Patent Application 17769321 - AUTOMATED TREATMENT OF MACROMOLECULES FOR

Title: AUTOMATED TREATMENT OF MACROMOLECULES FOR ANALYSIS AND RELATED APPARATUS

Application Information

Invention Title: AUTOMATED TREATMENT OF MACROMOLECULES FOR ANALYSIS AND RELATED APPARATUS
Application Number: 17769321
Submission Date: 2025-04-08T00:00:00.000Z
Effective Filing Date: 2022-04-14T00:00:00.000Z
Filing Date: 2022-04-14T00:00:00.000Z
National Class: 422
National Sub-Class: 063000
Examiner Employee Number: 94761
Art Unit: 1798
Tech Center: 1700

Rejection Summary

102 Rejections: 0
103 Rejections: 7

Cited Patents

The following patents were cited in the rejection:

Office Action Text

DETAILED ACTION

Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .

Preliminary Amendment
The preliminary amendments of claims, filed 10/26/2023, has been fully considered.

Status of Claims
Claim 1-4, 8-9, 11, 13, 15, 17-18, and 24-33 are pending and under examination.
Claims 5-7, 10, 12, 14, 16, 19-23, and 34-159 have been canceled.

Information Disclosure Statement
The information disclosure statement (IDS) document(s) submitted on 11/15/2022 and 10/26/2023 is/are compliant with the provisions of 37 CFR 1.97. Accordingly, the IDS document(s) has/have been fully considered by the examiner.

Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.

The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.

The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.

This application includes one or more claim limitations that use the word “means” or “step” but are nonetheless not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph because the claim limitation(s) recite(s) sufficient structure, materials, or acts to entirely perform the recited function. Such claim limitation(s) is/are:
“a porous means … to allow a liquid to pass through and evacuate the sample, while maintaining the immobilized macromolecule in the sample container” in claim 13.
“a means for accelerating a reaction … the means for accelerating the reaction is configured to apply microwave energy to accelerate the reaction” in claim 15.
“a means for monitoring the apparatus … configured to monitor temperature, pressure, flow, air bubble formation, position of one or more of the valves, refractive index and conductance”.

For purposes of examination, the examiner is interpreting claim limitation “porous means” as a porous material with a pore size capable of blocking macromolecules and allow a fluid to pass.
For purposes of examination, the examiner is interpreting claim limitation “means for accelerating a reaction” as a device that emits or produces microwave energy.
For purposes of examination, the examiner is interpreting claim limitation “means for monitoring the apparatus” as any device that measures, quantifies, or evaluates temperature, pressure, flow, bubble formation, position, refractive index and conductance.
Because this/these claim limitation(s) is/are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, it/they is/are not being interpreted to cover only the corresponding structure, material, or acts described in the specification as performing the claimed function, and equivalents thereof.
If applicant intends to have this/these limitation(s) interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, applicant may: (1) amend the claim limitation(s) to remove the structure, materials, or acts that performs the claimed function; or (2) present a sufficient showing that the claim limitation(s) does/do not recite sufficient structure, materials, or acts to perform the claimed function.

The interpretations of the following limitations are not interpreted under 112(f), but are set forth to make the record clear:
“one or more non-planar sample container(s) with a volume equal to or less than about 20 mL” in claim 1.
“the one or more non-planar sample container(s) is/are characterized by having a ratio between a height and a largest dimension from about 1:1 to about 100:1” in claim 1.

A review of applicant specification states “The term “about” as used herein refers to the usual error range for the respective value readily known to the skilled person in this technical field. Reference to “about” a value or parameter herein includes (and describes) embodiments that are directed to that value or parameter per se. For example, description referring to “about X” includes description of “X.”
For purposes of examination, claim limitation “one or more non-planar sample container(s) with a volume equal to or less than about 20 mL” is being interpreted as 20 mL or less within a usual error range known in the art.
For purposes of examination, claim limitation “the one or more non-planar sample container(s) is/are characterized by having a ratio between a height and a largest dimension from about 1:1 to about 100:1” is being interpreted as ratio’s within usual error ranges known in the art.

Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.

The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.

