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 .
Office Action: Notice
Any objection or rejection of record in the previous Office Action, mailed 7/2/2025,
which is not addressed in this action has been withdrawn in light of Applicants' amendments
and/or arguments. This action is FINAL.
Election/Restrictions
Applicant’s election without traverse of Group I in the reply filed on May 14, 2025 is acknowledged. Claims 61 and 80-86 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected Groups 2-3, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 5/14/2025.
Claim Status
Claims 5, 8-9, 11-16, 18-19, 21-22, 25-54, 56-60, 62-79 and 87-95 have been cancelled (9/29/2025). Claims 1-4, 6-7, 10, 17, 20, 23-24, 55, 61, 80-85 have been amended (9/29/2025). No new matter was added. Claims 61 and 80-86 are withdrawn from consideration (5/14/2025). Thus, claims 1-4, 6-7, 10, 17, 20, 23-24 and 55 are under examination (8/13/2021).
Priority
Claims 1-4, 6-7, 10, 17, 20, 23-24 and 55 receive a priority date of 2/15/2019, the filing date of US Provisional 62/806,174.
Objections Withdrawn
Specification:
The objections to the specification due to the use of a trademark or tradenames are withdrawn in view of Applicant’s amendments.
Rejections Maintained
Claim Rejections - 35 USC § 102
Claims 1-2, 4, 6-7, 10, 17, 20, 23-24 and 55 are rejected under 35 U.S.C. 102 (a)(1) and (a)(2) as being anticipated by Jaenisch et al. (WO 2018/035495 A1; published 2/22/2018).
Regarding claims 1-2 and 4, Jaenisch teaches methods of modifying DNA methylation by contacting a with a catalytically inactive site-specific nuclease fused to an effector domain having methylation or demethylation activity and one or more guide sequences (Abstract). Further, Jaenisch teaches genome editing involving at least two of the genomic sequences are on different chromosomes, where a genomic sequence may comprise a tag (i.e., an epitope tag or a fluorescent tag) or a transgene (i.e., a reporter gene) (Paragraph 103, lines 5-10). Specifically, Jaenisch teaches that a gene of interest encodes a transcription factor, a transcriptional co-activator or co-repressor, an enzyme, a chaperone, a heat shock factor, a heat shock protein, a receptor, a secreted protein, a transmembrane protein, a histone (i.e., HI, H2A, H2B, H3, H4) (Paragraph 136, lines 1-10).
Jaenisch also teaches applications of the method for modulating one or more genomic sequences in a cell can further comprise introducing an effector molecule (i.e., nucleic acid sequence; protein; organic molecule; inorganic molecule, small molecule) or physical trigger that associates with (i.e., binds to; specifically binds to) the effector domain to modulate the methylation or demethylation of a genomic sequence (i.e., an inducer molecule; a trigger molecule) (Paragraph 87, lines 1-5). Further, Jaenisch teaches a sequence to be inserted into a genome encodes a tag in an appropriate position such that a fusion protein comprising the tag is produced (Paragraph 133, lines 1-5). Jaenisch also teaches specific examples of genetic modifications of interest include modifying sequence(s), (i.e., gene(s)) to match sequence in different species (i.e., change mouse sequence to human sequence for any gene(s) of interest), alter sites of potential or known post-translational modification of proteins (i.e., phosphorylation, glycosylation, lipidation, acylation, acetylation), alter sites of potential or known epigenetic modification, alter sites of potential or known protein- protein or protein-nucleic acid interaction, inserting tag, epitope tag (or chromatin associated protein (ChAP)), and/or inserting or deleting splice sites (Paragraph 101, lines 1-10). Specifically, Jaenisch teaches that the previously described epitope tag or ChAP comprises a differentially methylated region that may also be differentially methylated between differentiation states (i.e., progenitor cells vs. terminally differentiated cells) (Paragraph 114, lines 5-10).
