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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 03/30/2026 has been entered.
Claim Status
The amendments of 03/30/2026 have been entered.
Claims 1, 4, 7, and 10-11 are pending and are being examined.
All previous objections and rejections not set forth below have been withdrawn in view of applicant’s amendments to the claims.
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.
Claims 1 and 4 are rejected under 35 U.S.C. 103 as being unpatentable over Maor et al. (US 2014/0298541 A1) in view of Li et al. (The Arabidopsis NFYA5 Transcription Factor Is Regulated Transcriptionally and Posttranscriptionally to Promote Drought Resistance, 2008, The Plant Cell, 20: 2238–2251) and in evidence of Chen et al. (CRISPR/Cas Genome Editing
and Precision Plant Breeding in Agriculture, 2019, Annu. Rev. Plant Biol., 70:667–97 15:16).
Maor et al. discloses a method of improving nitrogen use or utilization efficiency (NUE) in plants (page 1, abstract) by using microRNAs (miRNAs) (page 20, para 0077) under nitrogen deficient condition (page 69-70, para 0239). It describes making a microRNA-resistant target gene by introducing a mutation in the miRNA binding site of the target gene, so that the DNA and resulting RNA sequences are changed in a way that prevents miRNA binding, but the amino acid sequence of the protein encoded by the target gene is unchanged (page 7, para 0117; page 70, para 0243). Such mutation(s) abolish(es) binding of specific miRNA to its specific target gene in the genome. Maor et al. describe several miR169a sequences which are orthologues of maize miRNAs (page 24, para 0224; table 6) and involved in NUE. Maor et al. also describes rice miR169a, OsmiR169a (page 38, table 6), and a nucleotide sequence comprising 100% sequence identity to instant SEQ ID NO: 37, as shown below.
RESULT 6
US-14-438-763-359/c
Sequence 359, US/14438763
Patent No. 10190126
GENERAL INFORMATION
APPLICANT: A.B. SEEDS LTD.
APPLICANT: MAOR, Rudy
APPLICANT: NESHER, Iris
TITLE OF INVENTION: TRANSGENIC PLANTS WITH MODIFIED SUGAR CONTENT
TITLE OF INVENTION: AND METHODS OF GENERATING SAME
FILE REFERENCE: P34093US00
CURRENT APPLICATION NUMBER: US/14/438,763
CURRENT FILING DATE: 2015-04-27
PRIOR APPLICATION NUMBER: PCT/IL13/50880
PRIOR FILING DATE: 2013-10-28
PRIOR APPLICATION NUMBER: US 61/719,415
PRIOR FILING DATE: 2012-10-28
NUMBER OF SEQ ID NOS: 543
SEQ ID NO 359
LENGTH: 82
TYPE: DNA
ORGANISM: Medicago truncatula
Query Match 100.0%; Score 21; Length 82; Best Local Similarity 100.0%;
Matches 21; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CAGCCAAGGATGACTTGCCGA 21
|||||||||||||||||||||
Db 82 CAGCCAAGGATGACTTGCCGA 62
However, Maor et al. does not describe any target gene for miR169a or use any gene editing system.
Li et al. teaches that NF-YA5 is a target gene for miR169a (abstract), as recited in claim 4. It explains the post-transcriptional regulation by which degradation of NF-YA5 transcript (mRNA) is regulated by miR169a (page 2244, left column, para 1). Li et al. also describe the method to identify and to delete the exact upstream sequence of NF-YA5 transcript where miR169a binds and target the NF-YA5 transcript for cleavage (page 2242, Fig. 4).
Before the effective filing date of the claimed invention, it would have been obvious to
one of ordinary skill in the art to improve nitrogen utilization efficiency in plants using miR169a, as taught by Maor et al., by knocking-out the activity of miR169a using the well-known and standard gene editing system such as CRISPR/Cas9 (Chen et al., title and Abstract) by mutating, including deleting, the binding site of miR169a in the NF-YA5 gene in a plant. The CRISPR/Cas9 based targeted gene editing system is routine and efficient method which overcomes the challenges of random mutagenesis (e.g., by using transposons, T-DNA, physical, or chemical mutagenesis) by reducing random off-target mutations while deleting/mutating a specific target sequence in genome.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to knock-out the activity of miR169a using a targeted gene editing system by mutating the miR169a binding site of its target gene, NF-YA5, with a reasonable expectation of success to increase nitrogen use efficiency.
