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 Group V (claims 1, 2, 18 and 74-82) and C1 substrate being methanol in the reply filed on 02/05/2026 is acknowledged. The traversal is on the ground(s) that the “special technical feature linking these groups is the specific claimed iterative pathway. This is not found persuasive because as far as claim 1 is suggested by the prior art as discussed below, such iterative pathway is not a special technical feature that makes a contribution over the prior art.
The requirement is still deemed proper and is therefore made FINAL.
Claims 3-15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected Invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 02/05/2026.
In the interest of compact prosecution, claim 20 is not withdrawn and is examined herein.
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.
Claim 20 and 77 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 20 recites that the C1 substrate comprises formaldehyde, which is understood to directly include the C1 substrate only being formaldehyde. Due to dependency from claim 1, claim 20 sets forth “a first set of heterologous nucleic acids encoding one or more enzymes that convert the C1 substrate [being formaldehyde] to formyl-CoA and formaldehyde.” As such, it is unclear if claim 1 requires:
-conversion of formaldehyde to formyl-CoA wherein a portion of the starting formaldehyde remains formaldehyde; or
-conversion of formaldehyde to an intermediate compound that is reconverted to formaldehyde, since claim 20 appears to require that formaldehyde be converted to formaldehyde that requires a conversion rather no chemical change.
Since the scope of claim 20 is subject to multiple interpretations, an ordinarily skilled artisan cannot determine how to avoid infringement.
Claim 77 recites RuHACLG390N. The meaning of the substitution G390N is unclear in the absence of a specific sequence that serves as reference to define the meaning of G390 such that an ordinarily skilled artisan cannot determine how to avoid infringement. While the specification may reference databases outside of the specification that may be relevant, “Essential material” may be incorporated by reference, but only by way of an incorporation by reference to a U.S. patent or U.S. patent application publication. 37 CFR 1.57(d). Essential material includes information that “Describe the claimed invention in terms that particularly point out and distinctly claim the invention as required by 35 U.S.C. 112(b),” wherein the sequence of RuHACL is required to particularly point out the meaning of G390N. 37 CFR 1.57(d)(2).
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.
Claim(s) 1, 2, 18, 20, 74-77, and 79-82 is/are rejected under 35 U.S.C. 103 as being unpatentable over Chou, Alex. "Novel enzymes and pathways facilitating biological utilization of one carbon compounds." (2018) Diss., Rice University.
Chou, abstract, states:
Although biological systems hold great potential for the sustainable production of fuels and chemicals from one-carbon (C1) feedstocks, their C1 utilization reactions rely on specific acceptor molecules, complex metabolic pathways, and originate from difficult to engineer microorganisms, limiting applicability and implementation in the biotechnology industry. As a result, to date no non-native C1 utilizing organism has been engineered for growth or product synthesis from solely C1 substrates. In this thesis, we report that 2-hydroxyacyl-CoA lyase (HACL), an enzyme involved in the α-oxidation of long-chain fatty acids, catalyzes a novel C1 addition reaction resulting in the ligation of carbonyl-containing molecules with formyl-CoA to produce C1-elongated 2-hydroxyacyl-CoAs. We characterized the first prokaryotic variant of HACL and found that it can use a wide range of carbonyl substrates of different chain lengths, including both aldehydes and ketones, which when combined with enzymes comprising a de novo designed pathway, supported the conversion of C1 feedstocks to industrially relevant chemicals such as glycolate, ethylene glycol, ethanol, acetate, glycerate, and 2-hydroxyisobutyrate. Homology-guided mutagenesis allowed the identification of key residues influencing the in vivo activity of HACL and its ability to support C1 bioconversion. We implemented an HACL-based pathway in E. coli to utilize formaldehyde as the sole carbon substrate for glycolate production and demonstrated the potential of the pathway to support growth in a two-strain system, which was supported by genome scale modeling and flux balance analysis. The previously undescribed condensation reaction catalyzed by HACL is a direct and flexible means for C1 addition that can facilitate engineering of C1 bioconversion and synthetic methylotrophy/autotrophy in industrial organisms.
“Having successfully prototyped HACL-mediated pathways using both purified protein and in cell extract, we hypothesized that these pathways could function in vivo in whole cells. We focused in this work on the simplest version of the pathway, catalyzing the conversion of formaldehyde to glycolate. This would not only serve as a proof-of principle prototype of pathway function, but also serve as a basis for further expansion to other feedstocks and products. For example the conversions of methanol and formate to formaldehyde have been the subject of other studies. In addition, glycolate is a product of commercial interest with applications in areas such as cosmetics and polymers” Chou, page 94. “Our first aim was to demonstrate that the conversion of formaldehyde to glycolate is possible using whole cells either in a live or resting state. In this section, we describe our efforts to engineer strains of E. coli to express the pathway for the desired C1 conversion and our strategies for testing the engineered strains.” Chou, page 95.
