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
The Office acknowledges the receipt of Applicant’s Request for Continued Examination filed October 2, 2025. Claims 1-2, 5, 12, 14, 18-20, 26-27, 37-40, 52-54, and 83-84, are pending. Claims 37-40, 52-54, and 84, are withdrawn. Claims 3-4, 6-11, 13, 15-17, 21-25, 28-36, 41-51, and 55-82, are cancelled. Claims 1-2, 5, 12, 14, 18-20, 26-27, and 83, are examined in the instant application.
All previous rejections not set forth below have been withdrawn.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Response to Amendments
2. Rejections withdrawn from action:
The rejection for claims 1-2, 5, 12, 14, 19-20, 26-27, and 83, under 103 is modified in view of amendment.
Priority
3. This application is claiming the benefit of Provisional Application No. 63/117,173 filed November 23, 2020.
Claim Rejections - 35 USC § 112 (a) (New Matter)
4. 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.
5. Claims 1-2, 5, 12, 14, 18-20, 26-27, and 83, 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 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.
Applicant is invited to point to the paragraph number in the originally-filed disclosure where support for “the root-forming competent plant cell and a node” can be found. Paragraphs [0132] and [0154] state that the root-forming competent cell can be a node explant. This is not the same as a root-forming competent plant cell and a node. Absent of support, Applicant is required to cancel the new matter in response to the instant Office action.
Claim Rejections - 35 USC § 112(b) (Indefinite)
6. Claims 1-2, 5, 12, 14, 18-20, 26-27, and 83, 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 is unclear because it is not known whether “the root-forming competent plant cell and a node” is one part comprising two components or two separate, disconnected parts. It is further unclear how a root-forming competent plant cell is distinguishable from a node, as a node is also a root-forming competent cell. Moreover, it is unclear whether the introducing step applies only to the root-forming competent plant cell, because the node is not recited in the “introducing” step.
In claim 2, it is unclear whether the “capable of modifying” phrase refers to the portion or the editing system.
In claim 19, it is unclear whether the “modified nucleic acid” refers to the polynucleotide of claim 1. Clam 1 does not recite a modified nucleic acid. It is unclear how a modified nucleic acid is distinguishable from an unmodified nucleic acid.
Correction is required.
Claim Rejections - 35 USC § 112(d)
7. The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
8. Claim 14 rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Claim 1 recites a node. Claim 14, which depends from claim 1, states that the root is obtained from a shoot tip of the explant. The shoot tip of claim 14 does not further limit the node of claim 1.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 103
9. Claims 1-2, 5, 12, 14, 19-20, 26-27, and 83, are rejected under 35 U.S.C. 103 as being unpatentable over Súkeníková et al. (“Agrobacterium tumefaciens-mediated transformation of blackberry (Rubus fruticosus L.)”, 2015, Plant Cell Tiss Organ Cult 120, 351–354. (U)), in view of Bahramnejad et al. (“A critical review on use of Agrobacterium rhizogenes and their associated binary vectors for plant transformation”, Biotechnology Advances, vol. 37, no. 7, 8 June 2019, p. 1-14, (previously cited)).
a. Regarding claims 1 and 83, Súkeníková teaches Agrobacterium-mediated transformation on berry crops specifically on blackberries (Rubus fruticosus), (see page 351 right column middle section). Súkeníková teaches “[i]n vitro cultures were initiated from single-node segments with dormant buds on shoot multiplication medium (SMMA) … Multiple shoot cultures were used as a source of explants for transformation experiments.”(i.e., root forming competent plant cell and a node), (see page 351 right column middle section). Súkeníková teaches on rooting shoot explants (i.e. root-forming competent plant cell and node), (see Abstract and page 353 left column middle section). Overall, Súkeníková teaches how Agrobacterium can be used on Rubus plants, specifically on explants comprising the root-forming competent plant cell and a node.
b. In regard to claims 1 and 83, Súkeníková does not specifically teach the limitation of working with A. rhizogenes.
