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, 8-10, 12-25 and 27 are pending and examined. Claims 3-7, 11 and 26 have been cancelled.
Claim Rejections - 35 USC § 112
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.
Claims 1, 2, 8-10, 12-25 and 27 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while arguably enabling for A. tumefaciens strain EHA105 comprising the plasmid designated “pVIRD5specKO” and a method for introducing said plasmid into a banana plant cell, does not reasonably provide enablement for the bacterium as broadly claimed or its use in the genus of plant cells as claimed. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make/use the invention commensurate in scope with these claims.
In In re Wands (8 USPQ2d 1400 (CAFC 1988)), the CAFC considered the issue of enablement in molecular biology. The CAFC summarized eight factors to be considered in a determination of "undue experimentation". These factors include: (a) the quantity of experimentation; (b) the amount of guidance presented; (c) the presence or absence of working examples; (d) the nature of the invention; (e) the state of the prior art; (f) the predictability of the prior art; (g) the breadth of the claims; and (h) the relative skill in the art. The factors are analyzed in turn for the instant case as follows:
The instant claims are drawn broadly to any bacterium that transfers nucleotide sequences to a plant cell comprising a nucleotide sequence encoding vir genes wherein the expression of Vir5D is reduced or destroyed by insertion or mutation and deletion and a T-DNA sequence encoding at least a CRISPR-associated endonuclease.
Meanwhile, the specification teaches that virD5 was knocked out using a spectinomycin resistance cassette resulting in plasmid pVIRD5specKO and strain EHA105virD5 (p. 62). This strain was not impaired in transient expression of reporter genes in banana cells (see Example 2). This strain led to non-transgenic gene edited cells (p. 66; see also p. 68).
Here, the specification fails to teach or provide guidance for making and using the broad genus of bacterium as instantly claimed for transferring nucleic acids to any conceivable plant species, and further fails to provide working examples of bacterium that are capable of transferring nucleic acids into any plant type as broadly claimed.
This guidance is critical in light of the state of the art, which teaches that Agrobacterium can genetically transform various host cell including numerous dicot and some monocot angiosperm species and gymnosperms with the efficiency in some monocots including important crops lagging far behind (Hwang et al, 2017, The Arabidopsis Book, e0186, doi:10.1199/tab.0186, 1-31; p. 12, col. 2, last ¶; p. 20, ¶ 1).
Or see Hwang et al which teaches that one major limitation of Agrobacterium mediated transformation is that it cannot be efficiently used for many economically important plant species or elite varieties of particular species (2013, Plant Pathology, 62:1384-1397; see p. 1385, col. 1, ¶ 1).
Moreover, Gelvin teaches that the genetics of T-DNA integration is complex and that merely altering the levels of vir genes in Argobacterium strains does not predictably alter the ability of Agrobacterium to transfer and integration of T-DNA to plant cells, and that the chromosomal background of the Agrobacterium plays an important role in transformation efficiency (2003, Microbiology and molecular biology reviews, 67.1, 16-37; see p. 23, col. 2 ¶ 4 through p. 24, col. 1, ¶ 3).
Thus, in light of the breadth of the claims, the state of the art, and the fact that the specification only teaches a single strain of Agrobacterium that is modified for transforming a single plant species, the skilled artisan would resort to trial and error experimentation which is tantamount to excessive and impermissible undue experimentation.
Claims 1, 2, 8-10, 12-25 and 27 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.
Instant claims 1, 2, 8-10, 12-25 and 27 are drawn broadly to any bacterium that transfers nucleotide sequences to a plant cell comprising a nucleotide sequence encoding vir genes wherein the expression of Vir5D is reduced or destroyed by insertion or mutation and deletion and a T-DNA sequence encoding at least a CRISPR-associated endonuclease.
Meanwhile, the specification teaches that virD5 was knocked out using a spectinomycin resistance cassette resulting in plasmid pVIRD5specKO and strain EHA105virD5 (p. 62). This strain was not impaired in transient expression of reporter genes in banana cells (see Example 2). This strain led to non-transgenic gene edited cells (p. 66; see also p. 68).
