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 .
Status of the Claims
Claims 1-18 are pending.
Claims 3-6 and 12-18 are withdrawn from consideration as being drawn to a non-elected invention.
Claims 1-2 and 7-11 are examined herein.
Claims 1-2 and 7-11 are rejected.
Election/Restrictions
Applicant’s election without traverse of Group I, encompassing claims 1-2 and 7-11 (drawn to a guide nucleic acid that binds to a PIF gene with recited sequences and a method for editing a PIF gene with the same recited sequences) in the reply filed on 07/01/2026 is acknowledged.
Priority
Application No. 18/664,349 filed on 05/15/2024 is a continuation of 18/442,164 filed on 02/15/2024 and claims priority benefit to provisional application No. 63/485,263 filed on 02/16/2023.
Claim Interpretation
A bHLH domain (as recited in claim 9) is interpreted to be inherent to the structure of a PIF polypeptide.
Claim Objections
Claim 7 recites:
A method for editing a specific site in the genome of a plant cell, the method comprising introducing a gene editing system into the plant cell, the gene editing system comprising a CRISPR-Cas effector protein in association with a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to an endogenous Phytochrome Interacting Factor(PIF) gene and the CRISPR-Cas effector protein cleaving, in a site-specific manner, a target site within the endogenous PIF gene in the plant cell, the endogenous PIF gene:
(a) comprising a sequence having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:69, 70, 72, 73, 75, 76, 78, 79, 81, or 82;
(b) comprising a region having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:84-87, 88-91, 92-95, 96-108 or 109-112;
(c) encoding a polypeptide comprising a sequence having at least 80% sequence identity to any one of the amino acid sequences of SEQ ID NOs:71, 74, 77, 80,or 83; and/or
(d) encoding a region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO:113, thereby generating an edit in the endogenous PIF gene of the plant cell.
As written, the limitation in part (d) that reads “thereby generating an edit in the endogenous PIF gene of the plant cell” appears to only be required if the endogenous gene encoding the PIF transcription factor encodes a region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO:113 (i.e. part (d)). However, it is reasonably interpreted that this limitation is meant to be applied if the endogenous PIF gene comprises any of (a) through (d).
To improve clarity, Applicant should amend the claim so that “thereby generating an edit in the endogenous PIF gene of the plant cell” is a wherein clause. With the suggested amendment, the claim would read:
A method for editing a specific site in the genome of a plant cell, the method comprising introducing a gene editing system into the plant cell, the gene editing system comprising a CRISPR-Cas effector protein in association with a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to an endogenous Phytochrome Interacting Factor(PIF) gene and the CRISPR-Cas effector protein cleaving, in a site-specific manner, a target site within the endogenous PIF gene in the plant cell, the endogenous PIF gene:
(a) comprising a sequence having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:69, 70, 72, 73, 75, 76, 78, 79, 81, or 82;
(b) comprising a region having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:84-87, 88-91, 92-95, 96-108 or 109-112;
(c) encoding a polypeptide comprising a sequence having at least 80% sequence identity to any one of the amino acid sequences of SEQ ID NOs:71, 74, 77, 80,or 83; and/or
(d) encoding a region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO:113;
thereby generating an edit in the endogenous PIF gene of the plant cell;
wherein the gene editing system thereby generates an edit in the endogenous PIF gene of the plant cell.
Applicant should amend the claim as described above or in another manner of Applicant’s choosing that improves clarity of the claim limitations.
Improper Markush Grouping
Claims 1-2 and 7-8 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of:
SEQ ID NOs: 69, 70, 72, 73, 75, 76, 78, 79, 81, or 82 (claims 1 and 7)
SEQ ID NOs: 84-87, 88-91, 92-95, 96-108 or 109-112 (claims 1 and 7)
SEQ ID NOs: 71, 74, 77, 80, or 83 (claims 1 and 7)
SEQ ID NOs: 114-119 (claims 2 and 8)
is improper because the alternatives defined by the Markush grouping do
not share both a single structural similarity and a common use for the
following reasons:
Regarding group i), the sequences are either genomic DNA or cDNA of different
corn PIF genes (spec, p. 7-9 and 106-109) that do not share a single structural similarity. An ABSS sequence search of SEQ ID NO: 78 (first 15,000 basepairs; see SEQ ID NO: 78 search results in copending app no. 18, 442,164 for full length search of the identical sequence) which corresponds to the corn PIF gene Zm00001d033267 returned results having as low as 5% sequence identity to SEQ ID NO: 78. From the instant application, only edited alleles of the Zm00001d033267 appeared in the results and had high sequence identity to SEQ ID NO: 78. Additionally, SEQ ID NO: 79 appeared in the results and had only 6.2% sequence identity to SEQ ID NO: 78. All other sequences did not appear in the results, meaning they had below 5% sequence identity to instant SEQ ID NO: 78. That is, none of the other sequences in group i) listed above are structurally similar to SEQ ID NO: 78. Hence, the included species of the claimed invention, i.e. the other PIF genes, represent structurally distinct genes and do not share both a substantial structural feature and a common function that flows from the substantial structural feature.
