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 .
Claims 1, 5-8, 10-11, 18 and 20 are examined.
Withdrawn rejections
The rejection of claims 1, 5-12, 18 and 20 under 35 USC 112(a) for failing to comply with the enablement requirement is withdrawn in light of amendments and in consideration of arguments made by Applicant.
The rejection of claims 1, 5-9 and 18 under 35 USC 102(a)(1) is withdrawn in light of amendments made by Applicant.
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.
Claims 1, 5-8, 10-11, 18 and 20 remain 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.
Due to Applicant’s amendments of the claims, the rejection is modified from the rejection set forth in the Office action mailed 11/24/2025.
Applicant claims a monocot plant comprising a mutation that abolishes the expression or activity of a DA2 polypeptide comprising at least 95% identity to SEQ ID NO: 25-26, 28-31 or 33-35 wherein the plant has increased seed or organ size relative to a plant without the mutation.
Claim 5 is drawn to the DA2 comprising a RING domain of SEQ ID NO: 1.
Claim 6 is drawn to the DA2 polypeptide comprising a RING domain of SEQ ID NO: 2.
Claim 7 is drawn to the DA2 polypeptide comprising a consensus domain of SEQ ID NO: 36.
Claim 8 is drawn to the DA2 polypeptide comprising a consensus domain of SEQ ID NO: 37
Claims 10 is drawn to the plant being one from a Markush group of monocot crop plants.
Claim 11 is drawn to the plant being maize.
Independent claim 18 is drawn to a method of increasing the seed or organ size of a monocot plant comprising introducing within the cells of a plant a mutation that reduces the expression or activity of a DA2 polypeptide.
Claim 20 is drawn to the plant of claim 18 being maize.
Applicant describes obtaining a da2-1 mutant of Arabidopsis thaliana, SALK_150003, which is a T-DNA insertion line from the ABRC (paragraph 213). Applicant describes transforming the da2-1 mutant with Agrobacterium tumefaciens to introduce a plasmid to express DA2, i.e., restoring DA2 function in the publicly available da2-1 T-DNA insertion line (paragraph 214). Applicant describes screening multiple publicly available T-DNA insertion lines of predicted ubiquitin ligase genes expressed in Arabidopsis ovules or seeds and finding the seeds produced by da2-1 were larger and heavier than those of the wild-type (paragraph 228). Applicant describes that the effect of da2-1 on seed size was only observed when maternal plants are homozygous for the da2-1 mutation (paragraph 234). Applicant describes identification of the T-DNA insertion site of da2-1 in the gene At1g78420 (paragraph 239).
Applicant describes generating two mutated sequences of DA2, DA2C59S and DA2N91L using a multi-site directed mutagenesis kit (paragraph 220). Applicant describes that the DA2 gene (At1g78420) has a predicted RING domain at residues 59-101; therefore, the C59S mutation was predicted to disrupt E3 ubiquitin ligase activity. Applicant describes observing the E3 ligase activity was abolished in an in vitro ubiquination assay by expressing DA2 in Escherichia coli as a fusion protein with maltose binding protein (paragraph 241). Applicant describes that an in vitro assay of the N91L mutation did not affect E3 ligase activity (paragraph 242). Applicant noted in the Remarks filed 2/23/2026 that this mutation is not a member of the claimed genus, which only encompasses mutations that abolish the expression or activity of the DA2 polypeptide.
Applicant describes identifying homologs of Arabidopsis DA2 in other plant species by observing shared homology of sequences (paragraph 243).
Applicant does not describe a representative number of species across the claimed genus of plants comprising any mutation, which is functionally claimed and which abolishes the expression or activity of a DA2 polypeptide of the claimed target sequences wherein the plant has increased seed size or organ size. Applicant does not describe a structure-function relationship reduced to practice in a plant or plant cell wherein the expression or activity of a DA2 polypeptide is reduced other than in the SALK_150003 mutant of Arabidopsis thaliana, da2-1. Regarding the two additional mutants observed with in vitro assays, while the C59S mutation resulted in abolished E3 ligase activity, it was not expressed in a plant. Further, this single embodiment of a mutation beyond the publicly available T-DNA insertion line would not be representative of the broad genus of mutations and functions claimed. Applicant describes a N91L mutation of DA2, which Applicant noted in the Remarks filed 2/23/2026 that this mutation is not a member of the claimed genus, which only encompasses mutations that abolish the expression or activity of the DA2 polypeptide, resulted in smaller seeds (paragraph 242) as opposed to the claimed function of larger seed size or increased biomass yield.
Given the breadth of the genera encompassed by the claims, the described species are not sufficiently representative. The Applicant has not set forth the structure-function relationship for the claimed genus such that one of ordinary skill in the art would be able to recognize which members of the genus of mutants in any monocot plant species would have reduced expression or activity of the DA2 polypeptide nor would one of ordinary skill in the art be able to predict which members would have increase seed or organ size. The breadth of dependent claims does not overcome the lack of description for the scope of the claimed invention. Applicant has not described a representative number of species across the genus of the DA2 protein sharing only 95% identity to elected SEQ ID NO: 28, nor a structure-function relationship which would allow one of ordinary skill in the art to envision which members of this genus would comprise reduced expression or activity of the DA2 polypeptide nor would one of ordinary skill in the art be able to predict which members would have increase seed or organ size. Applicant has not described any embodiments other than in Arabidopsis thaliana. While Applicant has provided a description of DA2 homologs, it is not clear that a plant species other than Arabidopsis thaliana comprising the T-DNA insertion in the Arabidopsis line identified by Applicant as da2-1 would have reduced DA2 expression or activity or increased seed or organ size.
