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 without traverse of claims 1-4 in the reply filed on January 29, 2026 is acknowledged.
Status of Claims
Claims 1-9 are currently pending in the instant application. Claims 5-9 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions, there being no allowable generic or linking claim.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 are under examination on the merits in the instant application.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on May 31, 2023 has been considered by the examiner, except NPL Citation No. 6. It is noted that the English language translation submitted by applicant is illegible.
Specification
1. The specification is objected to for failing to comply with 37 CFR 1.77(b), which requires that the specification of a utility application should include sections in order with appropriate section headings. For instance, the instant specification does not contain “BACKGROUND OF THE INVENTION”, “BRIEF SUMMARY OF THE INVENTION”, and “DETAILED DESCRIPTION OF THE INVENTION”. Applicant is required to carefully review the entire specification and comply with the guidelines in 37 CFR 1.77(b).
2. The disclosure is objected because it contains an embedded hyperlink and/or other form of browser-executable code. See paragraph 75. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
3. The disclosure is objected to because it does not contain a "Sequence Listing" as a separate part of the disclosure or a CRF of the “Sequence Listing.”. Appropriate correction is required as instructed below. See under the heading “Nucleotide and/or Amino Acid Sequence Disclosures”.
Drawings
1. The drawings in FIG. 3B are objected to under 37 CFR 1.83(a) because they fail to show “green”, “pink”, and “gray” as described in the specification. Any structural detail that is essential for a proper understanding of the disclosed invention should be shown in the drawing. MPEP § 608.02(d). 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.
Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
2. The drawings in FIGs. 3A, 6, and 11-12 are objected to for containing sequence rule non-compliant subject matter. Appropriate correction is required as instructed below.
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency – The amino acid sequences appearing in FIG. 3A and the nucleotide sequences appearing in FIGs. 6 and 11-12 are not identified by sequence identifiers in accordance with 37 CFR 1.821(d). Sequence identifiers for nucleotide and/or amino acid sequences must appear either in the drawings or in the Brief Description of the Drawings.
Required response – Applicant must provide:
Replacement and annotated drawings in accordance with 37 CFR 1.121(d) inserting the required sequence identifiers;
AND/OR
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required sequence identifiers into the Brief Description of the Drawings, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825 because it does not contain a "Sequence Listing" as a separate part of the disclosure or a CRF of the “Sequence Listing.”.
Required response - Applicant must provide:
A "Sequence Listing" part of the disclosure; together with
An amendment specifically directing its entry into the application in accordance with 37 CFR 1.825(a)(2);
A statement that the "Sequence Listing" includes no new matter as required by 37 CFR 1.821(a)(4); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(a)(3).
If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
If the "Sequence Listing" part of the disclosure is submitted according to item 1) c) or d) above, applicant must also provide:
A CRF in accordance with 37 CFR 1.821(e)(1) or 1.821(e)(2) as required by 1.825(a)(5); and
A statement according to item 2) a) or b) above.
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 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 instant claims recite “the adenine base editor having a form in which an adenosine deaminase variant comprising a P48R mutation”.
The instant claims recite the adenine base editor (ABE) in the form of a tRNA adenosine deaminase variant (TadA) without any specific amino acid sequence assigned to the ABE or the TadA variant. Further, the specification does not define a specific amino acid sequence for the claimed subject matter. Now, it is noted that it was art-recognized knowledge before the effective filing date that there are a number of different ABE amino acid sequence variants or mutant TadA genotypes comprising P48. See Figure 2b and Extended Dana Figure 1 of Gaudelli et al. (Nature, 2017, 551:464-471). As such, the actual ABE or TadA variant sequence comprising P48, which is claimed to be mutated to arginine (R) reads on multiple different sequences. That is, the E. coli TadA amino acid sequence for “ABE1.1” modified to comprise P48R differs from that for “ABE5.3” modified to comprise P48R. Hence, the claimed adenine base editor encompasses variable, inconsistent amino acid sequences, and as such, one of ordinary skill in the art cannot ascertain the clear metes and bounds of the exact amino acid sequence of the claimed subject matter of claims 1-4.
In addition, “TadA7.10” required to comprise P48R as recited in claim 2 is not known to comprise P48 but instead was known to comprise A48, which is one of 14 modified amino acids compared to the wild-type. See “ABE7.10” of E. coli TadA is known to comprise A48 as shown in Figure 2b and Extended Data Figure 1 of Gaudelli et al. (Nature, 2017, 551:464-471). Hence, it is unclear how TadA7.10 comprising A48 can possibly have P48 that is to be mutated to arginine (R). Accordingly, claim 2 recites structurally conflicting limitations regarding the TadA.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-4 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, 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, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
The instant claims are broadly drawn to an ABE comprising an adenosine deaminase variant of any amino acid sequence having P48R that is fused to any Cas9 protein.
