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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 10/21/2025 has been entered.
Status of Claims
Claims 1, 4-16, 18, 21-22, 24-27, 33-34, 36-42 are under examination on the merits.
The objections to claims 8, 28, 36 & 38-39 are withdrawn in light of Applicant’s amendments.
The rejection of claims 33-36 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, is withdrawn in light of Applicant’s amendments.
The rejection of claims 1-10, 13-15, 20-23, 25-26, 33 & 36-39 under 35 U.S.C. 102(a)(1) as being anticipated by Guyomarc’h et al (2004) J of Experimental Botany, 55(397): 673-684 taken with the evidence of GenBank accession number AJ579629 is withdrawn in light of Applicant’s amendments.
The rejection of claims 1-8, 10, 13-15, 20-23, 25-26, 33 & 37-39 under 35 U.S.C. 102(a)(1) as being anticipated by Takeda et al (2004) Genes & Development. 18:782–793, taken with the evidence of GenBank accession number AY560347 is withdrawn in light of Applicant’s amendments.
The rejection of claims 1-10, 13-14, 20 & 37 under 35 U.S.C. 102(a)(1) as being anticipated by Suzuki et al (2004) Plant J. 38 (4), 673-684, taken with the evidence of GenBank accession number AB112744 is withdrawn in light of Applicant’s amendments.
The rejection of claims 1-15, 20-27, 33 & 37-39 under 35 U.S.C. 103 as being unpatentable over Gherbi et al (2001) EMBO reports. 2(4):287–291, in view of Wright et al (2005) The Plant Journal 44:693–705, hereafter Wright; in further view of Takeda et al (2004) Genes & Development. 18:782–793 is withdrawn in light of Applicant’s amendments.
The rejection of claim 1-15, 18, 20-27, 33 & 37-39 under 35 U.S.C. 103 as being unpatentable over Gherbi in view of Wright and Takeda, and further in view of Groth et al WO 2017/054832 A1 is withdrawn in light of Applicant’s amendments.
The rejection of claims 1-16, 20-27, 33 & 37-39 under 35 U.S.C. 103 as being unpatentable over Gherbi in view of Wright and Takeda, and further in view of Dubois et al (2011) PLoS One. 6(4), e18658 is withdrawn in light of Applicant’s amendments.
The rejection of claims 1-15, 20-32, 33-34 & 37-39 under 35 U.S.C. 103 as being unpatentable over Gherbi in view of Wright and Takeda, and further in view of GenBank accession number AB112744 is withdrawn in light of Applicant’s amendments.
Claim Objections
Claims 1, 12, 14, 24 & 33 are objected to because of the following informalities:
Claim 1 (line 18): the list of steps is missing a connecting word such as "and" between the penultimate and last steps.
Claim 24 recites a group consisting of both alfalfa (line 5) and lucerne (7). Since both terms refer to the plant species Medicago sativa, the list repeats this plant type.
Claim 12 (line 2) recites “ZFNs”. Claim 14 (line 1) recites “EMS”. These acronyms should be written out in their first use for clarity.
Claim 33 (line 10): “the plant with the trait of interest” should read --the trait of interest--, because it is the trait that is the result of the tandem duplication.
Appropriate correction is required.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 33 & 36 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon without significantly more. Claim 33 recite(s) identifying and/or selecting a plant with a trait of interest and genotyping the plant with the trait of interest. Claim 36 further recites the trait of interest is selected from a list of traits. This judicial exception is not integrated into a practical application because no active steps are required beyond genotyping, identifying and/or selecting. Genotyping and identifying are merely characterizing the plant and selecting is a thought process. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the steps of identifying, selecting, and genotyping are mental processes based on an observation of a natural phenomenon.
Claim 34 which further requires growing the plant to form a population of plants comprises a step that is more than a mental process and so is not included in this rejection.
Claims 37 is rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural phenomenon without significantly more. Claim 37 is drawn to a population of plant cells, plant parts or plants obtained by the method of claim 1. This judicial exception is not integrated into a practical application because claim 37 is a product by process claim and the population of plant cells, parts, or plants is limited only by the distinctive structural characteristics imparted by the method of claim 1. The claim(s) does/do not include additional elements that are sufficient to amount to significantly more than the judicial exception, because the step of reducing or abolishing expression, level, or activity of a TONSOKU nucleic acid or polypeptide in a population of plants in the method of claim 1 does not require reduced or abolished expression, level, or activity in the generated plant. Furthermore, “a population of plant cells, plant parts or plants obtained by the method of claim 1” does not exclude progeny, cells, or parts of the generated plant of claim 1 that may lack the tandem duplication due to e.g. random recombination during reproduction. The method of claim 1 comprises the recited steps but does not exclude additional steps such as crossing with a plant of another genotype. Thus, the method of generating the population of cells, parts, or plants of claim 37 imparts no markedly different characteristics that would differentiate such a population from a population found in nature.
