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 .
Priority
This application is acknowledged as a continuation of U.S. Application No. 17/905,733, filed September 6, 2022, which is a U.S. National Phase Application of PCT/US2021/021194, International Filing Date March 5, 2021, and which claims benefit of U.S. Provisional Application No. 62/985,778, filed March 5, 2020. As such, the effective filing date of Claims 1, 5-7, and 9-11 is 03/05/2020.
Status of the Claims
Amendments dated 03/02/2026 have been entered.
Claims 2-4 and 8 have been cancelled.
Claims 9-11 are newly added.
Claims 1, 5-7, and 9-11 are pending.
Claims 1, 5-7, and 9-11 are examined herein.
The objections to the specification and sequence disclosure are withdrawn in view of Applicant’s amendments to the specification.
The objection to Claim 6 is withdrawn in view of Applicant’s amendments to the claims.
The rejection of Claims 5-7 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or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention are withdrawn in view of Applicant’s amendments to the claims.
The rejections of Claims 1-2 and 8 under 35 U.S.C. 102(a)(1) as being anticipated by Liu et al. (Journal of integrative plant biology 59.7 (2017): 459-474; IDS Document) are withdrawn in view of Applicant’s amendments to the claims and cancellation of Claims 2 and 8.
The rejections of Claims 1 and 5-7 on the ground of nonstatutory double patenting as being unpatentable over Claims 1-4 of U.S. Patent No. 12,442,013 B2 are withdrawn in view of the Terminal Disclaimer filed and accepted on 03/02/2026.
Claim Objections
Claim 1 is objected to because of the following informalities:
Claim 1, line 4 should be amended to recite “…wherein the endogenous PARP encodes a PARP2 gene…”
Appropriate correction is required.
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.
---The following are new rejections from those set forth in the Office Action dated 11/24/2025 made in view of Applicant’s amendments to the claims.---
Claims 1 and 11 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.
The Federal Circuit has clarified the written description requirement. The court stated that a
written description of an invention "requires a precise definition, such as by structure, formula, [or] chemical name, of the claimed subject matter sufficient to distinguish it from other materials". University of California v. Eli Lilly and Co., 119 F.3d 1559, 1568; 43 USPQ2d 1398, 1406 (Fed. Cir. 1997).
The court also concluded that "naming a type of material generally known to exist, in the absence of
knowledge as to what that material consists of, is not description of that material". Id. Further, the court
held that to adequately describe a claimed genus, Patent Owner must describe a representative number
of the species of the claimed genus, and that one of skill in the art should be able to "visualize or recognize the identity of the members of the genus". Id.
Claims 1 and 11 are broadly directed to a method of obtaining a plant that has reduced non-edible biomass compared to a counterpart control plants which comprises disrupting expression of an endogenous PARP gene of the plant, and the said plant obtained by the method. The PARP gene encompassed by the instant claims is a PARP2 gene, wherein the plant is any tomato plant species. The claims broadly encompass any method of disrupting, inhibiting, or preventing the expression of any endogenous PARP2 gene from any tomato plant species plant known in the art.
In the instant claims, Applicant recites the disruption (i.e., inhibition or prevention) of a endogenous PARP2 gene from any tomato plant species known in the art, which encompasses modifications to upstream regulators of any endogenous PARP2 gene from any tomato plant species known in the art. The specification does not describe the co-factors, or regulators of any PARP2 gene from any tomato plant species known in the art, for example, that makes the endogenous PARP2 gene down-regulate and/or suppress in any tomato plant species known in the art. Applicant has not described what these upstream regulators are, or how they may be altered (i.e., increased or decreased) to affect expression of any endogenous PARP2 gene from any tomato plant species known in the art.
As such, neither the specification nor the prior art describe the identity or function of the co-factors, or regulators of endogenous PARP2 genes, for example, that interact with endogenous PARP2 genes causing the genes to down-regulate and/or be suppressed in any tomato plant species known in the art.
One of ordinary skill in the art would not recognize that the Applicant was in possession of the necessary common attributes or features of the claimed genus in view of the prior art.
Hence, Applicant has not, in fact, adequately described the broad genus of co-factors and regulators that could disrupt the expression of endogenous PARP2 genes in tomato plants.
To overcome this aspect of the written description rejection, Examiner suggest that Applicant amend the Claim 1 to recite, the “wherein” clause recited in Claim 5.
