Abstract: A vessel holder assembly is provided. A vessel holder, for receiving one or more vessels, includes a first set of attachment features. A cap assembly, for covering the vessel(s) includes a second set of attachment features. Respective attachment features of the vessel holder and the cap assembly may be complementary, such that engagement between complementary attachment members results in an attachment between the cap assembly and the vessel holder. Such an attachment may be manually removable, or may be locked so as to require a tool, or other suitable method, for detaching the cap assembly from the vessel holder.

Abstract: Systems and methods for processing tissue samples using acoustic energy. The tissue sample may be collected and placed on a substrate (e.g., microscope slide), or other sample holder. A transfer substrate may be positioned on the other side of the sample opposite the substrate. A microscope incorporated with the acoustic treatment system may be used to view, identify and select a portion of the sample to be transferred from the initial substrate to the transfer substrate. The selected portion of the sample is exposed to focused acoustic energy while disposed between the two substrates. The focused acoustic energy has characteristics (e.g., high frequency, small focal zone) that may be effective to transfer the selected portion of the sample from the initial substrate to the transfer substrate. Such transfer may occur with little to no damage to the sample, for example, at low temperature isothermal conditions and/or little to no cavitation of or around the sample.

Abstract: Methods and systems for treating material with focused acoustic energy and/or ultraviolet radiation are described. Sample material may be provided to a single batch vessel or may flow in a continuous or intermittent fashion into/out of a processing chamber within which the material is exposed to focused acoustic energy and/or ultraviolet radiation. Exposure to focused acoustics in a flow through environment may enhance the effects of the radiation on the sample material. Further, in flow-through or single batch arrangements, sample material may be retained exterior to or within a processing chamber by one or more retaining members (e.g., filter, valve, etc.) until a characteristic of the sample material reaches one or more particular criteria (e.g., physical, chemical, biological). Once the criteria of the sample material is attained (e.g., via further treatment), the material is then permitted to flow past the retaining member(s) and through the inlet or outlet of the chamber.

Abstract: Method and apparatus for controlling acoustic treatment of a sample to mediate a tagmentation process used on double stranded DNA.

Abstract: Method and apparatus for holding and/or transferring a sample material into a second holder. The sample holder may comprise a shoulder arranged on the outer surface to engage a second holder and to position a top opening of the sample holder for communication with the second holder. A sample may be expelled from a sample holder using a piston that moves from a lower portion to an upper portion of the sample holder.

Abstract: Method and apparatus for controlling acoustic treatment of a sample including a liquid. A processing volume in which the sample is acoustically treated may be controlled, e.g., by positioning a suitable element so as to reduce and/or eliminate a headspace at a sample/gas interface. An interaction between the acoustic energy and the sample may be controlled, e.g., by using an energy director positioned at least partially in the sample that helps to reduce splashing or other sample ejection that would otherwise occur.

Abstract: A treatment vessel may allow a user, or automated system, to manipulate sample material within a treatment area during processing (e.g., focused acoustic treatment), as well as subject the sample material to a staged processing protocol. The vessel may include openings for receiving/discharging the sample material. Walls within the vessel may be movable between various positions, to permit or obstruct flow of sample material into or out from a treatment area. The wall(s) may push the sample material within the vessel, as well as adjust pressure levels within the treatment area. In some embodiments, an acoustic treatment system may include a flexible coupling medium that may be deformed toward the vessel upon an application of suitable pressure thereto. When the medium presses up against the vessel, defects (e.g., particles, bubbles, interfaces, etc.) that may otherwise be present along the acoustic wave path may be reduced.

Abstract: The present disclosure relates to a composition that includes an apolipoprotein and a lipid bilayer, and methods and systems for preparing the composition. The apolipoprotein may be incorporated within at least a portion of the lipid bilayer. The lipid bilayer may form a liposome or other suitable carrier for transporting the apolipoprotein. The apolipoprotein incorporated lipid bilayer may provide a suitable delivery vehicle for the apolipoprotein to the body. Compositions of the present disclosure may be formed by exposing a mixture of an apolipoprotein and a lipid formulation to focused acoustic energy which, in some embodiments, may result in a liposome that at least partially encapsulates the apolipoprotein. In some embodiments, apolipoprotein A-V may be incorporated within a liposome, where the apolipoprotein A-V is suitably bioactive, or therapeutic, when delivered to cells and/or into the body of a patient.

Abstract: Systems and methods are described for transfer of tissue samples from a substrate to a vessel, for subsequent processing (e.g., focused acoustic treatment) within the vessel. A transfer apparatus, having a transfer end and a handle end, may be used to collect a sample material from the substrate. When the sample material is collected from the substrate, the transfer end may be placed within a vessel for treatment of the sample material while the transfer end is also located within the vessel. In some embodiments, the transfer end may be decoupled or otherwise separated from the handle end so that only the transfer end portion of the transfer apparatus is located within the vessel during treatment.