Claims 7 and 10-11 are rejected under 35 U.S.C. 103 as being unpatentable over Maor et al. in view of Li et al. as applied to claims 1 and 4 above, and further in view of Huynh et al. (US 8795987 B2) and in evidence of Cui et al. (Review of CRISPR/Cas9 sgRNA Design Tools, 2018, Interdisciplinary Sciences: Computational Life Sciences, 10:455–465).
Claim 7 is drawn to a method of producing a genome-edited rice plant with enhanced nitrogen utilization efficiency under a nitrogen-deficient condition using genome editing; and regenerating a rice plant from the rice plant cell that is obtained after the genome editing wherein the target nucleotide sequence of NF-YA5 gene derived from rice consists of the nucleotide sequence of SEQ ID NO: 41. Claim 10 is drawn to the genome-edited rice plant produced by the said method.
Maor et al. in view of Li et al. describe a method of enhancing nitrogen use/utilization efficiency (NUE) in a plant under a nitrogen-deficient condition, by inhibiting the activity of miR169a based on a mutation/deletion of the miR169a binding site in its target gene, NFYA5, as discussed above. Maor et al. also describes regenerating transformed plants into maturity (page 11, para 0165-0166). Maor et al. teaches that a plant's nitrogen use efficiency (NUE) is a result of an alteration in at least one of the traits including the uptake (as recited in claim 7), spread, absorbance and use (read on to “assimilation”, as recited in claim 7), accumulation, relocation of nitrogen absorbed by the plant (page 4, para 0053, line 1-4).
However, Maor et al. in view of Li et al. do not explicitly describe any gene editing system wherein the target nucleotide sequence of NF-YA5 gene derived from rice comprising the nucleotide sequence of SEQ ID NO: 41.
Huynh et al. teaches techniques for regulating gene expression using RNAi molecules (abstract) that either induce mRNA degradation or inhibiting translation of the mRNA (column 1, last 3 lines; and column 2, first 2 lines). It also teaches SEQ ID NO: 7287 from rice which maintains 100% identity to instant SEQ ID NO: 41, as shown below.
RESULT 1
US-12-183-204-7287/c
Sequence 7287, US/12183204
Patent No. 8795987
GENERAL INFORMATION
APPLICANT: International Business Machines Corporation
APPLICANT: Huynh, Tien
APPLICANT: Rigoutsos, Isidore
TITLE OF INVENTION: Ribonucleic Acid Interference Molecules of Oryza Sativa
FILE REFERENCE: YOR920070097US2
CURRENT APPLICATION NUMBER: US/12/183,204
CURRENT FILING DATE: 2008-07-31
NUMBER OF SEQ ID NOS: 24555
SEQ ID NO 7287
LENGTH: 96
TYPE: DNA
ORGANISM: Oryza sativa
Query Match 100.0%; Score 20; Length 96; Best Local Similarity 100.0%;
Matches 20; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 CGCCGGTGGCAATTCATCCT 20
||||||||||||||||||||
Db 46 CGCCGGTGGCAATTCATCCT 27
Before the effective filing date of the claimed invention, it would have been obvious to one of ordinary skill in the art to modify the method, as described by Maor et al in view of Li et al., by abolishing the repression of NF-YA5 gene, a target gene of miR169a, by mutating or knocking-out the target binding site of miR169a in NF-YA5 in rice, as described by Huynh et al. Identifying a specific gene, including NFYA5, based on several methods including homology search, especially in plant species with published genome (as in rice), is a routine practice in the art. It is also prudent to mention here that designing a guide RNA (gRNA) to mutate or knock-out any specific target sequence in a genome is also a routine and standard practice in the art (Cui et al., abstract), which can be used by an ordinarily skilled artisan. Using any specific sequence, including instant SEQ ID NO: 41 comprising 100% identity to the SEQ ID NO: 7287 as taught by Huynh et al., to mutate or knocking-out the miR169a binding site in the NF-YA5 gene in plants including in rice is an experimental design choice of any ordinarily skilled artisan without changing the outcome while mutating/deleting the miR169a binding site in NFYA5, as taught by Li et al, to increase NUE (which includes nitrogen uptake and/or nitrogen assimilation), as described by Maor et al.
