; et
al. |
October 16, 2014 |
MIXING CARTRIDGES, MIXING STATIONS, AND RELATED KITS, SYSTEMS, AND
METHODS
Abstract
Cartridges useful for mixing materials, such as fluidic
materials are provided. A cartridge typically includes a body
structure having surfaces that define a cavity with upper and lower
portions. A rotatable member generally extends along a horizontal
axis in the upper portion of the cavity. One or more protrusions
typically extend outward from the rotatable member and into the
lower portion of the cavity, and are configured to mix the material
when the material is disposed in the cavity. Related mixing
stations, systems, kits, and methods are also provided.
Inventors: |
Hofstadler; Steven A.;
(Vista, CA) ; Drader; Jared J.; (San Marcos,
CA) ; Gutierrez; Jose R.; (San Marcos, CA) ;
Bare; Rex O.; (Preston, CT) ; Miller; Robert D.;
(Costa Mesa, CA) ; Smith; Jeffrey C.; (Irvine,
CA) |
|
Applicant: |
Name |
City |
State |
Country |
Type |
Hofstadler; Steven A.
Drader; Jared J.
Gutierrez; Jose R.
Bare; Rex O.
Miller; Robert D.
Smith; Jeffrey C. |
Vista
San Marcos
San Marcos
Preston
Costa Mesa
Irvine |
CA
CA
CA
CT
CA
CA |
US
US
US
US
US
US |
|
|
Assignee: |
IBIS BIOSCIENCES, INC.
Carlsbad
CA
|
Family ID: |
41508816 |
Appl. No.: |
14/047436 |
Filed: |
October 7, 2013 |
Related U.S. Patent Documents
|
|
|
|
|
|
Application
Number |
Filing Date |
Patent Number |
|
|
12560982 |
Sep 16, 2009 |
8550694 |
|
|
14047436 |
|
|
|
|
61097507 |
Sep 16, 2008 |
|
|
|
Current U.S.
Class: |
366/279 |
Current CPC
Class: |
B01F 15/00467 20130101;
C12Q 1/6806 20130101; B01F 11/0088 20130101; B01F 13/1022 20130101;
B01F 7/00291 20130101; B01F 15/0048 20130101; B01F 15/065 20130101;
B01F 13/08 20130101; B01F 7/004 20130101; B01F 15/00207 20130101;
B01F 2215/0032 20130101; B01F 2215/0037 20130101; B01F 13/002
20130101; B01F 7/04 20130101; B01F 2015/062 20130101; B01F 11/0091
20130101; B01F 7/00233 20130101; B01F 13/003 20130101; B01F
2015/00649 20130101; B01F 13/1013 20130101 |
Class at
Publication: |
366/279 |
International
Class: |
B01F 7/00 20060101
B01F007/00; C12Q 1/68 20060101 C12Q001/68 |
Claims
1. A cartridge for mixing material, comprising: at least one body
structure comprising one or more surfaces that define a cavity
having upper and lower portions; at least one rotatable member
extending at least partially along an axis that is substantially
horizontally disposed in the upper portion of the cavity, which
rotatable member is configured to operably connect to a rotational
mechanism; and at least one protrusion extending outward from the
rotatable member and into the lower portion of the cavity, which
protrusion is configured to mix the material when the material is
disposed in the cavity, the rotatable member is operably connected
to the rotational mechanism, and the rotational mechanism at least
partially rotates the rotatable member about the axis.
2-70. (canceled)
Description
CROSS REFERENCE TO RELATED APPLICATIONS
[0001] The present Application claims priority to U.S. Provisional
Application Ser. No. 61/097,507 filed Sep. 16, 2008, and U.S.
Provisional Application Ser. No. 61/097,520 filed Sep. 16, 2008,
both of which are herein incorporated by reference in their
entireties.
FIELD OF THE INVENTION
[0002] The invention relates generally to mixing materials, and
provides cartridges, mixing stations, systems, methods, and kits
useful for this purpose.
BACKGROUND OF THE INVENTION
[0003] Uniform mixtures of materials, often in the forms of
suspensions or emulsions, are used in a wide variety of
applications. In the life sciences, for example, homogeneous
suspensions of magnetically responsive particles are commonly used
as part of cell, polypeptide, and polynucleotide purification
protocols. In the case of high-throughput nucleic acid
purification, numerous samples including genomic DNA or RNA, mRNA,
or amplification products are typically isolated or otherwise
purified in the wells of microplates or in other containers in
processes that involve the use of magnetic bead suspensions. Many
cell-based applications also utilize aliquots of uniform cell
density, for example, to screen vast compound libraries for
pharmaceutical candidates. Homogeneous mixtures of reagents are
also used in numerous biological and non-biological processes, such
as in nucleic acid amplification reactions, cell culturing
procedures, and inorganic chemical synthetic schemes, among many
others. Uniformly mixed materials are also used in a variety of
other contexts as well.
SUMMARY OF THE INVENTION
[0004] The present invention provides cartridges that are useful in
mixing materials, including fluidic materials. Typically, the
fluidic materials include particles, such as magnetically
responsive beads, cells, solid supports, or the like, which are
maintained in suspension using the cartridges described herein. In
some embodiments, the cartridges are consumable or disposable
components of mixing stations. Optionally, fluid mixing stations
are included as components of systems. To illustrate, in certain
embodiments, the cartridges described herein are used to maintain
substantially homogenous mixtures including magnetically responsive
beads, which are utilized in systems that perform nucleic acid
purification and detection. In addition, the invention also
provides related kits and methods.
[0005] In one aspect, the invention provides a cartridge for mixing
material (e.g., fluidic material, etc.). The cartridge includes at
least one body structure comprising one or more surfaces that
define a cavity having upper and lower portions. The cartridge also
includes at least one rotatable member extending at least partially
along an axis that is substantially horizontally disposed in the
upper portion of the cavity. The rotatable member is configured to
operably connect to a rotational mechanism. In addition, the
cartridge also includes at least one protrusion extending outward
from the rotatable member and into the lower portion of the cavity.
The protrusion is configured to mix the material when the material
is disposed in the cavity, the rotatable member is operably
connected to the rotational mechanism, and the rotational mechanism
at least partially rotates the rotatable member about the axis.
[0006] The cartridges described herein include various embodiments.
In certain embodiments, for example, cartridges are included as
components of the mixing stations, kits, and/or systems described
herein.
[0007] Typically, the cavity lacks substantial dead zones, e.g.,
areas where particles tend to fall out of suspension. In some
embodiments, the upper portion of the cavity comprises at least one
hole or indentation that receives at least a section of the
rotatable member. In certain embodiments, the cavity comprises a
volume capacity of about 500 mL or less.
[0008] In some embodiments, the body structures of the cartridges
of the invention comprise one or more dimensions selected from,
e.g., a height of about 10 cm or less, a width of about 15 cm or
less, and a length of about 20 cm or less. In certain embodiments,
the body structure comprises a weight of about 1 kg or less.
Typically, the body structure is dimensioned to be handheld. Also,
in some embodiments, the body structure, the rotatable member, the
protrusion, or any combination thereof are disposable. In certain
embodiments, the body structure comprises at least one alignment
feature configured to align the cartridge relative to a cartridge
support structure of a cartridge receiver/rotation assembly, when
the cartridge is positioned on the cartridge support structure of
the cartridge receiver/rotation assembly. In addition, in some
embodiments, the body structure comprises at least one retention
component configured to engage at least one retention mechanism of
a cartridge receiver/rotation assembly, when the cartridge is
positioned on a cartridge support structure of the cartridge
receiver/rotation assembly.
[0009] The rotatable members of the cartridges described herein are
typically configured to rotate about 180 degrees or less within the
cavities of the cartridges. In some embodiments, rotatable members
are configured to operably connect to the rotational mechanism via
a substantially vertically disposed side surface of the body
structure. To further illustrate, the rotatable member optionally
comprises at least a first magnetic coupler that is configured to
interact with at least a second magnetic coupler of the rotational
mechanism to effect rotation of the rotatable member when the first
and second magnetic couplers are within magnetic communication with
one another and the rotational mechanism effects rotation of the
second magnetic coupler.
[0010] In some embodiments, the protrusion of the cartridges
described herein comprises at least one paddle or at least on
blade. Optionally, the protrusion is fabricated integral with the
rotatable member. Typically, the rotatable member comprises a
plurality of protrusions.
[0011] In some embodiments, the cavity is fully enclosed within the
body structure. In some of these embodiments, an aperture is
disposed through a top surface of the body structure. The aperture
is generally configured to receive a fluid handling component that
fluidly communicates with the cavity. Typically, the aperture is
disposed through the top surface of the body structure relative to
the rotatable member and to the protrusion such that the fluid
handling component does not contact the rotatable member or the
protrusion when the rotatable member rotates the protrusion and the
aperture receives the fluid handling component. In certain
embodiments, a closure is disposed in or over the aperture. In some
embodiments, the closure comprises a septum. In certain
embodiments, the closure is re-sealable. In some embodiments, a
fill port is disposed through a top surface of the body structure.
In some embodiments, a vent port is disposed through a top surface
of the body structure.
[0012] In other embodiments, a top surface of the body structure
comprises an opening that communicates with the cavity. In some of
these embodiments, a sealing member is operably connected to the
body structure. The sealing member is generally structured to
substantially seal the opening. In some embodiments, the sealing
member comprises a removable cover that is structured to engage at
least one surface of the body structure. Optionally, the sealing
member comprises a film that overlays the opening on the top
surface of the body structure. In certain embodiments, the film
comprises a heat sealed film. Optionally, the film comprises an
adhesive. Typically, an aperture is disposed through the sealing
member. The aperture is generally configured to receive a fluid
handling component such that the fluid handling component can
fluidly communicate with the cavity. In some embodiments, the
aperture is disposed through the sealing member relative to the
rotatable member and to the protrusion such that the fluid handling
component does not contact the rotatable member or the protrusion
when the rotatable member rotates the protrusion and the aperture
receives the fluid handling component. In some embodiments, a
closure is disposed in or over the aperture. In certain
embodiments, the closure comprises a septum. In some embodiments,
the closure is re-sealable. In some embodiments, a fill port is
disposed through a sealing member. In some embodiments, a vent port
is disposed through a sealing member.
[0013] In certain embodiments, a fluidic material is disposed in
the cavity. In these embodiments, the fluidic material typically
comprises particles. To further illustrate, the particles are
optionally selected from, e.g., cells, biopolymers, and solid
supports. In some embodiments, the particles are maintained in
suspension within the fluidic material when the rotatable member is
operably connected to the rotational mechanism and the rotational
mechanism at least partially rotates the rotatable member about the
axis. Optionally, the particles comprise magnetically responsive
particles (e.g., magnetically responsive beads, etc.).
[0014] In some embodiments, at least a first surface of the body
structure is substantially symmetrical about the axis of the
cavity. In these embodiments, a distance between a lower portion of
the protrusion and the first surface of the cavity is typically
substantially identical at two or more positions about the axis of
the cavity. In some embodiments, the first surface of the cavity is
curved. For example, a radius of curvature of the first surface of
the cavity optionally varies along the length of the cavity. In
certain embodiments, a radius of curvature of the first surface of
the cavity is larger at a central portion of the cavity than the
radius of curvature near an end portion of the cavity.
[0015] In some embodiments, the rotatable member comprises a
proximal end which extends through a hole or an indentation in a
surface of the cavity. Typically, the proximal end is configured to
operably connect to the rotational mechanism. In certain
embodiments, at least one washer is disposed around the proximal
end of the rotatable member to seal the hole or indentation in the
surface of the cavity. In some embodiments, there is a projection
that extends outward from the rotatable member. The projection is
typically configured to activate a motion sensor when the motion
sensor is in sensory communication with the projection and the
rotatable member is rotated.
