DETAILED CORRESPONDENCE
Status of the Application
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s amendment to the claims, filed August 7, 2026, is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Claims 1, 2, 4, 6, 9, 10, and 12 are pending in the application and are being examined on the merits.
Applicant’s remarks filed August 7, 2026 in response to the non-final rejection filed May 7, 2026 are acknowledged and have been fully considered.
Claims 7 and 8 have been canceled by applicant’s amendment filed August 7, 2026 and rejections previously applied to these claims are withdrawn.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on July 17, 2026 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS has been considered by the examiner.
Claim Objections
Claims 10 and 12 are objected to because of the following informalities:
Claim 10 is objected to in the recitation of “the targeted site” and in the interest of improving claim form and consistency with claim 1, it is suggested that the noted phase be amended to recite (with markings to show changes made) “the target nucleotide sequence
Claim 12 is objected to in the recitation of “wherein said Vif variant is the sequence” and in the interest of improving claim form, it is suggested that the noted phase be amended to recite (with markings to show changes made) “wherein the amino acid sequence of said Vif variant is the sequence.”
Claim Rejections - 35 USC § 112(b)
The rejection of claim 12 under 35 U.S.C. 112(b) is withdrawn in view of applicant’s amendment to claim 12.
Claims 1, 2, 4, 6, 9, 10, and 12 are newly rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
This rejection is necessitated by applicant’s amendments to claims 1 and 12.
Claim 1 (claims 2, 4, 6, 9, 10, and 12 dependent therefrom) is indefinite in the recitation of “does not substantially promote degradation.” The term “substantially” is a term of approximation (MPEP 2173.05(b).III.D) and the examiner has reviewed the specification and can find no examples or teachings that can be used for ascertaining the approximation intended by the term “substantially.” Moreover, there is nothing in the specification or prior art of record to indicate that one of ordinary skill in the art could have ascertained the scope of the recited term of approximation. It is suggested that applicant clarify the meaning of the term “substantially” in the context of claim 1. In the interest of advancing prosecution, applicant may consider an amendment to delete the term “substantially” in claim 1.
Claim 12 recites the trademark/trade name “GenBank.” Where a trademark or trade name is used in a claim as a limitation to identify or describe a particular material or product, the claim does not comply with the requirements of 35 U.S.C. 112(b). See MPEP 2173.05(u). The claim scope is uncertain since the trademark or trade name cannot be used properly to identify any particular material or product. A trademark or trade name is used to identify a source of goods, and not the goods themselves. Thus, a trademark or trade name does not identify or describe the goods associated with the trademark or trade name. In the present case, the trademark/trade name is used to identify/describe a sequence database and, accordingly, the identification/description is indefinite.
Claim Rejections - 35 USC § 112(a)
Claims 1, 2, 4, 6, 9, 10, and 12 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor at the time the application was filed, had possession of the claimed invention.
This is a “new matter” rejection and is necessitated by applicant’s amendment to claim 1 to recite “does not substantially promote degradation of the APOBEC3 family cytidine deaminase via an E3 ubiquitin ligase complex.”
MPEP § 2163.II.A.3.(b) states, “when filing an amendment an applicant should show support in the original disclosure for new or amended claims”. See also MPEP 714.02. MPEP § 2163.II.A.3.(b) further states, “[i]f the originally filed disclosure does not provide support for each claim limitation, or if an element which applicant describes as essential or critical is not claimed, a new or amended claim must be rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112, para. 1, as lacking adequate written description”. According to MPEP § 2163.I.B, “While there is no in haec verba requirement, newly added claim limitations must be supported in the specification through express, implicit, or inherent disclosure” and “The fundamental factual inquiry is whether the specification conveys with reasonable clarity to those skilled in the art that, as of the filing date sought, applicant was in possession of the invention as now claimed. See, e.g., Vas-Cath, Inc., 935 F.2d at 1563-64, 19 USPQ2d at 1117”.