The instant specification does not appear to identify/disclose the amino acid sequence of the claimed ABE. Further, as broadly written, the claimed “adenosine deaminase variant comprising a P48R mutation” is not limited to a variant having only P48R mutation but is open to comprising mutations at other residues. Furthermore, as broadly written, the claimed “Cas9” protein reads on any Cas9 species known in the art. Hence, each of the instantly claimed “adenosine deaminase variant” and “(Cas9) protein” constituting the ABE reads on a myriad of structurally different species. Now, it appears that the instant specification at best appears to describe an increased TC sequence-specific cytosine base editing activity that is provided by a TadA comprising P48R as the only mutated or substituted amino acid, wherein the TadA is fused to a mutant Cas9(D10A). See FIG. 5. Indeed, ABEs are recognized to comprise “a Cas9 nickase” with D10A substitution or deficient Cas9 (dCas(A840H) as evidenced by page 1 of Rees et al. (Science Advances, 2019, 5:eaax5717) disclosing that “All ABEs reported to date” comprise “three fused protein components”, one of which is “a Cas9(D10A) nickase”. See also Figures 18 and 58 and paragraph 0202 of Liu et al. (US 2018/0073012 A1). Taken together, the prior art teaches that only two specific species of Cas9 protein is capable of being used in an ABE, wherein the single species of dCas9 disclosed in the specification is one of the two art-recognized Cas9 species suitable for an ABE. Given the breadth of the generically recited claim language that reads on any TadA variants and any Cas9 proteins, the single disclosed dCas9-containing species disclosed in FIG.5, which appears to comprise a single mutation P48R in the TadA, is not deemed to constitute a representative number of structurally different species encompassed by the genus claimed in the instant case because one cannot extrapolate an increased cytosine editing activity for other structures other than the single species disclosed in the instant application. That is, the required structure-function correlation is not sufficiently described for the entire genus as claimed.
Regarding claim 2, it is noted that the claim requires that “TadA7.10” comprises “a P48R mutation”. However, as noted in the §112(b) rejection above, TadA7.10 (or ABE7.10) is known to have “A” at position 48. Indeed, consistent with the knowledge in the prior art, the instant application appears to disclose that the amino acid residue at position 48 of “TadA7.10” is “A” as evidenced by FIG. 3A. Hence, it is prima facie apparent that the instant application fails to describe a “TadA7.10” comprising “a P48R mutation” because “TadA7.10” does not have “P” at position 48.
Accordingly, it is concluded that the instant specification fails to adequately describe the claimed subject matter “in such full, clear, concise, and exact terms” (e.g., amino acid sequence of the claimed ABE) and also fails to reasonably convey that the instant co-inventors had possession of the entire genus as of the filing date sought in the instant application.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-4 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Jeong et al. (Nature Biotechnology, published online on July 1, 2021, 39:1426-1433).
Applicant cannot rely upon the certified copy of the foreign priority application to overcome this rejection because a translation of said application has not been made of record in accordance with 37 CFR 1.55. When an English language translation of a non-English language foreign application is required, the translation must be that of the certified copy (of the foreign application as filed) submitted together with a statement that the translation of the certified copy is accurate. See MPEP §§ 215 and 216.
Jeong discloses “ABE-P48R-UGI”, which comprises TadA with P48R that is fused/linked to Cas9(D10A), which is linked to two copies of UGI. See pages 1429-1430; Figure 4a. Jeong discloses that the ABE variant can be “TadA7.10” or “ABEmax”. See page 1426.
Since all structural limitations claimed in the instant case are fully satisfied by Jeong’s ABE, it necessarily follows that Jeong’s ABE inherently possesses “increased thymine-cytosine (TC) sequence-specific cytosine base editing activity,” absent objective evidence to the contrary.
Accordingly, claims 1-4 are described by Jeong et al.
Claims 1-4 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Jeong et al. (Research Square, October 2, 2020, of record).
Jeong discloses an adenine base editor “ABEmax” comprising “fused elements” comprising “a partially inactive Cas nuclease” including “Cas9” and TadA7.10 having a P48R mutation (“TadA7.10-P48R”) forming “ABEmax-P48R”, which “has increased cytosine editing activity”, wherein two copies of uracil-DNA glycosylase (UGI) are linked to the C-terminus of ABEmax-P48R, thereby forming “ABE-P48R-UGI”. See pages 2-5.
Accordingly, all claim limitations are described by Jeong et al.
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 and 4 are rejected under 35 U.S.C. 103 as being unpatentable over Liu et al. (US 2018/0073012 A1).
Liu teaches making an ABE, which is a fusion protein comprising a Cas9 nickase (nCas9) and E. coli TadA (SEQ ID NO:1) that is modified at P48 to comprise “an P48X mutation in ecTadA SEQ ID NO: 1”, wherein “X indicates any amino acid other than the corresponding amino acid in the wild-type adenosine deaminase”, wherein Liu actually used “P48L”, “P48S”, “P48T”, or “P48A”, wherein a “UGI” is tethered to the ABE. See paragraphs 0009, 0202, 0206, 0266, 0270, 0274, and 0316; Table 4.