Response to Arguments
Applicant’s Remarks on pg. 4 of the reply filed on 03/02/2026 are acknowledged but do not overcome these new rejections. In particular Applicant’s Remarks rely on the premise that the amendment to the claim reciting a method to obtain a tomato plant with reduced non-edible biomass by disrupting expression of an endogenous PARP2 gene overcomes the previous written description rejection dated 11/24/2025.
This is not found persuasive for the reasons given in the new 35 U.S.C. 112(a) rejection above, made in view of Applicant’s amendments to the claims.
Claim Rejections - 35 USC § 103
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 11 are rejected under 35 U.S.C. 103 as being unpatentable over Liu et al. (Journal of integrative plant biology 59.7 (2017): 459-474; IDS Document) in view of D’Halluin et al. (US20190225974, published 07/25/2019), taken with evidence of the instant specification.
Regarding Claims 1 and 11, Liu et al. (herein referred to as Liu) teaches a method of inhibiting PARP expression in Arabidopsis thaliana using the PARP inhibitor 3-aminobenzamide (3-AB) and full-length Arabidopsis PARP1 and PARP2 in E. coli to analyze the expression activity of endogenous PARP genes in vitro, which resulted in the inhibition of PARP1 and PARP2 activity (Figure 1A and B). Liu further discloses a method of using anti-PARP2 antibody to detect the mobility shift of PARP2 proteins in Arabidopsis seed extracts that were co-incubated with 3-AB. The up-shifted smears originating from the self-modification of the PARP2 protein were weakened by co-incubation of 3-AB. These two methods of experimentation indicated that 3-AB inhibited PARP1 and PARP2 activities in vitro and in vivo. To observe the growth phenotype of plants treated with PARP inhibitors that disrupt the expression of PARP genes in a plant, Liu teaches growing Arabidopsis seeds on plates inoculated with 3-AB and observing their lateral and vertical growth, finding that plants treated with 3-AB exhibited more lateral roots than control plants (Figure 2A and B), with secondary lateral roots that created a more complicated overall root architecture (Figure 2B and C). The results also showed that seedlings grown with 3-AB had a higher average biomass than the control (Figure 2D). To measure the increase or decrease in plant biomass, Liu teaches several techniques to track the changes in the lateral root growth, by daily monitoring (6th day to 14th day after germination) and measuring several phenotypic indices (lateral root number, number of emerged lateral roots, lateral root length, lateral root elongation rate, and length of emerged lateral roots). The recited method of measuring phenotypic indices allowed Liu to quantitatively select which seedlings had different proportions of biomass tissues compared to the control.
However, Liu does not teach the feature of Claim 1, wherein the plant is a tomato plant.
D’Halluin et al. (herein referred to as D’Halluin) teaches a method of reducing the expression and/or activity of poly(ADP-ribose) polymerase (PARP) gene in the plant cells or plants, wherein the reduction in activity of the PARP genes increases abiotic stress tolerance in the plant cells or plants (pg. 16, paragraph 0214). D’Halluin further teaches that plants useful in the method of reducing the expression and/or activity of poly(ADP-ribose) polymerase (PARP) gene in the plant cells or plants which results in increased abiotic stress tolerance, include tomato plants (pg. 17, paragraph 0218).
It would have been obvious to one of ordinary skill in the art at the time of the effective filing date of the invention to perform the method of inhibiting PARP gene expression taught by Liu in the tomato plant taught by D’Halluin. Because of the teachings of D’Halluin, one of ordinary skill in the art would have been motivated to combine these two pieces of prior art because D’Halluin teaches that the method of reducing the expression and/or activity of poly(ADP-ribose) polymerase (PARP) gene in the plant cells or plants, wherein the reduction in activity of the PARP genes increases abiotic stress tolerance in the plant cells or plants taught by D’Halluin, can also be performed in Arabidopsis plant cells or plants (D’Halluin; pg. 17, paragraph 0218). Additionally, the reduction/inhibition of PARP2 gene activity taught by Liu performed in the tomato plant taught by D’Halluin, would reasonably be expected to produce a plant from the modified plant cell that has an increased proportion of non-edible biomass compared to the counterpart control plant, by virtue of the evidence from the instant specification (pgs. 17-18, paragraphs 0066-0068). The method of reducing/inhibiting of PARP2 gene activity taught by Liu performed in the tomato plant taught by D’Halluin, would be expected to disrupt expression of an endogenous PARP gene of the plant in the plant or plant cell, which increases the abiotic stress tolerance of the plant. The evidence of the specification shows that when PARP gene activity is disrupted in a tomato plant or plant cell, the proportion of non-edible biomass of the tomato plant is reduced when compared to a control plant. Therefore, by disrupting PARP2 gene expression using the method taught by Liu in the tomato plant taught by D’Halluin, and selecting plants for abiotic stress tolerance, a portion of the plants selected in this step would also have the desired trait of reduced non-edible biomass compared to a control plant. As such, and without evidence to the contrary, it is reasonable to conclude that the disruption of PARP2 gene expression taught by Liu, in the tomato taught by D’Halluin would inherently produce the recited properties claimed by Applicant. Applicant is reminded that the discovery of a new property does not render a claimed invention patentable, specifically, "[T]he discovery of a previously unappreciated property of a prior art composition, or of a scientific explanation for the prior art’s functioning, does not render the old composition patentably new to the discoverer" (See MPEP 2112). The rationale to support a conclusion that the claims would have been obvious is that all the claimed elements were known in the prior art, and one of ordinary skill could have combined these elements as claimed with no change to their respective functions. Thus the combination yielding predictable results would have been expected by a skilled artisan. Therefore, for all the reasons above, the claimed invention is prima facie obvious in view of the prior art.