“The ability of the HACL-based pathway to convert formaldehyde to glycolate, a native substrate for E. coli, provides the opportunity for the pathway to support growth on C1 substrates or C1-trophy. We evaluated the ability of the pathway to support growth using both computational and experimental methods.” Chou, page 111.
“[A]ppropriate amounts of carbon source (e.g. formaldehyde) was added to 25 mL Pyrex Erlenmeyer flasks (Corning Inc., Corning, NY) and sealed with foam plugs filling the necks. Flasks were incubated at 30°C and 200 rpm.” Chou, page 96.
Such HACL-mediated pathway expressed in E. coli is as follows in Fig. 6.1.2 of Chou:
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The above is a disclosure of an engineered microbial system and method (wherein the microbial system, i.e. E. coli, is not naturally able to use C1 substrate from growth) having a first set of heterologous nucleic acids encoding one or more enzymes that convert the C1 substrate to formyl-CoA, and a second set of heterologous nucleic acids encoding one or more enzymes being HACL that catalyzes the ligation of formyl-CoA and formaldehyde to form glycolyl-CoA and ACR that catalyzes the ligation of glycolyl-CoA to glycoaldehyde, wherein such glycoaldehyde enable use of glycolaldehyde (after oxidation to glycolate) to enable growth of the microbial system (i.e. E. coli).
Regarding recitation in claim 1 of “that convert C1 substrate to formyl-CoA and formaldehyde,” Chou directly suggests that the C1 substrate can be methanol. Chou, Fig. 5.1.1. teaches the following:
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While chapter 6 of Chou shows a C1 substrate being directly formaldehyde as recited in claim 20, Chou, Fig. 5.1.1 teaches that methanol (as recited in claim 18) can also serve as a C1 substrate that is converted to formaldehyde by activity of MDH and then to formyl-CoA by activity of ACR. Since Chou directly suggests that methanol be used as C1 carbon source, at the time of filing an ordinarily skilled artisan would have been motivated to modify any engineered E. coli taught by Chou to have a first set of heterologous nucleic acids encoding enzymes including ACR and MDH that converts a C1 substrate being methanol to formyl-CoA and formaldehyde.
Regarding claim 20 specifically, claim 20 requires “one or more enzymes that convert the C1 substrate [being formaldehyde] to formyl-CoA and formaldehyde.” The rejection of claim 20 under 35 U.S.C. 112(b) above is incorporated herein by reference. The provision of formaldehyde as a C1 substrate as taught in Chou is considered to meet the broadest reasonable interpretation of conversion of formaldehyde C1 substrate to formyl-CoA and formaldehyde as far as a portion (but not necessarily all) of formaldehyde is converted to formyl-CoA such that there is a remainder of formaldehyde.
Regarding a second iteration of activity of HACL and ACR as recited in claim 1, Chapter 6 of Chou teaches “Three version of the HACL-based pathway were evaluated, each of which we have demonstrated either in vitro or in vivo. . . . Finally, we simulated the ability of an HACL-based pathway to provide C3 units by way of glyceryl-CoA for the production of glycerate or glyceraldehyde (HACL-Glycerald) as described in Section 5.4.2. Both reactions for reduction of glyceryl-CoA to glyceraldehyde and hydrolysis of glyceryl-CoA to glycerate were included in the model.” Chou, pages 113-114. Table 6.1 of Chou shows the pathway for glyceraldehyde production as follows:
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The above is a description of a first iteration wherein a HACL catalyzes ligation of formyl-CoA and formaldehyde to glycolyl-CoA and an ACR catalyzes conversion of glycolyl-CoA to glycoaldehyde, and a second iteration wherein HACL catalyzes ligation of formyl-CoA and glycoaldehyde to form glyceryl-CoA and ACR catalyzes conversion of glyceryl-CoA to glyceraldehyde.
As discussed, Chou embodiments the first iteration as recited in a working embodiment using formaldehyde as a direct C1 substrate wherein Chou further directly teaches that methanol can substitute as a C1 substrate wherein methanol is oxidized to formaldehyde by activity of MDH. However, Chou in reference to Table 6.1 and related text, directly suggests that a second iteration of formyl-CoA ligation to glycoaldehyde can be employed to produce glyceraldehyde. As such, at the time of filing an ordinarily skilled artisan would have been motivated to further modify any embodiment of Chou to have a second iteration as recited wherein HACL catalyzes ligation of formyl-CoA and glycoaldehyde to form glyceryl-CoA and ACR catalyzes conversion of glyceryl-CoA to glyceraldehyde, since Chou directly suggests that the same is desirable.