As amended, claim 1 (claims 2, 4, 6, 9, 10, and 12 dependent therefrom) recites the limitation “wherein the Vif variant or fragment thereof binds to an apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3) family cytidine deaminase and does not substantially promote degradation of the APOBEC3 family cytidine deaminase via an E3 ubiquitin ligase complex.” According to applicant’s instant remarks at p. 4, support for this amendment is at specification paragraph [0032]. However, while the disclosure of specification paragraph [0032] provides descriptive support for “…when Vif is used, since Vif is known to bind to an E3 ubiquitin ligase complex and promote proteolysis of APOBEC3…, it is preferable to apply alteration that causes lack of bindability to proteins other than APOBEC3,” there is no apparent descriptive support for the limitation at issue. Applicant is invited to show support for the noted limitation.
Claims 1, 2, 4, 6, 9, 10, and 12 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor at the time the application was filed, had possession of the claimed invention.
This rejection has been modified from its previous version in order to address applicant’s amendment to the claims.
MPEP 2163.II.A.2.(a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention.”
For claims drawn to a genus, MPEP § 2163 states the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406.
MPEP § 2163 further states that “[s]atisfactory disclosure of a ‘representative number’ depends on whether one of skill in the art would recognize that the applicant was in possession of the necessary common attributes or features possessed by the members of the genus in view of the species disclosed. For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus…Instead, the disclosure must adequately reflect the structural diversity of the claimed genus, either through the disclosure of sufficient species that are ‘representative of the full variety or scope of the genus,’ or by the establishment of ‘a reasonable structure-function correlation.’ Such correlations may be established ‘by the inventor as described in the specification,’ or they may be ‘known in the art at the time of the filing date.’"
The factors considered in the Written Description requirement are (1) level of skill and knowledge in the art, (2) partial structure, (3) physical and/or chemical properties, (4) functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the (5) method of making the claimed invention. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would lead one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient." MPEP § 2163.
As amended, claim 1 (claims 2, 4, 6, 9, 10, and 12 dependent therefrom) recites a genus of variants of Virion infectivity factor (Vif) of a human immunodeficiency virus (HIV) or a simian immunodeficiency virus (SIV), or fragments thereof, the variants or fragments thereof binding to an apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3) family cytidine deaminase and do not substantially promote degradation of the APOBEC3 family cytidine deaminase via an E3 ubiquitin ligase complex.
According to specification paragraph [0032], “when Vif is used, since Vif is known to bind to an E3 ubiquitin ligase complex and promote proteolysis of APOBEC3…, it is preferable to apply alteration that causes lack of bindability to proteins other than APOBEC3. Examples of such alteration include deletion of several (e.g., 11, 10, 9, 8, 7 etc.) amino acids in the N terminal of Vif protein (refseq No. AAF20197) and substitution of the 145th leucine residue with other amino acid residue (e.g., alanine residue) and the like, but they are not limited to these alterations.”
Given a broadest reasonable interpretation in light of the specification, the structures of the Vif variant and fragments thereof are unlimited.
As amended, claim 12 recites said Vif variant is the sequence of GenBank Accession No. AAF20197 with at least one of (a) a deletion of 7 to 11 amino acids at the N-terminus of said sequence and (b) a substitution of the leucine residue at position 145 of said sequence.
Given a broadest reasonable interpretation in light of the specification, the term “with” in the phrase “with at least one of (a) a deletion of 7 to 11 amino acids at the N-terminus of said sequence and (b) a substitution of the leucine residue at position 145 of said sequence” is interpreted as being synonymous with “comprising,” which is inclusive or open-ended (MPEP 2111.0.I). The Vif variant of claim 12 is interpreted as requiring at least the modification(s) of (a) and/or (b) and any additional amino acid modifications (substitutions, insertions, deletions, and/or additions) relative to the sequence of GenBank Accession No. AAF20197.
The specification discloses the following representative species of the recited genus of Vif variants and fragments thereof – a variant Vif, wherein the variant Vif is Vif of HIV or SIV except for a deletion of 7 to 11 amino acids at the N-terminus. Other than a variant Vif, wherein the variant Vif is Vif of HIV or SIV except for a deletion of at least the 7 to 11 amino acids at the N-terminus, the specification fails to disclose any other variants of Vif that bind to an APOBEC3 family cytidine deaminase and do not substantially promote degradation of the APOBEC3 family cytidine deaminase via an E3 ubiquitin ligase complex.
