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 .
Status of the Claims
Claims 3, 5, and 7 are cancelled.
Claims 1-2, 4, 6, and 8-20 are pending.
Claims 1-2, 4, 6, and 8-20 are examined herein.
Claims 1-2, 4, and 11-20 are rejected.
Claims 6 and 8-10 are objected to.
Claim Objections
Claim 1 is objected to because of the following informalities: Claim 1 recites “Tm-22” three times. The first recitations are italicized, however the third recitation is not. The third recitation of “Tm-22” should be italicized to be consistent with the other recitations. Appropriate correction is required.
Claim 2 is objected to because of the following informalities: Claim 2 recites “The tomato plant of claim 1, being homozygotic for said at least one amino acid substitution”. To improve clarity, the claim should read “The tomato plant of claim 1, wherein the tomato plant is homozygotic for said at least one amino acid substitution”, or another grammatically appropriate equivalent. Appropriate correction is required.
Claims 6 and 8-10 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.
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.
This is a modified rejection from the previous rejection in the Office Action dated 10/20/2025.
Claim 20 is rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon without significantly more. The claim(s) recite(s) “ A food or processed product comprising the plant of claim 1 or parts thereof, wherein said processed product comprises DNA of the plant of claim 1 and wherein said processed product is selected from the group consisting of canned tomatoes, a tomato paste, a ketchup, a tomato sauce, a tomato soup, a dehydrated tomato, a tomato juice, a tomato powder, a tomato dice, a crushed tomato, a chopped tomato and a tomato concentrate”.
The claims encompass processed and purified products, such as a tomato paste, a tomato sauce, a tomato soup, a dehydrated tomato, a tomato juice, a tomato powder, a tomato dice, a crushed tomato, a chopped tomato and a tomato concentrate that could reasonably be expected to be identical to those occurring in nature. For example, a tomato juice may be interpreted simply as the liquid from the tomato and this tomato juice would reasonably be expected to be identical to any other tomato juice. Additionally, the claim only further requires “wherein said processed product comprises DNA of the plant of claim 1”. The DNA as claimed can be any DNA of the plant and does not limit the DNA to be a mutated DNA sequence encoding the mutated Tm-22 protein. Therefore, the processed product of the tomato as instantly claimed would reasonably be interpreted to be identical to those occurring in nature.
Therefore, the claims encompass a judicial exception that is a natural phenomenon. This judicial exception is not integrated into a practical application because are the claims are merely drawn to a product, and no additional elements or limitations are required that would make the product structurally different from that of a naturally occurring product.
To overcome this rejection, Applicant may amend the claim, e.g., to require the DNA comprise a mutated nucleotide sequence that encodes the mutated Tm-22 protein without adding new matter and without introducing amendments that may result in other rejections, e.g. antecedent basis issues.
Claim Rejections - 35 USC § 112
Written Description
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.
This is a modified rejection from the previous rejection set forth in the Office Action dated 10/20/2025.
Claims 1, 2, 4, and 11-20 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 1, 2, 4, and 11-20 are broadly drawn to a tomato plant or a part thereof, expressing a Tm- 22 protein having an amino acid sequence which comprises at least one amino acid substitution with respect to wild type Tm-22 protein as set forth in SEQ ID NO: 25, wherein said at least one amino acid substitution is in a leucine rich repeat (LRR) domain of said Tm-22 protein and renders the plant resistant to tomato brown rugose fruit virus (ToBRFV). Specifically, the written description requirement regards the broad limitation that any amino acid substitution in any LRR domain renders the plant resistant to ToBRFV.
Applicant describes in working examples three mutations including mutations at F528S, S604N, and I652M effectively conferred resistance to ToBRFV (p. 34, lines 25-33 through p. 35, lines 1-2). These recited mutations appear to be in regard to the Tm-2² protein represented by the amino acid sequence of instant SEQ ID NO: 25 (p. 9, lines 17-20).