Regarding group ii), the sequences are DNA regions specific to distinct PIF
genes described above. An ABSS sequence search of SEQ ID NO: 108
returned results having as low as 41% sequence identity to SEQ ID NO: 108. From the instant application, only SEQ ID NOs: 96-99 and 105-108 appeared in the results and had high sequence identity to SEQ ID NO: 108. All other sequences did not appear in the results or did not have high sequence identity, meaning none of the other sequences in group ii) listed above are structurally similar to SEQ ID NO: 108. Hence, the included species of the claimed invention, i.e. the other regions of PIF genes, represent structurally distinct genes and do not share both a substantial structural feature and a common function that flows from the substantial structural feature.
Regarding group iii), the sequences are amino acid sequence encoded by
different PIF genes described above. An ABSS sequence search of SEQ ID
NO: 80 returned results having as low as 19% sequence identity to SEQ ID NO: 80. From grouping iii), only SEQ ID NOs: 77 and 83 appeared in the results and had low sequence identity of about 22% to SEQ ID NO: 80. All other sequences in group iii) did not appear in the results, thus has less than 19% sequence identity to SEQ ID NO: 80. That is, none of the other sequences in group iii) listed above are structurally similar to SEQ ID NO: 80. Hence, the included species of the claimed invention, i.e. the other PIF polypeptides, are structurally distinct polypeptides and do not share both a substantial structural feature and a common function that flows from the substantial structural feature.
Regarding group iv) the sequences are nucleotide sequences of the PIF genes that the invention uses to produce complimentary spacers of guideRNAs. An ABSS sequence search of SEQ ID NO: 114 returned results having as low as 77.4% sequence identity to SEQ ID NO: 114. None of the sequences from the group (SEQ ID NOs: 115-119) appeared in the results. That is, none of the other sequences in group iv) listed above are structurally similar to SEQ ID NO: 114. Hence, the included species of the claimed invention, i.e. the other nucleotide sequence of the genes/ spacer sequences, are structurally distinct and do not share both a substantial structural feature and a common function that flows from the substantial structural feature.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
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.
Claims 1-2 and 7-11 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.
Claims 1-2 and 7-11 are broadly drawn to a guide nucleic acid or a method of editing a site in the genomic DNA of a plant cell comprising a guide nucleic acid that binds to a PIF gene, wherein the PIF transcription gene comprises
(a) a sequence having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:69, 70, 72, 73, 75, 76, 78, 79, 81, or 82;
(b) comprising a region having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:84-87, 88-91, 92-95, 96-108 or 109-112;
(c) encoding a polypeptide comprising a sequence having at least 80% sequence identity to any one of the amino acid sequences of SEQ ID NOs:71, 74, 77, 80, or 83; and/or
(d) encoding a region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO:113.
The corresponding sequences of SEQ ID NOs: 78, 108, 80, and 113 are used below as examples in this rejection, although the rejection applies to all sequences for the same reasons.
Applicant describes in working examples using CRISPR/Cas guide nucleic acids to target a region of a PIF gene that is 100% identical to the sequences, e.g. SEQ ID NO: 108 in corn (spec., p. 107-108). The gene comprising this region is 100% identical to SEQ ID NO: 78.
Applicant does not teach any DNA or amino acid sequence that is as low as 80% sequence identity to the PIF nucleotide and polypeptide sequences that is still able to confer the function of a PIF gene/polypeptide.