The written description requirement may be satisfied through sufficient description of a representative number of species by disclosing relevant and identifying characteristics such as structural or other physical and/or chemical properties, by disclosing functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the invention as claimed. See Eli Lilly,119 F.3d at 1568, 43 USPQ2d at 1406.
Here, the specification fails to describe a representative number of species from the broad genus of bacterium as instantly claimed for transferring nucleic acids to any conceivable plant species, and further fails to provide working examples of bacterium that are capable of transferring nucleic acids into any plant type as broadly claimed.
This description is critical in light of the state of the art, which describes that Agrobacterium can genetically transform various host cell including numerous dicot and some monocot angiosperm species and gymnosperms with the efficiency in some monocots including important crops lagging far behind (Hwang et al, p. 12, col. 2, last ¶; p. 20, ¶ 1).
Or see Hwang et al which describes that one major limitation of Agrobacterium mediated transformation is that it cannot be efficiently used for many economically important plant species or elite varieties of particular species (p. 1385, col. 1, ¶ 1).
Moreover, Gelvin describes that the genetics of T-DNA integration is complex and that merely altering the levels of vir genes in Argobacterium strains does not predictably alter the ability of Agrobacterium to transfer and integration of T-DNA to plant cells, and that the chromosomal background of the Agrobacterium plays an important role in transformation efficiency (see p. 23, col. 2 ¶ 4 through p. 24, col. 1, ¶ 3).
Thus, in light of the breadth of the claims, the state of the art, and the fact that the specification only describes a single strain of Agrobacterium that is modified for transforming a single plant species, the skilled artisan would not be of the opinion that Applicant was in possession of the genus of bacterium or the genus of plant cells comprising said bacterium as broadly claimed.
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 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.
Claim(s) 1, 2, 8-10, 12, 14, 20, 22, 23, 25 and 27 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gelvin et al (Pub. No. US 2022/0112510 A1) in view of Hamada et al (Pub. No. US 2017/0137833 A1) and Wang et al (2018, New Phytologist, 217:726-738).
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.
Instant claims 1, 2, 8-10, 12, 14, 20, 22, 23, 25 and 27 are drawn broadly to Agrobacterium capable of transferring nucleotide sequences to a plant cell comprising a nucleotide sequence encoding vir genes wherein the expression of Vir5D is reduced or destroyed by insertion or mutation and deletion and a T-DNA sequence encoding at least a CRISPR-associated endonuclease, wherein the nucleotide sequence is a plasmid such as a Vir-helper plasmid, wherein the mutation results in a selectable trait, a method of generating a plant comprising contacting said plant with said bacterium, wherein the genome of the plant does not comprise any integrated T-DNA sequence, generating a plant therefrom.
Gelvin et al teach mutant Agrobacterium strains generated by mutagenesis targeting the VirD2 gene for transient expression of T-DNA encoded transgenes which do not stably integrate into the plant genome (see Abstract; see ¶ 0009). Gelvin et al teach that is advantageous to generate Agrobacterium strains that can effectively transfer T-DNA but not integrate to deliver genome engineering reagents (¶ 0008).
Gelvin et al specifically claim an Agrobacterium strain comprising a VirD2 mutant comprising insertions or deletions that would reduce or destroy expression and a method of using said strain for genome editing in a plant wherein said genome editing is CRISPR/Cas9 (see claims 1, 2, 13, 14, 16, 17 and 18).
Gelvin et al teach, in fact, that the use of this strain results in mutations to the PDS2 gene in N. benthamiana wherein the vector comprises a sgRNA scaffold to express sgRNAs and a Vir helper plasmid (see ¶ 0071 and 0072; see also Figure 10; see claim 14).
Thus, while Gelvin et al reasonably teach, suggest and provide motivation for a bacterium comprising nucleotide sequences encoding vir genes and T-DNA sequence encoding CRISPR to mutate at least one target sequence in a plant cell, the issue is whether one would mutated VirD5 as opposed to VirD2 as taught by Gelvin et al.