Claims 1-4, 8-9, 11, 13, 15, 17-18, 24-33 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor, or for pre-AIA the applicant regards as the invention.

Claim 32 recites “a sample ... an apparatus … a non-planar sample container … a macromolecule analyte ... a reagent”. However, claim 32 incorporates the limitations of independent claim 1 which previously recites the terms above. It is unclear if applicant is referring to the terms from the apparatus in claim 1 or if applicant is introducing different features of the claimed invention. Perhaps applicant is intending to recite “the sample ... the apparatus … one of the non-planar sample container(s) … the macromolecule analyte … the reagent”?

Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.

The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.

Claims 1-2, 4, 8-9, 11, 24-25, 30 are rejected under 35 U.S.C. 103 as being unpatentable over Henzel (WO 0012994A1 – hereinafter “Henzel”) and further in view of Chen et al. (US 2008/0305142 – hereinafter “Chen”).

Regarding claim 1, Henzel disclose an apparatus for automated treatment of a sample comprising an immobilized macromolecule analyte (Henzel disclose an apparatus 10 for rapid protein sequence analysis of multiple samples 12; p. 5 line 32 through p. 6 line 4; fig. 1A. Specifically, Henzel disclose the apparatus 10 may be used for a method of immobilizing proteins and polypeptides of interest onto a PVDF membrane; p. 34 lines 11-13), which apparatus comprises:
one or more non-planar sample container(s) with a volume equal to or less than about 20 mL (Henzel disclose a sample cartridge 20 having a 1/16 inch internal diameter with a length of 15-20 mm; p. 34 lines 33-36. Accordingly, Henzel disclose a cylindrical having an internal diameter equal to 1.5875 mm (r=0.79375 mm) a maximum volume of