c. Regarding claims 1 and 83, Bahramnejad teaches on A. rhizogenes and their associated binary vectors for plant transformation specifically disclose the strains and the relevant prior art in each field, (See Tables 1-7). Specifically, teaches on A. rhizogenes strain MSU440, K599, A4 and the different applications from, “Inducible foreign gene expression in plants using modified strains of Agrobacterium rhizogenes”, “Gene silencing in hairy roots”, and “Genome editing in hairy roots mediated”, (See Tables 1-7). Additionally, Bahramnejad, discloses that “Ri transformed roots are genetically stable”… “ as the transformed root presumably develops from a single transformed cell”, (See page 4 Section 1.3), which reads on a root-forming competent plant cell. Furthermore, Bahramnejad teaches how the “hairy root systems offers the advantage of rapid setup and high scalability” for transient gene expression besides stable expression into the “nuclear or plastid genome”, (See page 10, Section 7, 1st paragraph). Moreover, Bahramnejad discloses that “the amenability and adaptability of hairy roots systems to make possible studying previously intractable research areas” and “Agrobacterium rhizogenes mediated hairy root induction has been adopted and practiced widely as an indispensable part of plant tissue culture techniques”, (See Abstract and Conclusion). Lastly, teaches the advantages of A. rhizogenes over A. tumefaciens, (see image below).
Overall, Bahramnejad teaches working with “A. rhizogenes as transformation host and the vectors systems to be used according to their experimental needs and feasibility”, (see conclusion last sentence).
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d. Given Súkeníková‘s teaching of the limitation of working with Agrobacterium and Rubus plants, specifically with explants comprising root-forming competent plants cells and nodes, and Bahramnejad addresses the advantages of working with specifically A. rhizogenes strain and its advantages over A. tumefaciens, it would have been obvious to adapt Súkeníková’s method of transformation of Rubus using A. rhizogenes. Additionally, A. rhizogenes have been engineered to be more infective and having a wide host range including Rubus plants as taught by Bahramnejad. This would have been considered a motivation to combine along with the technical ability to optimize given that Bahramnejad disclose teaching of using A. rhizogenes for transformation over A. tumefaciens. Therefore, substituting A. tumefaciens for A. rhizogenes in Rubus transformation to introduce a polynucleotide in a plant, given the known advantages of using A. rhizogenes strains on Rubus plants, plant culturing techniques to produce roots, and successful transformation strategies disclosed in the prior art, it would have been an obvious and routine optimization for one skill in the art to substitute the A. tumefaciens transformation vector with the A. rhizogenes transformation vector with a reasonable expectation of success. It is the Office’s position, based on the teachings, is that a method to transform a Rubus plant with A. rhizogenes, is well-known and well characterized in the art make it a well-known option to transform a root-competent plant cell. Therefore, the Office’s position is that it would be obvious for those ordinary skill in the art to transform a root-forming competent plant cell from a Rubus plant with known transformation techniques using A. rhizogenes.
In regard to claim 2, and the teachings of Súkeníková mentioned above in claim 1.
With respect to claim 2, Súkeníková does not teach wherein a CRISPR system is introgressed into Rubus plants using A. rhizogenes transformation.
However, Bahramnejad teaches that A. rhizogenes systems can allow for editing systems, such as CRISPR and TALENs, (See Section 6 Table 6).
It would have been obvious to modify the teachings of Súkeníková with Bahramnejad as the substitution of known equivalent techniques has been shown to produce predictable results when identified by the prior art as substitutable techniques. See MPEP 2144.06 (II).
Regarding claim 5, and the teachings of Súkeníková mentioned above in claim 1. Additionally, Súkeníková teaches using binary plasmids, (see page 351 right column last paragraph).
With respect to claim 5, Súkeníková does not teach wherein a Ti and Ri plasmid binary vector system is introgressed into Rubus plants using A. rhizogenes transformation.