To this point, Hamada et al teach there is a need in the art for Agrobacterium with increased gene targeting efficiency by providing an Agrobacterium that has lost or reduced chromosomal insertion ability (see Abstract; see also ¶ 0014). Hamada et al teach, in fact, that mutated VirD5 has T-DNA nuclear translocation ability and lacks chromosomal insertion ability (e.g., see Example 1; see also Table 3).
Or see Wang et al which teaches confirms that VirD5is required for Agrobacterium infection, reduces stable transformation efficiency and does not affect transient transformation efficiency (see Abstract).
Therefore, prior to the effective filing date of the instant invention it would have been prima facie obvious to one of ordinary skill in the art to substitute using VirD2 with reduced activity as taught by Gelvin et al by instead using VirD5 with reduced activity, for example, as taught by Hamada et al and Wang et al because they are functionally equivalent to one another and thus merely a design choice.
It is noted that the equivalency must be recognized in the prior art, and cannot be based on applicant’s disclosure or the mere fact that the components at issue are functional or mechanical equivalents. In re Ruff, 256 F.2d 590, 118 USPQ 340 (CCPA 1958). See MPEP 2144.06
Factors that will support a conclusion that the prior art element is an equivalent are: (1) the prior art element performs the identical function specified in the claim in substantially the same way, and produces substantially the same results as the corresponding element disclosed in the specification. Kemco Sales, Inc. v. Control Papers Co. , 208 F.3d 1352, 54 USPQ2d 1308 (Fed. Cir. 2000); or (2) a person of ordinary skill in the art would have recognized the interchangeability of the element shown in the prior art for the corresponding element disclosed in the specification. Caterpillar Inc. v. Deere & Co. , 224 F.3d 1374, 56 USPQ2d 1305 (Fed. Cir. 2000); or (3) there are insubstantial differences between the prior art element and the corresponding element disclosed in the specification. IMS Technology, Inc. v. Haas Automation, Inc., 206 F.3d 1422, 1436, 54 USPQ2d 1129, 1138 (Fed. Cir. 2000). See MPEP 2183.
Here, VirD5 with reduced activity is considered functionally equivalent to VirD2 with reduced activity because (1) they each perform an identical function in so far as they result in transient expression of T-DNA encoded transgenes which do not stably integrate into the plant genome; (2) one would have recognized that this feature is useful for transient expression; and (3) there are insubstantial differences between the two as each result in transient expression of T-DNA encoded transgenes which do not stably integrate into the plant genome.
One would have a reasonable expectation of success in doing so because each Gelvin et al, Hamada et al and Wang et al demonstrate that reducing or destroying activity of vir genes leads to the successfully transient expression of nucleic acid sequences of interest, and in particular, effectively utilize the CRISPR/Cas9 system to induce mutations in a gene of interest.
Claim(s) 1, 13, 15-21 and 24 is/are rejected under 35 U.S.C. 103 as being unpatentable over Gelvin et al (Pub. No. US 2022/0112510 A1) and Hamada et al (Pub. No. US 2017/0137833 A1) and Wang et al (2018, New Phytologist, 217:726-738) and view of Hu et al (2021, Plant Biotechnology, 19:654-656) and Zhou et al (2020, J Integr Plant Biol., 62(3)269-286) and Rodrigues et al (2021, PNAS, 118:1-8).
Claims 1, 13, 15-21 and 24 are drawn broadly to Agrobacterium capable of transferring nucleotide sequences to a plant cell comprising a nucleotide sequence encoding vir genes wherein the expression of Vir5D is reduced or destroyed by insertion or mutation and deletion and a T-DNA sequence encoding at least a CRISPR-associated endonuclease, wherein the plant cell is banana plant cell and the target sequence is ACO1 or PPO2 OR ALS, wherein an additional target sequence is mutated and that at least first mutation results in a selectable trait, and a method of generating a plant comprising said bacterium and mutations in a first and second gene, wherein the first mutation results in a selectable trait.
