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 .
Claim Status
Claims 1-20 are pending and being examined.
Claim Objections
Claim 9 is objected to because of the following informalities: It is suggested to recite the full names of the abbreviated terms viz., GRF4, IPT, GIF 1, WUS, STM and PLT5 in the claim.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(a)
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.
Enablement
Claims 3-4 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 enablement requirement. The claims contain subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Claim 3 recites, “… at least one gene for facilitating Agrobacterium delivery into nuclei of the plant cells.” The Applicant describes Agrobacterium infiltration (spec, p.42, line 30) and injecting the Agrobacterium solution into plant leaves (spec, p.43, line 5). The Applicant asserts that “overexpression VlrE2-INTERACTING PROTEIN (VIP 1) and the agrobacterium effector protein VirE2 facilitates a more efficient agrobacterium T-DNA delivery” (Spec, p.47, line 12-13).
The Applicant does not describe delivering the (whole) bacterium (Agrobacterium) being delivered into the plant cells, let alone into the “nuclei of the plant cells”, as recited in claim 3. The Applicant also does not provide any guidance to “facilitate Agrobacterium delivery into nuclei of the plant cells”.
Current status of the art asserts that agrobacterium never enters into the host plant cells. In fact, not even the whole Ti plasmid but only the T-DNA part of the Ti plasmid gets into the host plant cells and transported into the nucleus wherein the VirE2 and VIP1 proteins are involved in the process (Lacroix et al., Pathways of DNA Transfer to Plants from Agrobacterium tumefaciens and Related Bacterial Species, 2019, Annu. Rev. Phytopathol., 57:231–51; p.232, para 1, line 4-8; p.233, Fig.1), as also indicated by the Applicant.
Undue trial and error experimentations would be needed by a skilled artisan to facilitate Agrobacterium delivery into nuclei of the plant cells.
Based on breadth of the claims, lack of any working example, lack of guidance in the instant description or in prior art, the specification at the time of the application filed would not have taught one skilled in the art how to make and use the full scope of the claimed invention without performing undue experiments.
Claim Rejections - 35 USC § 112(b)
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.
Claims 1-20 are 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 1 recites the limitation "… the nucleic acid…" in line 2. There is insufficient antecedent basis for this limitation in the claim. There is no previous mention of any nucleic acid before “the nucleic acid”.
It is suggested to replace underlined “the” with “a”. All the claims depending from claim 1 inherit the indefiniteness.
Claim 11 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.
Regarding claim 11, the phrase “e.g., Yao” in line 2 renders the claim indefinite because it is unclear whether the limitation following the phrase are part of the claimed invention. See MPEP § 2173.05(d).
Claim 16 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 16 recites, “… maintaining said plant or part thereof in the dark to promote regeneration following said contacting and prior to exposing to light.” There is insufficient antecedent basis for this limitation in the claim.
Claim 16 depends from claim 1, which does not recite any (said) exposure to light. Further, the sequence(s) of events of light exposure in relation to “said contacting” and “maintaining the plants in the dark” are also unclear. It is not clear to the Examiner if-
the (said) plant or parts thereof always need(s) to be maintained in the dark (since germination), OR
the (said) plant or parts thereof need(s) to be maintained in light (exposed to light) before the “said contacting” and then kept in dark for certain period of time before exposing to light again.
Examiner interprets the claim as maintaining said plant or part thereof maintained in light, then the “said contacting” happened. Then the plant or parts thereof are kept in the dark to promote regeneration for certain period of time and then exposed to light.
Claim Rejections - 35 USC § 102(a)
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-2, 8-4 and 20 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Maren et al. (Genotype-independent plant transformation, 2022, Horticulture Research, 9: hac047) in evidence of Clough et al. (Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana, 1998, The Plant Journal, 16:735-743).
Maren et al. teaches several methods including the well-known CRISPR-Cas system using the genome editing agent Cas9 (as recited in claims 1 and 7-8) for producing genetically edited plants that do not require tissue culture while speeding up the breeding cycles (p.9, right column, para 2, line 9-13). The T0 plants used for genome editing would comprise any plant including non-transgenic plants, as recited in claims 1-2. Maren et al. describes several developmental regulators (DRs) that dramatically improve regeneration efficiency, shorten transformation (or genome editing) time, and make transformation of recalcitrant genotypes possible (abstract, line 5-6), as recited in claim 1. It teaches several vectors (reads on to “constructs”) encoding different developmental regulators including IPT (p.7, Fig. 3) which is induced by another DR, STM (p.8, right column, para 2, line 3-4), as recited in claim 9. Overexpression of STM results in (increased) regeneration of transgenic tobacco plants with a bushy phenotype (p.8, right column, para 2, line 11-13) while induced IPT (over-)expression improved transformation efficiency by 24.3 and 6.6 times in tobacco and lettuce (p.9, right column, para 1, line 2-4), respectively.
