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finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 11/25/2025 has been entered.
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 1-4, 8, 26, and 33 is 21 January 2020.
Status of the Claims
Amendments dated 10/27/2025 have been entered.
Claims 5-7, 9-25, 27-32, and 34-49 have been cancelled by Applicant.
Claims 1-4, 8, 26, and 33 are pending.
Claims 1-4, 8, 26, and 33 are examined herein.
The rejections to Claims 1-4, 6, 8, 26, 31, and 33 under 35 U.S.C. 103 as being unpatentable over Gilbertson et al. (US Patent No. 8,395,023 B2, issued 03/12/2013; IDS Document) in view of Kumar et al. (US 2015/0184178 A1, published 07/02/2015) and Niu et al. (WO 2018/140899 A1, published 08/02/2018) are withdrawn in view of Applicant’s amendments to the claims and rendered moot in view of Applicant’s cancellation of Claims 6 and 31.
Claim Rejections - 35 USC § 112
Scope of EnablementThe 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.
---These are new rejections from those set forth in the Office Action dated 06/26/2025 made in view of Applicant’s amendments to the claims dated 10/27/2025. Applicant’s Remarks dated 10/27/2025 have been reviewed and are deemed inapposite to the new rejections.---
Claims 1-4, 8, 26, and 33 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a plant cell and method of producing a plant comprising an endogenous miRNA recognition sequence that hybridizes to an endogenous microRNA (miRNA) comprising the nucleic acid sequence of SEQ ID NO: 198 and the gene encoding the polypeptide of interest comprises the nucleic acid sequence of SEQ ID NO: 564, does not reasonably provide enablement for a plant cell and method of producing a plant comprising an endogenous miRNA recognition sequence hybridizes to an endogenous microRNA (miRNA) comprising a nucleic acid sequence of any one of SEQ ID NOs: 1-554 and the gene encoding the polypeptide of interest comprises a nucleic acid sequence that is at least 80% identical to SEQ ID NO: 564. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make or use the invention commensurate in scope with these claims.
In re Wands, 858 F.2d 731 (Fed. Cir. 1988) lists the following eight factors for determining whether undue experimentation would be required to practice an invention: (1) quantity of experimentation necessary; (2) amount of direction or guidance supplied; (3) presence or absence of working examples; (4) nature of the invention; (5) state of the prior art; (6) relative skill of those in the art; (7) predictability or unpredictability or the prior art; (8) breadth of the claims.
Claims 1-4 and 8 are broadly directed to a plant cell comprising a targeted genetic modification in a genomic locus of an endogenous gene encoding a polypeptide of interest, the targeted genetic modification introducing into the genomic locus an endogenous microRNA (miRNA) recognition sequence, wherein the endogenous miRNA recognition sequence hybridizes to an endogenous microRNA (miRNA) comprising a nucleic acid sequence of any one of SEQ ID NOs: 1-554 and the gene encoding the polypeptide of interest comprises a nucleic acid sequence that is at least 80% identical to SEQ ID NO: 564, whereby expression of the endogenous miRNA that hybridizes to the endogenous microRNA recognition sequence decreases expression of the polypeptide of interest.
Claims 26 and 33 are broadly directed to method of producing a plant having decreased expression of a polypeptide of interest, the method comprising: (a) introducing in a regenerable plant cell a targeted genetic modification at a genomic locus of an endogenous gene encoding the polypeptide of interest, wherein the targeted genetic modification modifies the genomic locus to encode an endogenous microRNA (miRNA) recognition sequence, the endogenous miRNA recognition sequence hybridizing to an endogenous microRNA (miRNA) comprising a nucleic acid sequence of any one of SEQ ID NOs: 1-554 and the gene encoding the polypeptide of interest comprises a nucleic acid sequence that is at least 80% identical to SEQ ID NO: 564; and (b) generating the plant, wherein the plant comprises the targeted genetic modification.
Applicant teaches the polynucleotide sequence of SEQ ID NO: 564 (Specification, pg. 5). Applicant teaches that the sequence is isolated from maize and is a Zea mays Tasselless 1 (Zm-TSL1) nucleic acid sequence and the microRNA recognition sequence that decreases the expression of SEQ ID NO: 564 in a plant cell is SEQ ID NO: 198 (Specification, pg. 10). In Example 2, Applicant teaches that the down regulation of ZM-TSL1 reduces the size and appearance of a maize tassel. Applicant teaches that gene editing via CRISPR-Cas9 was utilized to place the tassel-specific miR529 target site (SEQ ID NO: 559) into the 3' untranslated region (3'UTR) of the ZM-TSL 1 (SEQ ID NO: 560) in a maize inbred. Guide RNA ZM-TSL 1-CRS (SEQ ID NO: 561) created the double-strand break within the maize genome and homology-directed repair (HOR) using a 200-bp oligonucleotide template (SEQ ID NO: 563) inserted the miR529 target site into the ZM-TSL1 3'UTR. The template was designed to create as few alterations as possible when compared to the endogenous ZM-TSL1 sequence while allowing for the presence of the 21 bp miR529 target site within the 3'UTR. The design also altered one base in the PAM motif within the template in order to prevent further double stranded breaks within any edited plants (Specification, pgs. 29-30, Example 2).