In regard to claim 5, However, Bahramnejad teaches that A. rhizogenes systems can allow for transformation using Ti and Ri plasmids, similar to known traditional Agrobacterium systems, (See page 4 Section 1.4 Table 2). Additionally, Bahramnejad discloses how T-DNAs are disarmed by removing non-essential genes via homologous recombination to produce binary vectors for transferring genes of interest into plants, (See pg. 4 Sec 1.4). Specifically, teaches how foreign genes can be expressed in binary vectors introduced via A. tumefaciens followed by A. rhizogenes for hairy root induction, or A. rhizogenes carrying both the Ri plasmid and the recombinant binary vector such as Ti plasmid with transgene insertion, (See page 4 section 1.4 and Table 2).
It would have been obvious to modify the teachings of Súkeníková with Bahramnejad as the T-DNA from a Ti/Ri plasmid is a known vehicle that has been shown to be very efficient in allowing transgene insertion when using plant transformation techniques.
Regarding claim 12, and the teachings of Súkeníková mentioned above in claim 1. Additionally, Súkeníková teaches inducing root formation of transformed Rubus explants in media (see page 352 left column middle paragraph).
With respect to claim 12, Súkeníková does not teach wherein roots are produced in the absence of exogenous plant growth substance.
However, Bahramnejad teaches how A. rhizogenes carry a Ri plasmid that induces root growth without exogenous plant growth substance because of its hairy root phenotypic trait, (See page 4 Section 1.3 left column).
It would have been obvious to modify the teachings of Súkeníková with Bahramnejad as the T-DNA from a Ri plasmid is a known to induce root formation and has been shown to be very efficient in serving as a visual marker without the need of antibiotic screening markers when using plant transformation techniques.
In regard to claim 14, and the teachings of Súkeníková mentioned above in claim 1. Additionally, Súkeníková teaches on generating roots from shoots, (see page 352 left column middle paragraph).
With respect to claim 19, and the teachings of Súkeníková mentioned above in claim 1. Additionally, Súkeníková does not teach wherein a Rubus plants using A. rhizogenes transformation was transgene-free.
However, Bahramnejad teaches that A. rhizogenes systems can allow for transient gene expression instead of genome integration, (See page 10, Section 7, 1st paragraph).
It would have been obvious to modify the teachings of Súkeníková with Bahramnejad as the substitution of known equivalent techniques has been shown to produce predictable results when identified by the prior art as substitutable techniques. See MPEP 2144.06 (II).
In regard to claim 20, Súkeníková teaches that “the rooted shoots were acclimatized by transferring them to pots filled with soil and covered with glass containers. Successfully acclimatized plants 10–15 cm high were used for molecular analyses.” (i.e. producing a plant from the root), (see page 352 left column middle paragraph). In order for a plant to be produce by a root it would need to produce shoots and all the developmental organs, not just the root.
Regarding claims 26-27, Súkeníková teaches using A. tumefaciens strains, LBA4404, C58 and AGL 0, on blackberry transformation, (see page 351 right column last paragraph).
With respect to claims 26-27, Súkeníková does not teach wherein a disarmed A. rhizogenes strain MSU440 is introgressed into Rubus plants using A. rhizogenes transformation, (See page 4 Section 1.4 Table 2).
However, Bahramnejad teaches disarmed A. rhizogenes strains MSU440, K599, A4 and the different applications, similar to known traditional Agrobacterium systems, (See Tables 1-7).
With respect to claims 26-27, it would have been obvious to modify the teachings of Súkeníková with Bahramnejad as the substitution of known equivalent techniques has been shown to produce predictable results when identified by the prior art as substitutable techniques. See MPEP 2144.06 (II).
Response to Applicant's Remarks:
10. To the extent that Applicant’s traversals may apply to the above rejection:
Firstly, Applicant argued that it is unpredictable and a lack of a reasonable expectation of success of A. rhizogenes to effectively infect Rubus. Secondly, the prior art does not teach transforming a “root-forming competent plant cell from a plant in the Rubus genus.” Thirdly, the prior does not teach “introducing a polynucleotide that encodes or comprises at least a portion of an editing system that is capable of modifying a target nucleic acid in the plant cell to provide a modified nucleic acid as recited in Claim 2”. (Remarks, 10/02/2025, pages 7-9). These arguments have been fully considered but not found persuasive.