Response to Arguments
Applicant’s Remarks on pg. 5 of the reply filed on 03/02/2026 are acknowledged but do not overcome these new rejections. In particular Applicant’s Remarks rely on the premise that the teachings of Liu do not provide a reasonable suggestion that reducing the expression of PARP2 in tomato plants can afford the plants with reduced non-edible biomass (Remarks, pg. 5).
This is not found persuasive. In response to Applicant’s arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). The obvious rationale of the rejection above relies on the combination of Liu and D’Halluin to teach the disruption of PARP2 expression in a tomato plant.
Applicant’s Remarks also rely on the premise that the teachings of D’Halluin do not provide a reasonable suggestion that disruption of a PARP gene could effect a reduction of non-edible biomass and the disclosure does not mention PARP 2 (Remarks, pg. 5).
This is not found persuasive. In response to Applicant’s arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). The obvious rationale of the rejection above relies on the combination of Liu and D’Halluin to teach the disruption of PARP2 expression in a tomato plant.
Additionally, Applicant does not provide any evidence or argument to the contrary to address the inherency argument presented in the new 35 U.S.C. 103 rejection above, wherein the evidence of the instant specification shows that when PARP2 gene activity is disrupted in a tomato plant or plant cell, the proportion of non-edible biomass of the tomato plant is reduced when compared to a control plant. Therefore, by disrupting PARP2 gene expression using the method taught by Liu in the tomato plant taught by D’Halluin, and selecting plants for abiotic stress tolerance, a portion of the plants selected in this step would also have the desired trait of reduced non-edible biomass compared to a control plant. As such, and without evidence to the contrary, it is reasonable to conclude that the disruption of PARP gene expression taught by Liu, in the tomato taught by D’Halluin would inherently produce the recited properties claimed by Applicant.
Therefore, for all the reasons above, the claimed invention remains prima facie obvious in view of the prior art.
Claims 5-7 and 9-10 are rejected under 35 U.S.C. 103 as being unpatentable over Liu et al. (Journal of integrative plant biology 59.7 (2017): 459-474; IDS Document) in view of D’Halluin et al. (US20190225974, published 07/25/2019), taken with evidence of the instant specification as applied to Claim 1 above, and further in view of Njuguna et al. (Afrika Focus 30.2 (2017): 66-76).
The teachings of Liu and D’Halluin as applied to Claim 1 are set forth previously herein and are incorporated by reference.
However, Liu and D’Halluin do not teach features of Claims 5-7 and 9-10, wherein the expression of the endogenous PARP gene is disrupted by introducing a nuclease into the plant, wherein the nuclease is an RNA-guided nuclease, a DNA-guided polypeptide, a zinc-finger nuclease (ZFN), a TALE endonuclease (TALEN), an engineered meganuclease, or a native meganuclease, wherein the RNA-guided nuclease is a Cas polypeptide, further wherein the Cas polypeptide is a Cas9 polypeptide or a Cpfl polypeptide, or wherein the DNA-guided polypeptide is Natronobacterium gregoryi Argonaute (NgAgo), Thermus thermophilics Argonaute (TtAgo), or Pyrococcusfuriosus Argonaute (PfAgo).