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, which is less than about 20 mL) wherein the one or more non-planar sample container(s) is/are characterized by having a ratio between a height and a largest dimension from about 1:1 to about 100:1 (Henzel disclose a diameter equal to about 1.6 mm and a length of about 16 mm; p. 34 lines 33-36. Accordingly, Henzel disclose a ratio of a height to a largest dimension from about 10:1); and
at least one of said sample container(s) is subjected to temperature control and configured for allowing fluid flow-through, or a holder or space configured for holding said sample container(s) (Henzel disclose a heater 74 for individually heating each sample cartridge 20; figs. 1A & 2A, p. 9 lines 6-21. The sample cartridge 20 comprises an inlet 52 and an outlet 62 to allow fluid flow through a chamber 64; figs. 1A & 2A, p. 8 lines 13-16. Sample cartages 20 are held by a cartridge holder 22; fig. 1A, p. 8 lines 22-24. Note: “container(s)” implies either 1 container or a plurality of containers. The claims to not positively define either (i) a single container or (ii) a plurality of containers. Accordingly, if the prior art teaches one of the alternatives (i.e., (i) one container or (ii) a plurality of containers) that meets the limitation, then the prior art reads on the claims);
a plurality of reagent reservoirs for containing a respective reagent (Henzel disclose reagents 30 are delivered to the sample cartridges 20 by a delivery device 14; fig. 1A, p. 6 lines 18-24),
a plurality of valves connected in a supply line having an upstream end and a downstream end (Henzel disclose a reagent delivery device 14 for delivering a predetermined volume of one or more selected solvents and reagents 30 to the apparatus sample cartridges 20; fig. 1A, p. 6 lines 18-22. A reagent tube 46 supplies the solvents and reagents 30 to an upstream end 44 from a downstream end 36; fig. 1A, p. 7 lines 5-10. Henzel also disclose a multi-port, multi-position, radial valve 43 connecting the upstream end of supply line 46 to a downstream supply tube 50; fig. 1A, p. 7, lines 6-19. The multi-port, multi-position, radial valve 43 comprises internal valves for selecting desired ports; p. 7 lines 11-31),
wherein at least one or each of said valves is positionable to provide alternate flow paths therethrough (Henzel disclose the reagents 30 are selectable through the reagent delivery device 14; p. 6 lines 18-22. The multi-purpose, radial valve 43 comprises internal valves for selecting desired ports; fig. 1A, p. 7 lines 11-31); and
a control unit to control delivery of said one or more reagent(s) to said sample container(s) (Henzel disclose an apparatus controller 24; fig. 1A, p. 5 line 32 through p. 6 line 4. The apparatus controller 24 is connected to control valve 43 so the solvents or reagents 30 can be independently delivered to the appropriate sample cartridge 20; p. 6 lines 18-19 and p. 7 lines 32-37 and p. 10 lines 3-14), wherein:
said apparatus is configured to hold at least 5 reagent reservoirs (Henzel; fig. 1A. See also Method 1, R1-R5, p. 18 line 10 through p. p. 30 line 30);
delivery of said one or more reagent is individually addressable (Henzel; p. 6 lines 18-19 and p. 7 lines 32-37),
said supply line connects said reagent reservoirs to said sample container(s) and said reagent reservoirs are fluidically connected to said sample container(s) (Henzel; fig. 1A, #46, #50), and
at least temperature control of said sample container(s), positioning of said valve(s) and/or delivery of said one or more reagent(s) to said sample container(s) is automated and controlled by said control unit (Henzel disclose at least temperature control of said sample container(s); p. 9 lines 14-30. Henzel disclose positioning of said valve(s); p. 10 lines 3-14. Lastly, Henzel disclose delivery of said one or more reagent(s) to said sample containers; p. 6 lines 18-19).
Henzel does not teach wherein at least one of said reagent reservoirs is subjected to temperature control, and contains an enzyme as a reagent, or temperature control of said reagent reservoir(s) is automated and controlled by said control unit. However, Chen teach the analogous art of an apparatus for automated treatment of a sample (Chen; fig. 5, [0038]) comprising a plurality of reagent reservoirs for containing a respective reagent, wherein at least one of said reagent reservoirs is subjected to temperature control, and contains an enzyme as a reagent, and temperature control of said reagent reservoir(s) is automated and controlled by said control unit (Chen; fig. 5, “(3)” [0038]). It would have been obvious to one of ordinary skill in the art before the effective filing date to modify the plurality of reagent reservoirs of Henzel to contain an enzyme and be subjected to temperature control by a control unit, as taught by Chen, because Chen teaches the plurality of reagents that contains an enzyme as a reagent can be used to produce large amounts of nucleic acids in small volumes, in short periods of time, with the need for only minimal and inexpensive purification procedures, thus producing high-quality therapeutic grade nucleic acids for any basic analytical or research purpose; [0025], wherein temperature control of the reagents can maintain shelf life, prevent degradation, and reduce contamination of the reagents. One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since Henzel and Chen teach automated systems for treatment of a sample with a plurality of reagents.

Regarding claim 2, modified Henzel teach the apparatus of claim 1 above, wherein at least one of the sample container(s) is subjected to active heating and active cooling (Henzel; p. 9 lines 14-15); and
at least one of the reagent reservoirs is subjected to active heating and/or active cooling (The modification of the plurality of reagent reservoirs of Henzel to contain an enzyme and be subjected to temperature control by a control unit, as taught by Chen, has previously been discussed in claim 1 above. Chen teach a temperature controlled environment for the reagents and is therefore capable of temperate adjustment).

Regarding claim 4, modified Henzel teach the apparatus of claim 1 above, which further comprises at least one pump for delivering the one or more reagents to the sample container(s) (Henzel disclose the apparatus prepares a pump for performing a method; p. 25, Step 22).

Regarding claim 8, modified Henzel teach the apparatus of claim 1 above, wherein the apparatus is configured to hold at least 10 reagent reservoirs (Henzel p. 28 R1-S2 through p. 29 S3-X3).

Regarding claim 9, modified Henzel teach the apparatus of claim 1 above, wherein the apparatus is configured to hold reagents.
Modified Henzel does not explicitly teach wherein the apparatus is configured to hold at least 20 reagent reservoirs. However, it would have been obvious to modify the apparatus to be configured to hold at least 20 reagents because modifying the apparatus to hold at least 20 reagents is merely a change in size/proportion which would provide the additional benefit of increasing the number of assays/protocols capable of being performed by the system. One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since the modification amounts to a change in size/proportion is considered routine expedients and does not patentably distinguish over the prior art (See MPEP 2144.04 (IV)(A)).