The prior art does not provide resolution for the lack of description provided by Applicant. Song (Song et al. 2007. Nature Genetics. 39:623-630) teaches that loss of function of a GW2 protein, a previously unknown protein with RING-type E3 ubiquitin ligase activity, resulted in increased seed size in rice (Abstract). Song teaches identification of homologous genes across plant species had limited sequence identity and were all functionally uncharacterized (page 624, right column paragraph 3). Song is silent regarding mutations outside of the sequence encoding the GW2 reducing GW2 expression or activity or increasing seed or organ size. It is therefore unclear whether the described embodiments would result in the claimed function across these genera.
Therefore, the specification fails to sufficiently describe the claimed invention in such full, clear, concise, and exact terms that a skilled artisan would recognize that Applicant was in possession of the invention as broadly claimed at the time of filing.
Applicant’s arguments regarding written description rejection
Applicant's arguments filed 2/23/2026 have been fully considered but they are not persuasive.
Applicant argues on pages 5 of the Remarks that the Specification describes DA2 polypeptides as RING-type E3 ubiquitin ligases comprising a RING domain (see, e.g., paragraphs [0044]-[0047]). Suitable RING domains are set forth in SEQ ID NO: 1 and, more specifically, SEQ ID NO: 2. The specification further identifies the location of the RING domain within DA2 polypeptides across diverse plant species, including the wheat, barley, maize, rice, or sorghum sequences (paragraph [0047]). The specification goes on to describe additional conserved domains that flank the RING domain, including a first consensus domain N-terminal to the RING domain and a second consensus domain C-terminal to the RING domain (see, e.g., paragraphs [0049]-[0052]).
This argument has been fully considered but is not persuasive. Applicant does not describe a representative number of species nor a structure function relationship such that one would be able to envision which members of the claimed genus comprise the claimed function other than the T-DNA insertion comprised by the SALK_150003 mutant of Arabidopsis thaliana, da2-1. The scope of Applicant’s claimed invention encompasses any monocot plant with any mutation abolishing the activity of a DA2 comprising the claimed sequences. The observation of a single mutation in a single dicot plant species does not adequately provide guidance across any monocot plant species, of which there may be many differences in seed development.
Applicant argues on page 6 of the Remarks that the reference presented by the examiner, Song, demonstrates the advancement provided by the instant disclosure, e.g., overexpression of rice GW2 in Arabidopsis, which shares only 43.1% amino acid identity with Arabidopsis DA2, produced smaller seeds and organs than wild-type plants, indicating a conserved function in seed and organ growth across dicots and monocots.
This argument has been fully considered but it is not persuasive. The observation that overexpression of a monocot gene in Arabidopsis reduced seed size does not adequately describe a representative number of species, nor a structure-function relationship that would allow one of ordinary skill in the art to envision which members of the claimed genus would have a reduced seed size if otherwise comprising the claimed limitations. While it is acknowledged that many aspects of seed development are known or would be expected to be conserved across plant taxa, there are also many differences not only between monocots and dicots but within monocots.
Applicant argues on page 7 of the Remarks that, regarding the examiner’s point that the N91L mutation appears to demonstrate a member of the claimed genus of mutations would not be expected to comprise the claimed function if it were expressed in a plant, Applicant notes that the N91L mutation is not a member of the claimed genus, which only encompasses mutations that abolish the expression or activity of the DA2 polypeptide. As discussed at paragraph [0242] of the specification as originally filed, an in vitro ubiquitination assay showed that the N91L mutant of DA2 had E3 ligase activity (i.e., the mutation did not abolish activity).
This note is acknowledged by the examiner with appreciation for the clarification.
Closest Prior Art
Claims 1, 5-8, 10-11, 18 and 20, drawn to abolishing activity of DA2 in a monocot plant, are not found to be obvious in light of the teachings in the prior art at the time of filing. While Alonso (Alonso, et al. 2003. Science 301(5633):653-7) discloses producing the SALK line, anticipating instant claims 1, 5-9 and 18, there were no prior art teachings that would have provided motivation and an expectation of success by abolishing DA2 activity in other plants. It is noted that the characterization of the SALK line produced by Alonso was only provided by Xie post-filing, therefore while this reference is used as evidence regarding Alonso it is not relied upon for obviousness.
Additionally, Allen (US20110247094) Allen teaches a maize plant cell comprising a recombinant DNA construct that expresses a polynucleotide to modulate expression of a protein of SEQ ID NO: 16-21. Allen identifies SEQ ID NO: 51 (Table 6), as a homolog of SEQ ID NO: 16-21 which shares 100% identity with elected SEQ ID NO: 28. Allen does not teach or suggest a function associated with SEQ ID NO: 51 which would have been motivated one of ordinary skill in the art to abolish activity of the encoded protein in a plant.
Conclusion
Claims 1, 5-8, 10-11, 18 and 20 remain rejected.
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 DAVID R BYRNES whose telephone number is (571)270-3935. The examiner can normally be reached 9:00 - 5:00 M-F.
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, Bratislav Stankovic can be reached at (571) 270-0305. 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.
/DAVID R BYRNES/Examiner, Art Unit 1662
Prosecution Insights