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 .
Priority
Acknowledgment is made of Applicant's claim for domestic benefit under 35 U.S.C. 119(e). As such, the effective filing date of Claims 1-3, 5, 7-9, 11-13, 16-17, 20-21, 29, 31-33, 36-41, 43-44, and 48-51 is 02 July 2021.
Status of the Claims
Amendments dated 09/16/2025 have been entered.
Claims 1-3, 5, 7-9, 11-13, 16-17, 20-21, 29, 31-33, 36-41, 43-44, and 48-51 are pending.
Claims 31-33, 36-41, 43-44, and 48-51 are withdrawn from consideration as being directed to a non-elected invention.
Claims 1-3, 5, 7-9, 11-13, 16-17, 20-21, and 29 are examined herein.
Information Disclosure Statement
The Information Disclosure Statement filed on 09/16/2025 is in compliance with the provisions of 37 CFR 1.97 and has been considered in full. A signed copy of the list of references cited is included with this Office Action.
Claim Interpretation
Regarding the recitation of “transcription regulatory region” in Claim 1, it is noted that the specification defines, in part, a “transcription regulatory region” to include promoters, translational
termination regions, transcriptional initiation start sites, operators, activators, enhancers, other
regulatory elements, ribosomal binding sites, an initiation codon, termination signals, and the
like, wherein a transcription regulatory region for a particular gene may be within the gene body (i.e., the entire sequence of the gene from the transcription start site to the transcription termination site),
upstream or downstream of the gene body (i.e., proximal to the gene), or located further away on
the same chromosome as the gene or on a different chromosome from the gene (i.e., distal to the
gene) (Specification, pg. 15, paragraph 0053).
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 1-2, 5, 7-8, 11-13, 16-17, 20-21, and 29 remain rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zhang et al. (Journal of Experimental Botany 69.12 (2018): 2897-2909, IDS Document) as evidenced by Ecker (Nature biotechnology 31.2 (2013): 119-120).
Regarding Claim 1, Zhang et al. (herein referred to as Zhang) discloses a Solanum lycopersicum Mill. cv. Ailsa Craig ripening inhibitor (rin) mutant plant (pg. 2899, Plant materials and conditions), wherein Zhang further discloses that RIN is a transcription regulatory region of Solyc07g052960 (also denoted as SlFSR) that modulates expression of Solyc07g052960 (pg. 2898, Introduction, right column, last paragraph) in tomato plants, by binding to the promoter region of SlFSR (pg. 2907, right column, first not-complete paragraph), wherein the expression of SlFSR is decreased in rin mutant tomato plants (Abstract) due to the disruption of the regular function of RIN.
Regarding Claims 1 and 2, in rin mutant tomato plants, the binding site of RIN (the CArG-box CNR promoter) is hypermethylated through an epimutation, which leads to the inhibition of the RIN transcription factor and the subsequent non-ripening phenotype of the rin mutant tomato fruit, as evidenced by Ecker (Nature biotechnology 31.2 (2013): 119-120). Ecker also provides evidence that the cytosine hypermethylation of the RIN binding site in rin mutant tomato plants is heritable.
Regarding Claim 5, Zhang discloses that the relative expression of SlFSR (total RNA) was decreased in the rin mutant tomato plant when compared to a WT Solanum lycopersicum Mill. cv. Ailsa Craig tomato plant (pg. 2900, Fig. 1B).
Regarding Claim 7, Zhang discloses that the expression of SlFSR (fruit shelf-life regulator) was significantly decreased in the tomato mutant rin (ripening inhibitor) when compared to the WT tomato plant, indicating that SlFSR expression is obstructed by the RIN mutation (pg. 2900, right column, Expression of SlFSR is inhibited in tomato ripening mutants and regulated by ethylene).
Regarding Claim 8, Zhang discloses that the modified tomato plant is from the Ailsa Craig variety (pg. 2899, left column, second paragraph).
Regarding Claims 11, 20-21 and 29, seeds, progeny plants, and methods of growing progeny plants are deemed inherent to the modified tomato plants which are anticipated by the disclosure of Zhang.
Regarding Claim 12, Zhang discloses tomato fruits produced by the rin mutant tomato plants (pg. 2904, Fig. 6A).