[0016] In certain embodiments, the protrusion comprises at least
one substantially vertically disposed segment that extends downward
from the rotatable member and at least one substantially laterally
disposed segment that extends outward from the substantially
vertically disposed segment. In some embodiments, the substantially
laterally disposed segment comprises an edge having a textured
surface that, for example, enhances the uniform mixing of materials
in a cartridge cavity relative to a protrusion lacking such an
edge.
[0017] In another aspect, the invention provides a mixing station
that includes at least one cartridge that comprises at least one
body structure comprising one or more surfaces that define a cavity
having upper and lower portions. The cartridge also comprises at
least one rotatable member extending at least partially along an
axis that is substantially horizontally disposed in the upper
portion of the cavity, and at least one protrusion extending
outward from the rotatable member and into the lower portion of the
cavity. In addition, the mixing station also includes a cartridge
receiver/rotation assembly that comprises at least one cartridge
support structure that supports the body structure of the
cartridge, and a rotational mechanism operably connected to the
rotatable member. In some embodiments, the mixing station includes
a thermal modulating component within thermal communication of the
cavity to modulate temperature of fluidic material when the fluidic
material is disposed in the cavity. Typically, the cartridge is
removable from the cartridge support structure. In some
embodiments, the body structure comprises at least one retention
component. In these embodiments, the cartridge receiver/rotation
assembly typically comprises at least one retention mechanism that
engages the retention component to retain the cartridge on the
cartridge support structure of the cartridge receiver/rotation
assembly. In certain embodiments, the rotatable member comprises at
least a first magnetic coupler. In these embodiments, the
rotational mechanism comprises at least a second magnetic coupler
that magnetically communicates with the first magnetic coupler to
effect rotation of the rotatable member when the rotational
mechanism rotates the second magnetic coupler. In some embodiments,
the rotational mechanism comprises a motor. Typically, the
rotational mechanism is mounted on the cartridge support structure.
In certain embodiments, the cartridge receiver/rotation assembly
comprises at least one controller operably connected at least to
the rotational mechanism. The controller is typically configured to
selectively direct the rotational mechanism to rotate the rotatable
member in an initiation mode or in a maintenance mode in which a
rate of rotation of the rotatable member is greater in the
initiation mode than in the maintenance mode.
[0018] In some embodiments, the cartridge receiver/rotation
assembly comprises a motion sensor that is configured to sense
motion of the rotatable member when the rotational mechanism
rotates the rotatable member. In these embodiments, a projection
typically extends outward from the rotatable member. The projection
is generally configured to activate the motion sensor when the
rotatable member is rotated.
[0019] In certain embodiments, the mixing station includes at least
one detection component in sensory communication with the cavity.
The detection component is typically configured to detect one or
more parameters of a fluidic material when the fluidic material is
disposed in the cavity. In some embodiments, for example, the
parameters are selected from, e.g., pH, temperature, pressure,
density, salinity, conductivity, fluid level, radioactivity,
luminescence, fluorescence, phosphorescence, and the like.
[0020] Optionally, the cartridge support structure comprises a
recessed region that receives at least part of the body structure.
In some embodiments, the recessed region comprises at least one
groove. In these embodiments, the body structure typically
comprises at least one alignment feature that is received within
the groove to align the cartridge relative to the cartridge support
structure of the cartridge receiver/rotation assembly.
[0021] In another aspect, the invention provides a kit that
includes at least one cartridge that comprises at least one body
structure comprising one or more surfaces that define a cavity
having upper and lower portions. The cartridge also includes at
least one rotatable member extending at least partially along an
axis that is substantially horizontally disposed in the upper
portion of the cavity. In addition, the cartridge further includes
at least one protrusion extending outward from the rotatable member
and into the lower portion of the cavity. The kit also includes at
least one fluidic material and/or at least one particle disposed in
the cavity and/or in at least one separate container. The kit
further includes instructions for mixing the fluidic material
and/or the particle in the cartridge and/or loading the fluidic
material and/or the particle into the cavity of the cartridge.
Typically, the kit also includes packaging for containing the
cartridge, the separate container, and/or the instructions. To
illustrate, the fluidic material generally includes water, a
buffer, a cell culture medium, or the like. In some embodiments,
the particle comprises at least one magnetically responsive
particle. In certain embodiments, the particle is a cell, a
biopolymer, a solid support, or the like.
[0022] In another aspect, the invention provides a system that
includes at least one mixing station that comprises a cartridge.
The cartridge includes at least one body structure comprising one
or more surfaces that define a cavity having upper and lower
portions. The cartridge also includes at least one rotatable member
extending at least partially along an axis disposed in the upper
portion of the cavity. In addition, the cartridge also includes at
least one protrusion extending outward from the rotatable member
and into the lower portion of the cavity. The mixing station also
includes at least one cartridge receiver/rotation assembly that
comprises at least one cartridge support structure that supports
the body structure of the cartridge, and a rotational mechanism
operably connected to the rotatable member. The system also
includes at least one additional system component selected from,
e.g., at least one nucleic acid amplification component, at least
one sample preparation component, at least one microplate handling
component, at least one material transfer component, at least one
sample processing component, at least one mass spectrometer, at
least one controller, at least one database, and/or the like.
[0023] In another aspect, the invention provides a method of mixing
a fluidic material. The method includes (a) providing a cartridge
that comprises at least one body structure comprising one or more
surfaces that define a cavity having upper and lower portions, at
least one rotatable member extending at least partially along an
axis that is substantially horizontally disposed in the upper
portion of the cavity, at least one protrusion extending outward
from the rotatable member and into the lower portion of the cavity,
and the fluidic material disposed in the cavity. The method also
includes (b) rotating the rotatable member to cause the protrusion
to agitate the fluidic material to thereby mix the fluidic
material. In some embodiments, (b) comprises rotating the rotatable
member back-and-forth about 180 degrees or less within the cavity.
Typically, the method includes adding and/or removing material to
and/or from the cavity. In some embodiments, one or more particles
are disposed within the fluidic material and (b) maintains the
particles in suspension within the fluidic material. In certain
embodiments, (b) includes (i) rotating the rotatable member in an
initiation mode to suspend the particles within the fluidic
material, and (ii) rotating the rotatable member in an maintenance
mode to maintain the particles in suspension within the fluidic
material in which a rate of rotation of the rotatable member is
greater in the initiation mode than in the maintenance mode.
[0024] In another aspect, the invention provides a method of
fabricating a cartridge. The method includes (a) forming at least
one body structure comprising one or more surfaces that define a
cavity having upper and lower portions and (b) forming at least one
rotatable member comprising at least one outwardly extending
protrusion, which rotatable member is configured to extend at least
partially along an axis that is substantially horizontally disposed
in the upper portion of the cavity. The method also includes (c)
coupling the rotatable member to the body structure such that the
protrusion extends into the lower portion of the cavity.
[0025] In another aspect, the invention provides a method that
includes (a) receiving an order from a customer for at least one
cartridge that comprises at least one body structure comprising one
or more surfaces that define a cavity having upper and lower
portions, at least one rotatable member extending at least
partially along an axis that is substantially horizontally disposed
in the upper portion of the cavity, and at least one protrusion
extending outward from the rotatable member and into the lower
portion of the cavity. The method also includes (b) supplying the
cartridge to the customer in response to the order. Optionally, (a)
comprises receiving the order via a personal appearance by the
customer or an agent thereof, via a postal or other delivery
service, via a telephonic communication, or via an email
communication or another electronic medium. In some embodiments,
(a) comprises receiving the order for a kit that comprises the
cartridge. In certain embodiments, (b) comprises supplying the
cartridge to the customer via a personal appearance by the customer
or an agent thereof, or via a postal or other delivery service.
BRIEF DESCRIPTION OF THE DRAWINGS
[0026] The description provided herein is better understood when
read in conjunction with the accompanying drawings which are
included by way of example and not by way of limitation. It will be
understood that like reference numerals identify like components
throughout the drawings, unless the context indicates otherwise. It
will also be understood that some or all of the figures may be
schematic representations for purposes of illustration and do not
necessarily depict the actual relative sizes or locations of the
elements shown.
[0027] FIG. 1A schematically illustrates a cartridge from a
perspective view according to one embodiment of the invention.
[0028] FIG. 1B schematically shows the cartridge of FIG. 1A from a
top view.
[0029] FIG. 1C schematically shows the cartridge of FIG. 1A further
including a sealing member from a perspective view.
[0030] FIG. 1D schematically illustrates the cartridge of FIG. 1C
from a top view.
[0031] FIG. 1E schematically depicts the cartridge of FIG. 1C from
a transparent top view.
[0032] FIG. 1F schematically shows the cartridge of FIG. 1C from a
bottom view.
[0033] FIG. 1G schematically illustrates the cartridge of FIG. 1C
from a transparent bottom view.
[0034] FIG. 1H schematically illustrates the cartridge of FIG. 1C
from a front elevation view.
[0035] FIG. 1I schematically depicts the cartridge of FIG. 1C from
a transparent front elevation view.
[0036] FIG. 1J schematically illustrates the cartridge of FIG. 1C
from a back elevation view.
[0037] FIG. 1K schematically shows the cartridge of FIG. 1C from a
transparent back elevation view.
[0038] FIG. 1L schematically illustrates the cartridge of FIG. 1C
from a side elevation view.
[0039] FIG. 1M schematically depicts the cartridge of FIG. 1C from
a transparent side elevation view.
[0040] FIG. 1N schematically shows the cartridge of FIG. 1C from a
cross-sectional side elevation view.
[0041] FIG. 2A schematically illustrates a cartridge from a
perspective view according to one embodiment of the invention.
[0042] FIG. 2B schematically shows the cartridge of FIG. 2A from a
top view.
[0043] FIG. 2C schematically shows components of the cartridge of
FIG. 2A from a partially exploded, cross-sectional side elevation
view.
[0044] FIG. 2D schematically depicts the cartridge of FIG. 2A from
a cross-sectional side elevation view.
[0045] FIG. 3A schematically shows the rotatable member and
protrusions from the cartridge of FIG. 1A from a perspective
view.
[0046] FIG. 3B schematically shows the rotatable member and
protrusions of FIG. 3A from a side elevation view.
[0047] FIG. 3C schematically illustrates the rotatable member and
protrusions of FIG. 3A from a front elevation view.
[0048] FIG. 3D schematically shows the rotatable member and
protrusions of FIG. 3A from a back elevation view.
[0049] FIG. 3E schematically shows the rotatable member of FIG. 3A
from a top view.
[0050] FIG. 3F schematically depicts the rotatable member and
protrusions of FIG. 3A from a bottom view.
[0051] FIG. 3G schematically shows the rotatable member and
protrusions of FIG. 3A with a projection attached to the rotatable
member from a perspective view.
[0052] FIG. 3H schematically illustrates the rotatable member and
protrusions of FIG. 3A disposed in a cartridge cavity from a
perspective view.
[0053] FIG. 4 schematically illustrates a cartridge having magnetic
coupler from a partially transparent bottom view according to one
embodiment of the invention.
[0054] FIG. 5A schematically illustrates a mixing station from a
perspective view according to one embodiment of the invention.
[0055] FIG. 5B schematically shows the mixing station of FIG. 5A
from a side elevation view.
[0056] FIG. 5C schematically depicts the mixing station of FIG. 5A
from a top view.
[0057] FIG. 6A schematically shows the cartridge receiver/rotation
assembly of the mixing station of FIG. 5A from a perspective
view.