Before the effective filing date of the claimed invention, there was a high level of unpredictability in the art of amino acid modification. For example, the reference of Singh et al. (Curr. Protein Pept. Sci. 18:1-11, 2017; cited on Form PTO-892 filed May 7, 2026) reviews various protein engineering methods and discloses that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility, and conformational changes (see p. 7, column 1, top). The unpredictability associated with amino acid modification is exemplified by the reference of Zhang et al. (Structure 26:1474-1485, 2018; cited on Form PTO-892 filed May 7, 2026), which discloses that even a mutation that was predicted to be benign caused significant structural changes and unexpected effects on the function of a polypeptide (p. 1475, column 1). As such, one of skill in the art would recognize a high level of unpredictability that a variant Vif as encompassed by the claims would exhibit binding to an APOBEC3 family cytidine deaminase and not substantially promote degradation of the APOBEC3 family cytidine deaminase via an E3 ubiquitin ligase complex.
Given that the claims recite a genus of Vif variants and fragments thereof encompassing unlimited modifications and having widely variant structures, the genus requires binding to an APOBEC3 family cytidine deaminase while simultaneously requiring that the members of the genus do not substantially promote degradation of the APOBEC3 family cytidine deaminase via an E3 ubiquitin ligase complex, there was a high level of unpredictability in the art of amino acid modification, and the specification discloses only a single representative species among a widely variant genus, one of skill would reasonably conclude that the applicant was not in possession of the claimed invention.
RESPONSE TO REMARKS: Applicant argues that in view of the specification’s disclosure (paragraph [0032]) of the N-terminal 7-11 amino acid deletion variant of Vif, which has the indicated function and the involvement of the N-terminal region in the E3-ligase/proteolysis pathway combined with the known Vif-CBFß-APOBEC3 binding interface, one of skill in the art would be able to visualize or recognize all members of the recited genus of Vif variants and fragments thereof.
Applicant’s arguments are not found persuasive. According to MPEP 2163.II.A.3.a).ii), for inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing only one species within the genus. Given that the genus of Vif variants and fragments thereof encompasses widely variant species, the state of the art of amino acid modification was highly unpredictable, and the specification discloses only a single representative species of the genus of recited Vif variants and fragments thereof, the specification fails to provide adequate description of the recited genus of Vif variants and fragments thereof.
While specification paragraph [0032] discloses the protein that binds to a DNA modifying enzyme can be appropriately modified based on the function of the protein, binding site with the target molecule, three-dimensional structure, and the like, and further discloses that those skilled in the art can appropriately design fragments, applicant’s disclosure appears to rely on a “make and test” rationale to satisfy the written description requirement of 35 U.S.C. 112(a). However, according to MPEP 2163.II.3, “An adequate written description of a chemical invention also requires a precise definition, such as by structure, formula, chemical name, or physical properties, and not merely a wish or plan for obtaining the chemical invention claimed.” In this case, such a “make and test” rationale is not sufficient to describe the members of the genus so that one of skill can “visualize or recognize” the members of the genus and one of skill in the art would reasonably conclude that applicant was not in possession of the recited genus of Vif variants and fragments thereof.
While applicant contends that “the Vif-CBFß-APOBEC3 binding interface is well known” to one of skill in the art, applicant does not elaborate and it is unclear to the examiner as to how one of skill in the art would apply the Vif-CBFß-APOBEC3 binding interface to establish adequate written description of the widely variant structures of the members of the genus of Vif variants and fragments thereof.
For these reasons, it is the examiner’s position that the specification fails to satisfy the written description requirement of 35 U.S.C. 112(a).
Claims 1, 2, 4, 6, 9, 10, and 12 are rejected under 35 U.S.C. 112(a) because the specification, while being enabling for a complex comprising
a nucleic acid sequence-recognizing module specifically binding to a target nucleotide sequence in a DNA, and
a DNA modifying enzyme-binding module bonded to each other,
wherein the nucleic acid sequence-recognizing module is a CRISPR-Cas system,
wherein at least one DNA cleavage ability of Cas is inactivated, and
wherein the DNA modifying enzyme-binding module is a variant Virion infectivity factor (Vif) that specifically binds to an APOBEC3 family cytidine deaminase, wherein the variant Vif is Vif of HIV or SIV except for a deletion of 7 to 11 amino acids at the N-terminus,
does not reasonably provide enablement for all complexes as encompassed by the claims, particularly with regard to the recited Vif variant and fragment thereof. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
This rejection has been modified from its previous version in order to address applicant’s amendment to the claims.
