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 1-2, 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 Claims 37-40, 52-54, and 84, are withdrawn.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All previous rejections not set forth below have been withdrawn.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
Rejections withdrawn from action:
The rejection for claims 1-2, 5, 12, 14, 18-20, 26-27, and 83, under 112(a) new matter is withdrawn in view of amendment.
The rejection for claims 1-2, 5, 12, 14, 18-20, 26-27, and 83, under 112(b) is withdrawn in view of amendment.
The rejection for claim 14, under 112(d) is withdrawn in view of amendment.
The rejection for claims 1-2, 5, 12, 14, 18-20, 26-27, and 83, under 103 is modified in view of amendment. Additionally, claim 18 was inadvertently omitted from the previous 103 rejection, as evidenced by the inclusion of claim 19, which depends from claim 18, in the rejection.
Priority
This application is claiming the benefit of Provisional Application No. 63/117,173 filed November 23, 2020.
Claim Rejections - 35 USC § 103
4. Claims 1-2, 5, 12, 14, 18-20, 26-27, and 83, REMAIN 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. (previously cited)), 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)).
Súkeníková teaches a method of transforming a root-forming competent plant cell in a Rubus fruticosus explant by contacting an Agrobacterium tumefaciens strain to the explant comprising the root-forming competent plant cell, wherein the explant is a single-node segment with dormant buds (same as Applicant’s node explant), introducing a polynucleotide from the A. tumefaciens strain into the root-forming competent plant cell to provide a transformed plant cell, thereby transforming the root-forming competent plant cell, wherein the polynucleotide is heterologous to the A. tumefaciens strain, and producing a root from the transformed plant cell (Title; Abstract; p. 351, second column, first full paragraph).
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 transformation using 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).
PNG
media_image1.png
367
520
media_image1.png
Greyscale
d. Given Súkeníková‘s teaching of transformation with Agrobacterium of 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 on an editing system capable of modifying a target sequence.
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 introduced 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).
In regard to claim 18, Bahramnejad teaches “the ability to induce hairy roots, a hallmark phenotype exhibited by host plants when infected by virulent A. rhizogenes” (pg. 2 col.2 last para.). The formation of hairy roots is an inherent property of an explant transformed by A. rhizogenes. Once the explant forms hairy roots, it would have been obvious to a person skilled in the art to transfer that rooted explant to a shoot-induction medium to generate a shoot from the root and produce a complete plant.
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:
5. To the extent that Applicant’s traversals may apply to the above rejection:
Firstly, Applicant argued that the prior art does not provide any “teaching, suggestion, or direction is provided in the combination of Sukenikova and Bahramnejad to use A. rhizogenes with a Rubus plant cell as claimed nor on how to do so.” Secondly, that the prior art utilizes “a "flag explant (petioles with basal part of the leaves) ... excised from in vitro plantlets” and not the claimed plant explants. (Remarks, 04/21/2026, page 8). 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 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).
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.
In response to applicant's second argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., the prior art utilizes “a "flag explant (petioles with basal part of the leaves) ... excised from in vitro plantlets” and not the claimed plant explants) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). In the instant case, the claim only requires that the Agrobacterium contact the explant (i.e. shoot node explant), which Súkeníková clearly teaches (see image below).
PNG
media_image2.png
231
388
media_image2.png
Greyscale
Conclusion
6. No claims are allowed.
7. 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.
Conclusion
8. No claims are allowed.
9. 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.
10. 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.
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, Amjad A Abraham can be reached on (571) 270-7058. 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.
/C.J.O./Examiner, Art Unit 1663
/PHUONG T BUI/ Primary Examiner, Art Unit 1663
Prosecution Insights