It is well-known, routine, and an inherent requirement/property to include cis-regulatory elements like promoter(s) and terminator(s) operatively linked to the polynucleotide sequence(s) (as recited in claims 10-11) to be expressed in any expression vector (or construct) including the ones described by Maren et al. (p.7, Fig. 3). It is also known the art to use a polynucleotide sequence encoding a selection agent, often antibiotic resistance, as taught by Maren et al. (p.3-4, table 1), (as recited in claim 12) to select positive transformants.
Maren et al. describes Agrobacterium-mediated transgene expression in multiple plant species (p.9, right column, para 2, line 1-3). Maren et al. teaches transforming and increasing transformation efficiency in several tree species including citrus (p.8, right column, para 2, line 5-8), as recited in claims 13-14 and 20.
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 5-7 and 18 are rejected under 35 U.S.C. 103 as being unpatentable over Maren et al. as applied to claims 1-2, 7-14, 18 and 20 above, and further in view of Trauterman et al. (US 2021/0139926 A1) and Ishii et al. (Proving that a genome-edited organism is not GMO, 2022, Trends in Biotechnology, Vol. 40:525-528; abstract).
Maren et al. describes a method of producing a genomically edited plant comprising using at least one nucleic acid construct under conditions which allow editing and regeneration, wherein the plant is non-transgenic at T0, wherein the nucleic acid construct(s) encode a genome editing agent (Cas9) and at least one developmental regulator, as discussed above.
Maren et al. teaches several proteins (e.g., PRC2) which are involved in gene silencing (as recited in claim 7) for specific genes (e.g., (AUX/IAA2, WOX5, and SHR) (p.5, left column, para 1, line 6-12). It also describes RNAi mediated silencing of CLV1 gene in Brassica napus leading to overexpression of another DR protein, WUS, which, in turn, increases transformation efficiency in plants (p.6, para 2, line .23-27).
Maren et al. describes Agrobacterium-mediated transgene expression in multiple plant species (p.9, right column, para 2, line 1-3). It is a well-known and routine process to immerse, i.e., dipping the plant in an agrobacterium solution with or without vacuum (as recites in claim 18), as evidenced by Clough et al. (abstract).
However, Maren et al. does not explicitly describe preventing T-DNA integration, directed against Polymerase θ (Polθ).
Trauterman et al. teaches knockout mutant plants lacking PolQ, which is also known as Polθ (p.1, para 0010, line 1-3), activity are incapable of integrating T-DNA molecules (as recited in claims 5-6) during Agrobacterium tumefaciens mediated plant transformation (p.2, para 0011, line 12-14). Trauterman et al. describes a method of editing a genome of a plant cell by introducing at least one oligonucleotide for silencing the POLQ gene using RNAi/shRNA (p.16, para 0223, line 1-4) in corn while a second polynucleotide sequence encodes a genome editing component (e.g., guide RNA) (p.2, para 0018; page 16, para 0223).
Before the effective filing date of the invention, it would have been obvious to a person with ordinary skill in the art to modify the genome editing method, as described by Maren et al., to include a polynucleotide sequence (e.g., RNAi or shRNA) to silence Polθ or PolQ, as described by Trauterman et al.
Before the effective filing date, the ordinarily skilled artisan would have been motivated to target and silence the host Polθ activity with a realistic goal to prevent or minimize integration of heterologous transgene(s) into the host genome and, thus, help the genome edited plants not to be considered as transgenic or GMO to avoid legal implications in many countries that ban transgenic plants but allow genome edited plants, as described by Ishii et al. (Proving that a genome-edited organism is not GMO, 2022, Trends in Biotechnology, Vol. 40:525-528; abstract).
Claims 15-16 are rejected under 35 U.S.C. 103 as being unpatentable over Maren et al. as applied to claims 1-2, 7-14, 18 and 20 above, and further in view of Dong et al. (HY5 functions as a systemic signal by integrating BRC1-dependent hormone signaling in tomato bud outgrowth, 2023, PNAS, 120:e2301879120), Dai et al. (Factors Affecting Plant Regeneration from Leaf Tissues of Buddleia Species, 2007, HortScience 42:1670–1673) and Xiao et al. (HY5: A Pivotal Regulator of Light-Dependent Development in Higher Plants, 2022, Front. Plant Sci., 12:800989).
