DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 02/11/2026 has been entered.
Drawings
The drawings filed on 10/28/2021 are accepted by the Examiner.
Priority
This application claims benefit of priority to Provisional Application 61/081,930 filed on 07/18/2008 and Provisional Application 61/492,602 filed on 06/02/2011. This application is also a Continuation of 13/487,030 filed on 06/01/2012 and 16/733,132 filed on 01/02/2020. Additionally, this application is a Continuation in Part of 12/504,764 filed on 07/17/2009.
Amendment and Claim Status
In the reply filed on 10/30/2025, Applicant amended claims 19, 25, 46, 48 and 51-54. Claims 1-18, 26-31, 34-38, 40-41 and 43-44 are canceled.
Claims 19-25, 32-33, 39, 42 and 45-55 are currently pending and under examination.
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 53-55 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
The term “low-level” in claim 53 is a relative term which renders the claim indefinite. The term “low-level” is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. It is unclear what amount the reporter must be present within the partition volume to be considered at a “low-level.” One of ordinary skill in the art would not be able to determine the metes and bounds of what is and is not a “low-level” because the Specification does define what constitutes a “low-level” nor does the claim define what constitutes a “low-level.” Additionally, it is unclear exactly what “the reporter is present at a uniform low-level through the partition” means. The detecting step involves detecting ‘a pattern of localization’ which is simply the area in which the fluorescence occurs within the partition. However, it is unclear if “the reporter is present at a uniform low-level through the partition” is referring to a ‘low-level’ of fluorescence being present throughout the partition or just the reporter itself is present at a ‘low-level’ throughout the partition. Regarding negative partitions, the instant Specification states “in order to identify and quantitate enzyme activity, droplets are identified as ‘negative’ and/or ‘positive’ droplets for the reaction catalyzed by the target enzyme, and the number of enzyme molecules within positive droplets (e.g., based on the quantized signal strength) is determined” (Page 2, Line 31 – Page 3, Lines 1-3). Thus, it appears if the partition is a ‘negative partition,’ it would not have any reporter present because there is no reaction taking place. Thus, it is generally unclear what “the reporter is present at a uniform low-level throughout the partition” means. Therefore, claim 53 and all claims dependent upon claim 53 are rendered indefinite.
Claim Rejections - 35 USC § 103
The following is a quotation of pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negated by the manner in which the invention was made.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
The factual inquiries for establishing a background for determining obviousness under pre-AIA 35 U.S.C. 103(a) 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 19-25, 32-33, 39, 42 and 45-55 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Quake et al. (US 20020058332 A1, 05/16/2002) (IDS Reference of 11/22/2021) in view of Monforte (US 20080124726 A1, 05/29/2008) (Of Record).
Regarding claims 19, 21 and 46, Quake et al. disclose a method for analyzing and sorting biological materials, including proteins, enzymes, viruses and cells (Abstract). The method includes the sorting and analysis of particles, including cells, virions and molecules, by encapsulating the particles into individual droplets, droplets of aqueous solution in oil (Paragraph [0059]). More specifically, a first fluid is partitioned into a droplet within a second incompatible fluid, wherein the first fluid contains molecules, particles or cells (Paragraph [0287]). In one embodiment, the first fluid, or aqueous solution, contains an enzyme, reading on a target molecule (Paragraph [0316]). Enzymes are proteins produced by a living organism that catalyze chemical reactions of other substances (Paragraph [0057]). As enzymes are produced by living organisms, under the broadest reasonable interpretation, an enzyme which is secreted from a cell as-claimed is a product-by-process limitation. The enzyme as-claimed is in no way different from the enzymes described by Quake et al. as the enzymes disclosed by Quake et al. can also be derived from a cell.
Quake et al. disclose cells are labeled with an optically detectable reporter (Paragraph [0164]). Further, the reporter may be an antibody having a detectable moiety, such as a dye that fluoresces (Paragraph [0171]), reading on a detection component comprising an antibody.
Quake et al. do not explicitly state the detection component comprises an antibody linked to a reporter enzyme.
However, Monforte discloses a method for monitoring, including detecting, quantitating and assaying, a plurality of biomolecules, including proteins, within individual cells (Paragraph [0007]). More specifically, a plurality of cells containing a reagent for detecting the presence of a biomolecule and that reagent generates a signal indicating the presence of such biomolecule in a first aqueous solution which is combined with a second solution that is immiscible with the first solution in a manner that results in the formation of a plurality of reaction vesicles, reading on a partition, which contain one cell from the plurality of cells and a reagent for detecting the presence of the biomolecule (Paragraph [0018]). Further, when the biomolecule is a cell surface protein, the protein can be detected with a first antibody specific for that protein. A second antibody, with specificity for the first antibody, can be conjugated to a signal producing enzyme, such as horseradish peroxidase, to detect the first enzyme. Monforte goes on to state a ‘label’ or ‘reporter’ is any moiety or property that is detectable, allows detection, or is associated with detection, and the label can be covalently attached (Paragraph [0212]). Thus, the antibody conjugated to the signal producing enzyme reads on a detection component comprising an antibody covalently linked to a reporter enzyme.