Regarding claim 11, modified Henzel teach the apparatus of claim 1 above, wherein the apparatus is configured to hold two or more sample containers, each is subjected to temperature control and configured for allowing fluid flow-through (Henzel; figs. 1A and 2A, p. 8 lines 34-37, p. 9 lines 14-30).

Regarding claim 24, modified Henzel teach the apparatus of claim 1 above, which comprises at least one reagent reservoir comprising a binding agent, at least one reagent reservoir comprising a reagent for transferring information, at least one reagent reservoir comprising a reagent for removing a terminal amino acid of a polypeptide, and at least one reservoir comprising a reagent for a capping reaction (Henzel disclose reagents 30 are delivered to the sample cartridges 20 by a delivery device 14; fig. 1A, p. 6 lines 18-24).
Note: Claim 24 contain a large amount of functional language or language related to intended use (e.g. “for transferring … for removing … for capping”). However, functional language does not add any further structure to an apparatus beyond that of a capability. Apparatus claims must distinguish over the prior art in terms of structure rather than function. The broadest reasonable interpretation of a system (or apparatus or product) claim having structure that performs a function, which only needs to occur if a condition precedent is met, requires structure for performing the function should the condition occur (see MPEP 2114). Therefore, if the prior art structure is capable of performing the function, then the prior art meets the limitation in the claims.

Regarding claim 25, modified Henzel teach the apparatus of claim 24 above, wherein at least two of the reagent reservoirs comprising a binding agent, reagents for transferring information, reagents for removing a terminal amino acid of a polypeptide, and reagents for a capping reaction are subjected to temperature control.
Note: Claim 25 contain a large amount of functional language or language related to intended use (e.g. “for transferring … for removing … for capping”). However, functional language does not add any further structure to an apparatus beyond that of a capability. Apparatus claims must distinguish over the prior art in terms of structure rather than function. The broadest reasonable interpretation of a system (or apparatus or product) claim having structure that performs a function, which only needs to occur if a condition precedent is met, requires structure for performing the function should the condition occur (see MPEP 2114). Therefore, if the prior art structure is capable of performing the function, then the prior art meets the limitation in the claims.

Regarding claim 30, modified Henzel teach the apparatus of claim1 above.
Modified Henzel does not teach wherein at least one of the reagent reservoirs with a smaller volume is located closer to the sample container(s) than a reagent reservoir with a larger volume. However, modified Henzel teach the apparatus of claim 1 comprising the reagent reservoirs and sample containers. It would have been obvious to one of ordinary skill in the art before the effective filing date to modify the arrangement of the reagent reservoirs to move a reagent reservoir with a smaller volume close to the sample container(s) than a reagent reservoir with a larger volume because the arrangement order is merely a rearrangement of parts which would require less tubing to fill with reagent in order to treat the sample, thus preserving the reagent having a lesser volume. One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since the modification is considered routine expedients (See MPEP 2144.04(VI)(c)).

Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Henzel in view of Chen, and further in view of Kalra et al. (US 2006/0153736 – hereinafter “Kalra”).

Regarding claim 3, modified Henzel teach the apparatus of claim 2 above, wherein the temperature of the sample container(s) subjected to temperature control and are individually controlled by the control unit, and the sample container(s) subjected to temperature control and are housed in separate thermal blocks (Henzel; fig. 2A, p. 9 lines 14-15).
Modified Henzel does not teach the temperature of the reagent reservoir(s) is subjected to temperature control are individually controlled by the control unit, and the reagent reservoir(s) subjected to temperature control are housed in separate thermal blocks.
However, Kalra teach the analogous art of an apparatus for automated treatment of a sample (Kalra; [00230]), a control unit (Kalra; figs. 6A-6C, #608, [0078]) configured to individually control a plurality of reagent reservoirs in separate thermal blocks (Kalra; figs. 6A-6C, #630, [0038-0039, 0078]).
It would have been obvious to one of ordinary skill in the art before the effective filing date to modify the temperature control unit and plurality of reagent containers of modified Henzel to comprise individually controlled thermal blocks to house the plurality of containers and individually control the temperature, as taught by Karla, because Karla teaches the individual control of thermal blocks allows the plurality of reagents to be maintained at different selected temperatures (Karla; [0039]). One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since modified Henzel and Karla both teach systems for automated treatment of a sample with temperature-controlled environments.