Maren et al. describes a method of producing a genomically edited plant comprising using at least one nucleic acid construct under conditions which allow editing and regeneration, wherein the plant is non-transgenic at T0, wherein the nucleic acid construct(s) encode(s) a genome editing agent (Cas9) and at least one developmental regulator, as discussed above.
However, Maren et al. does not explicitly describe pre-exposure to blue light or maintaining the transformed explant in the dark.
Dong et al. describes that blue light exposure (besides red light) induces an increase in the abundance of HY5 in the leaves (p.2, left column, para 3, line 2-3), which is known to induce regeneration/organogenesis by promoting accumulation of plant phytohormone auxin in the oscillation zone, leading to lateral growth and branching, as taught by Xiao et al. (p.3, right column, para 1, line 2-4). It is also noted that the Applicant acknowledges that Dong et al. in the prior art teaches that blue light pre-exposure is beneficial for improved regeneration (spec, p.35, line 23-24; p.49, line 26-27).
Dai et al. teaches that dark treatment (as recited in claim 16) for 3 to 5 weeks (after plant transformation) dramatically increases shoot regeneration (abstract, line 6-7; p.1670, right column, para 3, line 5-7; p. 1671, Table 1; p.1672, left column, para 1, line 2-14).
Before the effective filing date of the invention, it would have been obvious to a person with ordinary skill in the art to modify the genome editing method, as described by Maren et al., to include a blue light pre-treatment of the explant (as taught by Dong et al.) and maintaining the transformed explant(s) under dark condition for 3-5 weeks, as described by Dai et al.
Before the effective filing date, the ordinary skill artisan would have been motivated to include a blue light pre-treatment of the explant before transformation and then maintaining the transformed explant(s) under dark condition for 3-5 weeks with a realistic objective to improve regeneration of the transformed plants, especially shoot organogenesis and regeneration.
Claims 17 and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Maren et al. as applied to claims 1-2, 7-14, 18 and 20 above, and further in view of Maher et al. (Plant gene editing through de novo induction of meristems, 2020, Nature Biotechnology, 38:84-89) and Yang et al. (Heritable transgene-free genome editing in plants by grafting of wild-type shoots to transgenic donor rootstocks, 2023, Nature Biotechnology, 41:958–967).
Maren et al. describes a method of producing a genomically edited plant comprising using at least one nucleic acid construct under conditions which allow editing and regeneration, wherein the plant is non-transgenic at T0, wherein the nucleic acid construct(s) encode a genome editing agent (Cas9) and at least one developmental regulator, as discussed above.
However, Maren et al. neither explicitly describe using an apical site of an explant including in a seedling nor grafting using the genomically edited plant.
Maher et al. describes that shoot apical meristem is the progenitor of all aboveground organs, including leaves and flowers (p.84, left column, para 1, line 2-4) in a plant. Meristem identity is dictated, in part, by developmental regulators (DRs) like SHOOT MERISTEMLESS (STM) and WUSCHEL (WUS) (p.84, left column, para 1, line 4-6). Maher et al. also describes that ectopic (over)expression of the cytokinin biosynthesis genes like isopentenyl transferase (ipt) is sufficient to induce shoot organogenesis (p.84, left column, para 1, last 3 lines). Co-delivering transgenes like WUS (e.g., WUS2) expedites production of transgenic plants (p.84, left column, para 2, line 5-6). Maher et al. describes a method of producing genome edited or transgenic shoots directly on soil-grown plants using the site of apical and axillary meristems (as recited in claim 17) in a plant (p. 87, Fig. 4) which can be a seedling.
Yang et al. describes a graft-mobile gene editing system that enables the production of transgene-free offspring in one generation without the need for transgene elimination, culture recovery and selection (abstract, line 9-11). It also describes grafting using Arabidopsis seedlings (as a rootstock) and B. rapa seedlings (as scions) (abstract; Fig.1), in tobacco plants (p.961, left column, para 2, line 2-5; Fig.3), to induce genome edited or transgenic trait(s) in the non-transgenic or non-genome edited scions.
Before the effective filing date of the invention, it would have been obvious to a person with ordinary skill in the art to modify the genome editing method, as described by Maren et al., to develop genome edited plants using an apical site of a plant including a seedling, as described by Maher et al., and using the genome edited seedling as a rootstock for grafting (as recited in claim 19), as described by Yang et al.
Before the effective filing date, an ordinarily skilled artisan would have been motivated to develop genome edited plants/seedlings using an apical site and then using the genome edited seedling as a rootstock for grafting to produce transgene-free offspring in one generation without the need for transgene elimination, culture recovery and selection, as taught by Yang et al.
Conclusion
No claim is allowed.
Communication
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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J.C.
/Jay Chatterjee/ Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/ Supervisory Patent Examiner, Art Units 1661 & 1662
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