[0058] FIG. 6B schematically depicts the cartridge
receiver/rotation assembly of the mixing station of FIG. 5A from a
top view.
[0059] FIG. 6C schematically illustrates the cartridge
receiver/rotation assembly of the mixing station of FIG. 5A from a
bottom view.
[0060] FIG. 6D schematically depicts the cartridge
receiver/rotation assembly of the mixing station of FIG. 5A from a
side elevation view.
[0061] FIG. 6E schematically illustrates the cartridge
receiver/rotation assembly of the mixing station of FIG. 5A from a
front view.
[0062] FIG. 6F schematically shows the cartridge receiver/rotation
assembly of the mixing station of FIG. 5A from a back view.
[0063] FIG. 7 schematically illustrates a cartridge
receiver/rotation assembly of a mixing station that includes a
thermal modulating component from a perspective view according to
one embodiment of the invention.
[0064] FIG. 8 is a block diagram showing a representative logic
device in which various aspects of the present invention may be
embodied.
[0065] FIG. 9A schematically illustrates selected components of a
representative system that includes a mixing station as a
sub-system component from a perspective view according to one
embodiment of the invention.
[0066] FIG. 9B schematically shows the representative system of
FIG. 9A from a front elevation view.
[0067] FIG. 9C schematically depicts the representative system of
FIG. 9A from a rear elevation view.
[0068] FIG. 9D schematically shows the representative system of
FIG. 9A from a side elevation view.
[0069] FIG. 9E schematically illustrates the representative system
of FIG. 9A from a top elevation view.
[0070] FIG. 9F schematically depicts the representative system of
FIG. 9A from a cross-sectional view.
[0071] FIG. 9G schematically illustrates the representative system
of FIG. 9A from a cross-sectional view.
[0072] FIGS. 10A and 10B schematically show additional components
of the representative system of FIG. 9A from a perspective
view.
[0073] FIG. 11A schematically illustrates the representative system
of FIG. 9A with an external covering from a perspective view.
[0074] FIG. 11B schematically illustrates the representative system
of FIG. 9A with an external covering from a front elevation
view.
[0075] FIG. 11C schematically shows the representative system of
FIG. 9A with an external covering from a side view.
DETAILED DESCRIPTION
[0076] I. Definitions
[0077] Before describing the invention in detail, it is to be
understood that this invention is not limited to particular
cartridges, mixing stations, systems, kits, or methods, which can
vary. As used in this specification and the appended claims, the
singular forms "a," "an," and "the" also include plural referents
unless the context clearly provides otherwise. Thus, for example,
reference to "a cartridge" includes a combination of two or more
cartridge. It is also to be understood that the terminology used
herein is for the purpose of describing particular embodiments
only, and is not intended to be limiting. Further, unless defined
otherwise, all technical and scientific terms used herein have the
same meaning as commonly understood by one of ordinary skill in the
art to which this invention pertains. In describing and claiming
the invention, the following terminology, and grammatical variants
thereof, will be used in accordance with the definitions set forth
below.
[0078] The term "amplifying" or "amplification" in the context of
nucleic acids refers to the production of multiple copies of a
polynucleotide, or a portion of the polynucleotide, typically
starting from a small amount of the polynucleotide (e.g., a single
polynucleotide molecule), where the amplification products or
amplicons are generally detectable. Amplification of
polynucleotides encompasses a variety of chemical and enzymatic
processes. The generation of multiple DNA copies from one or a few
copies of a target or template DNA molecule during a polymerase
chain reaction (PCR) or a ligase chain reaction (LCR) are forms of
amplification. Amplification is not limited to the strict
duplication of the starting molecule. For example, the generation
of multiple cDNA molecules from a limited amount of RNA in a sample
using reverse transcription (RT)-PCR is a form of amplification.
Furthermore, the generation of multiple RNA molecules from a single
DNA molecule during the process of transcription is also a form of
amplification.
[0079] The term "base composition" refers to the number of each
residue comprised in an amplicon or other nucleic acid, without
consideration for the linear arrangement of these residues in the
strand(s) of the amplicon. The amplicon residues comprise,
adenosine (A), guanosine (G), cytidine, (C), (deoxy)thymidine (T),
uracil (U), inosine (I), nitroindoles such as 5-nitroindole or
3-nitropyrrole, dP or dK (Hill F et al. (1998) "Polymerase
recognition of synthetic oligodeoxyribonucleotides incorporating
degenerate pyrimidine and purine bases" Proc Natl Acad Sci U.S.A.
95(8):4258-63), an acyclic nucleoside analog containing
5-nitroindazole (Van Aerschot et al., Nucleosides and Nucleotides,
1995, 14, 1053-1056), the purine analog
1-(2-deoxy-beta-D-ribofuranosyl)-imidazole-4-carboxamide,
2,6-diaminopurine, 5-propynyluracil, 5-propynylcytosine,
phenoxazines, including G-clamp, 5-propynyl deoxy-cytidine,
deoxy-thymidine nucleotides, 5-propynylcytidine, 5-propynyluridine
and mass tag modified versions thereof, including
7-deaza-2'-deoxyadenosine-5-triphosphate,
5-iodo-2'-deoxyuridine-5'-triphosphate,
5-bromo-2'-deoxyuridine-5'-triphosphate,
5-bromo-2'-deoxycytidine-5'-triphosphate,
5-iodo-2'-deoxycytidine-5'-triphosphate,
5-hydroxy-2'-deoxyuridine-5'-triphosphate,
4-thiothymidine-5'-triphosphate,
5-aza-2'-deoxyuridine-5'-triphosphate,
5-fluoro-2'-deoxyuridine-5'-triphosphate,
O.sup.6-methyl-2'-deoxyguanosine-5'-triphosphate,
N.sup.2-methyl-2'-deoxyguanosine-5'-triphosphate,
8-oxo-2'-deoxyguanosine-5'-triphosphate or
thiothymidine-5'-triphosphate. In some embodiments, the
mass-modified nucleobase comprises .sup.15N or .sup.13C or both
.sup.15N and .sup.13C. In some embodiments, the non-natural
nucleosides used herein include 5-propynyluracil,
5-propynylcytosine and inosine. Herein the base composition for an
unmodified DNA amplicon is notated as A.sub.wG.sub.xC.sub.yT.sub.z,
wherein w, x, y and z are each independently a whole number
representing the number of said nucleoside residues in an amplicon.
Base compositions for amplicons comprising modified nucleosides are
similarly notated to indicate the number of said natural and
modified nucleosides in an amplicon. Base compositions are
calculated from a molecular mass measurement of an amplicon, as
described below. The calculated base composition for any given
amplicon is then compared to a database of base compositions. A
match between the calculated base composition and a single database
entry reveals the identity of the bioagent.
[0080] The term "communicate" refers to the direct or indirect
transfer or transmission, and/or capability of directly or
indirectly transferring or transmitting, something at least from
one thing to another thing. Objects "fluidly communicate" with one
another when fluidic material is, or is capable of being,
transferred from one object to another. In some embodiments, for
example, an aperture is disposed through a top surface of a
cartridge body structure. In these embodiments, the aperture is
typically configured to receive a fluid handling component that
fluidly communicates with the cavity (e.g., adds and/or removes
material to and/or from the cavity). Objects are in "thermal
communication" with one another when thermal energy is or can be
transferred from one object to another. In certain embodiments, for
example, a mixing station includes a thermal modulating component
that can transfer thermal energy to and/or receive thermal energy
from a cartridge cavity to modulate (e.g., raise and/or lower)
temperature of fluidic materials disposed in the cavity. Objects
are in "magnetic communication" with one another when one object
exerts or can exert a magnetic field of sufficient strength on
another object to effect a change (e.g., a change in position or
other movement) in the other object. In some embodiments, for
example, a rotational mechanism magnetically communicates with a
rotatable member of a cartridge via magnetic couplers that effect
the rotation of the rotatable member. Objects are in "sensory
communication" when a characteristic or property of one object is
or can be sense, perceived, or otherwise detected by another
object. In certain embodiments, for example, a projection that
extends outward from a rotatable member is configured to activate a
motion sensor such that movement of the rotatable member can be
monitored when the motion sensor is in sensory communication with
the projection. To further illustrate, in some embodiments, a
detection component is positioned in sensory communication with a
cartridge cavity so as to detect one or more parameters (e.g.,
temperature, pH, or the like) of a fluidic material disposed in the
cavity. It is to be noted that there may be overlap among the
various exemplary types of communication referred to above.
[0081] The phrase "dead zone" in the context of cartridge cavities
refers to an area of a cavity in which particles tend to fall out
of suspension or otherwise settle even when a fluidic material
comprising the particles is agitated or otherwise mixed within the
cavity, or to an area of a cavity in which materials are mixed less
uniformly or thoroughly than in others within the cavity.
[0082] The phrase "horizontally disposed" refers to something that
is positioned, and/or operates, in a plane that is parallel to the
horizon or to a baseline. In some embodiments, for example, a
rotatable member extends at least partially along an axis that is
substantially horizontally disposed in the cavity of a cartridge
during typical or intended use of the cartridge. An axis is
"substantially horizontally disposed" in a cavity when it is either
exactly parallel to the horizon or to a baseline, or forms an angle
with the horizon or a baseline that is less than 45.degree. (e.g.,
40.degree. or less, 35.degree. or less, 30.degree. or less,
25.degree. or less, 20.degree. or less, 15.degree. or less,
10.degree. or less, 5.degree. or less, etc.).
[0083] The term "kit" is used in reference to a combination of
articles that facilitate a process, method, assay, analysis or
manipulation of a sample. Kits can contain instructions describing
how to use the kit (e.g., instructions describing the methods of
the invention), cartridges, mixing stations, magnetically
responsive particles or other particles, chemical reagents, as well
as other components. Kit components may be packaged together in one
container (e.g., box, wrapping, and the like) for shipment,
storage, or use, or may be packaged in two or more containers.
[0084] The phrase "laterally disposed" refers to something that
extends outward from at least one side of the same or another
thing. In some embodiments, for example, a protrusion includes a
substantially vertically disposed segment that extends downward
from a rotatable member and a substantially laterally disposed
segment that extends outward from the substantially vertically
disposed segment.
[0085] The phrase "lower portion" in the context of a mixing
cartridge cavity refers to an area or region of the cavity having a
maximum height that is not more than 50% of the maximum height of
the entire cavity and which is disposed below another area or
region of the cavity during intended operation of the
cartridge.
[0086] The term "material" refers to something comprising or
consisting of matter. The term "fluidic material" refers to
material (such as, a liquid or a gas) that tends to flow or conform
to the outline of its container.
[0087] The term "microplate" refers to a plate or other support
structure that includes multiple cavities or wells that are
structured to contain materials, such as fluidic materials. The
wells typically have volume capacities of less than about 1.5 mL
(e.g., about 1000 .mu.L, about 800 .mu.L, about 600 .mu.L, about
400 .mu.L, or less), although certain microplates (e.g., deep-well
plates, etc.) have larger volume capacities, such as about 4 mL per
well. Microplates can include various numbers of wells, for
example, 6, 12, 24, 48, 96, 384, 1536, 3456, 9600, or more wells.
In addition, the wells of a microplate are typically arrayed in a
rectangular matrix. Microplates generally conform to the standards
published by the American National Standards Institute (ANSI) on
behalf of the Society for Biomolecular Screening (SBS), namely,
ANSI/SBS 1-2004: Microplates-Footprint Dimensions, ANSI/SBS 2-2004:
Microplates-Height Dimensions, ANSI/SBS 3-2004: Microplates-Bottom
Outside Flange Dimensions, and ANSI/SBS 4-2004: Microplates-Well
Positions, which are each incorporated by reference. Microplates
are available from a various manufacturers including, e.g., Greiner
America Corp. (Lake Mary, Fla., U.S.A.) and Nalge Nunc
International (Rochester, N.Y., U.S.A.), among many others.