Abstract: This invention relates to systems and methods for applying acoustic energy to a sample. According to one aspect of the invention, a system comprises a housing, a chamber for receiving the sample, an acoustic energy source for providing a focused acoustic field to the sample according to a treatment protocol, a processor for determining the treatment protocol, a sensor for detecting information about the sample, and a user interface for communicating with a user.

Abstract: Method and apparatus for processing paraffin embedded samples, e.g., to disassociate paraffin from tissue components and/or other biomolecules from the paraffin. The sample may be exposed to focused acoustic energy while held in a vessel containing a non-solvent, aqueous solution. Disassociated paraffin may be emulsified into the liquid or otherwise separated from the sample.

Abstract: Methods and systems for acoustically treating material using a continuous process in which material may be caused to flow in a continuous or intermittent fashion into/out of an acoustic treatment chamber where the material is exposed to focused acoustic energy. The methods and systems may be arranged to permit continuous processing for extended periods while an acoustic energy source operates at a relatively high power output. Treatment chambers may include features such as an acoustic window and/or a chamber wall which may comprise an acoustically reflective material or a gas/wall interface that serves to reflect acoustic energy to form one or more secondary focal zones. Treatment system configurations relating to arrangements of a treatment chamber relative to an acoustic source and coupling medium, material flow paths, and others are provided.

Abstract: Methods and systems for acoustically treating material using a continuous process in which material may be caused to flow in a continuous or intermittent fashion into/out of an acoustic treatment chamber where the material is exposed to focused acoustic energy. The methods and systems may be arranged to permit continuous processing for extended periods while an acoustic energy source operates at a relatively high power output. Treatment chambers may include features such as an acoustic window, a heat exchanger, inlet/outlet flow arrangements, an inspection window, insert elements that define a treatment volume size or shape, etc. Treatment system configurations relating to arrangements of a treatment chamber relative to an acoustic source and coupling medium, material flow paths, and others are provided.

Abstract: Systems and methods include processing devices used to fragment nucleic acids to average nucleic acid sizes ranging from between about 5 kbp and about 20 kbp. A processing device may include an inlet portion and a channel upstream from a shearing region arranged so that a relatively constant pressure is established and maintained (e.g., a pressure that changes by less than about 40%) at an entrance of the shearing region during a majority of sample flow through the shearing region. In some embodiments, after forcing the sample through the shearing region once, the processing device may be taken out of the centrifuge, inverted and placed back into the centrifuge so that the sample is forced through the shearing region again.

Abstract: Method and apparatus for holding and/or treating a sample material. A sample may be positioned in a vessel and a crushing force may be applied to the sample material while in the vessel, e.g., by a plunger that is part of a cap to pulverize the sample at cryogenic temperatures. The sample holder may include an acoustic window arranged to admit acoustic energy into the vessel for acoustic treatment of the sample. A flexible film may be used at a portion of the vessel, e.g., at the acoustic window, to cooperate with a plunger for crushing a sample.

Abstract: Method and apparatus for processing paraffin embedded samples, e.g., to disassociate paraffin from tissue components and/or other biomolecules from the paraffin. The sample may be exposed to focused acoustic energy while held in a vessel containing a non-solvent, aqueous solution. Disassociated paraffin may be emulsified into the liquid or otherwise separated from the sample.

Abstract: Methods and systems for acoustically treating material using a continuous process in which material may be caused to flow in a continuous or intermittent fashion into/out of an acoustic treatment chamber where the material is exposed to focused acoustic energy. The methods and systems may be arranged to permit continuous processing for extended periods while an acoustic energy source operates at a relatively high power output. Treatment chambers may include features such as an acoustic window and/or a chamber wall which may comprise an acoustically reflective material or a gas/wall interface that serves to reflect acoustic energy to form one or more secondary focal zones. Treatment system configurations relating to arrangements of a treatment chamber relative to an acoustic source and coupling medium, material flow paths, and others are provided.

Abstract: Method and apparatus for controlling acoustic treatment of a sample including a liquid. A processing volume in which the sample is acoustically treated may be controlled, e.g., by positioning a suitable element so as to reduce and/or eliminate a headspace size at a sample/gas interface. An interaction between the acoustic energy and the sample may be controlled, e.g., by using a headspace control element positioned at least partially in the sample that helps to reduce splashing or other sample ejection that would otherwise occur.

Abstract: Methods and systems for acoustically treating material are described. Acoustic energy is emitted into a waveguide having a wall with a shape that tapers away from the acoustic source. The wall may have a substantially conical or parabolic shape. When emitted therein, the waveguide causes convergence of the acoustic energy so as to form an acoustic focal zone at a vessel. In some embodiments, a substantial portion of the acoustic focal zone is located outside of the internal volume defined by the waveguide.

Abstract: Method and apparatus for controlling acoustic treatment of a sample including a liquid. A processing volume in which the sample is acoustically treated may be controlled, e.g., by using a bead positioned in the sample that helps to enhance the shearing effects of acoustic energy on genomic fragments.