Regarding Claims 5-7 and 9, Njuguna et al. (herein referred to as Njuguna) teaches a metabolic engineering approach to alter the expression of PARP genes in maize (Zea mays) by means of CRISPR/Cas9 gene-editing (pg. 1, Abstract). Njuguna knocked out PARP gene expression and activity, using a Cas9 gene editing system (a nuclease, specifically a RNA-guided nuclease that is a Cas polypeptide, and more specifically a Ca9 polypeptide), by developing constructs that targeted a large deletion in the ZmPARP2 catalytic domain and a large deletion in the ZmPARP1 catalytic domain (pg. 70, lines 15-20). Njuguna teaches that a pair of guide RNAs (gRNA) and single gRNAs were cloned using the Golden Gate system into the pBUN411-Sp expression vector that carried a Cas9 nuclease protein, which was then re-cloned into a super virulent EHA101 Agrobacterium vector, and subsequently transformed into maize (pg. 70, lines 21-24). The plants that succeeded in having the guide-RNAs directing the Cas9 protein to the target sites showed homozygous deletions between 201 and 233 base pairs long in the ZmPARP2 construct and homozygous single nucleotide insertions or a homozygous base pair deletion in the ZmPARP1 construct (pg. 70, lines 24-32) Njuguna also teaches a method of producing a plant from the PARP knockout maize plants wherein the T0 parents were self-fertilized to produce a T1 progeny that were genotyped for the Cas9-induced mutation, wherein the T1 progeny was found to largely maintain the large deletion of the PARP2 catalytic domain (pg. 70, lines 31-33).
Instead of using chemical inhibition to disrupt the expression of endogenous PARP genes in a tomato plant, it would have been obvious to one skilled in the art, before the effective filing date of the claimed invention to modify the method of inhibiting PARP2 expression taught by Liu with the CRISPR-Cas9 gene editing system taught by Njuguna to “knock-out” the activity of endogenous PARP2 genes, resulting in inhibition of targeted PARP2 gene expression that would be heritably carried over into the progeny of the plant. Because of the teachings of Njuguna, a person of ordinary skill in the art would have been motivated to combine these three pieces of prior art to achieve the claimed invention because modifying the technique described in Liu et al. (in the tomato plant taught by D’Halluin) with the CRISPR-Cas9 gene editing system taught in Njuguna et al. would predictably result in a method of gene expression modification that would not require multiple applications of a chemical inhibitor to decrease the expression of a gene of interest and would allow altered expression and activity of a gene that would be heritable in a line of progeny. One of ordinary skill in the art would reasonably expect this modification to be successful, because the requisite components of the invention disclosed in the reference are present in the in instant application’s described method of gene editing (e.g., a CRISPR-Cas9 system, where Cas9-sgRNA genes were transformed via Agrobacterium-mediated transformation), functioning in the same capacity as the components detailed in the reference.
Regarding Claim 10, it is noted that is the position of this Office that any “knock-out” of the activity of endogenous PARP2 genes, resulting in inhibition of targeted PARP2 gene expression that would be heritably carried over into the progeny of the plant introduced using any guide system in any gene location that disrupts the activity of any PARP2 gene is rendered obvious by the combined teachings of teachings of Liu, D’Halluin, and Njuguna. Although Njuguna does not specifically teach disrupting the expression of a PARP2 gene using an editing system that comprises a DNA-guided polypeptide such as NgAgo, TtAgo, PfAgo, there is no way to distinguish a tomato plant comprising a knockout of PARP2 using an editing system that comprises a Cas9 polypeptide from a tomato plant comprising a knockout of PARP2 using an editing system that comprises any Argonaute polypeptide, for example. As such, it would have been obvious to one of ordinary skill in the art to knockout the PARP2 gene taught by Liu in the tomato plant taught by D’Halluin to disrupt the expression of PARP2 using an editing system as taught by Njuguna. The method of using a gene editing system to disrupt the expression of an endogenous gene is a technique that was routine in the art at the time the application was filed, as taught by the cited references and the state of the art in general.
Therefore, the invention is prima facie obvious.
Response to Arguments
Applicant’s Remarks on pg. 5 of the reply filed on 03/02/2026 are acknowledged but do not overcome these new rejections. In particular Applicant’s Remarks rely on the premise that Njuguna does not disclose tomato nor does it suggest that the disruption of PARP expression may affect non-edible biomass.
This is not found persuasive. In response to Applicant’s arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). The obvious rationale of the rejection above relies on the combination of Liu, D’Halluin, and Njuguna to teach the disruption of PARP2 expression in a tomato plant using a gene editing system. Regarding any of Applicants Remarks on the merits of the disclosure of Liu and D’Halluin as they related to Claims 5-7 and 9-10, please see the Response to Arguments section above, as they are applied to Claim 1.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/KELSEY L MCWILLIAMS/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663