For these reasons, Chou suggest the features of claim 1, 2, 18, 20, 79 and 82.
Regarding claims 75 and 81, as discussed above, Chou in Fig. 6.1.2(A) suggests AldA (a third set of nucleic acids) converts glycoaldehyde to glycolic acid that supports cell growth as recited in claim 75. Although the second iteration as discussed requires glycolaldehyde to be converted to glyceryl-CoA, Chou in Fig. 6.1.2(A) nevertheless teaches that it is desirable for at least a portion of glycoaldehyde to be converted to glycerate to support cell growth. “[G]lycolate must be generated in sufficient quantity and rate to allow for measurable cell growth.” Chou, page 122. As such, an ordinarily skilled artisan at time of filing would have been motivated to provide for some degree of glycolate production to benefit cell growth even in embodiments wherein glycolyl-CoA to glycolate to support cell growth. Glycolate is understood to meet the recitation of glycolic acid wherein glycolate is the conjugate base of glycolic acid.
Regarding claim 76 and 77, “To this end, we combined our glycolate-producing strain (AC440 expressing RuHACLG390N, LmACR, and AldA) with a second E. coli strain capable of glycolate consumption.” Chou, page 122. This is understood as directly suggesting HACL meeting the features of claims 76 and 77 as embodiments of a HACL as recited. That is, Fig. 6.11 of Chou compares activities of RuHACLG390N with wild-type RuHACL, which both have activity for producing glycolate such that Chou is understood as directly suggesting use of HACL meeting the features of claims 76 and 77.
Regarding claims 74 and 80, Fig. 5.3 of Chou teaches the following:
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The above shows the following iterations:
First iteration of ligation of formyl-CoA and formaldehyde to form glycolyl-CoA that is converted to glycoaldehyde;
Second iteration of ligation of formyl-CoA and glycoaldehyde to from glyceryl-CoA that is converted to glyceraldehyde; and
Third iteration of ligation of formyl-CoA and glyceraldehyde to form tetrose (a polyhydroxyaldehyde).
While Chou (and the specification) does not teach a working embodiment of production of tetrose (a polyhydroxyaldehyde) through three iterations as discussed above, at the time of filing an ordinarily skilled artisan would have been motivated to implement the same in a microbial system (engineered E. coli host) as taught by Chou since Fig. 5.3 of Chou and related text directly indicate that performance of the same is desirable. That is, Chou teaches repeat iterative elongations with formyl-CoA catalyzed by HCAL to form polyhydroxyaldehyde products as desirable such that an ordinarily skilled artisan at time of filing would have been motivated to do the same in an E. coli host cell.
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 1, 2, 18, 20, 74-77, and 79-82 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-26 of U.S. Patent No. 11,186,834 B2 in view of Chou, Alex. "Novel enzymes and pathways facilitating biological utilization of one carbon compounds." (2018) Diss., Rice University.
The rejections over Chou under 35 U.S.C. 103 above are incorporated herein by reference.
Patented claims recite:
1. A genetically modified microorganism comprising:
a first heterologous DNA molecule encoding a 2-hydroxyacyl-CoA lyase or an oxalyl-CoA decarboxylase that catalyzes the condensation of an initial C(n)-aldehyde with formyl-CoA to produce a 2-hydroxy-C(n+1)-acyl-CoA, wherein the 2-hydroxy-C(n+1)-acyl-CoA is one carbon longer than the initial C(n) aldehyde, and wherein n is the number of carbons in the initial C(n)-aldehyde, and
at least one heterologous DNA molecule encoding one or more polypeptides that catalyzes the conversion of a single carbon substrate to formyl-CoA, and
at least one heterologous DNA molecule encoding a polypeptide that catalyzes a conversion of the 2-hydroxy-C(n+1)-acyl-CoA.
2. The genetically modified microorganism of claim 1, wherein the first heterologous DNA molecule encodes a 2-hydroxyacyl-CoA lyase.
The patented claims encompass the performance of a first iteration and sets of nucleic acids as recited in claim 1 being a C1 substrate converted to formyl-CoA and ligation with formaldehyde to produce glycolyl-CoA as a 2-hydroxy-C(n+1)-acyl-CoA. As discussed above, Chou teaches that a desirable embodiment of at least patented claim 1 for has conversion of glycolyl-CoA to glyceraldehyde in a manner having all of the features of the rejected claims. That is, patented claim 1 is more generic to and encompasses the rejected claims, wherein Chou teaches that an advantageous embodiment of patented claim 1 is a microbial system and methods meeting the features of the rejected claims such that an ordinarily skilled artisan at the time of filing would have produced embodiments of patented claim 1 having all of the features of the rejected claims to achieve the same benefits of producing glyceraldehyde from C1 substrates set forth in the rejections under 35 U.S.C. 103 over Chou set forth above.