Claim Rejections - 35 USC § 112
Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 27 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 27 recites repeating steps (iv) and (v), which are the steps of growing “the” plant to seed and growing the seeds obtained in step iv. The plant has antecedent basis in the plant comprising at least one tandem duplication resulting in a trait of interest (claim 1, step ii). Thus, claim 27 appears to require growing the same plant to seed, twice. However, the example of Arabidopsis in the instant specification (example 1, page 38, and example 4, page 40) and claim 24 encompass annual, determinate species that grow to seed once. It is unclear if 27 is strictly limited to a method of repeating steps (iv) and (v) and growing “the plant” to seed twice, or if claim 27 encompasses methods wherein the plants of the seeds of step (v) are grown to seed.
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.
Written Description
Claims 1, 4-16, 18, 21-22, 24-27, 33-34, 36-42 are 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 claims contain 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. This is a Written Description rejection.
Claims 1, 4-16, 18, 21-22, 24-27, 33-34, 36-42 are drawn to methods wherein a tandem duplication is generated in a plant by reducing or abolishing expression, level, or activity of an endogenous TONSOKU gene comprising SEQ ID NO: 3 or 4 or a plant homolog thereof. Thus, the claims broadly require any homolog to a TONSOKU endogenously present in any plant.
TONSOKU proteins and the genes encoding them are well known in the art. The specification provides a structure for a TONSOKU polypeptide comprising two protein-protein interaction domains, tetratricopeptide repeats, and leucine rich repeats (page 9, lines 28-30). Guyomarc’h et al (2004) J of Experimental Botany, 55(397): 673-684, hereafter Guyomarc’h, describes a MGO3/TONSOKU protein as comprising tetratricopeptide repeats (TPR) and leucine-rich-repeats (LRR) (page 680, figure 7). Takeda et al (2004) Genes & Development. 18:782–793, hereafter Takeda, describes a putative homolog of the TONSOKU gene in rice and that Arabidopsis has no other gene related to the TONSOKU gene (page 784, right column, paragraph 2). Blue et al (2022) Plant Gene. 32. 100384 (available online 9/23/2022, after the effective filing date of the instant application), hereafter Blue, describes domain structures of TONSOKU proteins that are highly conserved across species (page 9, left column, paragraph 1 and figure 4). Most land plant species have TONSOKU genes (Blue page 9, left column, paragraph 1), with copy numbers of genes in the family ranging from 0-7 (Blue figure 2c).
Thus, many TONSOKU genes are known in the art across many plant species, and the identification of a TONSOKU gene would have been routine to one of skill in the art. However, Blue describes plant homologs of TONSOKU that lack LRR domains involved in protein interactions or have shorter sequences or low sequence similarity relative to other TONSOKU homologs and suggests that these genes have different function (page 9, left column, paragraph 1).
Applicant has described Arabidopsis plants with TONSOKU mutation with tandem duplications. Applicant has not described the structural features of plant TONSOKU homologs necessary and sufficient for the function of generating tandem duplications. One of skill in the art would not recognize that Applicant was in possession of the necessary common attributes or features of the genus of endogenous TONSOKU plant homologs capable of generating tandem duplications in view of the disclosed species.
Because endogenous TONSOKU plant homologs capable of generating tandem duplications when reduced in activity, level or expression are not described over the full scope of the claims, the method of generating a plant comprising a tandem duplication is likewise not described, and the specification fails to provide an adequate written description of the claimed invention. Therefore, given the lack of written description in the specification with regard to the structural and functional characteristics of the compositions used in the claimed methods, Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
Scope of Enablement
Claims 1, 4-16, 18, 21-22, 24-27, 33-34, 36-42 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 reduced or abolished expression of one endogenous TONSOKU nucleic acid sequence or reduced or abolished levels of an endogenous TONSOKU polypeptide or reduced or abolished activity of an endogenous TONSOKU polypeptide in Arabidopsis, does not reasonably provide enablement for reduced expression, levels, or activity of TONSOKU in all species of plant. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims. This is an Enablement rejection.
The claims are drawn methods comprising a genus of endogenous TONSOKU genes and polypeptides. The term TONSOKU is defined in the specification to encompass a protein encoded by the TONSOKU gene (page 9, paragraph 2), including plant homologs of SEQ ID NO: 1 (page 9, lines 13-14) but not excluding polypeptides encoded by non-plant homologs (page 8, lines 25-26). The claims require an endogenous TONSOKU with a nucleic acid sequence of SEQ ID NO: 3 or 4 or a plant homologue thereof.
Thus, the claims are broad and read on any endogenous plant TONSOKU gene homologous to SEQ ID NO: 1 and the protein encoded thereby.
The species of TONSOKU protein described in the specification include SEQ ID NO: 1, from Arabidopsis, and a homolog in tomato (page 39, lines 20-21). MGOUN3 and BRUSHY1 are provided as synonyms for the TONSOKU gene in Arabidopsis (page 8, lines 9-13). Homologs in animals (page 8, lines 23-26) and yeast (page 9 line 30) are discussed.