Microplates are also commonly referred to by various synonyms, such
as "microtiter plates," "micro-well plates," "multi-well
containers," and the like
[0088] The term "molecular mass" refers to the mass of a compound
as determined using mass spectrometry, for example, ESI-MS. Herein,
the compound is preferably a nucleic acid. In some embodiments, the
nucleic acid is a double stranded nucleic acid (e.g., a double
stranded DNA nucleic acid). In some embodiments, the nucleic acid
is an amplicon. When the nucleic acid is double stranded the
molecular mass is determined for both strands. In one embodiment,
the strands may be separated before introduction into the mass
spectrometer, or the strands may be separated by the mass
spectrometer (for example, electro-spray ionization will separate
the hybridized strands). The molecular mass of each strand is
measured by the mass spectrometer.
[0089] The term "non-priority microplate" refers to a microplate
that is processed or otherwise handled after at least one other
microplate, or whose processing or handling is interrupted or
deferred in order to process or otherwise handle at least one other
microplate, in a given microplate handling system of the invention.
That is, the order, schedule, or timing of processing or handling a
non-priority microplate is subject to interruption or delay when a
higher priority microplate is presented, such as a microplate
including stat samples. In some embodiments, non-priority
microplates are introduced into a given system via non-priority
microplate storage units.
[0090] The term "nucleic acid molecule" refers to any nucleic acid
containing molecule, including but not limited to, DNA or RNA. The
term encompasses sequences that include any of the known base
analogs of DNA and RNA including, but not limited to,
4-acetylcytosine, 8-hydroxy-N.sup.6-methyladenosine,
aziridinylcytosine, pseudoisocytosine,
5-(carboxyhydroxyl-methyl)-uracil, 5-fluorouracil, 5-bromouracil,
5-carboxymethylaminomethyl-2-thiouracil,
5-carboxymethyl-aminomethyluracil, dihydrouracil, inosine,
N.sup.6-isopentenyladenine, 1-methyladenine, 1-methylpseudo-uracil,
1-methylguanine, 1-methylinosine, 2,2-dimethyl-guanine,
2-methyladenine, 2-methylguanine, 3-methyl-cytosine,
5-methylcytosine, N.sup.6-methyladenine, 7-methylguanine,
5-methylaminomethyluracil, 5-methoxy-amino-methyl-2-thiouracil,
beta-D-mannosylqueosine, 5'-methoxycarbonylmethyluracil,
5-methoxyuracil, 2-methylthio-N-isopentenyladenine,
uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid,
oxybutoxosine, pseudouracil, queosine, 2-thiocytosine,
5-methyl-2-thiouracil, 2-thiouracil, 4-thiouracil, 5-methyluracil,
N-uracil-5-oxyacetic acid methylester, uracil-5-oxyacetic acid,
pseudouracil, queosine, 2-thiocytosine, and 2,6-diaminopurine.
[0091] The term "priority microplate" refers to a microplate that
is processed or otherwise handled before the processing or handling
of a non-priority microplate is commenced or completed in a given
microplate handling system of the invention. In some embodiments,
one or more wells of priority microplates comprise stat or urgent
samples. In certain embodiments, priority microplates are
introduced into a given system via priority microplate storage
units.
[0092] The term "system" refers a group of objects and/or devices
that form a network for performing a desired objective. In some
embodiments, for example, mixing stations with cartridges having
fluidic materials with magnetically responsive particles are
included as part of systems in which nucleic acids are purified
using the magnetically responsive particles such that the molecular
masses of the nucleic acids can be more readily detected by mass
spectrometers of these systems.
[0093] The phrase "upper portion" in the context of a mixing
cartridge cavity refers to an area or region of the cavity having a
maximum height that is not more than about 65% of the maximum
height of the entire cavity and which is disposed above another
area or region of the cavity during intended operation of the
cartridge.
[0094] The phrase "vertically disposed" refers to something that is
positioned, and/or operates, in a plane that is perpendicular to
the horizon or to a baseline. In certain embodiments, for example,
the body structure of a cartridge includes a substantially
vertically disposed side surface during typical or intended use of
the cartridge. As side surface is "substantially vertically
disposed" when it is either exactly perpendicular to the horizon or
to a baseline, or forms an angle with the horizon or a baseline
that is more than 45.degree. and less than 90.degree. (e.g.,
between about 50.degree. and about 85.degree., between about
55.degree. and about 80.degree., between about 60.degree. and about
75.degree., between about 65.degree. and about 70.degree.,
etc.).
II. Introduction
[0095] The invention relates to material mixing, and in various
embodiments provides cartridges, mixing stations, systems, kits,
and related methods that are useful for this purpose. In some
applications, for example, fluidic materials are mixed such that
particles (e.g., magnetically responsive particles or other solid
supports, cells, and the like) are maintained in suspension and
uniformly distributed within the fluidic material. In other
exemplary applications, different particles are mixed with one
another, solid materials are dissolved in liquids, different
liquids are mixed with one another or emulsified, and gases are
distributed within liquid phases. Homogeneous mixtures of materials
are commonly used in a host of scientific and industrial processes,
including biopolymer purification procedures, compound screening
methods, and chemical synthesis schemes, among many others. The
cartridges, mixing stations, and other aspects described herein can
be used, or readily adapted for use, in these as well as
essentially any other application that involves mixtures of
materials. These and many other attributes will be apparent upon
reviewing the description provided herein.
III. Example Cartridges
[0096] FIGS. 1 A-N schematically illustrate a representative mixing
cartridge of the invention. As shown, cartridge 100 includes body
structure 102, which includes curved surface 104 that partially
defines cavity 106 having upper portion 108 and lower portion 110.
As further shown, cartridge 100 also includes rotatable member 112
extending along an axis that is substantially horizontally disposed
in upper portion 108 of the cavity 106. In addition, protrusions
114 extend outward from rotatable member 112 and into lower portion
110 of cavity 106, e.g., when rotatable member 112 is not being
rotated. Protrusions 114 (shown as a blade or paddle) are
configured to mix material when the material (e.g., a fluidic
material, etc.) is disposed in cavity 106 and a rotational
mechanism rotates rotatable member 112 about the substantially
horizontally disposed axis. Suitable rotational mechanisms are
described further herein.
[0097] Body structures are generally dimensioned to be handheld,
although other sizes are also optionally utilized. Handheld
cartridges are typically readily transportable (e.g., manually or
robotically), e.g., to and from cartridge receiver/rotation
assemblies in a given mixing station or system, via a carrier
service (e.g., the postal service or the like) as a kit component,
or the like. In some embodiments, for example, cartridge body
structures have heights of about 10 cm or less (e.g., about 9.5 cm,
about 9 cm, about 8.5 cm, about 8 cm, about 7.5 cm, about 7 cm,
about 6.5 cm, about 6 cm, about 5.5 cm, about 5 cm, about 4.5 cm,
about 4 cm, about 3.5 cm, about 3 cm, about 2.5 cm, etc.). In
certain embodiments, cartridge body structures have widths of about
15 cm or less (e.g., about 14.5 cm, about 14 cm, about 13.5 cm,
about 13 cm, about 12.5 cm, about 12 cm, about 11.5 cm, about 11
cm, about 10.5 cm, about 10 cm, about 9.5 cm, about 9 cm, about 8.5
cm, about 8 cm, about 7.5 cm, about 7 cm, about 6.5 cm, about 6 cm,
about 5.5 cm, about 5 cm, about 4.5 cm, about 4 cm, about 3.5 cm,
about 3 cm, about 2.5 cm, etc.). In some embodiments, cartridge
body structures have lengths of about 20 cm or less (e.g., about
19.5 cm, about 19 cm, about 18.5 cm, about 18 cm, about 17.5 cm,
about 17 cm, about 16.5 cm, about 16 cm, about 15.5 cm, about 15
cm, about 14.5 cm, about 14 cm, about 13.5 cm, about 13 cm, about
12.5 cm, about 12 cm, about 11.5 cm, about 11 cm, about 10.5 cm,
about 10 cm, about 9.5 cm, about 9 cm, about 8.5 cm, about 8 cm,
about 7.5 cm, about 7 cm, about 6.5 cm, about 6 cm, about 5.5 cm,
about 5 cm, about 4.5 cm, about 4 cm, about 3.5 cm, about 3 cm,
about 2.5 cm, etc.). In some exemplary embodiments, mixing
cartridge body structures include a height of about 3.0 cm (e.g.,
3.3 cm, 3.2 cm, 3.1 cm, 3.0 cm, 2.9 cm, 2.8 cm, 2.7 cm, etc.), a
width of about 5.5 cm (e.g., 5.8 cm, 5.7 cm, 5.6 cm, 5.5 cm, 5.4
cm, 5.3 cm, 5.2 cm, etc.), and a length of about 12.0 cm (e.g.,
12.3 cm, 12.2 cm, 12.1 cm, 12.0 cm, 12.9 cm, 12.8 cm, 12.7 cm,
etc.). To further illustrate, mixing cartridge body structures can
also include a variety of shapes. In some embodiments, for example,
body structures include substantially rectangular-shaped,
substantially square-shaped, substantially oval-shaped, and/or
substantially circular-shaped cross-sections. In addition, mixing
cartridges, or body structures thereof, generally include weights
of about 1 kg or less (e.g., about 750 grams, 500 grams, 250 grams,
200 grams, 150 grams, 100 grams, 50 grams, etc.). Cartridge
fabrication materials and techniques are described further
herein.
[0098] The cavities of the mixing cartridges include numerous
embodiments. For example, they can include various shapes and
volume capacities. A mixing cartridge cavity generally has a shape
that lacks substantial dead zones (e.g., areas where particles tend
to settle or otherwise not be mixed) when a given rotatable member
mixes materials in the cavity. In some embodiments, for example,
one or more surfaces of a body structure that define its cavity are
substantially symmetrical about a substantially horizontally
disposed axis (e.g., an axis about which a rotatable member
rotates) of the cavity. Curved surface 104 of cavity 106 illustrate
one of these embodiments. Further, a radius of curvature of a
surface of a given cavity optionally varies along the length of the
cavity in some embodiments. As shown, for example, in FIGS. 1 B and
K, the radius of curvature of curved surface 104 of cavity 106 is
larger at central portion 116 of cavity 106 than the radius of
curvature near end portion 118 of cavity 106. To further
illustrate, a distance between a lower portion of a protrusion of a
rotatable member and a surface of the cavity is substantially
identical at two or more positions about the axis of the cavity in
some embodiments. Protrusions 104 and curved surface 104 of
cartridge 100 show one of these embodiments. Typically, the upper
portions of cavities include holes, indentations, or the like that
receive sections of rotatable members, e.g., to position the
rotatable members within the cavities. As an example, cavity 106 of
cartridge 100 include indentation 120 and hole 122 that receive
sections of rotatable member 112. Although mixing cartridge
cavities optionally include other volume capacities, they include
volume capacities of about 500 mL or less (e.g., about 450 mL,
about 400 mL, about 350 mL, about 300 mL, about 250 mL, about 200
mL, about 150 mL, about 100 mL, about 50 mL, etc.).