Claims 1, 2, 18, 20, 74-77, 79-82 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-36 of U.S. Patent No. 12,391,937 B2 in view of Chou, Alex. "Novel enzymes and pathways facilitating biological utilization of one carbon compounds." (2018) Diss., Rice University.
The rejections over Chou under 35 U.S.C. 103 above are incorporated herein by reference.
Patented claims recite:
1. A method for the production of a product from a single carbon substrate, the method comprising the steps of:
a) growing a genetically modified microorganism in a culture comprising the single carbon substrate and a growth media,
b) converting said single carbon substrate to a formyl-CoA,
c) condensing an initial C(n)-aldehyde with the formyl-CoA to produce 2-hydroxy-C(n+1)-acyl-CoA, wherein the 2-hydroxy-C(n+1)-acyl-CoA is one carbon longer than the initial C(n) aldehyde and wherein n is the number of carbons in the initial C(n)-aldehyde;
d) converting the 2-hydroxy-C(n+1)-acyl-CoA to a C(n+1)-aldehyde;
e) isolating a product from said microorganism, or said growth media, or both;
wherein the single carbon substrate is selected from the group consisting of methane, methanol, formaldehyde, formate, carbon monoxide, carbon dioxide, and combinations thereof; and
wherein the microorganism expresses:
i. a 2-hydroxyacyl-CoA lyase or an oxalyl-CoA decarboxylase that catalyzes the condensation of the initial C(n)-aldehyde with the formyl-CoA to produce the 2-hydroxy-C(n+1)-acyl-CoA;
ii. one or more polypeptides that catalyze the conversion of the single carbon substrate to the formyl-CoA; and
iii. one or more polypeptides that catalyze a conversion of the 2-hydroxy-C(n+1)-acyl-CoA to the C(n+1)-aldehyde.
2. The method of claim 1, wherein the microorganism expresses a 2-hydroxyacyl-CoA lyase.
A generic C(n+1)-aldehyde as recited in at least patent claim 1 is understood to encompass any aldehyde with required number of carbon atoms including a hydroxylated C(n+1)-aldehyde.
The patented claims encompass the performance of a first iteration and sets of nucleic acids as recited in claim 1 being a C1 substrate (e.g. methanol, formaldehyde) converted to formyl-CoA and ligation with formaldehyde to produce glycolyl-CoA as a 2-hydroxy-C(n+1)-acyl-CoA which is then converted to glycolaldehyde as a C(n+1) aldehyde. As discussed above, Chou teaches that a desirable embodiment of at least patented claim 1 for has conversion of glycolyl-CoA to glyceraldehyde in a manner having all of the features of the rejected claims. That is, patented claim 1 is more generic to and encompasses the rejected claims, wherein Chou teaches that an advantageous embodiment of patented claim 1 is a microbial system and methods meeting the features of the rejected claims such that an ordinarily skilled artisan at the time of filing would have produced embodiments of patented claim 1 having all of the features of the rejected claims to achieve the same benefits of producing glyceraldehyde from C1 substrates set forth in the rejections under 35 U.S.C. 103 over Chou set forth above.
Allowable Subject Matter
Claim 78 is objected to as being dependent upon a rejected base claim, but would be allowable if rewritten in independent form including all of the limitations of the base claim and any intervening claims.
The following is a statement of reasons for the indication of allowable subject matter:
Nattermann et al. (Engineering a Highly Efficient Carboligase for Synthetic One-Carbon Metabolism, ACS Catal., 11, 2021, 5396-5404) teaches use of CaAbFfT in the following pathway (Fig. 2A):
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In the above pathway, ligation of formaldehyde with formyl-CoA to form glycolyl-CoA is the same as the first iteration recited in the claims. However, the action of AbfT produces glycolate from glycolyl-CoA without the formation of glycolaldehyde, which is needed as a substrate for ligation with formyl-CoA to produce glyceryl-CoA. It is understood that the diversion of some glycolyl-CoA to glycolate (rather than the second iteration) may be desirable to support cell growth. Without the benefit of applicant’s disclosure there is substantial uncertainty regarding how expression of AbfT may interfere with the second iteration by preventing glycolaldehyde formation even in applications wherein formate is used as a C1 substrate. As such, there is deemed insufficient motivation in the prior art to reach the features of claim 78.
Conclusion
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/TODD M EPSTEIN/Primary Examiner, Art Unit 1652