Claim 13 is rejected under 35 U.S.C. 103 as being unpatentable over Henzel in view of Chen, and further in view of Grenz et al. (US 2012/0103421 – hereinafter “Grenz”).

Regarding claim 13, modified Henzel teaches the apparatus of claim 1 above, comprising the at least one sample container(s).
Modified Henzel does not teach wherein at least one of the sample container(s) comprises: a porous means, a porous membrane or a frit to allow a liquid to pass through and evacuate the sample container, while maintaining the immobilized macromolecule in the sample container.
However, Grenz teach the analogous art of at least one sample container(s) (Grenz; fig. 1, #100, [0028]), wherein the at least one sample container(s) comprise: a porous means, a porous membrane (Grenz; fig. 2, #232, [0029]) or frit (Grenz; fig. 2, #234, 236, [0029]) to allow a liquid to pass through and evacuate the sample container, while maintaining the immobilized macromolecule in the sample container, while maintaining the immobilized macromolecule in the sample container (Grenz; [0029]).
It would have been obvious to one of ordinary skill in the art before the effective filing date to modify at least one sample container(s) of modified Henzel to comprise a porous means, a porous membrane or frit, as taught by Grenz, because Grenz teaches the sample container comprising a porous means, a porous membrane or frit functions to block the passage of particulates of a desired size range or retain analytes such as by adsorption in a manner analogous to solid phase extraction or chromatography (Grenz; [0029]). One of ordinary skill in the art would have expected the modification could have been performed with a reasonable expectation of success since modified Henzel and Grenz both teach sample container(s) comprising a sample.

Claim 15 is rejected under 35 U.S.C. 103 as being unpatentable over Henzel in view of Chen, and further in view of Lambert et al. (US 2008/0245787 – hereafter “Lambert”).

Regarding claim 15, modified Henzel teaches the apparatus of claim 1 above, which further comprises a means for accelerating a reaction in at least one of the sample container(s), wherein the means for accelerating the reaction (Henzel teach heater 74 expedites the reactions within the sample cartridges 20; p. 9 lines 6-7).
Modified Henzel does not teach the means for accelerating the reaction is configured to apply microwave energy to accelerate the reaction in the at least one of the sample container(s).
However, Lambert teach the analogous art of a means for accelerating a reaction in at least one sample container(s) (Lambert; [0001]), wherein the means for accelerating the reaction is configured to apply microwave energy to accelerate the reaction in the at least one of the sample container(s) (Lambert; [0001-0004]).

Claim 17 is rejected under 35 U.S.C. 103 as being unpatentable over Henzel in view of Chen, and further in view of Lebedev et al. (US 2016/0121326 – hereinafter “Lebedev”).

Regarding claim 17, modified Henzel teach the apparatus of claim 1 above, which further comprises a means for monitoring the apparatus, wherein the monitoring means is configured to monitor temperature (Henzel; p. 9 lines 22-30), pressure (Henzel; p. 16, lines 1-5), flow (Henzel; p. 15, lines 10-23), position of one or more of the valves (Henzel; p. 10, lines 3-14).
Modified Henzel does not teach the means for monitoring is configured to monitor air bubble formation. However, Kozikowski teach the analogous art of a monitoring means wherein the monitoring means is configured to monitor air bubble formation (Kozikowski; [0030]). It would have been obvious to one of ordinary skill in the art before the effective filing date to modify the monitoring mean of modified Henzel to comprise the monitoring means configured to monitor air bubble formation, as taught by Kozikowski, because Kozikowski teach the monitoring means configured to monitor air bubble formation can improve the accuracy of analysis results after treatment of a sample (Kozikowski; [0004]). One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since modified Henzel and Kozikowski both teach sample treatment techniques for preparing a sample for analysis.
Modified Henzel does not teach the means for monitoring is configured to monitor refractive index and conductance. However, Lebedev teaches the analogous art of a monitoring means wherein the monitoring means is configured to monitor refractive index and conductance (Lebedev; [0196]). It would have been obvious to one of ordinary skill in the art before the effective filing date to modify the monitoring means of modified Henzel to comprise monitoring means configured to monitor refractive index and conductance, as taught by Lebedev, because Lebedev teaches the monitoring means configured to monitor refractive index and conductance allows characterization of all or essentially off a fluid volume to be administered and detect microbial contamination (Lebedev; [0196]). One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since modified Henzel and Lebedev both teach monitoring means for a sample.