Jaenisch further teaches that the nucleic acid sequence or variant and an effector domain nucleic acid sequence are introduced into the cell as a chimeric sequence and the effector domain is fused to a molecule that associates with (i.e., binds to) Cas protein (i.e., the effector molecule is fused to an antibody or antigen binding fragment thereof that binds to Cas protein) (Paragraph 77, lines 5-10).
Regarding claims 6-7, Jaenisch teaches applications of the method for modulating one or more genomic sequences in a cell can further comprise introducing an effector molecule (i.e., nucleic acid sequence; protein; organic molecule; inorganic molecule, small molecule) or physical trigger that associates with (i.e., binds to; specifically binds to) the effector domain to modulate the methylation or demethylation of a genomic sequence (i.e., an inducer molecule; a trigger molecule) (Paragraph 87, lines 1-5). Further, Jaenisch also teaches that a tag or DNA molecule is a relatively small polypeptide, i.e., ranging from a few amino acids up to about 100 amino acids long (Paragraph 133, lines 5-10).
Regarding claims 10 and 17, Jaenisch teaches that one or more guide sequence comprised in the DNA molecule include sequences that recognize DNA in a site-specific manner, including guide sequences which can include guide ribonucleic acid (RNA) sequences utilized by a CRISPR system or sequences within a TALEN or zinc finger system that recognize DNA in a site-specific manner (Paragraph 62, lines 1-5). Jaenisch also teaches that the previously described tags comprise a solubility-enhancing tag (i.e., a SUMO tag, NUS A tag, SNUT tag, a Strep tag, or a monomelic mutant of the Ocr protein of bacteriophage T7) (Paragraph 133, lines 5-10).
Regarding claim 20, Jaenisch teaches a sequence to be inserted into a genome encodes a tag in an appropriate position such that a fusion protein comprising the tag is produced (Paragraph 133, lines 1-5). Further, each RNA sequence can vary in length from about 8 base pairs (bp) to about 200 bp. In some embodiments, the RNA sequence can be about 9 to about 190 bp; about 10 to about 150 bp; about 15 to about 120 bp; about 20 to about 100 bp; about 30 to about 90 bp; about 40 to about 80 bp; about 50 to about 70 bp in length (Paragraph 66, lines 1-5).
Regarding claims 23-24, Jaenisch teaches specific examples of genetic modifications of interest include modifying sequence(s), (i.e., gene(s)) to match sequence in different species (i.e., change mouse sequence to human sequence for any gene(s) of interest), alter sites of potential or known post-translational modification of proteins (i.e., phosphorylation, glycosylation, lipidation, acylation, acetylation), alter sites of potential or known epigenetic modification, alter sites of potential or known protein- protein or protein-nucleic acid interaction, inserting tag, epitope tag (or chromatin associated protein (ChAP)), and/or inserting or deleting splice sites (Paragraph 101, lines 1-10). Additionally, Jaenisch teaches that it is of interest to genetically modify a known or suspected differentially methylated region (DMR) and there are various examples of differentially methylated or concentrated regions between cells of different cell types (i.e., muscle cells vs neuron or skin cells vs hepatocytes) (Paragraph 114, lines 1-5).