The specification provides a structure for a TONSOKU polypeptide comprising two protein-protein interaction domains, tetratricopeptide repeats, and leucine rich repeats (page 9, lines 28-30). The specification discloses that TONSOKU forms a complex with MMS22L in yeast to mediate homologous recombination (page 9, lines 30-32). These structural features of TONSOKU polypeptides are well known in the art. Guyomarc’h et al (2004) J of Experimental Botany, 55(397): 673-684, hereafter Guyomarc’h, describes a MGO3/TONSOKU protein as comprising tetratricopeptide repeats (TPR) and leucine-rich-repeats (LRR) (page 680, figure 7). Guyomarc’h discloses that a deletion that cuts off the leucine-rich-repeats leads to a defective phenotype (page 680, right column second paragraph-page681, left column, first paragraph), demonstrating that the LRR motifs are required for normal activity of TONSOKU.
Blue et al (2022) Plant Gene. 32. 100384 (available online 9/23/2022 after the effective filing date of the instant application), hereafter Blue, teaches that domain structures of TONSOKU proteins are highly conserved across species (page 9, left column, paragraph 1 and figure 4). Blue teaches that most land plant species have TONSOKU genes (page 9, left column, paragraph 1), with copy numbers of genes in the family ranging from 0-7 (figure 2c). Tree species have higher copy numbers of TONSOKU genes than perennial or annual species (page 6, right column, paragraph 1). Thus, many TONSOKU genes are known in the art across many plant species.
However, Blue teaches that some plants have multiple copies of a TONSOKU gene, including Nicotiana tabacum, Oryza sativa ssp. japonica, and Carica papaya (figure 2c). Therefore, plants with multiple endogenous TONSOKU gene are encompassed in claims 1, 4-16, 18, 21-22, 24-27, 33-34, 36-42 and specifically in claim 24 (lines 2, 5, 7). Blue teaches that some homologous genes of TONSOKU lack LRR domains involved in protein interactions or have shorter sequences or low sequence similarity relative to other TONSOKU genes and suggests that these homologous genes have different function (page 9, left column, paragraph 1). In addition, Takeda et al (2004) Genes & Development. 18:782–793, hereafter Takeda, teaches that mutations in TONSOKU (referred to as BRU1 by Takeda) are recessive in the single-copy species Arabidopsis (page 783, right column, paragraph 3 and page 784, left column, paragraph 2-right column, paragraph 1).
The instant specification teaches a working example in Arabidopsis (page 38, lines 14-18). Arabidopsis has a single TONSOKU gene (Blue figure 2c). The prophetic example in tomato (page 39, lines 20-23) also is in a plant with a single TONSOKU copy (Blue figure 2c). The plants listed in prophetic example 3 (page 40, lines 5-10) include plants with multiple endogenous TONSOKU copies (Blue figure 2c), although these were not demonstrated in practice. In this prophetic example, a mutation in TONSOKU is identified or generated via mutagenesis or knockout or a plant is transformed with a construct encoding a TONSOKU inhibitory nucleic acid molecule or TONSOKU binding molecule.
However, as the art suggests TONSOKU homologs may have different functions relative to the Arabidopsis TONSOKU, and as the specification does not describe how to generate tandem duplications in a plant by reducing the expression, level, or activity of TONSOKU homologs that have a different function to Arabidopsis TONSOKU, undue trial and error experimentation would be required to generate a use for such a plant, if such use is possible. Thus, claims 1, 4-16, 18, 21-22, 24-27, 33-34, 36-42 are not enabled over the full scope of all plant homologs.
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.
Claim(s) 37 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Hammoudi et al (2016) New Phytologist. 211: 172-185. Published 3/2/2016, hereafter Hammoudi).
Claim 37 is drawn to a population of plant cells, plant parts or plants obtained by the method of claim 1.
Hammoudi discloses tandem duplication of the SUMO2 gene in Brassicaceae, leading to a neofunctionalized SUMO3 gene in Arabidopsis encoding a protein with different biochemical properties (Summary, page 172; page 173, left column, paragraph 4). Because the different function of SUMO3 reads on a trait of interest, the Arabidopsis plant therefore reads on a population of plant cells comprising a trait of interest resulting from a tandem duplication in the genome.
Because claim 37 is a product by process claim, the claim is not limited to the manipulations of the recited steps, only the structure implied by the steps. "[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process." In re Thorpe, 777 F.2d 695, 698, 227 USPQ 964, 966 (Fed. Cir. 1985).
The structure implied by the process steps should be considered when assessing the patentability of product-by-process claims over the prior art, especially where the manufacturing process steps would be expected to impart distinctive structural characteristics to the final product MPEP 2113 (I). In the instant case, the step of reducing or abolishing expression, level, or activity of a TONSOKU nucleic acid or polypeptide in a population of plants in the method of claim 1 does not require reduced or abolished expression, level, or activity in the generated plant, but rather encompasses transient methods of targeting TONSOKU. Thus, the only structural characteristic required of the plant generated by claim 1 is a tandem duplication within the genome resulting in a trait of interest. Hammoudi teaches a plant (Arabidopsis) with a tandem duplication in the genome resulting in the trait of interest of the potentially neofunctionalized gene SUMO3.
Furthermore, “a population of plant cells, plant parts or plants obtained by the method of claim 1” does not exclude progeny of the generated plant of claim 1 that may lack the tandem duplication due to e.g. random recombination during reproduction. The method of claim 1 comprises the recited steps but does not exclude additional steps such as crossing with a plant of another genotype. Thus, the population of plant cells, plant parts, or plants of claim 37 may read even on a plant without a tandem duplication in the genome.