[0099] In certain embodiments, a top surface of the body structure
comprises an opening that communicates with the cavity. As shown,
for example, in FIGS. 1 A and B, body structure 102 includes
opening 124 that communicates with cavity 106. In these
embodiments, a mixing cartridge typically includes a sealing member
that operably connects to the body structure, e.g., to seal the
cavity during operation, transport, or the like. In some
embodiments, the sealing member includes a removable cover that is
structured to engage one or more surfaces of the body structure. To
illustrate, the sealing member optionally includes a film (e.g., a
heat sealed or otherwise adhered film) that overlays the opening on
the top surface of the body structure. To facilitate communication
with the cavity, one or more apertures are generally disposed
through the sealing member. In some embodiments, for example,
apertures are configured to receive one or more fluid handling
components such that the fluid handling components can fluidly
communicate with the cavity (e.g., add and/or remove fluidic
material to/from the cavity). Fluid handling components are
described further below. Typically, an aperture is disposed through
the sealing member relative to the rotatable member and to
protrusions extending from the rotatable member such that the fluid
handling component does not contact the rotatable member or the
protrusions when the rotatable member rotates the protrusion and
the aperture receives the fluid handling component, e.g., to
minimize the chance of damaging these components during operation
of a given process. In some embodiments, a closure (e.g., a
re-sealable label, a septum, or the like) is disposed in or over
the aperture, e.g., to reduce the possibility of contaminating the
contents of the cavity, to prevent spillage during transport, to
minimize evaporation of fluidic materials in the cavity, etc. In
certain embodiments, a closure, such as a sealing label or the like
is removed from a cartridge during operation, whereas in other
embodiments, a closure such as a self-sealing septum remains
positioned in or over an aperture, e.g., when a fluid handling
component fluidly communicates with the cavity of the cartridge. To
further illustrate, in FIGS. 1 C and D, for example, cartridge 100
includes sealing member 126 (shown as a foil/laminate cover)
overlaying opening 124 of cavity 106. Although not within view, for
example, in FIGS. 1 C and D, an aperture or fill port is disposed
through sealing member 126, but has been covered and sealed by
closure 128 (shown as a round seal label). In some embodiments, a
fill port 131 and/or vent port 133 is disposed through the sealing
member 126.
[0100] As also shown, for example, in FIG. 1B, curved surface 104
of cartridge 100 also includes flattened area 105, which aligns
with the aperture disposed through sealing member 126 and with
closure 128. Flattened areas, such as flattened area 105 are
included in certain embodiments to reduce the possibility of a
fluid handling component (e.g., a pipette tip or needle) contacting
curved surface 104 and causing damage to the fluid handling
component and/or cartridge 100, when the fluid handling component
fluidly communicates with cavity 106.
[0101] In other exemplary embodiments, a cavity is fully enclosed
within a mixing cartridge body structure. That is, the body
structure does not include an opening comparable to opening 124 in
these embodiments. One or more apertures, however, are typically
disposed through a top surface of the body structure. In some of
these embodiments, for example, the top surface is fabricated
integral with the body structure or otherwise attached during
assembly. Suitable fabrication techniques and materials are
described further herein. The aperture is generally configured to
receive a fluid handling component that fluidly communicates with
the cavity. In these embodiments, the aperture is typically
disposed through the top surface of the body structure relative to
the rotatable member and to protrusions extending from the
rotatable member such that the fluid handling component does not
contact the rotatable member or the protrusions when the rotatable
member rotates the protrusions and the aperture receives the fluid
handling component. A closure (such as, a re-sealable label, a
septum, or the like) is typically disposed in or over the aperture,
e.g., at least prior to use. To further illustrate these
embodiments, FIGS. 2 A-D schematically show a representative mixing
cartridge having a cavity that is fully enclosed. As shown,
cartridge 200 includes top surface 202 fabricated integral (e.g.,
injection molded, machined, or the like) with other portions of the
cartridge's body structure. In this exemplary embodiment, cavity
portion 204 is fabricated separate from other components of the
cartridge (FIG. 2C) and attached to the remaining portion of the
body structure (via attachment components 206 (shown as
corresponding male and female elements that are structured to
engage one another) during device assembly to form cavity 208. As
further shown, cartridge 200 includes pre-pierced septum 210
positioned in an aperture disposed through top surface 202. During
operation, a fluid handling component (e.g., a manually or
robotically operated pipetting apparatus) typically fluidly
communicates with cavity 208 via septum 210.
[0102] In some embodiments, mixing cartridge body structures
include alignment features that align the cartridges relative to
other components, such as the cartridge support structure of a
cartridge receiver/rotation assembly. To illustrate, cartridge 100
includes alignment features 130, which align cartridge 100 relative
to a cartridge support structure when cartridge 100 is positioned
on a cartridge receiver/rotation assembly (not shown in FIGS. 1
A-N). In addition, in certain embodiments, body structures also
include retention components that engage retention mechanisms of
cartridge receiver/rotation assemblies. As shown, cartridge 100
includes retention component 132 (shown as a lip at the base of
body structure 102) that engages a retention mechanism of a
cartridge receiver/rotation assembly (not shown in FIGS. 1 A-N) to
hold cartridge 100 in place when body structure 102 is positioned
on the assembly and, e.g., when a rotational mechanism of the
assembly rotates rotatable member 112 of cartridge 100. Exemplary
cartridge receiver/rotation assemblies are described further
herein.
[0103] The rotatable members and protrusions of the mixing
cartridges of the invention also include a wide variety of
embodiments. To further illustrate one exemplary embodiment, FIGS.
3 A-H show additional views of rotatable member 112 and protrusions
114 of cartridge 100. Rotatable members are typically configured to
rotate about 180 degrees or less (e.g., about 135 degrees, about 90
degrees, about 45 degrees, etc.) within the cavities of the
cartridges described herein. Although rotatable member 112 of
cartridge 100 extends along an entire length of a substantially
horizontally disposed axis in upper portion 108 of the cavity 106,
other configurations are also optionally utilized. In some
embodiments, for example, rotatable members extend less than the
entire length of a substantially horizontally disposed rotational
axis. As an additional option, multiple rotatable members are used
in certain embodiments.
[0104] Rotatable members are generally configured to operably
connect to rotational mechanisms. Rotational mechanisms, which are
described further herein, effect the rotation of the rotatable
members. In some embodiments, rotatable members operably connect to
rotational mechanisms via substantially vertically disposed side
surfaces of cartridge body structures. For example, rotatable
member 112 includes proximal end 134 that extends through hole 122
in a substantially vertical surface of cavity 106. As also shown,
washer 136 is disposed around proximal end 134 of rotatable member
112, e.g., to seal in the surface of cavity 106. Proximal end 134
is configured to operably connect to a rotational mechanism that
mechanically effects the rotation of rotatable member 112.
Rotatable member rotation can also effected using other approaches.
In some embodiments, for example, rotatable members include
magnetic couplers that are configured to interact with magnetic
couplers of the rotational mechanisms to effect rotation of the
rotatable members when the magnetic couplers are within magnetic
communication with one another. To illustrate, FIG. 4 schematically
shows one embodiment of a cartridge that includes a magnetic
coupler from a partially transparent bottom view. As shown,
cartridge 400 includes rotatable member 402 disposed within cavity
404. In addition, magnetic coupler 406 is attached to rotatable
member 402 and magnetic coupler 408 is rotatably connected to a
rotational mechanism (not shown) via shaft 410. During operation,
magnetic coupler 406 and magnetic coupler 408 are positioned within
magnetic communication with one another such that when the
rotational mechanism effects the rotation of magnetic coupler 408,
magnetic coupler 408, in turn, effects the rotation of magnetic
coupler 406 and rotatable member 402. Magnetic coupling mechanisms
that are optionally adapted for use with the cartridges of the
invention are also described in, e.g., U.S. Pat. No. 6,461,034,
entitled "USE OF A BUBBLE PADDLE TUMBLE STIRRER TO MIX THE CONTENTS
OF A VESSEL WHILE THE CONTENTS ARE BEING REMOVED," which issued
Oct. 8, 2002 to Cleveland, which is incorporated by reference in
its entirety. Rotational mechanisms and related cartridge
receiver/rotation assemblies are described further herein.
[0105] Typically, mixing cartridges include mechanisms that
facilitate the monitoring and regulation of mixing processes
performed using the cartridges. In certain embodiments, for
example, there is a projection that extends outward from the
rotatable member. In these embodiments, the projection is generally
configured to activate a motion sensor when the motion sensor is in
sensory communication with the projection and the rotatable member
is rotated. As an illustration, projection 138 is positioned in
housing 139 near proximal end 134 of rotatable member 112. During
operation, the rate of rotatable member 112 rotation is typically
tracked and adjusted when a motion sensor detects the motion of
projection 138. Motion sensors are typically included as components
of cartridge receiver/rotation assemblies, which are described
further herein.
[0106] The protrusion or protrusions that extend from a given
rotatable member also include a number of different embodiments.
Essentially any number and configuration of protrusions that can
effect the mixing of materials in the cartridges of the invention
can be utilized. Typically, protrusions are configured (e.g., in
conjunction with cavity surface shapes and/or textures) to minimize
dead zones within cavities and to facilitate fluid communication
with cartridge cavities concurrent with the rotation of rotatable
members. In some embodiments, for example, a protrusion includes at
least one substantially vertically disposed segment (e.g.,
substantially vertically disposed segment 140) that extends
downward from the rotatable member (e.g., rotatable member 112) and
at least one substantially laterally disposed segment (e.g.,
substantially laterally disposed segment 142) that extends outward
from the substantially vertically disposed segment. In some
embodiments, protrusions typically include one or more edges having
textured surfaces (e.g., edge 144 of substantially laterally
disposed segment 142). The use of textured surfaces typically
enhances the uniformity of mixing materials within cartridge
cavities. Protrusions are optionally fabricated as separate
components and attached to rotatable members during cartridge
assembly processes. In other embodiments, protrusions fabricated
integral with rotatable members (e.g., as an integrated molded
part, etc.). Cartridge fabrication is described further herein.
IV. Example Mixing Stations
[0107] FIGS. 5 A-C schematically illustrate a mixing station
according to one embodiment of the invention. As shown, mixing
station 500 includes cartridge 100 (depicted in various transparent
views) and cartridge receiver/rotation assembly 502 (shown in
various partially transparent views). To further illustrate, FIGS.
6 A-F schematically show cartridge receiver/rotation assembly 502
without cartridge 100. Cartridge receiver/rotation assembly 502
includes cartridge support structure 504 and rotational mechanism
506. Cartridge support structure 504 is structured to position and
support cartridge 100, which is removable from cartridge
receiver/rotation assembly 502. In some embodiments, cartridges are
not removable components of mixing stations, e.g., are fabricated
integral with cartridge receiver/rotation assemblies. In certain
embodiments, cartridge support structure 504 is attached to or
mounted on another support surface via mounting holes 505. As
shown, cartridge support structure 504 includes recessed region 508
that receives body structure 102 of cartridge 100. Recessed region
508 includes grooves 510 that receive alignment features 130 of
cartridge 100 via notched regions 512 of cartridge
receiver/rotation assembly 502 to align cartridge 100 relative to
cartridge support structure 504 and rotational mechanism 506 of
cartridge receiver/rotation assembly 502. As mentioned above,
cartridge 100 includes retention component 132 (shown as a lip at
the base of the body structure of cartridge 100). When alignment
features 130 of cartridge 100 are received within grooves 510 of
cartridge support structure 504, retention component 132 engages
retention mechanism 514 (shown as a spring loaded clamp) of
cartridge receiver/rotation assembly 502 to reversibly hold
cartridge 100 in place within recessed region 508, e.g., to secure
cartridge 100 when rotational mechanism 506 rotates rotatable
member 112.