Regarding claim 55, Jaenisch teaches methods or collections of parts used for modifying DNA methylation by contacting a with a catalytically inactive site-specific nuclease fused to an effector domain having methylation or demethylation activity and one or more guide sequences (Abstract). Further, Jaenisch teaches genome editing involving at least two of the genomic sequences are on different chromosomes, where a genomic sequence may comprise a tag (i.e., an epitope tag or a fluorescent tag) or a transgene (i.e., a reporter gene) (Paragraph 103, lines 5-10). Specifically, Jaenisch teaches that a gene of interest encodes a transcription factor, a transcriptional co-activator or co-repressor, an enzyme, a chaperone, a heat shock factor, a heat shock protein, a receptor, a secreted protein, a transmembrane protein, a histone (i.e., HI, H2A, H2B, H3, H4) (Paragraph 136, lines 1-10). Jaenisch also teaches applications of the method for modulating one or more genomic sequences in a cell can further comprise introducing an effector molecule (i.e., nucleic acid sequence; protein; organic molecule; inorganic molecule, small molecule) or physical trigger that associates with (i.e., binds to; specifically binds to) the effector domain to modulate the methylation or demethylation of a genomic sequence (i.e., an inducer molecule; a trigger molecule) (Paragraph 87, lines 1-5). Further, Jaenisch teaches a sequence to be inserted into a genome encodes a tag in an appropriate position such that a fusion protein comprising the tag is produced (Paragraph 133, lines 1-5). Jaenisch also teaches specific examples of genetic modifications of interest include modifying sequence(s), (i.e., gene(s)) to match sequence in different species (i.e., change mouse sequence to human sequence for any gene(s) of interest), alter sites of potential or known post-translational modification of proteins (i.e., phosphorylation, glycosylation, lipidation, acylation, acetylation), alter sites of potential or known epigenetic modification, alter sites of potential or known protein- protein or protein-nucleic acid interaction, inserting tag, epitope tag (or chromatin associated protein (ChAP)), and/or inserting or deleting splice sites (Paragraph 101, lines 1-10). Specifically, Jaenisch teaches that the previously described epitope tag or ChAP comprises a differentially methylated region that may also be differentially methylated between differentiation states (i.e., progenitor cells vs. terminally differentiated cells) (Paragraph 114, lines 5-10).
Jaenisch teaches each and every limitation of claims 1-2, 4, 6-7, 10, 17, 20, 23-24 and 55, and therefore Jaenisch anticipates claims 1-2, 4, 6-7, 10, 17, 20, 23-24 and 55.
Applicant’s Response: The Applicant argues that Jaenisch does not expressly or inherently disclose a recombinant nucleosome, as required by independent claim 1, but instead teaches intracellular DNA modification using catalytically inactive nucleases fused to effector domains, which is fundamentally different from the claimed in-vitro recombinant nucleosome constructs. Applicant further contends that Jaenisch fails to disclose a DNA barcode indicative of a chromatin-associated protein (ChAP) capture epitope, a required claim element, and does not teach nucleosome-based panels, arrays, or kits.
Examiner’s Response to Traversal: Applicant’s arguments have been carefully and fully considered but are not found persuasive, as discussed below.
Under the broadest reasonable interpretation (MPEP 2111), the claims are not limited to isolated, in-vitro-reconstituted nucleosomes, but broadly encompass nucleosome structures generated using recombinant or genetic constructs. Jaenisch expressly teaches inserting tag or epitope tag sequences, including ChAP tags, into nucleic acid such that tagged fusion products are produced (Paragraphs 101, 133), and further teaches that the engineered gene products may include histones H1. H2A, H2B, H3, and H4 (Paragraph 136). Thus, Jaenisch expressly contemplates generating tagged histone proteins via genetic/recombinant manipulation, which reasonably meets the “recombinant” aspect included in the amended claim set (9/29/2025) under BRI.
The claimed “DNA barcode indicative of a ChAP capture epitope” is met by Jaenisch’s teaching of inserted tag/epitope/ChAP nucleic acid sequences, (Paragraph 101), as well as insertion of a sequence such that a tagged product is produced (Paragraph 133), which under BRI reasonably read on a DNA sequence that identifies or corresponds to the capture epitope; anticipation does not require the reference to use the word “barcode” verbatim (MPEP 2111, 2132; Verdegaal Bros. v. Union Oil, 814 F. 2d 628 (Fed. Cir. 1987)). Further, the claim does no require a particular barcode design beyond being DNA and being “indicative of” the capture epitope, and under BRI, the claimed “DNA barcode indicative of” a ChAP capture epitope is satisfied by a tag/inserted nucleic acid sequence that corresponds to the ChAP/epitope/tag used for capture (see MPEP 2114 regarding functional/”capable of” style limitations in apparatus/product claims).
Accordingly, the Applicant’s traversal does not overcome the anticipation of Jaenisch, who teaches either expressly (i.e., tag/epitope/ChAP insertion; histones as targets; sequence insertion producing tagged products) or inherently (MPEP 2131.01). Therefore, the 35 USC 102 rejection of claims 1-2, 4, 6-7, 10, 17, 20, 23-24 and 55 is maintained.