In order to overcome the art, claim 37 would need to recite that the population of plant cells, plant parts, or plants comprise distinctive characteristics resulting from the method of claim 1, including the trait of interest, the at least one tandem duplication, and the reduced level, activity, or expression of TONSOKU.
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.
Claims 1, 4-8, 10, 13-15, 21, 22, 25-26, 33, 34, & 37-42 are rejected under 35 U.S.C. 103 as being unpatentable over Takeda et al (2004) Genes & Development. 18:782–793, hereafter Takeda, taken with the evidence of GenBank accession number AY560347 (available online 4/13/2004).
This is a new rejection necessitated by Applicant’s amendment of the claims. Applicant’s arguments filed 10/21/2025 have been considered below as they apply to the new rejection but they are not persuasive.
Claims 1, 4-8, 10, 13-15, 21, 22, 25-26, 33, 34, & 37-42 are drawn to a method of generating a plant with a trait of interest by reducing or abolishing the level of a TONSOKU polypeptide in a population of plants, as well as a plant obtained by this method.
Takeda teaches Arabidopsis mutants in the BRUSHY1 gene generated by T-DNA random insertion mutagenesis (page 783, right column, paragraph 3). The instant specification describes BRUSHY1 as the same gene as TONSOKU (page 8, paragraph 4). Takeda teaches a method of screening the mutant plants for traits of interest, namely sensitivity to methane sulfonate (page 783, right column, paragraph 3). The method of screening involved growing the plants (page 790, right column, final paragraph). Takeda teaches multiple alleles, and describes the two mutants with less severe phenotypes as partial loss of function mutants (page 784, left column, paragraph 2). Takeda teaches the mutations as recessive (page 783, right column, paragraph 3).
Takeda identifies the gene involved as encoding an amino acid sequence with the sequence of GenBank accession no. AY560347 (page 784, right column, second paragraph). AY560347 has 100% sequence homology to instant SEQ ID NO: 1; see alignment above.
Takeda teaches mutations in the gene as a deletion, a substitution, and an insertion in the gene (page 784, right column, third paragraph-page 785, left column, paragraph 1; figure 3B). Takeda teaches that bru1-1 mutants exhibit epistasis with fas1-1 and fas2-2 mutants based on double mutant lines (page 788, left column, paragraph 4). Takeda teaches that expression of BRU1 is detectable in suspension culture cells (page 785, left column, paragraph 2).
Takeda teaches that mutations in BRU1 lead to fourfold higher rates of homologous recombination (page 785, right column, paragraph 1). Takeda teaches that mutations in BRU1 had less transcriptional gene silencing (page 786, left column paragraph 2). Takeda teaches a method for testing homologous recombination wherein a heterozygous bru1-1 mutant was crossed with a plant comprising a recombination trap, an F2 generation was created, and progeny was genotyped for homozygous bru1-1 mutants (page 786, figure 4 caption).
Takeda does not teach the sequence of BRU1 directly but identifies the gene as At3g18730 and GenBank accession number AY560347 (page 784, right column, paragraph 2).
GenBank accession number AY560347 teaches a nucleotide that encodes an amino acid sequence with 99% homology to SEQ ID NO: 1. See alignment below/next page.
PNG
media_image1.png
252
520
media_image1.png
Greyscale
PNG
media_image1.png
252
520
media_image1.png
Greyscale
Before the filing of the instant application, the method of identifying a plant with a trait of interest, genotyping the plant, and growing the plant to form a population (instant claims 33 & 34) would have been obvious over Takeda, because Takeda identified plants with a trait of interest (sensitivity to methane sulfonate), crossed these plants, and genotyped the resulting plants. Although claim 33 recites the trait of interest is a result of at least one tandem duplication within the genome of the plant, tandem duplications inherently result from the reduced activity, expression, or level of TONSOKU in an Arabidopsis plant. The instant specification describes de novo tandem duplication events to occur at a rate of 7 per generation; no Arabidopsis lines had 0 tandem duplications in a generation (figure 3, page 40, line 33-page 41 line 3). Thus, the TONSOKU-deficient Arabidopsis lines of Takeda would comprise tandem duplications, even though Takeda is silent about this feature, and some tandem duplications would inherently confer traits that would be uncovered by the method of screening in Takeda’s Arabidopsis lines. Therefore, the method of Takeda would make obvious the methods of claims 33-34 prior to the filing of the instant application.
Likewise, claim 1 & 8-10 & 13-14 are drawn to the method of providing a population of plants comprising an endogenous TONSOKU nucleic acid, reducing or abolishing TONSOKU expression or activity in the population of plants to generate a plant comprising at least one tandem duplication within the genome of the plant, and identifying or selecting a plant with the trait of interest. Although Takeda is silent about the presence or absence of tandem duplications in the genome of the TONSOKU mutant plants, these Arabidopsis lines of Takeda would inherently comprise tandem duplications. The screening of plants for a trait of interest, as taught by Takeda, would make obvious before the filing of the instant application a method wherein the screening uncovered a trait of interest that resulted from a tandem duplication. The plant of Takeda, which reads on a population of plant cells, comprises an insertion mutation in the TONSOKU gene (claims 8 & 10). The mutation was generated by a T-DNA insertion mutagenesis (claims 13-14). Plants were screened to identify those that were homozygous for the mutation (claim 15). Plants were assayed for sensitivity to sensitivity to methane sulfonate which reads on selecting the plant by assessing the behavior of at least one plant cell in a phenotypic assay (claim 42).