Applicant does not teach a plant cell or a method of producing a plant having decreased expression of SEQ ID NO: 564 [Zea mays Tasselless 1 (Zm-TSL1) nucleic acid sequence] across the range of claimed variants without undue experimentation. The claims encompass a plant cell encoding any polypeptide of interest having at least 80% sequence identity relative to SEQ ID NO: 564, wherein the polypeptide of interest has a targeted genetic modification in its genomic locus that is introduced through hybridization to an endogenous miRNA from any one of SEQ ID NOs: 1-554. Additionally, Applicant does not teach in the instant disclosure if all of SEQ ID NOs: 1-197 and 199-554 would be enabled for targeted genetic modification in a genomic locus of an endogenous gene encoding a nucleic acid sequence that is at least 80% identical to SEQ ID NO: 564 without undue experimentation, particularly SEQ ID NOs: 199-554, as those sequences are drawn to Glycine max miRNA sequences. When examining the prior and post-filing art in regards to SEQ ID NO: 564, neither the prior nor post filing art provide evidence that there are sequences having 80% identity relative to SEQ ID NO: 564 that are from Glycine max, much less sequences from Glycine max that have at least 80% sequence identity relative to SEQ ID NO: 564 that would be able to have some degree of hybridization with any one of SEQ ID NOs: 199-554 (See NCBI BLAST for SEQ ID NO: 564 located in file wrapper).
Claims 1 and 26 encompass polynucleotides with only 80% identity to instant SEQ ID NO: 564. Polynucleotides with 80% identity to 4,350 bp long SEQ ID NO: 564 would encompass polynucleotides with up to 870 substitutions, additions, deletions, or insertions relative to the 4,350 nucleotides of SEQ ID NO: 564, for a total of 4870x 3! possible variants. Applicant does not teach any plant cells comprising a targeted genetic modification in a genomic locus of any of the claimed sequence variants of SEQ ID NO: 564, much less when the endogenous miRNA recognition sequences of the variants of SEQ ID NO: 564 hybridize to SEQ ID NO: 198, much less when the endogenous miRNA recognition sequences of the variants of SEQ ID NOs: 564 hybridize to any one of SEQ ID NOs: 1-197 and 199-554. Applicant does not teach any functional fragments of SEQ ID NO: 564. Applicant does not teach any fragments as small as dinucleotides. The instant application fails to provide guidance for which nucleic acids of SEQ ID NO: 564 can be altered and/or duplicated, and to which nucleic acids, and also which nucleic acids must not be changed, to maintain the functional activity of the encoded TSL-1 polynucleotide when down-regulated in a plant cell by targeted genetic modification due to introduction of an endogenous miRNA recognition sequence which is hybridized by an endogenous microRNA, resulting in the decrease in expression of the encoded sequence variants of TSL-1. The specification also fails to provide guidance for which nucleic acids can be deleted and which region of SEQ ID NO: 564 can tolerate insertions and still have the function of reducing the size and appearance of a maize tassel with decreased expression by targeted genetic modification due to introduction of an endogenous miRNA recognition sequence which hybridizes to SEQ ID NO: 198, resulting in the decrease in expression of the encoded sequence variant of TSL-1—much less when the endogenous miRNA recognition sequence hybridizes to SEQ ID NOs: 1-197 and 199-554.
Applicant fails to provide guidance for how to make all polynucleotides with 80% identity to SEQ ID NO: 564 that can still undergo a targeted genetic modification in a genomic locus of the sequence variant of SEQ ID NO: 564 due to introduction of an endogenous miRNA recognition sequence which hybridizes to SEQ ID NOS: 1-554, resulting in the decrease in expression of the encoded sequence variant of SEQ ID NO: 564 which have the function of reducing the size and appearance of a maize tassel with decreased expression.
Teaching the exemplified species of polynucleotide insertions, deletions and substitutions of SEQ ID NO: 564 is unpredictable. These insertions, deletions, and substitutions in the polynucleotide encoded by SEQ ID NO: 564 would in many cases result in a change in the amino acids they encode and the resulting polypeptide. The amino acid, which is the primary structure of the polypeptide, is the basis for the spatial structure of the polypeptide, which in turn directly determines its function. Small changes in the amino acid sequences produced by transcription and translation of SEQ ID NO: 564 may lead to large changes in spatial structure, in turn altering the function of the polypeptide. Such differences in sequence structure will result in changes or even loss of function in certain nucleic acids/polypeptide molecules. While it is known that many amino acid substitutions, additions or deletions are generally possible in any given protein, the positions within the protein’s sequence where such amino acid changes can be made with a reasonable expectation of success (without altering protein function) are limited. Certain positions in the sequence are critical to the protein’s structure/function relationship, for example various sites or regions directly involved in binding, activity, and in providing the correct three-dimensional spatial orientation of binding and active sites. These regions can tolerate only relatively conservative substitutions or no substitutions at all. See Keskin et al., 2004, Protein Science 13: 1043-1055, who teach that proteins with similar structure may have different functions (Abstract; pages 1043-1044). See also Guo et al., 2004, Proceedings of the National Academy of Sciences USA 101: 9205-9210, who teach that there is a probability factor of 34% that a random amino acid replacement in a given protein will lead to its inactivation (Abstract; page 9206; Table 1). In the instant case, such a probability factor will be much higher as the claims encompass more than a single amino acid change in the proteins encoded by the polynucleotide selected from SEQ ID NO: 564. Furthermore, Thornton et al. (2000) (Nature Structural Biology, structural genomic supplement, November 2000: 991-994), teach that structural data may carry information about the biochemical function of a protein, while its biological role in the cell or organism is much more complex and additional experimentation is needed to elucidate actual biological function (page 992, left column, paragraph 2).