Claim 18 is rejected under 35 U.S.C. 103 as being unpatentable over Henzel in view of Chen, and further in view of Woudenberg et al. (US Patent No. 7,381,571 – hereinafter “Woudenberg”).

Regarding claim 18, modified Henzel teach the apparatus of claim 1 above.
Modified Henzel does not teach which further comprises a sensor for detecting a fluorescent signal. However, Woudenberg teach the analogous art of an apparatus for treating samples (Woudenberg; figs. 1A and 1B, col. 4 lines 41-44) wherein the apparatus comprises a sensor for detecting a fluorescent signal (Woudenberg; claim 13). It would have been obvious to one of ordinary skill in the art before the effective filing date to modify the apparatus of modified Henzel to comprise a sensor for detecting a fluorescent signal, as taught by Woudenberg, because Woudenberg teaches the sensor for detecting a fluorescent signal measures a reaction of an analyte-specific reagent with a sample (Woudenberg; col. 20 lines 12-14). One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since modified Henzel and Woudenberg both teach an apparatus for treating a sample with a reagent.

Claims 26-29, and 31-33 are rejected under 35 U.S.C. 103 as being unpatentable over Henzel in view of Chen, and further in view of Chee et al. (US 2020/0348308 – hereinafter “Chee”).

Regarding claim 26, modified Henzel teach the apparatus of claim 1 above, which is for treating a plurality of polypeptides, wherein the sample container(s) is loaded with a sample comprising the plurality of polypeptides (Henzel; p. 3 lines 5-6).
Modified Henzel does not teach each polypeptide of the plurality of polypeptides is associated with a nucleic acid recording tag. However, Chee teach the analogous art of treatment of a sample (Chee teach analyzing macromolecules including peptides, polypeptides, proteins, and employing nucleic acid encoding; [0003]), wherein the sample comprises the plurality of polypeptides and each polypeptide of the is associated with a nucleic acid recording tag (Chee; figs. 31A-D, [1403]). It would have been obvious to one of ordinary skill in the art before the effective filing date to modify the sample container(s) of modified Henzel with the sample loaded with a plurality of polypeptides wherein each of the polypeptides of the plurality of polypeptides is associated with a nucleic acid recording tag, as taught by Chee, because Chee teaches the plurality of polypeptides associated with a nucleic acid recording tag associates directly or indirectly with an analyte; [0008]. One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since modified Henzel and Chee both teach treating samples comprising a plurality of polypeptides.
Note: What the apparatus is for relates to function/intended use. However, functional language does not add any further structure to an apparatus beyond that of a capability. Apparatus claims must distinguish over the prior art in terms of structure rather than function. (see MPEP 2114 and 2111.04). Therefore, if the prior art structure is capable of performing the function, then the prior art meets the limitation in the claims.

Regarding claim 27, modified Henzel teach the apparatus of claim 26 above, wherein each polypeptide of the plurality of polypeptides is covalently joined to a solid support (The modification of the sample container(s) of modified Henzel with the sample loaded with a plurality of polypeptides wherein each of the polypeptides of the plurality of polypeptides is associated with a nucleic acid recording tag, as taught by Chee, has previously been discussed in claim 26 above. Chee further teach each polypeptide of the plurality of polypeptides is covalently joined to a solid support; figs. 31 & 34).