Because the method would have been obvious over Takeda, a plant produced by the method would have also been obvious (claim 37).
Additionally, the method of Takeda comprising growing plants comprising the TONSOKU homolog mutation in order to make crosses up to at least the F2 generation (page 786, figure 4 caption) inherently involves growing a mutant plant to seed (claim 25) and growing the seeds obtained (claim 26), which would result in an F1 generation. Takeda’s method also reads on a method that comprises growing the plant with the trait of interest (claim 40) to seed to obtain progeny (claim 41).
Some, if not all, of the generated plants from reduced or abolished TONSOKU activity would inherently also comprise two tandem duplications (instant claim 4) or three tandem duplications (instant claim 5) and these tandem duplications would occur at random locations (instant claim 6) and comprise a repeated sequence of 50-500 Kb (instant claim 7), because de novo tandem duplication events at random locations in the genome inherently occur at a rate of 7 per generation in an Arabidopsis mutant for TONSOKU, and some of these random duplications will comprise repeated sequences of at least 50Kb (instant specification, figure 3, page 40, line 33-page 41 line 3).
The Arabidopsis mutant line taught by Takeda reads on a population. However, the instant specification defines a plant to encompass a plant cell (page 35, lines 1-5). Takeda teaches plant tissues and plant parts by provided pictures of the plants where leaves and floral structures are visible (figure 2), which read on a population of plant cells obtained from plant tissue (claim 21) and plant tissue comprising a plant part (claim 22), including where the plant tissue or plant part is leaves (claims 38-39).
Applicant urges that amended claims clarify the link between reducing TONSOKU expression resulting in tandem duplication and selecting a plant with a trait of interest. Applicant urges that because the cited prior art does not disclose nor suggest that reducing or abolishing the expression/activity of TONSOKU results in at least one tandem duplication event or linking the tandem duplication to selecting a plant (Remarks, page 8, paragraphs 3-4).
This argument is unpersuasive, because while method of Takeda does not comprise identifying a tandem duplication within the genome of a plant or selecting a plant with a tandem duplication, the amended claims do not in fact require identifying a tandem duplication or directly selecting for a plant with a tandem duplication. Because the amended claims merely require identifying a plant with a trait of interest, and because the TONSOKU mutants of Takeda would have tandem duplications due to decreased TONSOKU expression/activity, selecting for plants with a trait of interest in this population of plants would likely select plants with traits of interest due to tandem duplication even if the duplication itself was unknown to be the cause. An active step requiring the identification of a tandem duplication would not be obvious over Takeda.
Applicant urges that because plant cells are not being claimed in the instant application, just the use of the plant cells, the inherent trait of increased tandem duplications would not make the method obvious to one of ordinary skill in the art (Remarks, page 8, paragraph 5-page 9, paragraph 1).
This argument is unpersuasive, because the methods of the amended claims do not require that a practitioner know that the plant or plant cells being used have tandem duplications. The method of screening for a trait of interest in a TONSOKU mutant line, as Takeda did, reads on the instant claims because the claims require selection of a plant with a tandem duplication indirectly, by selection of a plant with a trait of interest. A step requiring the identification of a tandem duplication directly in a TONSOKU mutant line would not have been obvious to one of skill in the art over Takeda for the reasons the Applicant provides.
Claims 1, 4-15, 21, 22, 24-27, 33, 34, & 36-42 are rejected under 35 U.S.C. 103 as being unpatentable over Gherbi et al (2001) EMBO reports. 2(4):287–291 (published 4/1/2001, hereafter Gherbi); in view of Wright et al (2005) The Plant Journal 44:693–705 (published 10/18/2005 hereafter Wright); in further view of Takeda et al (2004) Genes & Development. 18:782–793 (published 2004, hereafter Takeda).
This is a new rejection from the rejection mailed 4/21/2025. Applicant' s arguments filed 10/21/2025 have been fully considered below as they apply to the current rejection but they are not persuasive.
Claims 1, 4-8, 10, 13-15, 21, 22, 25-26, 33, 34, & 37-42 are summarized above. Claim 9 requires a loss of function mutation. Claim 24 is drawn to a method of reducing or abolishing the level of a TONSOKU polypeptide in a plant selected from a list of plants. Claims 11-12 are drawn to a method of modifying a TONSOKU gene via targeted mutagenesis. Claim 36 is drawn to a method wherein the trait of interest is from a list of traits.