Given the teachings of Thornton, Keskin, and Guo, it is reasonable to conclude that the structures required for the recited functions are unpredictable. The only working example provided that utilizes SEQ ID NO: 564 shows hybridization of SEQ ID NO: 198 to SEQ ID NO: 564— not a sequence variant of SEQ ID NO: 564, and without hybridization to any of SEQ ID NOs: 1-197 and 199-554. Applicant fails to provide any teachings or evidencee that SEQ ID NOS: 1-197 and 199-554 can be used as endogenous miRNA that can hybridize to the inserted miRNA recognition sequence of SEQ ID NO: 564, much less sequence variants having as little as 80% sequence identity relative to SEQ ID NO: 564, without undue experimentation.
When looking at the broadest scope of the claims, it is unpredictable whether SEQ ID NO: 564 can hybridize to all of SEQ ID NOs: 1-197 and 199-554 and whether the claimed sequence variants of SEQ ID NO: 564 can hybridize to all of SEQ ID NOs: 1-554, resulting in the decreased expression of the protein encoding by SEQ ID NO: 564 or variants thereof. The state of the prior art regarding miRNA teaches not all protein coding sequences in plants can be targeted by miRNAs, and that miRNAs typically bind to specific sequences in untranslated regions, wherein only a subset of coding sequences have the necessary complementary sites for miRNA binding—meaning, not every protein coding gene is able to be regulated by a miRNA [See Ivashuta et al. (2011) and Bartel (2009)].
As such, it would require undue experimentation to one of ordinary skill in the art to determine whether SEQ ID NO: 564 and the claimed variants thereof could be used in the plant cell and methods of the invention for targeted genetic modification via the introduction of an endogenous miRNA recognition sequence into the genomic locus of SEQ ID NO: 564 and variants thereof, whereby endogenous miRNA set forth in SEQ ID NOS: 1-554 are able to hybridize to the introduced miRNA recognition sequence in sequences having at least 80% sequence identity relative to SEQ ID NO: 564 to decrease the expression of the polypeptide of interest in said plant cell, or whereby endogenous miRNA set forth in SEQ ID NOS: 1-197 and 199-554 are able to hybridize to the introduced miRNA recognition sequence in SEQ ID NO: 564 to decrease the expression of the polypeptide of interest in said plant cell.
Given limited guidance supplied by Applicant, the breadth of the claims and the nature of the invention, as well as the unpredictability in the art, it would have required one skilled in the art undue trial and error experimentation to practice the claimed invention through the full scope of its claims.
Closest Prior Art
Claims 1-4, 8, 26, and 33 appear to be free of the prior art, in regards to SEQ ID NO: 564, as the prior art does not reasonably suggest the embodiment of the claimed invention wherein the miRNA comprising a nucleic acid sequence of SEQ ID NO: 198 (elected species), drawn to a maize miR529 tassel preferred microRNA involved with plant reproductive development that has been shown to target squamosa promoter binding protein-like (SBP-box) genes, would be able to decrease expression of the ZM-TSL1 gene encoded by SEQ ID NO: 564 after hybridizing to the introduced miRNA recognition sequence introduced into SEQ ID NO: 564 in a maize plant cell. The prior art also does not teach any known miRNA sequences that would interact and modulate the expression of an endogenous Zm-TSL1 gene or polypeptide in maize, or the alternative name for Zm-TSL1 denoted as ZmNIP3;1, nor any motivation to modify any genomic locus of Zm-TSL1 to include an miRNA recognition sequence.
The closest prior art in regards to SEQ ID NO: 564 is found in GenBank Accession AY108821.1 (dated 06/06/2008), which is a Zea mays PCO070928 mRNA sequence with 97.54% sequence identity and 26% query identity to instant SEQ ID NO: 564. However, the sequence and its associated publication do not teach the integration of the sequence into a plant cell comprising a targeted genetic modification in a genomic locus of GenBank Accession AY108821.1 to introduce an endogenous miRNA recognition sequence wherein GenBank Accession AY108821.1 hybridizes to SEQ ID NO: 198 resulting in decreased expression of GenBank Accession AY108821.1, or any motivation to do so.
Conclusion
No claims are allowed.
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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/KELSEY L MCWILLIAMS/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663