Regarding Claim 13, Zhang discloses that the shelf-life of rin mutant tomato plants was extended when compared to WT tomato fruit, due to delayed ripening of rin mutant tomato plant fruits (pg. 2904, Fig. 6A).
Regarding Claim 16, Zhang discloses that rin mutant tomato fruits (3 months post-harvest) had delayed signs of cell wall deterioration and no visible infection (pg. 2905, Fig. 7A), and that compared to the WT tomato plant, rin mutants also had decreased ethylene production (pg. 2904, Fig. 6C) and decreased transcription of cell-wall modifying genes (pg. 2906, Fig. 8).
Regarding Claim 17, Zhang discloses that the rin mutant tomato fruits (3 months post-harvest) exhibited delayed water loss in stored fruits (pg. 2905, Discussion, right column, first full paragraph).
Response to Arguments
Applicants Remarks on pgs. 7-10 in the reply filed on 09/16/2025 are acknowledged but do not
overcome these rejections. In particular, Applicant’s Remarks rely on the premise that Zhang does not disclose an introduced modification comprising hypermethylation of genomic DNA at the SIFSR gene or a transcription regulatory region thereof (Remarks, pg. 8) because "a genomic DNA at a fruit shelf-life regulator (SIFSR) gene or a transcription regulatory region thereof' would be understood to be a portion of genomic DNA that directly associated with expression the SIFSR gene, and as such, a portion of genomic DNA that is not directly associated with expression of the SIFSR gene would be outside the broadest reasonable interpretation of the term. For example, Applicant argues that a portion of genomic DNA that is associated with expression another gene that encodes a protein that plays a role in expression of the SIFSR gene would not be transcription regulatory region of the SIFSR gene (such as the RIN gene taught by Zhang) (Remarks, pgs. 8-9).
This is not found persuasive. Please see the following definition for “transcription regulatory region” that was entered into the record by Applicant in the Specification (paragraph 0053) dated 07/01/2022:
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Applicant does not define the term “transcription regulatory region” in the claims or specification in such a way that would disqualify the disclosure of Zhang. According to the Applicant’s own definition of “transcription regulatory region” in paragraph 0053 of the instant specification, the disclosure of Zhang anticipates the instantly claimed “transcription regulatory region” of the SlFSR gene recited in Claim 1, because Zhang discloses a RIN transcription factor that that modulates expression of Solyc07g052960 (pg. 2898, Introduction, right column, last paragraph) in tomato plants, by binding to the promoter region of SlFSR. As such, the RIN transcription factor disclosed by Zhang is a “nucleotide sequence that is able to regulate transcription of a particular gene in a cell or organism of interest” and can be found on a different chromosome relative to the instantly claimed SlFSR gene— meeting the criteria set forth in Applicant’s definition of “transcription regulatory region” to be a transcription regulatory region of SlFSR in tomato. If Applicant intends to narrow the scope of the claim, they should amend the claim to limit the “transcription regulatory region” to the genomic DNA of the instantly claimed SlFSR gene or the promoter region of the instantly claimed SlFSR gene.
Applicant also argues that the disclosure of Zhang and Ecker do not teach that there is any introduced modification comprising hypermethylation of genomic DNA at the SlFSR gene or a transcription regulatory region thereof (Remarks, pg. 9).
This is not found persuasive. As discussed above, the RIN transcription factor disclosed by Zhang is a “nucleotide sequence that is able to regulate transcription of a particular gene in a cell or organism of interest” and can be found on a different chromosome relative to the instantly claimed SlFSR gene— meeting the criteria set forth in Applicant’s definition of “transcription regulatory region” to be a transcription regulatory region of SlFSR in tomato. As such, because the evidence of Ecker discloses that the binding site of RIN (the CArG-box CNR promoter which is comprised within the RIN gene, and wherein the RIN gene is transcription regulatory region of SlFSR; See arguments above) is hypermethylated through an epimutation, which leads to the inhibition of the RIN transcription factor and the subsequent non-ripening phenotype of the rin mutant tomato fruit (Ecker; pg. 120, Figure 1) and the disclosure of Zhang provides evidence that the relative expression of SlFSR (total RNA) was decreased in the rin mutant tomato plant when compared to a WT Solanum lycopersicum Mill. cv. Ailsa Craig tomato plant (pg. 2900, Fig. 1B), the disclosure of Zhang and Ecker does teach that there is an introduced modification comprising hypermethylation of transcription regulatory region of SlFSR.