Exemplary rationales that may support a conclusion of obviousness include combining prior art elements according to known methods to yield predictable results. See MPEP 2143(I)(A). As such, it would have been prima facie obvious to one of ordinary skill in the art to utilize an antibody conjugated to a signal producing enzyme as the detection component in the method of Quake et al. as the two methods are very similar, both being drawn to evaluation of proteins within a single partition via detection components, and conjugating an enzyme to an antibody was a known and effective detection component as taught by Quake et al. as it amounts to combining prior art elements according to known methods to yield predictable results.
Quake et al. disclose each droplet is passed into the detection region where it is examined using the detector to determine if a signal is produced or not (Paragraph [0078]). The strength of the signal indicates a chemical reaction of a substrate catalyzed by an enzyme (Paragraph [0078]).
Regarding the limitation of ‘a pattern of localization of the target molecules,’ it is noted the instant Specification does not explicitly define what a ‘pattern of localization’ is. The instant Specification states “localization of the fluorescent molecules onto the bead surface can be detected as an increased signal on the bead surface, a decreased signal in a portion of the fluid partition (e.g., throughout the partition volume), or both” (Specification, Page 88, Lines 13-15). The instant specification goes on to state “any method can be used to detect the pattern of localization fluorescence within a fluid partition … in certain embodiments, fluid droplets are flowed through a narrow channel that forces the droplets to exhibit an elongated shape … as the droplets pass a laser detector, reaction-negative droplets give a uniform low-level fluorescence along their length, while reaction-positive droplets show a spike corresponding to when the bead-bound fluorescent reporter passes the laser detector” (Specification, Page 88, Lines 17-22). Thus, under the broadest reasonable interpretation, a ‘pattern of localization’ is interpreted simply as the area inside the partition in which the fluorescence occurs. The ‘pattern of localization’ is not a specific ‘pattern,’ it is simply the area, or location, where the fluorescence occurs within the partition due to the presence of the reporter in that specific area. Therefore, under the broadest reasonable interpretation, the area within the partition that fluoresces and produces a signal reads on a ‘pattern of localization.’ As such, the disclosure of Quake et al. of detecting the signal, being the fluorescence, from the droplet reads on detecting a pattern of localization of the target molecules within the partitions.
Regarding claim 20, Quake et al. disclose the aqueous solution comprises ultra-pure water (Paragraph [0015]). Additionally, as discussed above, the aqueous solution is in oil. Quake et al. further disclose their method can produce a wide variety of droplet shapes and patterns in emulsions, e.g., water in oil (Paragraph [0296]).
Regarding claim 22, Quake et al. disclose the aqueous solution contains an enzyme, reading on a target molecule (Paragraph [0119]). Enzymes are proteins.
Regarding claim 23, Quake et al. disclose the droplets contain no more than one particle of the biological material (Paragraph [0015]).
Regarding claim 24, Quake et al. disclose a cell is any cell with a size similar to or smaller than a biological cell, including bacterial cells (Paragraph [0060]).
Regarding claim 25, Quake et al. disclose populations of E. coli cells expressing green fluorescent protein were separated and enriched from non-fluorescent E. coli cells, and the bacteria were still viable after extraction from the sorting device (Paragraph [0193]). The E. coli cells expressing green fluorescent protein indicates the cells were in conditions suitable to secrete the target molecules as they expressed the fluorescent protein.
Regarding claims 32 and 33, Quake et al. disclose cells that produce a desired monooxygenase enzyme can be detected in the presence of a suitable substrate and can be collected based on the enzyme catalyzing a reaction where a detectable fluorescent product is produced from the substrate (Paragraph [0170]). As it was disclosed the cell could be collected if fluorescence was detected, this reads on monitoring the reaction and detecting a signal to determine the presence of a secreted target molecule. As the instant claim states the detectable label is released in response to the enzymatic reaction, it is interpreted the product of the reaction is what is released. Thus, the disclosure of Quake et al. of the enzyme catalyzing a reaction where a detectable fluorescent product is produced, interpreted as released, reads on this limitation.
Regarding claim 39, Quake et al. disclose the invention is useful for high throughput screening, wherein screening for about 106 to 107 or even 1012 or 1013 members of a library, including a protein library containing proteins with one or more mutations (Paragraph [0326]). As discussed regarding claim 24, cells of the invention include bacterial cells (Paragraph [0060]). Further, as discussed regarding claim 22, Quake et al. disclose the aqueous solution contains an enzyme (Paragraph [0119]).
Regarding claim 42, Quake et al. disclose as each droplet passes into the detection region, the signal produced is measured. Further, the strength of the signal may indicate the size of a molecule or the potency or amount of an enzyme expressed by a cell (Paragraph [0078]). Under the broadest reasonable interpretation, the signal strength representing the potency or amount of an enzyme expressed by the cell, reads on determining the distribution of the target molecules, the enzymes, among the partition, the droplet.
Regarding claim 45, Quake et al. disclose the stream of cells being sorted for a detectable characteristic or reporter is moved through the detection region where a signal from each cell is detected or measured and compared to a set range of values to determine whether the cell possesses the desired characteristic based on the amount of reporter detected (Paragraph [0176]).