Applicant has not described the broadly claimed genus of any amino acid modification is in the leucine rich repeat (LRR) domain of said Tm-2² protein that would effectively confer resistance. The prior art fails to remedy this deficiency. There is a dearth of description in the prior art of any Tm-2² protein having an amino acid sequence that is able to confer resistance to ToBRFV. Furthermore, Lindbo (US-20240049668-A1, published 02/15/2024 (after the effective filing date)) provides evidence that any mutation to an LRR domain of Tm-22 does not provide recognition of and resistance to ToBRFV. Specifically, Lindbo describes the amino acid sequence of wild-type Tm-22 is 100% identical to instant SEQ ID NO: 25. In table 4 (p. 17), Lindbo describes the LRR domain (SEQ ID NO: 11 of Lindbo) is at positions 477 to 861 of the Tm-22 protein (¶0053-0055, 0062). Within this LRR domain, Lindbo describes a single F655L mutation was similar to WT Tm-22 in that the mutation was insufficient for the Tm-22 protein to recognize and respond to the ToBRFV MP (Table 4). Alternatively, a C848R mutation elicited a detection and response to ToBRFV (Table 4), however a mutation at 848 to an amino acid other than R was observed to have a similar detection and response to ToBRFV MP as the WT Tm-22 (Table 5, ¶0229). Lindbo describes more mutation examples including double mutations (Table 6), where a mutation of C848R in combination with 857K or K857Q elicits the recognition and response to ToBRFV MP, however when C848R is in combination with K857E, K857 T, K857R, or K857I, the Tm-22 protein no longer recognizes the ToBRFV MP and is similar to WT Tm-22 (Table 6). Furthermore, Lindbo describes a mutation at either position 767 or 769 alone did not allow the Tm-22 protein to detect and respond to ToBRFV MP (Table 7-8). Lindbo clearly provides several examples of mutations in the LRR region that do not recognize the ToBRFV MP and would not confer resistance to ToBRFV.
Therefore, the specification fails to provide an adequate written description to support the claim of any amino acid modification is in the leucine rich repeat (LRR) domain of said Tm- 2² protein that would effectively confer resistance to ToBRFV. The broadly claimed genus is furtehr invalidated by the evidenced described by Lindbo who provides multiple examples of mutations in the LRR domain of an identical protein that do not confer recognition and response to ToBRFV. The limited examples of mutations at F528S, S604N, and I652M in SEQ ID NO: 25 which conferred resistance to ToBRFV do not describe the claimed genus by virtue of example. Therefore, one of ordinary skill in the art would not have recognized the Applicant to be in possession of the claimed invention at the time the application was filed.
Closest Prior Art
Claims 1-2, 4, 6, and 8-20 appear free of the prior art.
Regarding claims 1-2, 4, 6, and 8-20, the closest prior art is Ykema (WO-2020148021-A1). Ykema teaches an invention related to genomic sequences that provide tomato plants with resistance to Tomato brown rugose fruit virus (ToBRFV) (title, abstract, entire document). However, Ykema does not disclose, teach, or otherwise render obvious the resistance to ToBRFV is due to expressing a Tm-2² protein having an amino acid sequence that renders the plant resistant to tomato brown rugose fruit virus. In working examples, Ykema explicitly teaches the TBRFV resistant plant did not contain the Tm2² gene (p. 14, lines 6-8). For these reasons, the claims appear free of the prior art.
Response to Arguments
Applicant argues beginning on p. 5 of remarks dated 01/20/2026 the
following arguments:
The Examiner has rejected claim 20 because the claim allegedly does not include additional limitations that would render it different than the naturally occurring product.
The claim has been amended with traverse and without prejudice to refer to specific products (which do not occur in nature) and which comprise DNA of the plant of claim 1.
Accordingly, the rejection is rendered moot
This argument has been fully considered and is found not persuasive for
the following reason(s):
This is not persuasive because most of the specified products can still be reasonably interpreted as identical to those occurring in nature. For example, liquid from a tomato occurring in nature may be considered tomato juice and is reasonably interpreted to be identical to tomato juice from any other tomato plant. Additionally, the limitation of “wherein said processed product comprises DNA of the plant of claim 1” also does not render the food of processed product different from those that are naturally occurring because the referenced DNA can refer to any segment of DNA in the entire tomato genome, therefore the product is reasonably interpreted to be identical to those occurring in nature.
Applicant argues beginning on p. 5 of remarks dated 01/20/2026 the
following arguments:
The Examiner states that claims 3, 4 and 6 lack sufficient antecedent basis for a number of limitations and claims 5 and 7-10 are rejected as a function of their dependency.
While traversing the rejection, yet in the interest of expediting prosecution, claim 3 has been cancelled and claim 4 has been amended to render the rejection moot.
This argument has been fully considered and is found persuasive for
the following reason(s):
In view of Applicant’s amendments and cancellation of claims, the rejections under 112(b) have been withdrawn.
Applicant argues beginning on p. 6 of remarks dated 01/20/2026 the
following arguments:
The Examiner has rejected claims 1-5 and 11-20 under 35 U.S.C. §112(a), stating that "Applicant has not described the broadly claimed genus of any other Tm-22 protein having an amino acid sequence that is able to effectively confer the function of rendering the plant resistant to tomato brown rugose fruit virus (ToBRFV)." This rejection is respectfully traversed.
