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 .
Election/Restrictions
Applicant's election with traverse of claims 2, 4, 6, 11-12, 14, 16, 18, 21, 24-30, 32-35, 45, 49, 54, and 61 with species election of NaM for X, TPT3 for Y, GXU-AYC base pair, and AzK in the reply filed on November 14, 2025 is acknowledged. The traversal is on the ground(s) that the description of the inventive groups is incorrect. This is not found persuasive because “a method of synthesizing an unnatural polypeptide comprising NXN-NYN in a cell” in group II is not meant to state that the “polypeptide” comprises NXN-NYN. The “method of synthesizing an unnatural polypeptide comprising” is expressly recited in the preamble of claim 1, and “NXN-NYN” is what is used to perform the method of group II. In addition, it is prima facie apparent that a polypeptide cannot comprise a 3-bp nucleic acid thus the 3-bp nucleic acid should be interpreted as the material used in performing the method of group II. Applicant argues it is not clear whether the election requirement pertains to only the first unnatural anticodon or both anticodons and the election of a single anticodon would exclude embodiments encompassed by the claims. In response, it is noted that neither claim 1 nor any of the claims included in group II expressly requires that the two anticodons should differ from each other. Furthermore, the claims elected by applicant will be examined in their entirety thus, should any of the elected claims require that the two anticodons should differ, such claims would be examined in accordance with the required claim limitations.
The requirement is still deemed proper and is therefore made FINAL.
Status of Claims
Claims 1-4, 6, 9, 11-12, 14, 16, 18, 21, 24-30, 32-35, 42, 45, 49, 54, and 61 are currently pending in the instant application. Claims 9 and 42 withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to nonelected inventions, there being no allowable generic or linking claim. Accordingly, claims 1-4, 6, 11-12, 14, 16, 18, 21, 24-30, 32-35, 45, 49, 54, and 61 are under examination on the merits in the instant application.
Drawings
The drawings in FIG. 1 are objected to because the numerical values (e.g., “103”, “105”) in FIG. 1 are not identified either in the figure itself or in the description of FIG. 1 in the specification.
The drawings are objected to because the legends in FIG. 5D-5G are not clearly distinguishable from each other as shown below, thereby rendering the correct interpretation of FIG. 5G impossible.
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The drawings are objected to because the legends in FIG. 9B and FIG. 14 are not clearly distinguishable from each other as shown below, thereby rendering the correct interpretation of the graphs impossible.
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Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Rejections - Improper Markush Grouping
Claims 6 and 21 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination of process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP §706.03(y).
The Markush grouping of bases recited in claim 6 is improper because the alternatives defined by the Markush grouping do not share a single structural similarity that is shared by all of the recited bases. See the following two base species for instance.
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Similarly, the Markush grouping of unnatural amino acid species recited in claim 21 is improper because all of the unnatural amino acid species (e.g., N6-azidoethoxy-carbonyl-L-lysine vs. O-allytyrosine) do not share a substantial structural similarity.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternatives within a single claim in fact share a single structural similarity as well as a common use.
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, 6, 11-12, 14, 16, 18, 21, 24-30, and 32-35 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.
Claim 1 and dependent claims thereof recite steps “b” and “c”, each of which identically recites “transcribing the at least one unnatural DNA molecule”. The only difference between the two steps as written is the intended purpose such that step “b” is “to afford the mRNA” and step “c” is “to afford the at least first and second tRNA molecules”. As such, the two steps “b” and “c” fail to particularly point out and distinctly claim the differences in method steps/elements other than the mere intended purpose for each step “b” and “c”.
Claim 1 recites the limitation "the unnatural mRNA molecule" in line 14. There is insufficient antecedent basis for this limitation in the claim.
Claim 2 recites the unnatural codon comprises a first unnatural nucleotide “at a first position, a second position, or a third position of the codon, optionally”. It is noted that a codon consists of three nucleotide positions: first, second, and third positions. As such, the recitation regarding the first unnatural nucleotide position being at a first, second, or third position of the 3-mer codon fails to particularly point out and distinctly claim the exact position of the unnatural nucleotide, especially in light of the “optionally” limitation that is not a required limitation.