[0108] As also shown, proximal end 134 of rotatable member 112 of
cartridge 100 operably connects to rotational mechanism 506 via
rotatable shaft 516. Rotatable shaft 516 is operably connected to
motor 518 (shown as a stepper motor), which is mounted on cartridge
support structure 504 via motor mounting bracket 520. Motor 518
effects the rotation of rotatable shaft 516 and rotational
mechanism 506. As described herein, in other exemplary embodiments,
rotatable shaft rotation and material mixing is effected by
magnetic coupling mechanisms. For example, as described above with
respect to FIG. 4, rotatable members and rotational mechanisms
include magnetic couplers that magnetically communicate with one
another to effect rotation in some of these embodiments.
[0109] As referred to above, mixing stations optionally include
mechanisms for monitoring and regulating mixing processes performed
using the cartridges described herein. To illustrate, cartridge
receiver/rotation assembly 502 of mixing station 500 includes
motion sensor 522 (shown as a reflective solder terminal
phototransistor) mounted on cartridge support structure 504 via
motion sensor mounting bracket 524. Suitable motion sensors are
available from a variety of commercial supplier including, e.g.,
Omron Electronics LLC (Schaumburg, Ill., U.S.A.). During operation,
the rotation of rotatable member 112 of cartridge 100 is typically
monitored when motion sensor 522 detects the motion of projection
138 within housing 139 of cartridge 100.
[0110] In some embodiments, mixing stations include thermal
modulating components (e.g., resistive heating coils, or the like)
that modulate the temperature of materials disposed in the cavities
of mixing cartridges during a given mixing process. For example,
FIG. 7 schematically depicts cartridge receiver/rotation assembly
700, which includes heating element 702 disposed in recessed region
704. Heating element 702 is configured to thermally communicate
with the cavity of a mixing cartridge to regulate the temperature
of materials (e.g., a cell culture suspension, viscous fluidic
materials, etc.) within the cavity when the cartridge is positioned
within recessed region 704. Although not shown in FIG. 7, heating
element 702 operably connects to a power source. Typically, thermal
modulating components are operably connected to controllers
(described below), e.g., via such power sources.
[0111] The controllers of the mixing stations and systems described
herein are generally configured to effect, e.g. the rotation of
rotatable members to mix materials disposed within the cavities of
mixing cartridges, the monitoring of rotatable member rotation, the
detection of one or more parameters of materials disposed in mixing
cartridge cavities, and the like. Controllers are typically
operably connected to one or more system components, such as motors
(e.g., via motor drives), thermal modulating components, detectors,
motion sensors, fluidic handling components, robotic translocation
devices, or the like, to control operation of these components.
More specifically, controllers are generally included either as
separate or integral system components that are utilized to effect,
e.g., the rotation of rotatable members in mixing cartridges
according to one or more selectable rotational modes, the transport
of mixing cartridges between system areas or components, the
transfer of materials to and/or from mixing cartridges, the
detection and/or analysis of detectable signals received from
sample materials by detectors, etc. Controllers and/or other system
components is/are generally coupled to an appropriately programmed
processor, computer, digital device, or other logic device or
information appliance (e.g., including an analog to digital or
digital to analog converter as needed), which functions to instruct
the operation of these instruments in accordance with preprogrammed
or user input instructions (e.g., mixing mode selection, mixing
cartridge cavity temperature, fluid volumes to be conveyed, etc.),
receive data and information from these instruments, and interpret,
manipulate and report this information to the user.
[0112] A controller or computer optionally includes a monitor which
is often a cathode ray tube ("CRT") display, a flat panel display
(e.g., active matrix liquid crystal display, liquid crystal
display, etc.), or others. Computer circuitry is often placed in a
box, which includes numerous integrated circuit chips, such as a
microprocessor, memory, interface circuits, and others. The box
also optionally includes a hard disk drive, a floppy disk drive, a
high capacity removable drive such as a writeable CD-ROM, and other
common peripheral elements. Inputting devices such as a keyboard or
mouse optionally provide for input from a user. An exemplary system
comprising a computer is schematically illustrated in FIG. 8.
[0113] The computer typically includes appropriate software for
receiving user instructions, either in the form of user input into
a set of parameter fields, e.g., in a GUI, or in the form of
preprogrammed instructions, e.g., preprogrammed for a variety of
different specific operations. The software then converts these
instructions to appropriate language for instructing the operation
of one or more controllers to carry out the desired operation,
e.g., rotating a rotatable member of a mixing cartridge, aspirating
fluidic materials from a mixing cartridge, dispensing materials
into a cavity of a mixing cartridge, or the like. The computer then
receives the data from, e.g., sensors/detectors included within the
system, and interprets the data, either provides it in a user
understood format, or uses that data to initiate further controller
instructions, in accordance with the programming, e.g., such as in
monitoring detectable signal intensity, mixing cartridge cavity
temperature, or the like.
[0114] More specifically, the software utilized to control the
operation of the mixing stations of the invention typically
includes logic instructions that selectively direct, e.g., the
rotational mechanism to rotate the rotatable member in an
initiation mode or in a maintenance mode in which a rate of
rotation of the rotatable member is greater in the initiation mode
than in the maintenance mode. The logic instructions of the
software are typically embodied on a computer readable medium, such
as a CD-ROM, a floppy disk, a tape, a flash memory device or
component, a system memory device or component, a hard drive, a
data signal embodied in a carrier wave, and/or the like. Other
computer readable media are known to persons of skill in the art.
In some embodiments, the logic instructions are embodied in
read-only memory (ROM) in a computer chip present in one or more
system components, without the use of personal computers.
[0115] The computer can be, e.g., a PC (Intel x86 or Pentium
chip-compatible DOS.TM., OS2.TM.., WINDOWS.TM.., WINDOWS NT.TM..,
WINDOWS98.TM., WINDOWS2000.TM., WINDOWS XP.TM., WINDOWS Vista.TM.,
LINUX-based machine, a MACINTOSH.TM., Power PC, or a UNIX-based
(e.g., SUN.TM. work station) machine) or other common commercially
available computer which is known to one of skill. Standard desktop
applications such as word processing software (e.g., Microsoft
Word.TM. or Corel WordPerfect.TM.) and database software (e.g.,
spreadsheet software such as Microsoft Excel.TM., Corel Quattro
Pro.TM., or database programs such as Microsoft Access.TM. or
Paradox.TM.) can be adapted to the present invention. Software for
performing, e.g., rotatable member rotation, material conveyance to
and/or from mixing cartridges, mixing process monitoring, assay
detection, and data deconvolution is optionally constructed by one
of skill using a standard programming language such as Visual
basic, C, C++, Fortran, Basic, Java, or the like.
[0116] The mixing stations and related systems of the invention
optionally include detection components configured to detect one or
more detectable signals or parameters from a given mixing process,
e.g., from materials disposed within mixing cartridge cavities. In
some embodiments, systems are configured to detect detectable
signals or parameters that are upstream and/or downstream of a
given mixing process involving the mixing cartridges and mixing
stations described herein. Suitable signal detectors that are
optionally utilized in these systems detect, e.g., pH, temperature,
pressure, density, salinity, conductivity, fluid level,
radioactivity, luminescence, fluorescence, phosphorescence,
molecular mass, emission, transmission, absorbance, and/or the
like. In some embodiments, the detector monitors a plurality of
signals, which correspond in position to "real time" results.
Example detectors or sensors include PMTs, CCDs, intensified CCDs,
photodiodes, avalanche photodiodes, optical sensors, scanning
detectors, or the like. Each of these as well as other types of
sensors is optionally readily incorporated into the mixing stations
and systems described herein. The detector optionally moves
relative to mixing cartridges or stations, sample containers or
other assay components, or alternatively, mixing cartridges or
stations, sample containers or other assay components move relative
to the detector. Optionally, the mixing stations and systems of the
invention include multiple detectors. In these stations and
systems, such detectors are typically placed either in or adjacent
to, e.g., a mixing cartridge cavity or other vessel, such that the
detector is in sensory communication with the mixing cartridge
cavity or other vessel (i.e., the detector is capable of detecting
the property of the cavity or vessel or portion thereof, the
contents of a portion of the cavity or vessel, or the like, for
which that detector is intended).
[0117] The detector optionally includes or is operably linked to a
computer, e.g., which has system software for converting detector
signal information into assay result information or the like. For
example, detectors optionally exist as separate units, or are
integrated with controllers into a single instrument. Integration
of these functions into a single unit facilitates connection of
these instruments with the computer, by permitting the use of a few
or even a single communication port for transmitting information
between system components. Detection components that are optionally
included in the systems of the invention are described further in,
e.g., Skoog et al., Principles of Instrumental Analysis, 6.sup.th
Ed., Brooks Cole (2006) and Currell, Analytical Instrumentation:
Performance Characteristics and Quality, John Wiley & Sons,
Inc. (2000), which are both incorporated by reference.
[0118] The stations and systems of the invention optionally also
include at least one robotic translocation or gripping component
that is structured to grip and translocate mixing cartridges or
other containers between components of the stations or systems
and/or between the stations or systems and other locations (e.g.,
other work stations, etc.). In certain embodiments, for example,
systems further include gripping components that move mixing
cartridges between cartridge receiver/rotation assemblies,
incubation or storage components, and the like. A variety of
available robotic elements (robotic arms, movable platforms, etc.)
can be used or modified for use with these systems, which robotic
elements are typically operably connected to controllers that
control their movement and other functions.
[0119] FIG. 8 is a schematic showing a representative system
including an information appliance in which various aspects of the
present invention may be embodied. Other exemplary systems are also
described herein. As will be understood by practitioners in the art
from the teachings provided herein, the invention is optionally
implemented in hardware and software. In some embodiments,
different aspects of the invention are implemented in either
client-side logic or server-side logic. As will also be understood
in the art, the invention or components thereof may be embodied in
a media program component (e.g., a fixed media component)
containing logic instructions and/or data that, when loaded into an
appropriately configured computing device, cause that apparatus or
system to perform according to the invention. As will additionally
be understood in the art, a fixed media containing logic
instructions may be delivered to a viewer on a fixed media for
physically loading into a viewer's computer or a fixed media
containing logic instructions may reside on a remote server that a
viewer accesses through a communication medium in order to download
a program component.
[0120] FIG. 8 shows information appliance or digital device 800
that may be understood as a logical apparatus (e.g., a computer,
etc.) that can read instructions from media 817 and/or network port
819, which can optionally be connected to server 820 having fixed
media 822. Information appliance 800 can thereafter use those
instructions to direct server or client logic, as understood in the
art, to embody aspects of the invention. One type of logical
apparatus that may embody the invention is a computer system as
illustrated in 800, containing CPU 807, optional input devices 809
and 811, disk drives 815 and optional monitor 805. Fixed media 817,
or fixed media 822 over port 819, may be used to program such a
system and may represent a disk-type optical or magnetic media,
magnetic tape, solid state dynamic or static memory, or the like.
In specific embodiments, the aspects of the invention may be
embodied in whole or in part as software recorded on this fixed
media. Communication port 819 may also be used to initially receive
instructions that are used to program such a system and may
represent any type of communication connection. Optionally, aspects
of the invention are embodied in whole or in part within the
circuitry of an application specific integrated circuit (ACIS) or a
programmable logic device (PLD). In such a case, aspects of the
invention may be embodied in a computer understandable descriptor
language, which may be used to create an ASIC, or PLID.
[0121] In addition, FIG. 8 also shows mixing station 802, which is
operably connected to information appliance 800 via server 820.
Optionally, mixing station 802 is directly connected to information
appliance 800. During operation, mixing station 802 typically mixes
materials with mixing cartridge cavities (e.g., to maintain
particles in fluidic materials in suspension, etc.), e.g., as part
of an assay or other process. FIG. 8 also shows detector 824, which
is optionally included in the systems of the invention. As shown,
detector 824 is operably connected to information appliance 800 via
server 820. In some embodiments, detector 824 is directly connected
to information appliance 800. In certain embodiments, detector 824
is configured to detect detectable signals produced in a cavity of
a mixing cartridge positioned on a cartridge support structure of
mixing station 802.