“The test of enablement is not whether any experimentation is necessary, but whether, if experimentation is necessary, it is undue.” In re Angstadt, 537 F.2d 498, 504, 190 USPQ 214, 219 (CCPA 1976). Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands (858 F.2d 731, 737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988)) as follows: (A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the inventor; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. See MPEP § 2164.01(a). The Factors considered to be most relevant to the instant rejection are addressed in detail below.
The nature of the invention: The claimed invention encompasses a complex of a fusion of a catalytically impaired Cas (corresponding to “a nucleic acid sequence-recognizing module specifically binding to a target nucleotide sequence in a DNA in claim 1) and a variant of Virion infectivity factor (Vif) of human immunodeficiency virus (HIV) or simian immunodeficiency virus (SIV) (corresponding to “a DNA modifying enzyme- binding module” in claim 1) and a guide RNA (corresponding to a component of the “CRISPR-Cas system” in claim 1). The specification discloses Vif binds to APOBEC, particularly APOBEC3 as the DNA modifying enzyme (specification at paragraph [0032]).
The breadth of the claims: As amended, claims 1, 2, 4, 6, 9, 10, and 12 are drawn to a complex comprising
a nucleic acid sequence-recognizing module specifically binding to a target nucleotide sequence in a DNA, and
a DNA modifying enzyme-binding module bonded to each other,
wherein the nucleic acid sequence-recognizing module is a CRISPR-Cas system,
wherein at least one DNA cleavage ability of Cas is inactivated, and
wherein the DNA modifying enzyme-binding module is a variant of Virion infectivity factor (Vif) of human immunodeficiency virus (HIV) or simian immunodeficiency virus (SIV) or a fragment of said Vif variant, wherein the Vif variant or fragment thereof binds to an apolipoprotein B mRNA-editing enzyme, catalytic polypeptide-like 3 (APOBEC3) family cytidine deaminase and does not substantially promote degradation of the APOBEC3 family cytidine deaminase via an E3 ubiquitin ligase complex.
According to specification paragraph [0032], “when Vif is used, since Vif is known to bind to an E3 ubiquitin ligase complex and promote proteolysis of APOBEC3…, it is preferable to apply alteration that causes lack of bindability to proteins other than APOBEC3. Examples of such alteration include deletion of several (e.g., 11, 10, 9, 8, 7 etc.) amino acids in the N terminal of Vif protein (refseq No. AAF20197) and substitution of the 145th leucine residue with other amino acid residue (e.g., alanine residue) and the like, but they are not limited to these alterations.”
Given a broadest reasonable interpretation in light of the specification, the structures of the Vif variant and fragment thereof are unlimited.
As amended, claim 12 recites said Vif variant is the sequence of GenBank Accession No. AAF20197 with at least one of (a) a deletion of 7 to 11 amino acids at the N-terminus of said sequence and (b) a substitution of the leucine residue at position 145 of said sequence.
Given a broadest reasonable interpretation in light of the specification, the term “with” in the phrase “with at least one of (a) a deletion of 7 to 11 amino acids at the N-terminus of said sequence and (b) a substitution of the leucine residue at position 145 of said sequence” is interpreted as being synonymous with “comprising,” which is inclusive or open-ended (MPEP 2111.0.I). The Vif variant of claim 12 is interpreted as requiring at least the modification(s) of (a) and/or (b) and any additional amino acid modifications (substitutions, insertions, deletions, and/or additions) relative to the sequence of GenBank Accession No. AAF20197.
The amount of direction provided by the inventor and The existence of working examples: The specification discloses that while Vif binds to APOBEC3, Vif also binds to an E3 ubiquitin ligase complex and promotes proteolysis of APOBEC3 and that it is preferable to alter the Vif so that it binds only to APOBEC3 (specification at paragraph [0032]). The specification discloses the following working example of a Vif protein that binds to APOBEC3 without also binding to an E3 ubiquitin ligase complex and promoting proteolysis of APOBEC3 – a variant Vif, wherein the variant Vif is Vif of HIV or SIV except for a deletion of 7 to 11 amino acids at the N-terminus. Other than a variant Vif, wherein the variant Vif is Vif of HIV or SIV except for a deletion of at least the 7 to 11 amino acids at the N-terminus, the specification fails to disclose any other variants of Vif that bind to an APOBEC3 family cytidine deaminase without substantially promoting degradation of the APOBEC3 family cytidine deaminase via an E3 ubiquitin ligase complex.