Liu discloses SEQ ID NO:1 in paragraph 0199 as reproduced below, wherein a box is added for the wild-type “P” at amino acid residue 48.
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78
460
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50
456
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Liu teaches that “the adenosine deaminase is from a bacterium, for example, E. coli and S. aureus”, wherein the “S. aureus TadA is “a homolog of ecTadA”. See paragraphs 0007 and 0112.
Liu discloses that S. aureus TadA (SEQ ID NO:8) has “R” at position 48. See paragraph 0201. See the following, wherein a box is added for the “R” at amino acid residue 48.
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156
454
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Liu shows amino acid alignment between the two TadA species, ecTadA and saTadA, in Figure 10 such that the two sequences are each aligned from amino acid residue 1 such that ecTadA has “RLIDATL” at positions 74-80 and saTadA has “RLEGCTL” at positions 74-80. Hence, it is prima facie apparent that the “P” amino acid residue at position 48 of ecTadA is homologous to “R” at position 48 of saTadA.
It would have been obvious to one of ordinary skill in the art before the effective filing date to try “R” for the “X” amino acid in “P48X” of Liu’s SEQ ID NO:1 when making Liu’s fusion protein comprising a mutated ecTadA, dCas9, and UGI. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success because making an ABE that is a fusion protein comprising a modified ecTadA amino acid sequence having “P48X” was expressly suggested in the art as evidenced by Liu, and because there are only a finite number of identified, predictable amino acid residues other than “P” at position 48 of SEQ ID NO:1. Since Liu had already made fusion protein species each comprising one of “P48L”, “P48S”, “P48T”, and “P48A”, one of ordinary skill in the art would have tried amino acid residues other than L, S, T, and A at position 48 that were already tried by Liu in order to make and test new fusion ABE species whose P48 is mutated, thereby providing a total of 15 art-recognized standard amino acid residue choices (R, N, D, C, E, Q, G, H, I, K, M, F, W, Y, V) for the “X” in “P48X”. In particular, one of ordinary skill in the art would have more than reasonably included “R” for the 15 remaining “X” amino acids constituting “P48X” of Liu’s SEQ ID NO:1 (ecTadA) because S. aureus TadA (saTadA) was deemed “a homolog of ecTadA”, and because it is art-recognized knowledge and a scientific fact that saTadA comprises “R” at position 48 as evidenced by Liu’s SEQ ID NO:8. As such, one of ordinary skill in the art would have reasonably pursued the finite number of known amino acid residue options for “X” in “P48X”, which definitely includes “R” especially in view of “R” being at position 48 of the analogous ecTadA, and would have thus obtained the instantly claimed TadA comprising P48R with a reasonable expectation of success.
“When there is a design need or market pressure to solve a problem and there are a finite number of identified, predictable solutions, a person of ordinary skill has good reason to pursue the known options within his or her technical grasp. If this leads to the anticipated success, it is likely that not of innovation but of ordinary skill and common sense.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007).
Since the ABE comprising an ecTadA that is modified to comprise P48R for the reasons stated above fully satisfies all structural limitations set forth in claim 1, it necessarily follows that the ABE would inherently have an increased cytosine base editing activity, absent objective evidence to the contrary.
Accordingly, clams 1 and 4 taken as a whole would have been prima facie obvious before the effective filing date.
Claim 3 is rejected under 35 U.S.C. 103 as being unpatentable over Liu et al. (US 2018/0073012 A1) as applied to claim 1 above, and further in view of Rees et al. (Science Advances, 2019, 5:eaax5717).
The obviousness of claim 1 and the teachings of Liu are set forth in the above rejection, which is fully incorporated by reference herein thus will not be repeated.
Liu does not teach using ABEmax.
Rees teaches that “ABEmax” is an “improved” ABE, which has been “improved through codon and nuclear localization sequence optimization”. See page 1.
It would have been obvious to one of ordinary skill in the art before the effective filing date to utilize Rees’ “ABEmax” for introducing Liu’s SEQ ID NO:1 that has been modified to comprise P48R, which is rendered obvious as explained in the above rejection. One of ordinary skill in the art would have been motivated to do so with a reasonable expectation of success in order to make an ABE having “improved” properties because “ABEmax” was generated with “improved” properties as evidenced by Rees.
Accordingly, claim 3 taken as a whole would have been prima facie obvious before the effective filing date.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DANA H SHIN whose telephone number is (571)272-8008. The examiner can normally be reached Monday-Thursday: 8am - 6:30pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, RAM SHUKLA can be reached at 571-272-0735. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/DANA H SHIN/Primary Examiner, Art Unit 1635