V. Example System and Related Process Embodiments
[0122] To further illustrate exemplary embodiments of the
invention, FIGS. 9 A-G schematically depict a portion of a
representative system for nucleic acid amplification product
desalting and molecular mass measurement that includes a mixing
station as a sub-system component. The measured molecular masses of
the amplification products are typically used to determine base
compositions of the corresponding amplification products, which are
then generally correlated with the identities or organismal sources
of the initial template nucleic acids, for example, as part of a
research or in-vitro diagnostic application, among many others.
[0123] As shown in FIGS. 9 A-G, components of representative system
900 include microplate handling component or system 10, material
transfer component 902, mixing station 904, wash stations 906 and
908, sample processing component 910, and sample injector 912.
During operation, microplates are typically stored or positioned in
input non-priority microplate storage unit 12, output non-priority
microplate storage unit 14, priority microplate storage unit 16,
microplate processing area 18, and non-priority microplate holding
area 20 (e.g., on non-priority microplate holding component 22) of
microplate handling component 10. As also shown, microplate
handling component 10 also includes barcode reader 36. In the
exemplary embodiment shown, barcode reader 36 is configured to read
barcodes disposed on microplates when the microplates are disposed
in or proximal to non-priority microplate holding area 20, e.g., to
track the microplates or samples contained in the microplates in
microplate handling system 10. In some embodiments, for example,
non-priority microplates are stored in input non-priority
microplate storage unit 12 and priority microplates are stored in
priority microplate storage unit 16 after target regions of
template nucleic acids in those plates have been amplified, e.g.,
at a separate thermocycling station or nucleic acid amplification
component. Essentially any thermal cycling station or device is
optionally adapted for use with a system of the invention, such as
system 900. Examples of suitable thermocycling devices that are
optionally utilized are available from many different commercial
suppliers, including Mastercycler.RTM. devices (Eppendorf North
America, Westbury, N.Y., U.S.A.), the COBAS.RTM. AMPLICOR Analyzer
(Roche Molecular Systems, Inc., Pleasanton, Calif., U.S.A.),
MyCycler and iCycler Thermal Cyclers (Bio-Rad Laboratories, Inc.,
Hercules, Calif., U.S.A.), and the SmartCycler System (Cepheid,
Sunnyvale, Calif., U.S.A.), among many others. In other exemplary
embodiments, sample preparation components, nucleic acid
amplification components, and related fluid handling or material
transfer components are integrated with the systems described
herein, e.g., to fully automate a given nucleic acid amplification
and analysis process. Instruments that can be adapted for this
purpose include, for example, the m2000.TM. automated instrument
system (Abbott Laboratories, Abbott Park, Ill., U.S.A.), the
GeneXpert System (Cepheid, Sunnyvale, Calif., U.S.A.), and the
COBAS.RTM. AmpliPrep.RTM. System (Roche Molecular Systems, Inc.,
Pleasanton, Calif., U.S.A.), and the like.
[0124] Microplates are transferred from input non-priority
microplate storage unit 12 or priority microplate storage unit 16
to microplate processing area 18 using platform 28 of a microplate
transport mechanism. As referred to above and as shown in, e.g.,
FIGS. 9 F and G, platform 28 is operably connected to X-axis linear
motion component 38. X-axis linear motion component 38 includes
gantry 40. Platform 28 is operably connected to carriage 42, which
moves along gantry 40. As further shown in FIGS. 9 F and G,
microplate transport mechanism 26 also includes Y-axis linear
motion component 44 operably connected to carriage 42 and to
platform 28. Y-axis linear motion component 44 is configured to
raise and lower platform 28 along the Y-axis. Suitable linear
motion components, motors, and motor drives are generally available
from many different commercial suppliers including, e.g.,
Techno-Isel Linear Motion Systems (New Hyde Park, N.Y., U.S.A.), NC
Servo Technology Corp. (Westland, Mich., USA), Enprotech Automation
Services (Ann Arbor, Mich., U.S.A.), Yaskawa Electric America, Inc.
(Waukegan, Ill., U.S.A.), ISL Products International, Ltd.
(Syosset, N.Y., U.S.A.), AMK Drives & Controls, Inc. (Richmond,
Va., U.S.A.), Aerotech, Inc. (Pittsburgh, Pa., U.S.A.), HD Systems
Inc. (Hauppauge, N.Y., U.S.A.), and the like. Additional detail
relating to motors and motor drives are described in, e.g., Polka,
Motors and Drives, ISA (2002) and Hendershot et al., Design of
Brushless Permanent-Magnet Motors, Magna Physics Publishing (1994),
which are both incorporated by reference. Microplate handling
components are also described in, e.g., Attorney Docket No.
DIBIS-0116US.L, entitled "MICROPLATE HANDLING SYSTEMS AND RELATED
COMPUTER PROGRAM PRODUCTS AND METHODS" filed Sep. 16, 2008 by
Hofstadler et al., which is incorporated by reference in its
entirety.
[0125] Material transfer component 902 includes sample input gantry
914 and sample output gantry 916. Input gantry head 918 is
configured to move along sample input gantry 914, whereas output
gantry head 920 is configured to move along sample output gantry
916. Input gantry head 918 and output gantry head 920 each include
needles that are configured to aspirate and dispense fluidic
materials. Further, input gantry head 918 and output gantry head
920 are each configured to be raised and lowered along the Y-axis.
During operation of exemplary system 900, the needle or pipetting
tip of input gantry head 918 is typically used to aspirate an
aliquot of magnetically responsive particles (e.g., magnetically
responsive beads, such as BioMag.RTM. Plus Amine superparamagnetic
microparticles available from Bangs Laboratories, Inc., Fishers,
Ind., U.S.A.) that bind nucleic acids from a mixing cartridge
positioned at mixing station 904. Nucleic acid purification
involving magnetically responsive particles is also described in,
e.g., U.S. Patent App. Pub. No. US 2005/0164215, entitled "METHOD
FOR RAPID PURIFICATION OF NUCLEIC ACIDS FOR SUBSEQUENT ANALYSIS BY
MASS SPECTROMETRY BY SOLUTION CAPTURE," filed May 12, 2004 by
Hofstadler et al., and U.S. Patent App. Pub. No. US 2005/0130196,
entitled "METHOD FOR RAPID PURIFICATION OF NUCLEIC ACIDS FOR
SUBSEQUENT ANALYSIS BY MASS SPECTROMETRY BY SOLUTION CAPTURE,"
filed Sep. 17, 2004 by Hofstadler et al., which are both
incorporated by reference in their entirety. Optionally before, but
typically after aspirating the aliquot of magnetically responsive
particles (e.g., to minimize the possibility of cross-contaminating
samples), the needle of input gantry head 918 is also generally
used to aspirate an aliquot of an amplification product sample from
a selected well of a microplate positioned in microplate processing
area 18 of microplate handling system 10. The resulting mixture of
magnetically responsive particle and amplification product sample
aliquots disposed within the needle of input gantry head 918 is
then typically transferred to sample processing component 910 along
sample input gantry 914. After dispensing the mixture at sample
processing component 910, the needle of input gantry head 918 is
typically washed at wash station 906, e.g., to minimize the
probability of cross-contaminating samples, prior to repeating this
transfer cycle for other amplification product samples contained in
the wells of a given microplate (e.g., priority or non-priority
microplates) positioned in microplate processing area 18 of
microplate handling system 10.
[0126] In the embodiment shown, sample processing component 910 is
a desalting station that is used to desalt or otherwise purify
nucleic acid amplification products in the sample mixture prior to
mass spectrometric analysis. Sample processing component 910
includes carrier mechanism 922 (shown as a carousel), which
includes a plurality of sample processing units 924. In the
illustrated embodiment, each sample processing unit 924 includes
cuvette 926 and magnet 928. After a mixture of magnetically
responsive particle and amplification product sample aliquots is
dispensed into a given cuvette 926, that cuvette is typically
rotated in a clockwise direction on carrier mechanism 922 to
various positions within sample processing component 910 where
various reagents are added to and/or removed from that cuvette
(e.g., via various fluidic handling components of manifold 930) as
part of the process of purifying the amplification products
captured or otherwise bound to the magnetically responsive
particles in the mixture. When fluidic materials are removed from
the cuvette at a given position within sample processing component
910, the cuvette is typically moved proximal to the magnet of the
particular sample processing unit (e.g., cuvette 926 is moved
proximal to magnet 928 of sample processing unit 924) using a
conveyance mechanism to establish sufficient magnetic communication
between the magnet and the magnetically responsive particles such
that the magnetically responsive particles are moved to and
retained on an internal surface of the cuvette while fluidic
materials are removed from the cuvette. At the conclusion of a
purification process for a given sample, the purified amplification
products are then typically aspirated from the particular cuvette
using the needle of output gantry head 920. During or prior this
step, the nucleic acid amplification products are eluted from the
magnetically responsive particles. After purified amplification
products have been removed from a given cuvette, that cuvette is
then generally rotated on carrier mechanism 922 into communication
with cuvette wash station 927, where the cuvette is washed prior to
commencing another purification cycle involving the cuvette and
another sample. Sample processing components, such as sample
processing component 910 and related desalting/purification methods
are also described in, e.g., Attorney Docket No. DIBIS-0107US.L,
entitled "SAMPLE PROCESSING UNITS, SYSTEMS, AND RELATED METHODS"
filed Sep. 16, 2008 by Hofstadler et al., U.S. Patent App. Pub. No.
US 2005/0164215, entitled "METHOD FOR RAPID PURIFICATION OF NUCLEIC
ACIDS FOR SUBSEQUENT ANALYSIS BY MASS SPECTROMETRY BY SOLUTION
CAPTURE," filed May 12, 2004 by Hofstadler et al., and U.S. Patent
App. Pub. No. US 2005/0130196, entitled "METHOD FOR RAPID
PURIFICATION OF NUCLEIC ACIDS FOR SUBSEQUENT ANALYSIS BY MASS
SPECTROMETRY BY SOLUTION CAPTURE," filed Sep. 17, 2004 by
Hofstadler et al., and Hofstadler et al. (2003) "A highly efficient
and automated method of purifying and desalting PCR products for
analysis by electrospray ionization mass spectrometry" Anal
Biochem. 316:50-57, which are each incorporated by reference in
their entirety.
[0127] Purified and eluted amplification products that have been
aspirated from a particular cuvette of sample processing component
910 are typically transported along sample output gantry 916 to
sample injector 912 (shown as a two channel time-of-flight
injector) using output gantry head 920. That is, the amplification
products are typically dispensed from the needle or pipetting tip
of output gantry head 920 into one of the two channels of sample
injector 912, which generally comprise two independent sample
injection syringe pumps that are configured to receive the
amplification products. After dispensing the amplification products
at sample injector 912, the needle of output gantry head 920 is
typically washed at wash station 908 prior to aspirating another
purified amplification product sample from sample processing
component 910, e.g., to reduce the potential for carryover
contamination between samples.
[0128] Now referring to FIG. 10, which schematically shows
additional components of representative system 900 (sample
processing component 910 not shown) from a perspective view. As
shown, the additional components include dual sprayer module 932,
which includes two independent electrospray ionization sprayers,
and time-of-flight mass spectrometer 934. Amplification product
samples received at sample injector 912 are typically injected into
one of the two sprayers of dual sprayer module 932 for electrospray
ionization and mass measurement in time-of-flight mass spectrometer
934. As further shown, the additional components of representative
system 900 also include input/output device 936 (shown as a touch
screen monitor), computer 937, output device 939 (shown as a
printer), reagents and waste module 938, and chassis 940.