Regarding claim 46 and 50-52, Quake et al. disclose the reporter, reading on a detection component, can be fluorescently or chemically labeled amino acids or antibodies (Paragraph [0108]). Further, antibodies can in turn be detected using an optically-detectable reporter via directly conjugated reporters or labeled secondary antibodies (Paragraph [0171]).
Regarding claims 47-49, Quake et al. do not disclose the antibody is conjugated to a bead, particle or solid support, or wherein the antibody is linked to biotin.
However, Monforte et al. disclose a specific characterization of the invention is one or more biochemical reagents being linked to a solid phase (e.g., a bead) wherein the solid phase is in contact with the aqueous phase comprising the cell or cells (Paragraph [0216]). The utilization of a solid-phase biochemical reagent enables the capture of certain reaction products to the solid phase during the biochemical detection process (Paragraph [0216]). The beads of the invention are typically coupled to a second molecule that provides a capture function, for example, a bead coupled to an antibody (Paragraph [0268]). In addition to the beads carrying antibodies, the beads can also utilize other tethering mechanisms for connecting a protein or nucleic acid target to the bead, such as biotin-mediated binding (Paragraph [0269]).
Thus, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have conjugated the antibody functioning as a detection component in the method of Quake et al. to a bead with biotin because Monforte et al. disclose biotin-mediated binding is a means for connecting a protein target, such an antibody, to a bead, motivated by the desire to effectively capture the antibody to the bead and the use of a bead allows for the capture of reaction products to the bead during the biochemical detection process as taught by Monforte et al.
Regarding claim 53, see 112b above. As disclosed above, Quake et al. disclose each droplet is passed into the detection region where it is examined using the detector to determine if a signal is produced or not, reading on positive or negative partition (Paragraph [0078]). The strength of the signal may indicate the size of a molecule, the potency or amount of an enzyme expressed by a cell, or a positive or negative reaction such as binding of one molecule to another or a chemical reaction of a substrate catalyzed by an enzyme (Paragraph [0078]). Under the broadest reasonable interpretation, detecting the signal reads on detecting localization of a reporter because the reporter is detected within the droplet and the signal is produced by the presence of the reporter. Regarding the limitation of “in a negative partition, the reporter is present at a uniform low-level through the partition volume,” this is interpreted to be inherent to this type of method. As just discussed above, Quake et al. also disclose positive and negative droplets which are determined as each droplet passes into the detection region to determine if a signal is produced or not. Thus, it would be expected these negative droplets would also have the reporter present at a low-level throughout the droplet.
Regarding claim 54, as discussed above, Quake et al. disclose the reporter can be fluorescently or chemically labeled amino acids or antibodies (Paragraph [0108]) and each droplet is passed into the detection region where it is examined using the detector to determine if a signal is produced or not (Paragraph [0078]). As discussed above regarding claim 19, the detecting the pattern of localization within the partition of the fluorescent reporter is simply detecting the area inside the partition in which the fluorescence occurs. Therefore, detecting the signal, or the fluorescence, reads on detecting the pattern of localization within the partition of the fluorescent reporter.
Regarding claim 55, Quake et al. disclose to detect a reporter, the detection region may include an apparatus for stimulating a reporter for that characteristic to emit measurable light energy, for example, a light source such as a laser (Paragraph [0110]). Further, as disclosed above, Quake et al. disclose each droplet is passed into the detection region where it is examined using the detector to determine if a signal is produced or not, reading on a positive or negative partition (Paragraph [0078]). Under the broadest reasonable interpretation, the detection region including a laser to stimulate the reporter reads on passing the partitions by a laser detector and the partitions are what contain the reporter and the production of a signal, as compared to not producing a signal, reads on a spike when positive partitions pass the laser detector.
35 USC § 103 – Response to Arguments
Applicant's arguments filed 02/11/2026 have been fully considered but they are not persuasive.
Applicant argued on Page 7 that neither Quake nor Monforte teach the detection of a pattern of localization within a partition nor do they disclose a pattern of localization is a category of pattern that exists.
It is the Examiner’s position that while neither Quake nor Monforte specifically use the phrase ‘a pattern of localization,’ the teaching is present because a ‘pattern of localization’ is simply the area, or location, where the fluorescence occurs within the partition due to the presence of the reporter in that specific area, as stated above. Therefore this limitation is met.
Applicant further argued on the bottom of Page 6 that the cited prior art does not teach or suggest detecting partitions that contain target molecules secreted from the cells.
As stated above regarding claim 19, it is the Examiner’s position that an enzyme which is secreted from a cell as-claimed is a product-by-process limitation. The enzyme as-claimed is in no way different from the enzymes described by Quake et al. as the enzymes disclosed by Quake et al. can also be derived from a cell.
Conclusion
Claims 19-25, 32-33, 39, 42 and 45-55 are rejected.
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ASHLEY T WHITE whose telephone number is (571)272-0683. The examiner can normally be reached Monday - Friday 8:30 - 5:00 EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Sharmila Landau can be reached at (571)272-0614. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/A.T.W./Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
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