The state of the prior art; The level of one of ordinary skill; and The level of predictability in the art: According to MPEP 2164.03, “…what is known in the art provides evidence as to the question of predictability” and “[I]f one skilled in the art cannot readily anticipate the effect of a change within the subject matter to which that claimed invention pertains, then there is lack of predictability in the art.”
Before the effective filing date of the claimed invention, there was a high level of unpredictability in the art of amino acid modification. For example, the reference of Singh et al. (Curr. Protein Pept. Sci. 18:1-11, 2017; cited on Form PTO-892 filed May 7, 2026) reviews various protein engineering methods and discloses that despite the availability of an ever-growing database of protein structures and highly sophisticated computational algorithms, protein engineering is still limited by the incomplete understanding of protein functions, folding, flexibility, and conformational changes (see p. 7, column 1, top). The unpredictability associated with amino acid modification is exemplified by the reference of Zhang et al. (Structure 26:1474-1485, 2018; cited on Form PTO-892 filed May 7, 2026), which discloses that even a mutation that was predicted to be benign caused significant structural changes and unexpected effects on the function of a polypeptide (p. 1475, column 1). As such, one of skill in the art would recognized a high level of unpredictability that a variant Vif and a fragment thereof as encompassed by the claims would exhibit binding to an APOBEC3 family cytidine deaminase without substantially promoting degradation of the APOBEC3 family cytidine deaminase via an E3 ubiquitin ligase complex.
In view of the breadth of the claims, the lack of guidance and working examples provided in the specification, and the high degree of unpredictability in the relevant art, undue experimentation would be necessary for a skilled artisan to make and use the entire scope of the claimed invention. Applicants have not provided sufficient guidance to enable one of ordinary skill in the art to make and use the claimed invention in a manner reasonably correlated with the scope of the claims. The scope of the claims must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA 1970)). Without sufficient guidance, determination of having the desired biological characteristics is unpredictable and the experimentation left to those skilled in the art is unnecessarily, and improperly, extensive and undue. See In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988).
RESPONSE TO REMARKS: Applicant argues that in view of the specification’s disclosure of the working example of a Vif protein with an N-terminal deletion of 7-11 amino acids and the known Vif-CBFß-APOBEC3 binding interface, one of skill in the art would be able to make and use the full scope of the claimed invention and the references of Singh et al. and Zhang et al. fail to establish that undue experimentation would be required to make and use the claimed invention.
Applicant’s arguments are not found persuasive. Examiner acknowledges the specification’s working example of a Vif protein with an N-terminal deletion of 7-11 amino acids and also acknowledges that the references of Singh et al. and Zhang et al. by themselves fail to establish undue experimentation. However, the instant rejection is supported by a detailed analysis of relevant Factors of In re Wands and is not solely based on the references of Singh et al. and Zhang et al. to establish undue experimentation. Contrary to applicant’s position, in view of a detailed analysis of the relevant Factors of In re Wands as set forth above, it is the examiner’s position that the specification fails to enable the full scope of the claimed invention. While applicant contends that “the Vif-CBFß-APOBEC3 binding interface is well known” to one of skill in the art, applicant does not elaborate and it is unclear to the examiner as to how one of skill in the art would apply the Vif-CBFß-APOBEC3 binding interface to making and using the broad scope of Vif variants and fragments thereof.
For these reasons, it is the examiner’s position that the specification fails to satisfy the enablement requirement of 35 U.S.C. 112(a).
Conclusion
Status of the claims:
Claims 1, 2, 4, 6, 9, 10, and 12 are pending.
Claims 1, 2, 4, 6, 9, 10, and 12 are rejected.
No claim is in condition for allowance.
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 nonprovisional extension fee (37 CFR 1.17(a)) 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 mailing date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DAVID J STEADMAN whose telephone number is (571)272-0942. The examiner can normally be reached Monday to Friday, 7:30 AM to 4:00 PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, MANJUNATH N. RAO can be reached on 571-272-0939. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/David Steadman/Primary Examiner, Art Unit 1656