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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 11/19/25 has been entered.
Response to Amendment
This action is written in response to applicant’s amendments received on 11/19/25.
Any rejection or objection not reiterated herein has been overcome by amendment.
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.
Claims 52 and 54 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a product of nature without significantly more. The claim recites a polypeptide comprising Eubacterium rectale (E.r.) maturase or a variant of E. r. maturase having greater than 96% identity to SEQ ID NO: 14 and comprising either any mutation or a mutation of any amino acid at specific locations. As evidenced by E.r. reverse transcriptase this can occur naturally. See appendix and the mutations present at positions 65, 171, and other locations along the sequence. As evidenced by Karcher, E. rectale is one of the most common human gut bacteria (abstract). One of ordinary skill in the arts understands that the human gut (container) commonly contains a variety of salts. One of ordinary skill would likewise understand that as the bacteria and the enzyme are naturally occurring in the presence of salt this meets the imitation of “reaction buffer” as the enzyme is functional. This judicial exception is not integrated into a practical application because the naturally occurring amino acid sequence is not markedly different from its naturally occurring counterpart because it conveys the same genetic information. The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claimed kit does not require any additional element that renders the claimed product markedly different from the natural counterpart.
Step 1: This part of the eligibility analysis evaluates whether the claim falls within any statutory category. MPEP 2106.03. The claims recites a polypeptide comprising Eubacterium rectale (E.r.) maturase or a variant of E. r. maturase having greater than 96% identity to SEQ ID NO: 14 and comprising either any mutation or a mutation of any amino acid at specific locations. Because a polypeptide comprising Eubacterium rectale (E.r.) maturase or a variant of E. r. maturase having greater than 90% identity to SEQ ID NO: 14 are made of matter, a polypeptide comprising Eubacterium rectale (E.r.) maturase or a variant of E. r. maturase having greater than 90% identity to SEQ ID NO: 14 are a composition of matter. Thus, the claim is to composition of matter, which is one of the statutory categories of invention (Step 1: YES).
Step 2A Prong One: This part of the eligibility analysis evaluates whether the claim recites a judicial exception. As explained in MPEP 2106.04(II) and the October 2019 Update, a claim “recites” a judicial exception when the judicial exception is “set forth” or “described” in the claim. The claim recites a polypeptide comprising Eubacterium rectale (E.r.) maturase or a variant of E. r. maturase having greater than 96% identity to SEQ ID NO: 14 and comprising either any mutation or a mutation of any amino acid at specific locations, which are a nature-based product limitation. Because claims 52 and 54 recite a nature-based product a polypeptide comprising Eubacterium rectale (E.r.) maturase or a variant of E. r. maturase having greater than 96% identity to SEQ ID NO: 14 and comprising either any mutation or a mutation of any amino acid at specific locations, the markedly different characteristics analysis is used to determine if the nature-based product limitation is a product of nature exception. MPEP 2106.04(c)(I). The markedly different characteristics analysis is performed by comparing the nature-based product limitation in the claim to its naturally occurring counterpart to determine if it has markedly different characteristics from the counterpart. MPEP 2106.04(c)(II). Here the closest naturally occurring counterpart is the naturally occurring E.r. maturase, therefore claims 52 and 54are a product of nature exception. Additionally, instant specification (PGPUB 0007) indicates that SEQ ID NO:14 is a wildtype (natural) sequence. Association for Molecular Pathology v. Myriad Genetics Inc., 569 U.S. 576, 589-90 (2013) (naturally occurring things are “products of nature” which cannot be patented). Accordingly, the claim recites a judicial exception, and the analysis must therefore proceed to Step 2A Prong Two.
Step 2A Prong Two: This part of the eligibility analysis evaluates whether the claim as a whole integrates the recited judicial exception into a practical application of the exception. This evaluation is performed by (a) identifying whether there are any additional elements recited in the claim beyond the judicial exception, and (b) evaluating those additional elements individually and in combination to determine whether the claim as a whole integrates the exception into a practical application. 2019 PEG Section III(A)(2), 84 Fed. Reg. at 54-55. The claimed kit does not require any additional elements that renders the claimed product markedly different from the natural counterpart. To the extent Applicant might argue that the “container” is different from the naturally occurring counterpart, the recitation of a generic container is recited at such a high level of generalization as to not meaningfully limit the claims (any liquid composition would necessarily be in some “container”). Accordingly, the limitations laid out in claims 52 and 54 do not integrate the recited judicial exception into a practical application and the claim is therefore directed to the judicial exception. See MPEP 2106.05(h), discussing the administration step in Mayo Collaborative Servs. v. Prometheus Labs. Inc., 566 U.S. 66, 78
(2012) (Step 2A: YES).