Claim Rejections - 35 USC § 103
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Jaenisch et al. (WO 2018/035495 A1; published 2/22/2018) as applied to claims 1-2, 4, 6-7, 10, 17, 20, 23-24 and 55 above, and in view of Hill et al. (US PGPub 2010/0199364 A1; published 8/5/2010), Taylor et al. (US PGPub 2010/0112602 A1; published 5/6/2010); Marks et al. (US PGPub 2002/0155114 A1; published 10/24/2002); Hay et al. (US PGPub 2002/0132327 A1; published 9/19/2002); Iwata et al. (US PGPub 2004/0191869 A1; published 9/30/2004); Inoue et al. (US PGPub 2002/0123101 A1; published 9/5/2002); and Rizzuto et al. (US PGPub 2002/0192721 A1; published 12/19/2002).
As discussed above, Jaenisch teaches methods of modifying DNA methylation by contacting a with a catalytically inactive site-specific nuclease fused to an effector domain having methylation or demethylation activity and one or more guide sequences (Abstract). Further, Jaenisch teaches genome editing involving at least two of the genomic sequences are on different chromosomes, where a genomic sequence may comprise a tag (i.e., an epitope tag or a fluorescent tag) or a transgene (i.e., a reporter gene) (Paragraph 103, lines 5-10). Specifically, Jaenisch teaches that a gene of interest encodes a transcription factor, a transcriptional co-activator or co-repressor, an enzyme, a chaperone, a heat shock factor, a heat shock protein, a receptor, a secreted protein, a transmembrane protein, a histone (i.e., HI, H2A, H2B, H3, H4) (Paragraph 136, lines 1-10).
Regarding claim 3, Jaenisch teaches that the previously described tag comprises an HA, TAP, Myc, 6XHis, Flag, V5, or GST tag, to name few examples (Paragraph 133, lines 10-12). Further, Jaenisch also teaches that the previously described tags comprise a solubility-enhancing tag (i.e., a SUMO tag, NUS A tag, SNUT tag, a Strep tag, or a monomelic mutant of the Ocr protein of bacteriophage T7) (Paragraph 133, lines 5-10).
Jaenisch does not teach or suggest the specific tags in SEQ ID No: 1-7.
Hill teaches a trimeric complex or as an oligomer where the fusion protein, the nucleic acid, and the cell is suitable as a pharmaceutical composition or for therapeutic, diagnostic and/or research applications (Abstract). Further, Hill teaches a FLAG-tag (SEQ ID NO: 52), as shown
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[AltContent: textbox (Figure 1: Hill teaches SEQ ID NO: 52, a FLAG-tag, a 100% query match to SEQ ID NO: 1. )]in Figure 1, that is a 100% query match to SEQ ID NO: 1, as claimed in the instant application.
Taylor teaches methods and reagents for identifying an agent, such as by screening a library of agents, that modulates the interaction of two or more polypeptides, the method comprising: introducing into a cell at least a first polypeptide, each comprising a binding domain, wherein the first polypeptide comprises a localization domain of the second polypeptide; and detecting the cellular location of the first polypeptide, the second polypeptide or a combination thereof, wherein a change in the cellular location of the first polypeptide, the second polypeptide or a combination thereof indicates that the agent (Abstract). Further, Taylor teaches a HA-tag (SEQ ID NO: 33), as shown in Figure 2, that is a 100% query match to SEQ ID NO: 2, as claimed in the instant application.
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[AltContent: textbox (Figure 2: Taylor teaches SEQ ID NO: 33, a HA-tag, a 100% query match to SEQ ID NO: 2. )]
Marks teaches antibodies and derivatives thereof and/or other antibodies that specifically bind to the neutralizing epitopes provided herein can be used to neutralize botulinum neurotoxin and are therefore also useful in the treatment of botulism (Abstract). Further, Marks teaches a His-tag (SEQ ID NO: 5), as shown in Figure 3, that is a 100% query match to SEQ ID NO: 3, as claimed in the instant application.