Regarding claim 28, modified Henzel teach the apparatus of claim 26 above, wherein the apparatus comprises at least one reagent reservoir comprising a binding agent; the binding agent comprises a protein or an aptamer; and the binding agent is configured to bind a target comprising a single terminal amino acid residue, a dipeptide, a tripeptide or a post-translational amino acid modification of a polypeptide from the plurality of polypeptides (The modification of the sample container(s) of modified Henzel with the sample loaded with a plurality of polypeptides wherein each of the polypeptides of the plurality of polypeptides is associated with a nucleic acid recording tag, as taught by Chee, has previously been discussed in claim 26 above. Chee teach a single cycle protein identification via N-terminal dipeptide binders to peptides immobilized partition barcoded beads; fig. 52, [1425]).

Regarding claim 29, Chee teach the apparatus of claim 28 above, wherein the binding agent further comprises a coding tag with identifying information regarding the binding agent, wherein the coding tag is DNA molecule, an RNA molecule, a BNA molecule, an XNA molecule, a LNA molecule, a PNA molecule, a yPNA molecule, or a combination thereof (The modification of the sample container(s) of modified Henzel with the sample loaded with a plurality of polypeptides wherein each of the polypeptides of the plurality of polypeptides is associated with a nucleic acid recording tag, as taught by Chee, has previously been discussed in claims 26 and 27 above. Chee teach a single cycle protein identification via N-terminal dipeptide binders to peptides immobilized partition barcoded beads. The encoding tag and/or the recording tag (and/or the di-tag, the compartment tag, or the partition tag, if applicable), or any portion thereof (e.g., a universal primer, a spacer, a UMI, a recording tag barcode, an encoder sequence, a binding cycle-specific barcode, etc.), may comprise or be replaced with a sequenceable polymer, such as a non-nucleic acid sequenceable polymer; fig. 52, [1425]).

Regarding claim 31, modified Henzel teach the apparatus of claim1 above.
Modified Henzel does not teach the apparatus which is configured to generate an output sample comprising a nucleic acid encoded library with information that represents a binding history of the macromolecule analyte, wherein the nucleic acid encoded library is compatible for analysis with a DNA sequencer. However, Chee teach the analogous art of treatment of a sample (Chee teach analyzing macromolecules including peptides, polypeptides, proteins, and employing nucleic acid encoding; [0003]), which is configured to generate an output sample comprising a nucleic acid encoded library with information that represents a binding history of the macromolecule analyte, wherein the nucleic acid encoded library is compatible for analysis with a DNA sequencer (Chee; [1448]). It would have been obvious to one of ordinary skill in the art before the effective filing date to modify the apparatus of modified Henzel to be configured to generate an output sample comprising a nucleic acid encoded library with information that represents a binding history of the macromolecule analyte, wherein the nucleic acid encoded library is compatible for analysis with a DNA sequencer, as taught by Chee, because Chee teaches the creation of a nucleic acid encoded library of binding information is useful in another way in that it enables enrichment, subtraction, and normalization by DNA-based techniques that make use of hybridization; [1448]. One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since modified Henzel and Chee both teach treating samples comprising an immobilized macromolecule analyte.

Regarding claim 32, modified Henzel teach the apparatus of claim 31 above.
Modified Henzel does not teach the apparatus which is configured to perform high-throughput sample processing. However, Chee teach the analogous art of treatment of a sample (Chee teach analyzing macromolecules including peptides, polypeptides, proteins, and employing nucleic acid encoding; [0003]), which is configured to perform high-throughput sample processing (Chee; [0003]).

Regarding claim 33, modified Henzel disclose a method for automated treatment of a sample (Henzel; p. 18 line 10 through p. 38 line 35), which method is conducted using an apparatus of claim1 (Henzel disclose an apparatus 10 for rapid protein sequence analysis of multiple samples 12; p. 5 line 32 through p. 6 line 4; fig. 1A. Specifically, Henzel disclose the apparatus 10 may be used for a method of immobilizing proteins and polypeptides of interest onto a PVDF membrane; p. 34 lines 11-13), and which method comprises:
a) providing to said apparatus a sample a macromolecule analyte in a non-planar sample container (Henzel disclose a sample cartridge 20 having a 1/16 inch internal diameter with a length of 15-20 mm; p. 34 lines 33-36. Accordingly, Henzel disclose a cylindrical having an internal diameter equal to 1.5875 mm (r=0.79375 mm) a maximum volume of