Claim 3 recites that the unnatural anticodon comprises “NXN”; however, there is no limitation pertaining to the pair comprising “NXN” as the unnatural anticodon. Hence, claim 3 fails to particularly point out and distinctly claim the base pair comprising the expressly recited “NXN” as one of the unnatural anticodon species.
Claim 3 recites “with X-Y forming the unnatural base pair in DNA.” It is noted that claim 3 recites “NNX-XNN”, which does not comprise “X-Y forming the unnatural base pair”. Hence, it is unclear whether or not X-X in the expressly recited “NNX-XNN” forms an unnatural base pair.
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 (i.e., changing from AIA to pre-AIA ) 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.
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 1-4, 6, 11-12, 14, 16, 18, 21, 24-30, 32-35, 45, 49, 54, and 61 are rejected under 35 U.S.C. 103 as being unpatentable over Feldman et al. (JACS, 2019, 141:10644-10653, applicant’s citation) in view of Zhang et al. (Nature, 2017, 551:644-647, applicant’s citation), Liu (US 2013/0078671 A1), and Romesberg et al. (WO 2017/223528 A1, applicant’s citation).
Feldman discloses a method of producing proteins in vivo comprising site-specific three “noncanonical amino acids (ncAAs)” that are “N6-(2-azidoethoxy)-carbonyl-L-lysine (AzK)” in a strain of E. coli constitutively expressing a nucleoside triphosphate transporter from P. tricornutum (PtNTT2), wherein the method comprises using a plasmid comprising three site-specific “AXC” (X is dNaM) for the codon template at codon positions 149, 151, and 153 and the base-pairing “GYT” (Y is dTPT3) for the anticodon template for M. mazei Pyl tRNA, which is charged with AzK by the M. barkeri pyrrolysyl-tRNA synthetase (PylRS), wherein the unnatural mRNA is transcribed by T7 RNAP and the protein with “incorporation of three AzK residues” is translated in E. coli. See pages 10644-10645 and 10649-10651; Figures 7A-7C.
Feldman discloses the RNA analogues of “NaM” and ATPT3 in Figures 4A-B as shown below.
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Feldman does not teach that the protein comprises four AzK residues are site-specifically incorporated. However, Feldman teaches a goal “to produce protein with a higher density of ncAAs.” See page 10652.
Feldman does not teach using two unnatural tRNA molecules each comprising a different unnatural anticodon and charging the tRNA molecules by two different tRNA synthetases.
Zhang teaches producing a protein in E. coli comprising a site-specific noncanonical amino acid “p-azido-phenylalanine (pAzF)” comprising a plasmid with the AXC codon (X denotes NaM) at position 151, the GYT anticodon (Y denotes TPT3), and “an evolved Methanococcus jannaschii TryRS-tRNATyr pair (pAzFRS-tRNApAzF).” See pages 645-645; Figure 3b.
Zhang teaches that “the nucleoside triphosphate transporter from P. tricornutum (PtNTT2) is able to import both the deoxy- and ribotriphosphates of both unnatural nucleotides”. See page 644.
Liu teaches a method of site-specifically incorporating a plurality of different noncanonical amino acids or “at least two different noncanonical amino acids” into a single target protein using multiple aminoacyl-tRNA synthetase/tRNA pairs, wherein the protein comprising different noncanonical amino acids is useful “to enhance functional studies of the proteins.” See paragraphs 0004-0008.
Romesberg teaches an “in vivo method of increasing the production of a nucleic acid molecule containing an unnatural nucleotide” such as dNaM forming a base pair with dTPT3, wherein the nucleic acid molecule is produced by an engineered E. coli cell utilizing a modified nucleoside triphosphate transporter from P. tricornutum (PtNTT2), which is SEQ ID NO:4. See paragraphs 0007-0010; claims 11, 18-22, 69-71, 79-80, and 88.
It is noted that Romesberg’s SEQ ID NO:4 is a truncated amino acid sequence of SEQ ID NO:1 claimed in the instant case.
It would have been obvious to one of ordinary skill in the art before the effective filing date to modify Feldman’s method by increasing the number of site-specific “AXC” to at least four from three as used by Feldman, thereby incorporating at least four AzK residues in the translated protein. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success in order to produce a protein comprising a higher density of AzK residues than “three AzK residues” already produced by Feldman because it was an art-recognized goal “to produce protein with a higher density of ncAAs” as expressly disclosed by Feldman, wherein one of ordinary skill in the art would have been equipped with technical skills to make and use a plasmid comprising at least four site-specific “AXC” at codon positions, for instance 149, 151, 153, and 155, instead of the three codon positions 149, 151, and 153 used by Feldman.