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[AltContent: textbox (Figure 3: Marks teaches SEQ ID NO: 5, a His-tag, a 100% query match to SEQ ID NO: 3. )]
Hay teaches a fusion protein including a reporter polypeptide linked to a linker polypeptide comprising a protease cleavage Site, and a repressor polypeptide that represses the activity of the reporter polypeptide (Abstract). Hay further teaches a protease (SEQ ID NO: 1), as shown in Figure 4, that is a 100% query match to SEQ ID NO: 4, as claimed in the instant application.
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[AltContent: textbox (Figure 4: Hay teaches SEQ ID NO: 1, a protease, a 100% query match to SEQ ID NO: 4. )]
Iwata teaches a recombinant vector comprising, (i) a promoter sequence and (ii) a nucleotide sequence encoding a first protein which, when crystallized with a second protein, is capable of accommodating the second protein in the crystal lattice, said recombinant vector further allowing for the insertion of a further nucleotide sequence encoding a second protein to be located, when crystallized, in the crystal lattice of the first protein (Abstract). Iwata further teaches a Strep-tag (SEQ ID NO: 9), as shown in Figure 5, that is a 100% query match to SEQ ID NO: 5, as claimed in the instant application.
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[AltContent: textbox (Figure 6: Inoue teaches SEQ ID NO: 3, a Strep-tag, a 100% query match to SEQ ID NO: 6. )]Inoue teaches a process for producing a peptide or a peptide derivative by using a reaction system of transcribing a DNA into an RNA and then translating the RNA produced or a reaction system of translating an RNA in vitro characterized in that a part or all of protein components constituting the transcription/translation reaction system are labeled with one of a pair of substances adhering to each other and the other substance is used as an adsorbent for capturing said labeled protein components after translating (Abstract). Inoue further teaches a Strep-tag (SEQ ID NO: 3), as shown in Figure 6, that is a 100% query match to SEQ ID NO: 6 as claimed in the instant application.
Rizzuto teaches Modular Molecular Clasps and methods of using these Modular Molecular Clasps in a wide range of applications in the health care industry, i.e., in therapy, in clinical diagnostics, in in vivo imaging or in drug discovery (Abstract). Further, Rizzuto teaches a Protein C tag (SEQ ID NO: 5), as shown in Figure 7, that is a 100% query match to SEQ ID NO: 7 as claimed in the instant application.
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[AltContent: textbox (Figure 7: Rizzuto teaches SEQ ID NO: 5, a Protein-C tag, a 100% query match to SEQ ID NO: 7. )]
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the nucleosome of Jaenisch to include the specific short peptide tags (i.e., HA, TAP, Myc, 6XHis, Flag, V5, or GST tag) with specified SEQ ID Nos as taught by Hill, Taylor, Marks, Hay, Iwata, Inoue, and Rizzuto. Specifically, Jaenisch teaches nucleosomes comprising epitope tags and discloses that genomic sequences may comprise tags such as epitope tags, including histones (Paragraph 136, lines 1-10). Further, Jaenisch teaches various epitope tags (i.e., HA, TAP, Myc, 6XHis, Flag, V5, or GST tag) (Paragraph 133, lines 10-12), establishing that epitope tags are known for use with nucleosome-related methodology. Further, the specific peptide sequences recited in instant claim 3 are well-known in the art, as evidenced by exact 100% sequence matches found in multiple prior art references; Hill teaches the FLAG tag sequence (SEQ ID NO: 52), Taylor teaches the HA tag sequence (SEQ ID NO: 33), Marks teaches the His-tag sequence (SEQ ID NO: 5), Hay teaches the protease sequence (SEQ ID NO: 1), Iwata teaches the Strep-tag sequence (SEQ ID NO: 9), Inoue teaches another Strep-tag sequence (SEQ ID NO: 3) and Rizzuto teaches the Protein C tag sequence (SEQ ID NO: 5). These references demonstrate that each individual peptide tag was known in the art for protein labeling and purification applications.