Step 2B: This part of the eligibility analysis evaluates whether the claim as a whole amounts to significantly more than the recited exception, i.e., whether any additional element, or combination of additional elements, adds an inventive concept to the claim.
MPEP 2106.05. As discussed with Step 2A prong 2, the addition of the intended use in claims 52 and 54 of a kit is at best the equivalent of merely adding the words “apply it” as the claimed kit does not require any additional elements that are sufficient to amount to significantly more than the judicial exception. Mere instructions to apply an exception cannot provide an inventive concept (Step 2B: NO).
Claims 52 and 54 are not eligible.
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 39-40 and 51-53 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.
Claims 39 and 52 require newly added ranges amino acids 29-56, 82-143, 161-190, 201-225, or 315-423. There is no support for the claimed ranges in the specification. There are a series of individual amino acid substitutions recited in paragraphs 10, 13-15, and 82, but there is not a range associated with the recited points. The specification does not support the new matter of ranges between the discrete positions acids 29-56, 82-143, 161-190, 201-225, or 315-423 as discrete positions do not support the claimed ranges.
Claims 39-41, 51-54 and 64 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.
Regarding claim 39-40 and 51, claim 39 requires a mutation at some point along specific regions of SEQ ID NO 14 leading to desired properties presented in claim 39. Claims 39, 40 and 51 encompass any potential mutation or combination of mutations that gives rise to the recited function(s). Unlimited functional claim limitations that extend to all means or methods of resolving a problem may not be adequately supported by the written description or may not be commensurate in scope with the enabling disclosure, both of which are required by 35 U.S.C. 112(a) and pre-AIA 35 U.S.C. 112, first paragraph. While the instant specification describes a number of specific mutations (e.g., as in claim 42), the specification does not describe a sufficient number of species to support the breadth of the claims encompassing all possible mutations nor any structure-function relationship or other guidance that would allow one of skill in the art to identify functional mutations within the claimed genus. Moreover, as evidenced by Non-proteinogenic amino acids, there are thousands of possible unnatural amino acids that can occur in nature or be created in a laboratory (p1 first full paragraph). While unnatural amino acids are mentioned as being a possibility in instant specification [0107], there are no examples of even one unnatural amino acid variant of SEQ ID NO. 14 being created. Given that there are thousands of possible unnatural amino acids that any one or more of the specified ranges can be mutated in SEQ ID NO 14 can be substituted, one of ordinary skill in the arts understands is essentially an endless number of possible proteins that can be created and therefore applicant’s do not possess a representative sample of the genus that as claimed encompasses unnatural amino acids. The specification does not provide guidance on how the incorporation of unnatural amino acids alters the activity or structure of the protein, and therefore no structure-function relationship for unnatural amino acids is disclosed. The specification provides support for a variety of mutations at specific locations such as those listed in new claims 41 and 42, but the specification does not provide support for at least one mutation in the claimed ranges in SEQ ID NO 14. There is an insufficient number of species described in the specification to claim the broad genus of any amino acid substitution at any location and therefore the claim lacks written description support. Additionally, while claim 39 now requires a desired property outcome in specific ranges, this is not sufficiently supported by structure-function relationship as is in claim 42 for example.
Regarding claim 41, the claim requires a deletion of one or more amino acids from SEQ ID NO 14. One of ordinary skill in the arts understands is essentially an endless number of possible proteins that can be created and therefore applicant’s do not possess a representative sample of the genus as claimed. Further, at some point the number of deletions would render the protein non-functional. The specification does not provide guidance on how the one or more deletions alters the activity or structure of the protein, and therefore no structure-function relationship for one or more deletions is disclosed. Instant specification only discloses deletions in the α-loop which is insufficient to claim the extremely broad genus of a deletion of one or more amino acids from any position in SEQ ID NO 14. There is an insufficient number of species described in the specification to claim the broad genus of any one or more deletions at any location and therefore the claim lacks written description support.