It would also have been obvious to further modify Feldman’s method by providing site-specific incorporation of two different noncanonical amino acids (ncAAs) such as Feldman’s Azk and Zhang’s pAzF using two different unnatural tRNA synthetases for each of the two different ncAAs. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success in order to enhance the functional understanding/studies of proteins because producing a protein comprising site-specific incorporation of multiple (or at least two) different ncAAs using multiple (or at least two) different aminoacyl-tRNA synthetase/tRNA pairs was an art-recognized goal “to enhance functional studies of the proteins”, and because site-specific incorporation of another ncAA, pAzF, using the pAzFRS-tRNApAzF pair in combination with a plasmid comprising the AXC codon template as used by Feldman was shown to be effective and successful in pAzF site-specific incorporation into the target protein as evidenced by Zhang. That is, the plasmid comprising the AXC codon comprising NaM (or dNaM) base pairing with the GYT (or GYU) anticodon comprising TPT3 (or dTPT3) would have been deemed useful for producing a single protein comprising at least four UBPs with at least two different ncAAs: AzK and pAzF.
It would have been obvious to one of ordinary skill in the art to replace the PtNTT2 used by both Feldman and Zhang with Romesberg’s SEQ ID NO:4, which is a truncated PtNTT2, because Romesberg’s SEQ ID NO:4 was suggested to be useful in an “in vivo method of increasing the production of a nucleic acid molecule containing an unnatural nucleotide” comprising dNaM base pairing with dTPT3, thereby suggesting a reasonable expectation that Romesberg’s SEQ ID NO:4 would be useful in increasing in vivo production of a protein comprising unnatural protein that is synthesized from the nucleic acid comprising the unnatural base pairs formed by dNaM and dTPT3.
Accordingly, claims 1-4, 6, 11-12, 14, 16, 18, 21, 24-30, 32-35, 45, 49, 54, and 61 taken as a whole would have been prima facie obvious before the effective filing date.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Section 33(a) of the America Invents Act reads as follows:
Notwithstanding any other provision of law, no patent may issue on a claim directed to or encompassing a human organism.
Claims 45, 49, 54, and 61 are rejected under 35 U.S.C. 101 and section 33(a) of the America Invents Act as being directed to or encompassing a human organism. See also Animals - Patentability, 1077 Off. Gaz. Pat. Office 24 (April 21, 1987) (indicating that human organisms are excluded from the scope of patentable subject matter under 35 U.S.C. 101).
The instant claims are broadly drawn to a “cell” comprising unnatural codon-anticodon base pairs, wherein the term “cell” is defined to read on a “human cell” and “the cell is present in an organism”. See paragraph 00155. As such, the scope of the “cell” of claims 45, 49, 54, and 61 encompasses a human organism comprising the cell, which is patent ineligible under §101.
Recitation of an “isolated” cell would be remedial.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 45, 49, 54, and 61 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-25 of U.S. Patent No. 11,834,689 B2 in view of Feldman et al. (JACS, 2019, 141:10644-10653, applicant’s citation).
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims would have been obvious over the ‘689 patent claims drawn to a cell comprising at least two different tRNA synthetases, wherein the anticodon (“GYT or GYC”) of the tRNAs pairs with the codon (“AXC or GXC”) of the mRNA, wherein the Y is TPT3 and X is NaM, wherein the cell comprises a PtNTT. It would have been obvious to incorporate a plurality of UBPs because the terms “an anticodon” and “a codon” claimed in the ‘689 patent claims are defined to include a plurality as evidenced by the ‘689 specification’s definition that “the singular forms “a,” “an”, and “the” include plural referents unless the context clearly dictates otherwise.” It would have bene obvious to incorporate at least 4 UBPs into the cell of the ‘689 patent claims because it was an art-recognized goal “to produce protein with a higher density of ncAAs” as expressly disclosed by Feldman (see page 10652), wherein one of ordinary skill in the art would have been equipped with technical skills to make a plasmid comprising at least four UBPs instead of the three UBPs in Feldman.