Applicant also argues that Zhang does not teach that the decreased expression of the SlFSR protein was due to hypermethylation at the SlFSR gene or a transcription regulatory region thereof (e.g., promoter) (Remarks, pg. 10).
This is not found persuasive. The evidence of Ecker discloses that the binding site of RIN (the CArG-box CNR promoter which is comprised within the RIN gene, and wherein the RIN gene is transcription regulatory region of SlFSR; See arguments above) is hypermethylated through an epimutation, which leads to the inhibition of the RIN transcription factor and the subsequent non-ripening phenotype of the rin mutant tomato fruit (Ecker; pg. 120, Figure 1) and the disclosure of Zhang explicitly teaches that RIN modulates expression of Solyc07g052960 (pg. 2898, Introduction, right column, last paragraph) in tomato plants, by binding to the promoter region of SlFSR (pg. 2907, right column, first not-complete paragraph), wherein the expression of SlFSR is decreased in rin mutant tomato plants (Abstract) due to the disruption of the regular function of RIN. As such, the disclosure of Zhang, taken with evidence provided by Ecker, explicitly teaches that the decreased expression of the SlFSR protein was due to hypermethylation at the a transcription regulatory region of SlFSR, based on Applicant’s own definition of “transcription regulatory region” (See arguments above).
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (Journal of Experimental Botany 69.12 (2018): 2897-2909, IDS Document) as evidenced by Ecker (Nature biotechnology 31.2 (2013): 119-120).
The teachings of Zhang, as evidenced by Ecker, as they are applied to Claim 1 are set forth previously herein and are incorporated by reference.
Regarding Claim 9, Zhang teaches that the modified tomato plant is of the Ailsa Craig variety (pg. 2899, left column, second paragraph), which is a commercially available heirloom tomato variety. As such, it would have been obvious to one of ordinary skill in the art to modify a Brandywine tomato plant, as a substitute of the Ailsa Craig tomato plant taught in Zhang, to target an endogenous SlFSR gene transcription regulatory region in a tomato plant from the Brandywine variety because it’s a known heirloom variety of tomato that is commercially available. The Brandywine tomato variety would be a reasonable substitute in the place of the Ailsa Craig variety because one of ordinary skill could have substituted these elements as claimed with no change to their respective functions. Thus, the substitution yielding predictable results would have been expected by a skilled artisan. Therefore, for all the reasons above, the claimed invention is prima facie obvious.
Response to Arguments
Applicant’s Remarks on pgs. 10-11 in the reply filed on 09/16/2025 are acknowledged but do not overcome these rejections for the reasons given above in regards to the 35 U.S.C. 102 (a)(1) rejection applied to Claims 1-2, 5, 7-8, 11-13, 16-17, 20-21, and 29.
Closest Prior Art
Claim 3 appears to be free of the prior art. The closest prior art in regard to Claim 3 can be found in Zhang et al. (herein referred to as Zhang) as evidenced by Ecker (Nature biotechnology 31.2 (2013): 119-120). Zhang discloses a Solanum lycopersicum Mill. cv. Ailsa Craig ripening inhibitor (rin) mutant plant (pg. 2899, Plant materials and conditions), wherein Zhang further discloses that RIN is a transcription regulatory region of Solyc07g052960 (also denoted as SlFSR) that modulates expression of Solyc07g052960 (pg. 2898, Introduction, right column, last paragraph) in tomato plants, by binding to the promoter region of SlFSR (pg. 2907, right column, first not-complete paragraph). In rin mutant tomato plants, the binding site of RIN (the CArG-box CNR promoter) is hypermethylated through an epimutation, which leads to the inhibition of the RIN transcription factor and the subsequent non-ripening phenotype of the rin mutant tomato fruit, as evidenced by Ecker (Nature biotechnology 31.2 (2013): 119-120). However, the disclosure of Zhang does not suggest or provide any motivation to hypermethylate a region that is within 1 kb of the translation start site of the endogenous SlFSR gene in a modified tomato plant.
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 KELSEY L. MCWILLIAMS whose telephone number is (703)756-4704. The examiner can normally be reached M-F 08:00-17:30.
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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.
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/KELSEY L MCWILLIAMS/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663