Input/output device 936, computer 937, and output device 939 are
components of a controller of system 900. Controllers are described
further herein. Reagents and waste module 938 provide reagent
sources and waste receptacles for system 900. Chassis 940 provides
mechanical support for microplate handling system 10, sample
processing component 910, and other components of system 900. To
further illustrate, FIGS. 11 A-C schematically show representative
system 900 with an external covering from various views.
[0129] In some embodiments, the base compositions of amplification
products are determined from detected molecular masses. In these
embodiments, base compositions are typically correlated with the
identity of an organismal source, genotype, or other attribute of
the corresponding template nucleic acids in a given sample.
Databases with base compositions and other information useful in
these processes are also typically included in these systems.
Suitable software and related aspects, e.g., for determining base
compositions from detected molecular masses and for performing
other aspects of base composition analysis are commercially
available from Ibis Biosciences, Inc. (Carlsbad, Calif.,
U.S.A.).
[0130] Particular embodiments of molecular mass-based detection
methods and other aspects that are optionally adapted for use with
the systems described herein are described in various patents and
patent applications, including, for example, U.S. Pat. Nos.
7,108,974; 7,217,510; 7,226,739; 7,255,992; 7,312,036; and
7,339,051; and US patent publication numbers 2003/0027135;
2003/0167133; 2003/0167134; 2003/0175695; 2003/0175696;
2003/0175697; 2003/0187588; 2003/0187593; 2003/0190605;
2003/0225529; 2003/0228571; 2004/0110169; 2004/0117129;
2004/0121309; 2004/0121310; 2004/0121311; 2004/0121312;
2004/0121313; 2004/0121314; 2004/0121315; 2004/0121329;
2004/0121335; 2004/0121340; 2004/0122598; 2004/0122857;
2004/0161770; 2004/0185438; 2004/0202997; 2004/0209260;
2004/0219517; 2004/0253583; 2004/0253619; 2005/0027459;
2005/0123952; 2005/0130196 2005/0142581; 2005/0164215;
2005/0266397; 2005/0270191; 2006/0014154; 2006/0121520;
2006/0205040; 2006/0240412; 2006/0259249; 2006/0275749;
2006/0275788; 2007/0087336; 2007/0087337; 2007/0087338
2007/0087339; 2007/0087340; 2007/0087341; 2007/0184434;
2007/0218467; 2007/0218467; 2007/0218489; 2007/0224614;
2007/0238116; 2007/0243544; 2007/0248969; WO2002/070664;
WO2003/001976; WO2003/100035; WO2004/009849; WO2004/052175;
WO2004/053076; WO2004/053141; WO2004/053164; WO2004/060278;
WO2004/093644; WO 2004/101809; WO2004/111187; WO2005/023083;
WO2005/023986; WO2005/024046; WO2005/033271; WO2005/036369;
WO2005/086634; WO2005/089128; WO2005/091971; WO2005/092059;
WO2005/094421; WO2005/098047; WO2005/116263; WO2005/117270;
WO2006/019784; WO2006/034294; WO2006/071241; WO2006/094238;
WO2006/116127; WO2006/135400; WO2007/014045; WO2007/047778;
WO2007/086904; and WO2007/100397; WO2007/118222, which are each
incorporated by reference as if fully set forth herein.
[0131] Exemplary molecular mass-based analytical methods and other
aspects of use in the systems described herein are also described
in, e.g., Ecker et al. (2005) "The Microbial Rosetta Stone
Database: A compilation of global and emerging infectious
microorganisms and bioterrorist threat agents" BMC Microbiology
5(1):19; Ecker et al. (2006) "The Ibis T5000 Universal Biosensor:
An Automated Platform for Pathogen Identification and Strain
Typing" JALA 6(11):341-351.; Ecker et al. (2006) "Identification of
Acinetobacter species and genotyping of Acinetobacter baumannii by
multilocus PCR and mass spectrometry" J Clin Microbiol.
44(8):2921-32.; Ecker et al. (2005) "Rapid identification and
strain-typing of respiratory pathogens for epidemic surveillance"
Proc Natl Acad Sci USA. 102(22):8012-7; Hannis et al. (2008)
"High-resolution genotyping of Campylobacter species by use of PCR
and high-throughput mass spectrometry" J Clin Microbiol.
46(4):1220-5; Blyn et al. (2008) "Rapid detection and molecular
serotyping of adenovirus by use of PCR followed by electrospray
ionization mass spectrometry" J Clin Microbiol. 46(2):644-51;
Sampath et al. (2007) "Global surveillance of emerging Influenza
virus genotypes by mass spectrometry" PLoS ONE 2(5):e489; Sampath
et al. (2007) "Rapid identification of emerging infectious agents
using PCR and electrospray ionization mass spectrometry" Ann N Y
Acad Sci. 1102:109-20; Hall et al. (2005) "Base composition
analysis of human mitochondrial DNA using electrospray ionization
mass spectrometry: a novel tool for the identification and
differentiation of humans" Anal Biochem. 344(1):53-69; Hofstadler
et al. (2003) "A highly efficient and automated method of purifying
and desalting PCR products for analysis by electrospray ionization
mass spectrometry" Anal Biochem. 316:50-57; Hofstadler et al.
(2006) "Selective ion filtering by digital thresholding: A method
to unwind complex ESI-mass spectra and eliminate signals from low
molecular weight chemical noise" Anal Chem. 78(2):372-378.; and
Hofstadler et al. (2005) "TIGER: The Universal Biosensor" Int J
Mass Spectrom. 242(1):23-41, which are each incorporated by
reference.
[0132] In addition to the molecular mass and base composition
analyses referred to above, essentially any other nucleic acid
amplification technological process is also optionally adapted for
use in the systems of the invention. Other exemplary uses of the
systems and other aspects of the invention include immunoassays,
cell culturing, cell-based assays, compound library screening, and
chemical synthesis, among many others. Many of these as well as
other exemplary applications of use in the systems of the invention
are also described in, e.g., Current Protocols in Molecular
Biology, Volumes I, II, and III, 1997 (F. M. Ausubel ed.); Perbal,
1984, A Practical Guide to Molecular Cloning; the series, Methods
in Enzymology (Academic Press, Inc.); Sambrook et al., 2001,
Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring
Harbor Laboratory Press, Cold Spring Harbor, N.Y.; Oligonucleotide
Synthesis, 1984 (M. L. Gait ed.); Nucleic Acid Hybridization, 1985,
(Hames and Higgins); Transcription and Translation, 1984 (Hames and
Higgins eds.); Animal Cell Culture, 1986 (R. I. Freshney ed.);
Berger and Kimmel, Guide to Molecular Cloning Techniques, Methods
in Enzymology volume 152 Academic Press, Inc., San Diego, Calif.
(Berger), DNA Cloning: A Practical Approach, Volumes I and II, 1985
(D. N. Glover ed.); Immobilized Cells and Enzymes, 1986 (IRL
Press); Gene Transfer Vectors for Mammalian Cells, 1987 (J. H.
Miller and M. P. Calos eds., Cold Spring Harbor Laboratory); and
Methods in Enzymology Vol. 154 and Vol. 155 (Wu and Grossman, and
Wu, eds., respectively), which are each incorporated by
reference.
VI. Example Kits and Related Methods
[0133] In certain embodiments, the mixing cartridges of the
invention are provided in kits. To illustrate, in some embodiments,
kits include only empty mixing cartridges, whereas in other
exemplary embodiments kits also include material disposed in the
cavities of mixing cartridges and/or in separate containers. The
material included in a given kit typically depends on the intended
purpose of the mixing cartridges (e.g., for use in a nucleic acid
or protein purification process, for use in a cell culture process
or screening application, for use in a painting or printing
application, for use in chemical synthetic processes, etc.).
Accordingly, non-limiting examples of materials optionally included
in kits are magnetically responsive particles (e.g., magnetically
responsive beads, etc.), water, solvents, buffers, reagents, cell
culture media, cells, paint, ink, biopolymers (e.g., nucleic acids,
polypeptides, etc.), solid supports (e.g., controlled pore glass
(CPG), etc.), and the like. Kits typically also include
instructions for mixing the fluidic materials in the cartridges
and/or loading the materials into the cavity of the cartridge. In
addition, kits also generally include packaging for containing the
cartridge(s), the separate container(s), and/or the
instructions.
[0134] Kits are typically provided in response to receiving an
order from a customer. Orders are received through a variety of
mechanisms including, e.g., via a personal appearance by the
customer or an agent thereof, via a postal or other delivery
service (e.g., a common carrier), via a telephonic communication,
via an email communication or another electronic medium, or any
other suitable method. Further, kits are generally supplied or
provided to customers (e.g., in exchange for a form of payment) by
any suitable method, including via a personal appearance by the
customer or an agent thereof, via a postal or other delivery
service, such as a common carrier, or the like.
VII. Example Fabrication Methods and Materials
[0135] Mixing cartridges or components thereof, cartridge
receiver/rotation assemblies, and system components (e.g., mixing
stations, microplate storage units, microplate transport
mechanisms, support bases, sample processing components, etc.) are
optionally formed by various fabrication techniques or combinations
of such techniques including, e.g., machining, embossing,
extrusion, stamping, engraving, injection molding, cast molding,
etching (e.g., electrochemical etching, etc.), or other techniques.
These and other suitable fabrication techniques are generally known
in the art and described in, e.g., Molinari et al. (Eds.), Metal
Cutting and High Speed Machining, Kluwer Academic Publishers
(2002), Altintas, Manufacturing Automation: Metal Cutting
Mechanics, Machine Tool Vibrations, and CNC Design, Cambridge
University Press (2000), Stephenson et al., Metal Cutting Theory
and Practice, Marcel Dekker (1997), Fundamentals of Injection
Molding, W. J. T. Associates (2000), Whelan, Injection Molding of
Thermoplastics Materials, Vol. 2, Chapman & Hall (1991),
Rosato, Injection Molding Handbook, 3.sup.rd Ed., Kluwer Academic
Publishers (2000), Fisher, Extrusion of Plastics, Halsted Press
(1976), and Chung, Extrusion of Polymers: Theory and Practice,
Hanser-Gardner Publications (2000), which are each incorporated by
reference. Exemplary materials optionally used to fabricate mixing
cartridges, mixing stations, or components thereof include
polymethylmethacrylate, polyethylene, polydimethylsiloxane,
polyetheretherketone, polytetrafluoroethylene, polystyrene,
polyvinylchloride, polypropylene, polysulfone, polymethylpentene,
and polycarbonate, among many others. In some embodiments, mixing
cartridges or components thereof are fabricated as disposable or
consumable components of mixing stations or related systems. In
certain embodiments, following fabrication, system components are
optionally further processed, e.g., by coating surfaces with a
hydrophilic coating, a hydrophobic coating (e.g., a Xylan
1010DF/870 Black coating available from Whitford Corporation (West
Chester, Pa.), etc.), or the like, e.g., to prevent interactions
between component surfaces and reagents, samples, or the like.
[0136] While the foregoing invention has been described in some
detail for purposes of clarity and understanding, it will be clear
to one skilled in the art from a reading of this disclosure that
various changes in form and detail can be made without departing
from the true scope of the invention. For example, all the
techniques and apparatus described above can be used in various
combinations. All publications, patents, patent applications,
and/or other documents cited in this application are incorporated
by reference in their entirety for all purposes to the same extent
as if each individual publication, patent, patent application,
and/or other document were individually indicated to be
incorporated by reference for all purposes.
* * * * *