Thus, one of ordinary skill in the art would have been motivated to combine Jaenisch’s teaching of epitope-tagged nucleosomes with the well-known specific epitope tag sequences taught by the other references because epitope tags serve standard functions in protein research including purification, detection, and localization. The selection of any particular epitope tag from the known repertoire would have been obvious as a matter of routine design choice based on the intended application and experimental requirements. There would have been a reasonable expectation of success because epitope tags are modular elements that retain their binding properties when incorporated into different protein contexts, and Jaenisch already established the feasibility of using epitope tags with nucleosomes.
Applicant’s Response: The Applicant argues that claim 3 is not obvious because Jaenisch does not teach recombinant nucleosomes or DNA barcodes indicative of a ChAP capture epitope, and therefore cannot supply the fundamental elements of the instant claims. The Applicant further argues that, even if the individual tag sequences are taught by Hill, Taylor, Marks, Hay, Iwata, Inoue, or Rizzuto, there is no motivation for a person of ordinary skill in the art to combine Jaenisch’s gene-modification methods with these unrelated references, which are directed to disparate technologies and not quantitative mapping of chromatin-associated proteins.
Examiner’s Response to Traversal: Applicant’s arguments have been carefully and fully considered but are not found persuasive, as discussed below.
As recited above, Jaenisch teaches nucleosome-related constructs in which genomic sequences comprise epitope tags, including histones H1, H2A, H2B, H3, and H4, and identifies multiple well-known tags suitable for use in such constructs (Paragraphs 133, 136), which reasonably reads on recombinant nucleosome components formed from those tagged histones. The instant claim does not require Jaenisch to explicitly use the term “nucleosome”, nor do they require modification of a pre-assembled nucleosome rather than recombinant production of tagged histone components that inherently assemble into nucleosomes in the cellular context (see MPEP 2111, 2141).
Additionally, the Applicant’s assertion that a histone is not an epitope tag mischaracterizes the rejection. The rejection does not equate histones with epitope tags; rather, Jaenisch teaches epitope tags fused to proteins, including histones, thereby satisfying the epitope-tag limitation. Further, the claimed “DNA barcode indicative of a ChAP capture epitope” is reasonably met by Jaenisch’s disclosure of inserted nucleic acid sequences encoding tags/epitopes, which identify and enable capture of the associated chromatin protein under BRI; anticipation or obviousness does not require the reference to use the term “barcode” verbatim (see MPEP 2111, 2131).
Further, the specific short sequences recited in instant claim 3 (SEQ ID NOs: 1-7) are taught in the art by Hill (FLAG), Taylor (HA), Marks (His), Hay (protease tag), Iwata and Inoue (Strep-tags), and Rizzuto (Protein C), each demonstrating exact sequence matches and established use in protein labeling, purification, and detection. These sequences all represent well-known interchangeable potential tags that could be used as a routine design choice with a reasonable expectation of success.
A person of ordinary skill in the art would have been motivated to combine Jaenisch with these references because epitope tags are modular, interchangeable tools routinely selected from a known repertoire based on experimental needs, and Jaenisch already establishes the feasibility of using tags in nucleosome-associated contexts. The substitution of one known epitope tag for another represents a predictable variation involving routine design choice with a reasonable expectation of success, rendering claim 3 obvious (MPEP 2141, 2143; KSR Int’l Co., v Teleflex Inc.). Accordingly, claim 3 is unpatentable under 35 USC 103 over Jaenisch in view of Hill, Taylor, Marks, Hay, Iwata, Inoue, and Rizzuto.
Conclusions
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ELIZABETH ROSE LAFAVE whose telephone number is (703)756-4747. The examiner can normally be reached Compressed Bi-Week: M-F 7:30-4:30.
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/ELIZABETH ROSE LAFAVE/ Examiner, Art Unit 1684
/HEATHER CALAMITA/ Supervisory Patent Examiner, Art Unit 1684