Gherbi teaches Arabidopsis mutants homozygous for a T-DNA insertion in the RAD50 gene (page 290, left column, paragraph 3) have increased homologous recombination, including gene conversion relative to heterozygotes (page 288, right column, paragraph 1-2 and figure 4). Gherbi teaches a method of crossing RAD50 mutants with GUS recombination tester lines and screening for a trait of interest (antibiotic resistance) in the F3 generation (page 290, left column, paragraph 3). Gherbi does teach genotyping the plants for zygosity of the mutation by PCR prior to screening for increased recombination (page 288, left column, paragraph 1, figure 2). Thus, Gherbi teaches a method of increasing genome modification in a plant cell by mutating the gene encoding a polypeptide.
Gherbi does not teach a TONSOKU protein or gene, nor a method of reducing the level of a TONSOKU protein in a plant cell, nor a plant created by the method of reducing the level of a TONSOKU protein. Gherbi does not teach introducing a mutation into a TONSOKU gene, nor a method of mutation involving targeted genome modification, nor a method to reduce protein levels involving RNA interference or an inhibitor. Gherbi does not teach an increase in tandem duplications due to the method. Gherbi does not teach the reduction of a TONSOKU gene in a population of cells and growing the cells into a plant. Gherbi does not teach the method in any of the plants listed in claim 24 nor the traits in claim 36.
Wright teaches a method to increase homologous recombination in tobacco by introducing a construct encoding a zinc-finger nuclease via leaf disk transformation (page703, right column, paragraphs 2-3). Wright teaches a motivation to increase homologous recombination in plants, in that homologous recombination can create precise deletions, insertions, or mutations and that plant chromosomal modification through homologous recombination “has been a long sought after goal of plant biology” (page 693, left column, paragraph 1). Wright teaches a method of introducing zinc-finger nucleases and donor DNA into plant cells (page 696, right column, second paragraph) to specifically mutate a reporter gene (page 695, left column, paragraph 3). Wright teaches a motivation to use targeted genome modification in plant to perform gene targeting of valuable traits like increased resistance to disease or stress or altered oil or carbohydrate profiles (page 693, right column, paragraph 1) while allowing for greater public acceptance than other transformation methods (page 703, left column, paragraph 3), as well as a motivation to use zinc-finger nucleases because they can recognize extended sequence patterns with great specificity and affinity (page 694, right column first paragraph). Wright teaches a method where shoot cultures are grown from transformed leaf disks and the expression of the target gene in T0 plants is verified with RT-PCR (page703, right column, paragraphs 3). Wright also teaches protoplast cultures derived from shoot cultures, transformed by electroporation, and regenerated into plants (page 703, right column, paragraphs 3- page 401, left column, first paragraph).
The teachings of Takeda are summarized above.
Before the date of filing of the instant application, it would have been obvious to one having ordinary skill in the art to modify the method taught by Gherbi to mutate a RAD50 gene to increase homologous recombination in a plant cell with the method of Takeda to reduce the level of a TONSOKU/BRUSHY1 polypeptide to increase homologous recombination. One would have been motivated to increase recombination in a plant cell because Wright taught that increasing homologous recombination in plants had long been a goal for mutating DNA sequences within native chromosomal contexts (page 693, left column, paragraph 1). Because mutations in both RAD50 (Gherbi, abstract) and TONSOKU/BRUSHY1 (Takeda abstract) had been known in the art to increase homologous recombination, one of ordinary skill in the art would have had reasonable expectation of success in mutating TONSOKU in increase homologous recombination.
Although Gherbi, Wright, and Takeda are silent with regard to the presence or absence of tandem duplications, or traits that result from tandem duplications, a plant with a reduced or abolished expression, activity, or level of TONSOKU would inherently have tandem duplications, as presented above.
Regarding claims 1, 4-8, 10, 13-15, 21, 22, 25-26, 33, 34, & 37-42, the limitations of the claims are taught by Takeda, as summarized above.
Regarding claim 9, it would have been obvious before the time of filing from Takeda that a loss of function mutation would increase the homologous recombination phenotype observed, and Takeda indirectly suggests that bru1-3 is a loss of function mutation compared to the weaker phenotypes in the bru1-1 and bru1-2 mutants, hypothesized to be partial loss-of-function mutations (page 784, left column paragraph 2). Thus, in light of Takeda, a method of reducing the level of a TONSOKU polypeptide further comprising a mutation in a TONSOKU gene comprising a loss of function mutation would have been obvious at the time of filing.
Regarding claims 11-12, before the time of filing of the instant application, one of ordinary skill in the would have been motivated to modify the method taught by Gherbi/Takeda to reduce the level of a TONSOKU polypeptide by the method taught by Wright of targeted mutagenesis using zinc-finger nucleases. One of ordinary skill in the art would have been motivated to do so because zinc-finger nucleases for targeted mutagenesis allows for changing plant genomes in a specific and controlled manner, which could allow for greater public acceptance than other transformation methods and enables creating crops with valuable traits. One of ordinary skill in the art would have had reasonable expectation of success because zinc-finger nuclease mediated gene targeting had been widely used at the time of filing of the instant application.