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, which is less than about 20 mL);
b) providing a reagent to separate reagent reservoirs of said apparatus (Henzel disclose reagents 30 are delivered to the sample cartridges 20 by a delivery device 14; fig. 1A, p. 6 lines 18-24);
c) delivering the reagent reservoir to the sample container (Henzel disclose an apparatus controller 24; fig. 1A, p. 5 line 32 through p. 6 line 4. The apparatus controller 24 is connected to control valve 43 so the solvents or reagents 30 can be independently delivered to the appropriate sample cartridge 20; p. 6 lines 18-19 and p. 7 lines 32-37 and p. 10 lines 3-14);
d) delivering the reagent from the reagent reservoir to the sample container (Henzel disclose an apparatus controller 24; fig. 1A, p. 5 line 32 through p. 6 line 4. The apparatus controller 24 is connected to control valve 43 so the solvents or reagents 30 can be independently delivered to the appropriate sample cartridge 20; p. 6 lines 18-19 and p. 7 lines 32-37 and p. 10 lines 3-14).
Modified Henzel does not teach wherein the sample comprises and an associated nucleic acid recording tag joined to a solid support, b) providing a binding agent and a reagent for transferring information, wherein at least one of said reagent reservoirs comprises the binding agent and at least one of said reagent reservoirs comprises the reagent for transferring information, c) delivering the binding agent, wherein the binding agent comprises a coding tag with identifying information regarding the binding agent, d) delivering the reagent for transferring information to transfer information from the coding tag of the binding agent to the recording tag to generate an extended recording tag, and e) generating an output sample comprising a nucleic acid encoded library with information that represents a binding history of the macromolecule analyte, wherein the encoded library is compatible for analysis with a DNA sequencer. However, Chee teach the analogous art of a method for automated treatment of a sample (Chee; [Abstract, 0098-0361]), wherein the sample comprises a macromolecule analyte and an associated nucleic acid recording tag joined to a solid support (Chee; [01447-1449]) providing a binding agent and a reagent for transferring information (Chee; [1405, 1409, 1412]), wherein at least one of said reagent reservoirs comprises the binding agent and at least one of said reagent reservoirs comprises the reagent for transferring information (Chee; [1405, 1447-1448]), c) delivering the binding agent, wherein the binding agent comprises a coding tag with identifying information regarding the binding agent (Chee; fig. 52, [1425]), d) delivering the reagent for transferring information to transfer information from the coding tag of the binding agent to the recording tag to generate an extended recording tag (Chee; [1404-1405, 1407, 1419, 1421, 1427, 1432, 1435, 1447-1448]) and e) generating an output sample comprising a nucleic acid encoded library with information that represents a binding history of the macromolecule analyte, wherein the encoded library is compatible for analysis with a DNA sequencer (Chee; [0003, 1448]). One of ordinary skill in the art would have expected this modification could have been performed with a reasonable expectation of success since modified Henzel and Chee both teach treating samples comprising an immobilized macromolecule analyte.

Other References Cited
The prior art of made of record and not relied upon is considered pertinent to Applicant’s disclosure include:
Kochar et al. (US 2007/0116600) disclose a fluid handling system comprising flow control valves, a manifold, and reagent controlled valves.
Kopp et al. (US 2009/0227066) disclose reagent station and temperature control means for heating or cooling.
Jacobson et al. (US 2013/0296194) disclose a method and apparatus related to synthesis of polynucleotides having a predefined sequence on a support.

Citations to art
In the above citations to documents in the art, an effort has been made to specifically cite representative passages, however rejections are in reference to the entirety of each document relied upon. Other passages, not specifically cited, may apply as well.

Conclusion
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/C.A.T./Examiner, Art Unit 1798

/BENJAMIN R WHATLEY/Primary Examiner, Art Unit 1700

Patent Application 17769321 - AUTOMATED TREATMENT OF MACROMOLECULES FOR - Rejection

Patent Application 17769321 - AUTOMATED TREATMENT OF MACROMOLECULES FOR

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Rejection Summary

Cited Patents

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