Claims 1-4, 6, 11-12, 14, 16, 18, 21, 24-30, 32-35, 45, 49, 54, and 61 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-28 of U.S. Patent No. 12,319,944 B2 in view of Feldman et al. (JACS, 2019, 141:10644-10653, applicant’s citation) and Romesberg et al. (WO 2017/223528 A1, applicant’s citation).
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims would have been obvious over the ‘944 patent claims drawn to a method of producing a protein comprising an unnatural amino acid in an E. coli cell comprising at least two different tRNA synthetases that aminoacylate the tRNA with the unnatural amino acid, wherein the anticodon (“GYU or GYC”) of the tRNAs pairs with the codon (“AXC or GXC”) of the mRNA, wherein the Y is TPT3 and X is NaM, wherein the unnatural amino acid is pAzF or PrK, and “at least one unnatural nucleoside is introduced into the cell via the nucleoside triphosphate transporter”. It would have been obvious to incorporate a plurality of UBPs because the terms “an unnatural amino acid”, “an anticodon”, and “a codon” claimed in the ‘944 patent claims are defined to include a plurality as evidenced by the ‘944 patent specification’s definition that “the singular forms “a,” “an”, and “the” include plural referents unless the context clearly dictates otherwise.” It would have bene obvious to incorporate at least 4 UBPs into the cell of the ‘944 patent claims because it was an art-recognized goal “to produce protein with a higher density of ncAAs” as expressly disclosed by Feldman (see page 10652), wherein one of ordinary skill in the art would have been equipped with technical skills to make a plasmid comprising at least four UBPs instead of the three UBPs in Feldman. It would also have been obvious to use Romesberg’s SEQ ID NO:4 for the generically claimed nucleoside triphosphate transporter of the ‘944 patent claims because Romesberg’s SEQ ID NO:4 was suggested to be useful in an “in vivo method of increasing the production of a nucleic acid molecule containing an unnatural nucleotide”, which thus would have been reasonably expected to increase the in vivo production of a polypeptide comprising at least four unnatural amino acids.
Claims 1-4, 6, 11-12, 14, 16, 18, 21, 24-30, 32-35, 45, 49, 54, and 61 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 55-76 of copending Application No. 19/196,915 in view of Feldman et al. (JACS, 2019, 141:10644-10653, applicant’s citation) and Romesberg et al. (WO 2017/223528 A1, applicant’s citation).
Although the claims at issue are not identical, they are not patentably distinct from each other because the instant claims would have been obvious over the ‘915 claims drawn to kit/method for “producing a protein comprising an unnatural amino acid” using the kit, wherein the kit comprises an E. coli cell comprising at least two different tRNA synthetases, wherein the mutant anticodon such as “GYU” and “GYC” of the tRNAs pairs with the mutant codon “AXC” and “GXC” of the mRNA, wherein the Y is TPT3 and X is NaM, wherein the cell further comprises PtNTT and unnatural amino acids pAzF and PrK. It would have been obvious to incorporate a plurality of UBPs because the terms “an unnatural amino acid”, “a mutant anticodon”, and “a mutant codon” claimed in the ‘915 claims are defined to include a plurality as evidenced by the ‘915 specification’s definition that “the singular forms “a,” “an”, and “the” include plural referents unless the context clearly dictates otherwise.” See paragraph 0039. It would have bene obvious to incorporate at least 4 UBPs into the cell of the ‘915 claims because it was an art-recognized goal “to produce protein with a higher density of ncAAs” as expressly disclosed by Feldman (see page 10652), wherein one of ordinary skill in the art would have been equipped with technical skills to make a plasmid comprising at least four UBPs instead of the three UBPs in Feldman. It would also have been obvious to use Romesberg’s SEQ ID NO:4 for the PtNTT of the ‘915 claims because Romesberg’s SEQ ID NO:4 was suggested to be useful in an “in vivo method of increasing the production of a nucleic acid molecule containing an unnatural nucleotide”, which thus would have been reasonably expected to increase the in vivo production of a polypeptide comprising at least four unnatural amino acids.
Conclusion
No claim is allowed.
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/DANA H SHIN/Primary Examiner, Art Unit 1635