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 Application
1. Claims 33-35, 38, and 62-64 are pending and subject to examination on the merits. Claim 63 is withdrawn from consideration as being drawn to non-elected subject matter. Claims 33-35, 38, and 62-64 are currently under examination. The elected species of SEQ ID NO: 99 is free of the prior art; thus, the Examiner selects the next species of their choice for examination. The Examiner has searched the additional species: 100-110. SEQ ID NOs: 100, 103, and 104 are not free of the prior art.
Priority
2. Acknowledgment is made for the Applicant’s claim for domestic priority based on the US provisional application PRO 63/476,393 filed 21 December 2022.
Election/Restrictions
3. Group III, claims 33-35 and 38-39, was elected. SEQ ID NO: 99 is the elected species. Therefore, claim 63 is withdrawn from consideration, since it does not read on the elected species (SEQ ID NO: 99). Election was made without traverse in the reply filed on 05 February 2026.
Withdrawn Rejections
4. The 35 U.S.C. 112(b) indefiniteness rejection of claims 38-39 is withdrawn, since the phrase “at least about” was deleted from the claim and replaced with “comprising.”
5. The 35 U.S.C. 112(a) written description rejection is withdrawn, since the claimed cells are adequately described in the specification and the techniques are also known in the art.
6. The 35 U.S.C. 103 obviousness rejection over Bothmer et al (Bothmer et al., 2021, WO 2021/178720 A2—cited previously) is withdrawn, since the claims were amended to recite comprising SEQ ID NOs instead of at least 70% sequence identity. Bothmer et al. does not teach a sequence comprising SEQ ID NO: 99 but rather a sequence with 99.8% identity to SEQ ID NO: 99 with a non-conservative point mutation (a proline instead of a glycine) at position 330. The new 35 U.S.C. 103 obviousness rejection of the claims is found below.
New Rejections—necessitated by amendments
Claim Rejections - 35 USC § 103
7. 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.
8. 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.
9. Claims 33-35, 38, 62, and 64 are rejected under 35 U.S.C. 103 as being unpatentable over Bothmer et al (Bothmer et al., 2021, WO 2021/178720 A2—cited previously) and Halperin (US 2023/0076357 A1—cited herein). Regarding claims 33-35 and 38-39, drawn to a method of modifying a target nucleic acid in any cell, specifically, a plant cell to produce a plant comprising the modified target nucleic acid (claim 34), wherein the method comprises introducing an expression cassette with a promoter sequence (claim 33 and 62) consisting of a CRISPR-Cas effector protein (claim 64), a polypeptide comprising SEQ ID NO: 103, and an extended guide nucleic acid (claims 38-39), and wherein the introducing is carried out at a temperature of about 20-42oC, Bothmer et al. teaches novel compositions, systems, and methods for altering a genome at one or more locations in a host cell in vivo or in vitro (p. 2, Summary of Invention). Specifically, Bothmer et al. teaches the utilization of Gene Writer systems to modify a plant or plant part to increase the fitness of a plant, where the plant is contacted by the Gene Writer™ system, encoded by a vector, wherein nucleic acid are introduced into a plant or a part of plant (p. 1286-1287, “A. Delivery to a Plant”). Bothmer et al. continues to teach that the Gene Writer™ system can be delivered to a part of the plant or to a plant embryo, resulting in a plant with the genetic alteration (p. 1292, paragraph 3). Bothmer et al. teaches that the system or components of the system may be delivered to the cells utilizing a vector, a plasmid or virus, containing a retrotransposase, template nucleic acid, and a ribonuclear protein (p. 1294). Notably, the Gene Writer™ polypeptide may comprise a CRISPR-associated endonuclease domain that binds a template RNA, comprising a gRNA, which binds a DNA sequence (p. 1056, “Endonuclease domain”). Lastly, Bothmer et al. teaches some embodiments, where the Gene Writer™ polypeptide system is introduced to a host cell at room temperature (25oC) and then further incubated at 37oC for 3 days (p. 1110, last paragraph).
Bothmer et al., does not teach the specific transfection of a plant cell with a gene expression cassette encoding CRISPR/Cas effector protein system, SEQ ID NO: 103 polypeptide, and a guide nucleic acid (claim 38). Halperin teaches the utilization of the reverse transcriptase encoded by SEQ ID NO: 18, which shares 100% sequence identity with SEQ ID NO: 103 of the instant claims (See Supplemental file: 20260226_082810_us-18-391-959-103.rapm, Result 2: Duplicate 2) in CRISPR/Cas systems for genome editing (paragraph 0101).
Therefore, it 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 to combine to teachings of Bothmer et al. and Halperin to transfect a plant cell to produce a plant utilizing a CRISPR/Cas ribonuclear protein, guide RNA, and SEQ ID NO: 103 at a temperature of about 20-42oC to efficiently modify the target genome as taught by Halperin. One skilled in the art would be motivated to transfect a plant seed to produce a transgenic plant to increase the fitness of the plant as taught by Bothmer et al (p. 1287, “A. Delivery to a Plant,” first paragraph). Specifically, an increase in fitness could be manifested in a number of ways, e.g. better production of the plant, improved yield, improved vigor, improved pre- or post-harvest traits, and/or improvement of traits beneficial to humans, i.e. decrease in allergen production (p. 1288, second paragraph). There would be a reasonable expectation of success in transfecting a plant cell to produce a plant utilizing a method involving contacting a plant cell with a gene expression cassette comprising a guide RNA, CRISPR/Cas protein, and SEQ ID NO: 103 to produce a plant, since Bothmer et al. teaches the modification of a plant cell utilizing a CRISPR/Cas system.
Applicant’s Arguments and Examiner’s Rebuttal:
The applicant traverses the previous 35 U.S.C. 103 obviousness over Bothmer et al. because Bothmer et al. fails to teach the utilization of SEQ ID NOs: 96-133 as recited in the amended claims. The examiner agrees insofar that Bothmer et al. does not teach SEQ ID NO: 99 but rather a sequence that shares 99.8% sequence identity with SEQ ID NO: 99. To address this, the new obviousness rejection is found above includes the art from Halperin, where specifically, Halperin utilizes a reverse transcriptase that does share 100% sequence identity with SEQ ID NO: 103 of the instant claims.
The examiner does not find the arguments presented by the Applicant persuasive, and for these reasons, the rejections of record above apply.
Conclusion
10. All claims are rejected.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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 CIARA A MCKNIGHT whose telephone number is (703)756-4791. The examiner can normally be reached M-F 8:00am-4:30pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Manjunath Rao can be reached on (571) 272-0939. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/CIARA A MCKNIGHT/Examiner, Art Unit 1656
/MANJUNATH N RAO/Supervisory Patent Examiner, Art Unit 1656
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