The test for written description is whether the disclosure reasonably conveys to those skilled in the art that the inventor had possession of the claimed subject matter as of the filing date. Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010). For genus claims, possession may be demonstrated through disclosure of representative species and/or relevant identifying characteristics. Regents of the Univ. of Cal. v. Eli Lilly & Co., 119 F.3d 1559, 1568-69 (Fed. Cir. 1997).
Amended claim 1 now requires that the Tm-22 protein comprises at least one amino acid substitution with respect to wild type Tm-22 protein (SEQ ID NO: 25), wherein the substitution is in the LRR domain and renders the plant resistant to ToBRFV. This amendment establishes a clear structure-function relationship between the location of the mutation (LRR domain) and the acquired resistance phenotype (ToBRFV resistance).
The specification provides written description support for this amended claim through disclosure of representative species and identifying characteristics. The specification discloses three specific LRR domain substitutions that confer ToBRFV resistance: F528S, S604N, and I652M. Each mutation was generated, tested for MPToBRFV recognition via hypersensitive response, and validated for resistance against a resistance-breaking virus (Figures 6A-D, Figures 7A-F). These working examples demonstrate that amino acid substitutions in the LRR domain can confer the desired resistance phenotype.
Beyond these specific examples, the specification establishes the identifying characteristics of the claimed genus. The specification explains that the LRR domain (amino acids 388-861) determines effector recognition specificity in Tm-22 and other NLR proteins. This structure-function relationship i.e., that LRR domain substitutions alter MP binding (as in claim 4), thereby conferring ToBRFV resistance, is thoroughly described.
The specification also demonstrates that the claimed genus is predictable and reproducible. The directed evolution screen yielded 13 Tm-22 mutant alleles recognizing MPToBRFV, with the three specific mutations (F528, S604, 1652) independently appearing in multiple clones (Figure 5C). This convergent evolution demonstrates that one skilled in the art would understand that multiple different LRR substitutions can achieve the desired phenotype.
The Examiner's concern that the specification does not describe "any other Tm- 22 protein" beyond the three disclosed mutations is addressed by the amended claim language, which now explicitly ties the location of the substitution (LRR domain) to the function (ToBRFV resistance). The specification conveys to one skilled in the art that the inventors possessed the genus of Tm-22 proteins with LRR domain substitutions that confer ToBRFV resistance, as evidenced by: (1) three representative working examples; (2) disclosure of the structural basis for the structure-function relationship; (3) demonstration that multiple independent mutations in the LRR domain achieve the same result; and (4) explanation of the mechanistic basis (altered MP recognition) by which LRR substitutions confer resistance.
Applicant submits herewith a Declaration under 37 CFR 1.132 providing supplemental data regarding an additional LRR domain mutation (H817R) generated post-filing. This Declaration demonstrates that the structure-function relationship disclosed in the original specification is predictable and that one skilled in the art, based on the original disclosure, would have understood that LRR domain substitutions beyond the three specifically disclosed mutations can confer ToBRFV resistance. This supplemental evidence confirms that Applicant was in possession of the claimed genus as of the filing date.
In view of the foregoing, Applicant respectfully requests reconsideration and withdrawal of the outstanding rejections.
This argument has been fully considered and is found not persuasive for
the following reason(s):
Despite Applicant’s amendments and submission of a declaration providing one more example of a mutation in the LRR domain of Tm-22, the claims remain rejected under a modified written description rejection (see above). Applicant has now provided 4 mutation examples that allow Tm-22 to recognize the ToBRFV MP. However, the LRR domain is very large (388 amino acids) as evidenced by Lindbo (US-20240049668-A1, published on 02/15/2024 (after the effective filing date)) (¶0053-0055, 0062), and the four specific amino acid substitutions do not represent the broad genus by virtue of example. Additionally, Lindbo provides evidence that many mutations in the LRR domain of the identical Tm-22 protein fail to recognize and elicit a response to ToBRFV. Moreover, in several instances a substitution of different amino acids at the same position did not always confer recognition and response to ToBRFV. Because there is a dearth of description in the prior art of any mutation in Tm-22 protein that would confer the recognition of ToBRFV, and at least the publication of Lindbo has proven that only specific mutations to Tm-22 may confer a response to ToBRFV, Applicant arguments and declaration are not found persuasive. The claims remain rejected under a modified 35 USC 112(a) rejection.
Conclusion
No claims are allowed.
THIS ACTION IS MADE FINAL. 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 JESSICA N STOCKDALE whose telephone number is (703)756-5395. The examiner can normally be reached M-F 8:30-5:00 CT.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad Abraham can be reached at (571) 270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
JESSICA N. STOCKDALE
Examiner
Art Unit 1663
/JESSICA NICOLE STOCKDALE/Examiner, Art Unit 1663
/CHARLES LOGSDON/Primary Examiner, Art Unit 1662
Prosecution Insights