Regarding claim 52-54, claim 52 requires a mutation at some point along specific ranges in SEQ ID NO 14. As evidenced by Non-proteinogenic amino acids, there are thousands of possible unnatural amino acids that can occur in nature or be created in a laboratory (p1 first full paragraph). While unnatural amino acids are mentioned as being a possibility in instant specification [0107], there are no examples of even one unnatural amino acid variant of SEQ ID NO. 14 being created. Given that there are thousands of possible unnatural amino acids that any one or more of the ranges of amino acids in SEQ ID NO 14 can be substituted, one of ordinary skill in the arts understands is essentially an endless number of possible proteins that can be created and therefore applicant’s do not possess a representative sample of the genus that as claimed encompasses unnatural amino acids. The specification does not provide guidance on how the incorporation of unnatural amino acids alters the activity or structure of the protein, and therefore no structure-function relationship for unnatural amino acids is disclosed. The specification provides support for a variety of mutations at specific locations such as those listed in new claims 41 and 42, but the specification does not provide support for at least one mutation at any location on SEQ ID NO 14. There is an insufficient number of species described in the specification to claim the broad genus of any amino acid substitution at any location and therefore the claim lacks written description support.
Regarding claim 64, Additionally, while claim 64 now requires a desired property outcome, this is not sufficiently supported by structure-function relationship as is in claim 42 for example. Additionally, unlimited functional claim limitations that extend to all means or methods of resolving a problem may not be adequately supported by the written description or may not be commensurate in scope with the enabling disclosure, both of which are required by 35 U.S.C. 112(a) and pre-AIA 35 U.S.C. 112, first paragraph. There is an insufficient number of species described in the specification to claim the broad genus of any of the desired property outcome and therefore the claim lacks written description support.
Allowable Subject Matter
Claims 43-50 and 56-63 are 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.
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.
Modified rejection necessitated by amendment Claims 39-42 and 52-55 are rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of U.S. Patent No. 11,667,899 (reference claims). Although the claims at issue are not identical, they are not patentably distinct from each other because reference claim 1 anticipates instant claims.
Claims 39, 41-42, 52 and 53-55 requires a mutation relative to SEQ ID NO 14. Reference claim 1 provides several point mutations within SEQ ID NO 14. Therefore, the specific point mutations provided in reference claim 1 anticipate claims 39 and 41-42.
Claim 40 and 53 requires an reaction buffer comprising Tris, claim 15 likewise requires an reaction buffer comprising Tris.
Response to Arguments
Applicant's arguments filed 11/19/25 have been fully considered but they are not persuasive. Applicant argues that claim 52 is not directed to a product of nature as the enzyme and the reaction buffer are both provided within a container, vial, tube, or bottle, and that the natural variant would not retain the functional properties (p9 second full paragraph). This is not persuasive as laid out in the 101 rejection above. Further, if applicant is arguing that the enzyme container is separate from the reaction buffer container, the claim as written does not require separate vials, container, tubes or bottles for the enzyme and the reaction buffer. Arguments of counsel regarding the inability of the naturally occurring enzyme variants retaining the claimed activity are not found to be persuasive in the absence of a factual showing. MPEP 716.01(c) makes clear that:
“The arguments of counsel cannot take the place of evidence in the record. In re Schulze , 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965). Examples of attorney statements which are not evidence and which must be supported by an appropriate affidavit or declaration include statements regarding unexpected results, commercial success, solution of a long - felt need, inoperability of the prior art, invention before the date of the reference, and allegations that the author(s) of the prior art derived the disclosed subject matter from the applicant.”
The polypeptide is found in naturally occurring bacteria, the stomach can be considered a container, and one of ordinary skill in the arts understands that humans consume salt.
Applicant argues that the claims as amended now recite amino acid ranges between points that were found allowable (p9-10). There is a lack of support for the ranges as detailed above.
Applicants request the double patenting rejection over US patent 11, 667, 899 be held in abeyance (p10 last paragraph). A request to hold a rejection in abeyance is not a proper response to a rejection. Rather, a request to hold a matter in abeyance may only be made in response to an OBJECTION or REQUIREMENTS AS TO FORM (see MPEP 37 CFR 1.111(b) and 714.02). Thus, the double patenting rejections of record have been maintained as no response to these rejections has been filled by applicants at this time.
Conclusion
Claims 39-42, 51-55, and 64 are rejected
Claims 43-50 and 56-63 are objected to.
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 TREVOR L KANE whose telephone number is (571)272-0265. The examiner can normally be reached M-F 7:00 am-4:00pm.
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/TREVOR KANE/Examiner, Art Unit 1657
/ROBERT J YAMASAKI/Primary Examiner, Art Unit 1657