Regarding claim 24, before the time of filing of the instant application, one of ordinary skill in the art would have found it obvious to use tobacco instead of Arabidopsis in the method of Gherbi because Wright taught a method to increase homologous recombination using tobacco plants and cell lines (abstract). One would have had reasonable confidence of success because a homolog of BRU1 was known in tobacco (Takeda, page 785, left column, paragraph 3). Thus, the method of claim 24 to reduce the level of a TONSOKU polypeptide in a plant cell in a tobacco plant would have been obvious at the time of filing of the instant application.
Regarding claim 27, claim 27 is drawn to a method comprising repeating steps (iv) and (v) of claims 25 and 26. Step (iv) of claim 25 comprises growing to seed the plant that has the trait of interest in step (ii) of claim 1. To repeat step (iv) would encompass re-growing the plant from step (ii) to seed, such as from an asexual propagation of the plant of step (ii). Repeating step (ii) would not be satisfied by growing the seeds obtained from step (v) to seed.
Before the time of filing of the instant application, it would have been obvious to one of ordinary skill in the art to modify the method taught by Gherbi/Takeda to reduce the level of a TONSOKU polypeptide in a plant cell with the method taught by Wright to maintain transformed plants via aseptic shoot cultures. It would have been obvious before the time of filing to generate and maintain shoot cultures for a transgenic plant such as tobacco, because transformation methods such as leaf disk transformation involve regenerating plants in aseptic shoot cultures. Growing shoot cultures to seed and then growing the seeds obtained would have been obvious for experiments involving crossing of mutants with reporter lines (eg Gherbi). To repeat the process of growing the plant to seed and growing the seeds obtained, as recited in claim 27, would have likewise been obvious because more than one cross between TONSOKU mutants and other genetic lines was desired. Takeda made double mutant lines with two other genes to test interactions. Thus, before the time of filing of the instant application it would have been obvious to modify the method of Gherbi/Takeda with the method of Wright to maintain the original plant line in shoot culture in order to repeat the steps of growing the plant to seed and growing seeds. One of skill in the art would have been motivated to do so in order to cross the mutant line with other genetic lines. One of ordinary skill would have been reasonably confident of success because shoot culture methods were routine at the time of filing of the instant application.
Finally, it would have been obvious to one of ordinary skill in the art to modify the method to screen for a trait such as altered carbohydrate profiles or disease or stress resistance (instant claim 36) rather than or in addition to sensitivity to methane sulfonate. One of skill in the art would have been motivated to screen for these traits of interest, because Wright teaches that these are traits of high-value crops. One of ordinary skill in the art would have had reasonable expectation of success in screening for these traits, because methods of screening for plant traits was routine in the art prior to the filing of the instant application.
Claims 1, 4-15, 21, 22, 24-27, 33, 34, & 36-42 are obvious over Gherbi, Wright, and Takeda.
Applicant urges that amended claims clarify the link between reducing TONSOKU expression resulting in tandem duplication and selecting a plant with a trait of interest. Applicant urges that because the cited prior art does not disclose nor suggest that reducing or abolishing the expression/activity of TONSOKU results in at least one tandem duplication event or linking the tandem duplication to selecting a plant (Remarks, page 8, paragraphs 3-4).
This argument is unpersuasive, because while method of Takeda does not comprise identifying a tandem duplication within the genome of a plant or selecting a plant with a tandem duplication, the amended claims do not in fact require identifying a tandem duplication or directly selecting for a plant with a tandem duplication. Because the amended claims merely require identifying a plant with a trait of interest, and because the TONSOKU mutants of Takeda would have tandem duplications due to decreased TONSOKU expression/activity, selecting for plants with a trait of interest in this population of plants would likely select plants with traits of interest due to tandem duplication even if the duplication itself was unknown to be the cause. An active step requiring the identification of a tandem duplication would not be obvious over Takeda.
Applicant urges that because plant cells are not being claimed in the instant application, just the use of the plant cells, the inherent trait of increased tandem duplications would not make the method obvious to one of ordinary skill in the art (Remarks, page 8, paragraph 5-page 9, paragraph 1).
This argument is unpersuasive, because the methods of the amended claims do not require that a practitioner know that the plant or plant cells being used have tandem duplications. The method of screening for a trait of interest in a TONSOKU mutant line, as Takeda did, reads on the instant claims because the claims require selection of a plant with a tandem duplication indirectly, by selection of a plant with a trait of interest. A step requiring the identification of a tandem duplication directly in a TONSOKU mutant line would not have been obvious to one of skill in the art over Takeda for the reasons the Applicant provides.
Claim 16 is rejected under 35 U.S.C. 103 as being unpatentable over Gherbi in view of Wright and Takeda, as applied to claims 1, 4-15, 21, 22, 24-27, 33, 34, & 36-42 above, and further in view of Dubois et al (2011) PLoS One. 6(4), e18658.
This is a new rejection from the rejection mailed 4/21/2025.
Claim 16 is drawn to a method comprising using RNA interference to reduce the expression of at least one TONSOKU nucleic acid sequence.
The teachings of Gherbi, Wright, and Takeda are summarized above. Of emphasis, Takeda teaches that at least one mutant of a TONSOKU gene, bru1-3, has a phenotype causing reduced seed set, and the mutation is recessive (page 784, left column, paragraph 2-page 784, right column, paragraph 1).