It is known in the art that the genome edited rice plants and the seeds from the plants (as recited in claims 10-11) produced by the said method would maintain/inherit the trait of enhanced nitrogen utilization efficiency under nitrogen deficient condition.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to mutate or knock-out the target binding site for miR169a in NF-YA5 gene using a gene editing system to increase nitrogen utilization efficiency in rice.
Regarding claim 11, Maor et al. discloses regenerating transgenic T0 plants to maturity and harvesting seeds (page 69, para 0233).
Response to Applicant’s Arguments
The argument set forth in the Applicant’s reply on 3/30/2026 to the rejection of claims under 35 U.S.C. 103 has been fully considered but is not found persuasive.
In regard to USC 103 ejections, the Applicant argues that “the amendments to claims 1, 7, and 10 overcome the rejections by: (1) Explicitly reciting the functional requirement that the mutation abolishes miR169a binding (claims 1, 7, 10); (2) Specifying the enhanced NUE phenotype in measurable terms (increased nitrogen uptake/assimilation) (claim 7); (3) Identifying the target sequence as a miR169a binding site in NF-YA5 (claim 7); 3) Specifying the enhanced NUE phenotype in measurable terms (increased nitrogen uptake/assimilation) (claim 7); (4) Converting claim 10 from product-by-process to a structural claim explicitly reciting a genome-edited mutation at the endogenous NF-YA5 locus (response, page 13, para 7, line 2-7).
The Examiner disagrees. As discussed above, Moar et al. describes a method of improving nitrogen use or utilization efficiency (NUE) in plants by making a miRNA-resistant target gene by introducing mutation(s) in the miRNA binding site of the target gene, so that the target gene can be overexpressed, as discussed above. On the other hand, Li et al. teaches that NFYA5 is a target gene for miR169a. Li et al. also describes a method to identify and delete the exact upstream sequence of NF-YA5 transcript where miR169a binds and target the NF-YA5 transcript for cleavage, as discussed above. Nitrogen uptake and/or assimilation is part of NUE, as taught by Maor et al (page 4, para 0053, line 1-4).
Identifying a specific gene, including NFYA5, based on several methods including homology search, especially in plant species with published genome and/or published cDNA sequences (as in rice1), verifying target sequences of any miRNA molecule in a plant are routine practices in the art. Using CRISPR/Cas based gene editing technique to delete/mutate any specific sequence is also a well-known and a standard practice in the art. Targeted gene editing as CRISPR/Cas technique has many benefits over more traditional/older mutagenesis techniques, as described above. It would have been obvious to any ordinarily skilled artisan to use CRISPR/Cas based gene editing technique to delete the miR169a binding site in NF-YA5 gene to overexpress NF-YA5 gene with a realistic motivation to increase NUE in rice.
There would have been a realistic expectation of success in rice if a method to increase NUE works in Arabidopsis or maize (which is also a monocot as rice). The Applicant does not provide any evidence to show the contrary. Applicant’s opinion cannot take the place of evidence (MPEP 716.01(c)(II), 2145(I)).
Conclusion
All claims are rejected.
Correspondence
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JAY CHATTERJEE whose telephone number is (703)756-1329. The examiner can normally be reached (Mon - Fri) 8.30 am to 5.30 pm..
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/Jay Chatterjee/ Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/ Supervisory Patent Examiner, Art Units 1661 & 1662
1 Kikuchi et al. (GenBank Accession No. CI115347; published on 4th Mar. 2006; and Kikuchi et al., Collection, Mapping, and Annotation of over 28,000 cDNA Clones from Japonica Rice. 2003, Science, 301: 376–379) provide the evidence of a rice genome project sequencing 28,000 cDNA clones including the cDNA having 100% sequence identity to instant SEQ ID NO: 41.
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