MPEP says, "the Board stated that when there is motivation to solve a problem and there are a finite number of identified, predictable solutions, a person of ordinary skill has good reason to pursue the known options within his or her technical grasp. If this leads to anticipated success, it is likely the product not of innovation but of ordinary skill and common sense. KSR, 550 U.S. at 402-03, 82 USPQ2d at 1390” (MPEP, 2143/section E).
In the instant application, Applicant is reminded that this is a 103-obviousness rejection and not a 102-anticipation rejection. Regarding the first argument, that the prior art does not teach working with A. rhizogenes in Rubus plants. The combination of Súkeníková, which discloses transforming a Rubus plant, and Bahramnejad’s teachings on that “In nature, Agrobacterium rhizogenes infects multiple plants species”, (see page 1 introduction 1st paragraph left column), and the advantages over A. tumefaciens, (see above), make it obvious to substitute Súkeníková A. tumefaciens with A. rhizogenes. This is because there are only a limited number of these transformation tools available and the advantages over A. tumefaciens.
Súkeníková taught the fundamental method and components needed to achieve the desired transformation in Rubus plants. Bahramnejad, on the other hand, focused on the specific A. rhizogenes technique and advantages, which uses identical methods and techniques. Therefore, Súkeníková does not need to explicitly teach “working with A. rhizogenes in Rubus plants.” Since both Súkeníková and Bahramnejad identified a limited number of transformation solutions and Agrobacterium species, combining these reference makes the claimed invention obvious. Furthermore, as for “A. rhizogenes could, with any reasonable expectation of success, be used in a method of transforming a plant cell in the Rubus genus,” (see arguments page 7 last paragraph). Porter et al. (“Host range and implications of plant infection by Agrobacterium rhizogenes”, 1991, Critical Reviews in Plant Sciences, 10(4), 387–421(previously cited)), teaches on A. rhizogenes and Rubus. Specifically, Porter teaches on the wide host range that A. rhizogenes can inoculate, including Rubus plants, (see page 400-401). Additionally, Porter states that “A. rhizogenes, a number of strains have been engineered to be more infective or to carry more easily detected markers with which to confirm transformation.”, (see page 411 left column bottom paragraph), which clearly shows the expectation of success is high with regard to A. rhizogenes infecting Rubus.
Regarding the second argument, that the prior art does not teach using a root-forming plant cell. Applicant specification discloses that “A "root-forming competent cell" as used herein refers to a cell that has potential and/or capability to form a root upon being transformed. Exemplary root-forming competent cells include, but are not limited to, cambium layer cells in a plant stem. In some embodiments, the plant cell is a cell (e.g., a root-forming competent cell) in an explant such as, but not limited to, a shoot stem nodal explant, shoot tip explant, node explant, shoot node explant, leaf node explant, a shoot meristem explant, axillary shoot, an etiolated shoot, and/or any portion thereof.”, (See paragraph [130] in Applicants specification). Therefore, as long as the plant explant is able to form roots then it reads on the claim limitation. As it pertains to the prior art, both Súkeníková and Bahramnejad teach using either plant explants such as nodes or plant cells, respectively. Additionally, Bahramnejad specifically discloses that “Ri transformed roots are genetically stable”… “as the transformed root presumably develops from a single transformed cell”, (See page 4 Section 1.3), which reads on a root-forming competent plant cell.
Regarding the third argument, Applicant argues that “a polynucleotide that encodes or comprises at least a portion of an editing system that is capable of modifying a target nucleic acid in the plant cell to provide a modified nucleic acid as recited in Claim 2”. Bahramnejad, (See Section 6 Table 6), clearly teaches on genome editing systems that can improve transformation of these species.
At least for these reasons, the rejection is maintained.
Conclusion
11. No claims are allowed.
12. Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHRISTIAN JOSE ORDAZ whose telephone number is (703)756-1967. The examiner can normally be reached 8:30 am-5:00 pm.
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/C.J.O./Examiner, Art Unit 1663
/PHUONG T BUI/Primary Examiner, Art Unit 1663