Gherbi, Wright, and Takeda do not teach using RNA interference to reduce the expression of at least one TONSOKU nucleic acid sequence.
Dubois teaches a method using RNA interference by placing an RNAi construct under control of the pAlcA promoter to conditionally knock out the DUT1 gene in Arabidopsis (page 3, left column, paragraph 1). Dubois teaches a motivation to use a conditional RNA interference system because inactivation of the AtDUT1 gene is lethal (page 3, left column, paragraph 1). Dubois teaches that RNAi/DUT1 transformed plants have reduced expression of the target gene (page 3, left column, paragraph 2- right column paragraph 1, figure 3 A). Dubois teaches that RNAi/DUT1 plants had more than two recombination events per seedling, whereas control plants had no observed recombinant events, demonstrating that homologous recombination was increased in RNAi/DUT1 plants (page 5 right column paragraph 2-page 6, left column, paragraph).
Before the time of filing of the instant application, it would have been obvious to one of ordinary skill in the art to modify the method taught by Gherbi, Wright, and Takeda with the method of Dubois to further use RNA interference to reduce the expression of at least one TONSOKU nucleic acid sequence. One would have been motivated to do so in order to achieve a homozygous TONSOKU mutant phenotype with enhanced homologous recombination in a heterozygous mutant, or wildtype, line. Because the TONSOKU mutation is recessive, a heterozygous line would not have suffered from very low seed set (Takeda, page 784, left column, paragraph 2). Higher yield in stock lines are an obvious improvement to one of ordinary skill in the art. One would have had reasonable expectation of success because both Dubois and Gherbi, Wright, and Takeda taught methods to disrupt genes and proteins involved in the DNA repair and homologous recombination process in plants, and the methods of RNA interference were well understood at the time of filing. Thus, the method of reducing the level of TONSOKU polypeptide in a plant cell further comprising using RNA interference to reduce the expression of at least on TONSOKU nucleic acid sequence would have been obvious at the time of filing in view of Gherbi, Wright, Takeda, and Dubois.
Claims 1, 4-16, 21, 22, 24-27, 33, 34, & 36-42 are obvious in view of Gherbi, Wright, Takeda, and Dubois.
Claim 18 is rejected under 35 U.S.C. 103 as being unpatentable over Gherbi in view of Wright and Takeda, as applied to claims 1, 4-15, 21, 22, 24-27, 33, 34, & 36-42 above, and further in view of Groth et al WO 2017/054832 A1 (published 4/6/2017, filed 9/30/2016), hereafter Groth.
This is a new rejection from the rejection mailed 4/21/2025.
Claim 18 is drawn to a method of reducing levels of a TONSOKU polypeptide in a plant cell comprising using an inhibitor to reduce or abolish an activity of the TONSOKU polypeptide.
The teachings of Gherbi, Wright, and Takeda are presented above. Gherbi, Wright, and Takeda do not teach using an inhibitor to abolish an activity of the TONSOKU polypeptide.
Groth teaches that an activity of the TONSL protein in human cells is to bind to post-replicative chromatin (page 52, lines 16-26 and figure 20) and that recognition of histone modification H4K20me0 is critical to this function (page 52 line 35-page 53, line4). TONSL is a homolog of TONSOKU protein found in animals (instant specification, page 9, paragraph 4). Groth teaches that mutated proteins are impaired in this function (page 52, lines 35-36 and figure 25 and 26). Groth also teaches a method of using an inhibitor to competitively bind TONSL to prevent normal chromatin binding activity (page 61, lines 9-14). Groth teaches that TONSL is involved in the repair of double strand breaks and damaged replication forks through homologous recombination (page 4, lines 22-25).
Before the time of filing of the instant application, it would have been obvious to one of ordinary skill in the art to modify the methods taught by Gherbi, Wright, and Takeda to reduce levels of a TONSOKU polypeptide in a plant cell with the method taught by Groth to reduce activity of a TONSOKU polypeptide in a plant cell by applying an inhibitor. Wright taught a motivation to increase homologous recombination (page 693, left column, paragraph 1) as well as a motivation to minimize untargeted genome mutations to improve public acceptance (page 703, left column, paragraph 3). Thus, one having ordinary skill in the art at the time of filing of the instant application could have been motivated to substitute the method comprising random mutation of Gherbi, Wright, and Takeda with the method of Groth to inhibit TONSOKU-homolog function using an inhibitor in order to improve public acceptance of the resulting plant. One would have had reasonable expectation of success because TONSOKU and TONSL are homologs and both were known in the art to play similar roles in the regulation of homologous recombination, and TONSL mutants phenocopy the effects of TONSL inhibitors (Groth, page 5, lines 17-19).
Thus, claims 1, 4-15, 18, 21, 22, 24-27, 33, 34, & 36-42 are obvious in view of Gherbi, Wright, and Takeda, in further view of Groth.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Victoria L DeLeo whose telephone number is (703)756-5998. The examiner can normally be reached M-F 8:00am-12pm EST.
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.
/VICTORIA L DELEO/Examiner, Art Unit 1662
/Anne Kubelik/Primary Examiner, Art Unit 1663
Prosecution Insights