Gelvin et al teach mutant Agrobacterium strains generated by mutagenesis targeting the VirD2 gene for transient expression of T-DNA encoded transgenes which do not stably integrate into the plant genome (see Abstract; see ¶ 0009). Gelvin et al teach that is advantageous to generate Agrobacterium strains that can effectively transfer T-DNA but not integrate to deliver genome engineering reagents (¶ 0008).
Gelvin et al specifically claim an Agrobacterium strain comprising a VirD2 mutant comprising insertions or deletions that would reduce or destroy expression and a method of using said strain for genome editing in a plant wherein said genome editing is CRISPR/Cas9 (see claims 1, 2, 13, 14, 16, 17 and 18).
Gelvin et al teach, in fact, that the use of this strain results in mutations to the PDS2 gene in N. benthamiana wherein the vector comprises a sgRNA scaffold to express sgRNAs and a Vir helper plasmid (see ¶ 0071 and 0072; see also Figure 10; see claim 14).
Hamada et al teach there is a need in the art for Agrobacterium with increased gene targeting efficiency by providing an Agrobacterium that has lost or reduced chromosomal insertion ability (see Abstract; see also ¶ 0014). Hamada et al teach, in fact, that mutated VirD5 has T-DNA nuclear translocation ability and lacks chromosomal insertion ability (e.g., see Example 1; see also Table 3).
Or see Wang et al which teaches confirms that VirD5is required for Agrobacterium infection, reduces stable transformation efficiency and does not affect transient transformation efficiency (see Abstract).
Thus, while Gelvin et al, Hamada et al and Wang et al reasonably teach, suggest and provide motivation with a reasonable expectation of success for making a bacterium comprising nucleotide sequences encoding vir genes and reduced or destroyed expression and/or activity of VirD5 and a T-DNA sequence encoding CRISPR to mutate at least one target sequence in a plant cell as noted supra, the issue is whether one would have used said bacterium to mutate a second target sequence such as ACO1 or ALS in a banana plant cell.
To this point and with respect to claim 13, Hu et al teaches CRISPR/Cas9 mediated genome editing of MaACO1 to promote the shelf life of banana fruit which is a main staple food in developing countries (see Abstract; see also p. 654, col. 1, ¶ 1; see also p. 656, col. 1, penultimate ¶).
Regarding claim 15, Zhou et al teaches the successful inhibition of ALS using CRISPR/Cas9 to create transgene-free herbicide resistant plants (p. 6, ¶ 2). Zhou et al also teaches that traditional breeding of banana is difficult but that CRISPR/Cas9 maybe successfully used to genetically improve one of the most economically important fruit crops.
Regarding claim 18, Rodriques et al teach that base editing was known in the art and uses either a nuclease-dead Cas9 or Cas9 nickase that can still bind the target DNA but does not induce double stranded breaks yet still results in mutations (p. 2, col. 1, ¶ 1 and 2).
Therefore, prior to the effective filing date of the instant invention it would have been prima facie obvious to one of ordinary skill in the art to apply the teachings of Gelvin et al and Hamada et al and Wang et al to introduce mutations into two target sequences such as the ACO1 and ALS gene, for example, as taught by Hu et al and Zhou et al, because to do so would result in a transgene free plant that is also herbicide tolerant with improved shelf life in one of the most economically important fruit crops which banana.
One would have a reasonable expectation of success in doing so because each of Hu et al and Zhou et al teach the successful use of CRISPR/Cas9 in banana.
One would have found it prima facie obvious to follow the teachings of Gelvin et al and Hamada et al and Wang et al by instead using a base editor as encompassed by instant claim 18 because to do so is a functional design choice that is not substantially different from using CRISPR/Cas9 that does not have a base editor.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JASON DEVEAU-ROSEN whose telephone number is (571)272-2828. The examiner can normally be reached 7:30am - 4pm.
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/JASON DEVEAU ROSEN/Primary Examiner, Art Unit 1662
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