The prior art fails to remedy this deficiency. Regarding SEQ ID NO: 78, which is a PIF gene identified as Zm00001d033267 in the specification (p. 106), there appears to be a dearth of description of the nucleotide sequences that would be expected to have the function of a PIF gene at as low as 80% sequence identity. A review of sequences that share identity with elected SEQ ID NO: 78 reveals a large identity gap between two sequential search results of SEQ ID NO: 78 (see file wrapper 20260219_110106_us-18-442-164-78.align45.rnpbm in co-pending application no. 18/442,164 for full length search of the identical sequence (SEQ ID NO: 78)). Both search results are from the instant application, the first having 99.9% sequence identity and the next most similar having 76.1% sequence identity.
SEQ ID NO: 108 is a region of SEQ ID NO: 78 and the prior art fails to remedy the deficiency for the same reason.
Regarding SEQ ID NO: 80, which is a PIF polypeptide sequence encoded by SEQ ID NO: 78 according to the spec (p. 8), there appears to be a dearth of description of the polypeptide sequences that would be expected to have the function of a PIF protein at as low as 80% sequence identity. A review of sequences that share identity with elected SEQ ID NO: 80 reveals a large identity gap between sequential search results of SEQ ID NO: 80 (see file wrapper 20260429_152208_us-18-664-349-80.rapbm), where the sequences also fail to describe the sequences as PIF polypeptides. Specifically, no sequences between result 1 and result 6 describe the polypeptide as being a PIF polypeptide. Additionally, a large identity gap exists between result 6 which has 91.4% sequence identity and result 7 which has 67% sequence identity to SEQ ID NO: 80.
SEQ ID NO: 113 is a region of SEQ ID NO: 80 and the prior art fails to remedy the deficiency for the same reason.
Additionally, Sharma (published after the effective filing date) provides a review of PIFs and describes their function as regulated by various transcription factors that function upstream of them, and describes various proteins heterodimerize with PIFs at various levels and regulate downstream target genes (p. 2, ¶2). Sharma further notes variation has been seen in APB motif, bHLH domain, and length of PIFs in some of the plants discussed above which might be responsible for their diverse functions, and this is a potential area of research to understand how such variations affect the function of PIFs (p. 2, ¶11). That is, Sharma describes how structural variation affects function of PIFs is not understood. Because the full scope of how the structure of PIFs affects their function remains unknown, Applicant could not have described the full genus of the claimed sequences at 80% sequence identity that retain the function of a PIF gene/ protein.
The instant specification does not provide enough sequences to describe the genus of PIF sequences at as low as 80% sequence identity by virtue of example. There also is a dearth of description in the prior art of the sequences that would be expected to have the required function of a PIF gene or polypeptide, and given the complex protein interactions that regulate PIF function and because the structure-function relationship of PIF proteins in not fully understood, a skilled artisan would not have recognized the Applicant to be in possession of the claimed PIF sequences at as little as 80% sequence identity that retain the function of PIF genes/proteins. As such, the structural features that distinguish nucleotides or polypeptides with as low as 80% identity to SEQ ID NOs: 78, 108, 80, or 113 that are PIF sequences from other nucleotides or polypeptides with 80% identity to SEQ ID NOs: 78, 108, 80, or 113 are not described in the specification nor the prior art. The specification fails to provide an adequate written description to support the sequences recited in claims 1-2 and 7-8 with 80% identity that are able to effectively confer the functions of a PIF gene or protein. The limited examples of 100% identity to the recited sequences do not describe the claimed genus by virtue of example. Therefore, one of ordinary skill in the art would not have recognized the Applicant to be in possession of the claimed invention at the time the application was filed.
Claim Rejections - 35 USC § 102
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, 7, and 9-11 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Wu (Wu, G., Zhao, Y., Shen, R., Wang, B., Xie, Y., Ma, X., ... & Wang, H. (2019). Characterization of maize phytochrome-interacting factors in light signaling and photomorphogenesis. Plant physiology, 181(2), 789-803.) and as evidenced by maizeGDB GRMZM2G165042 (maizeGDB, GRMZM2G165042 (bhlh43 - bHLH-transcription factor 43), B73 RefGen_v3, published online and last updated 07/23/2017).
Claim 1 is drawn to a guide nucleic acid that binds to a target site within an endogenous gene encoding a Phytochrome Interacting Factor (PIF) transcription factor, the endogenous gene:
comprising a sequence having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:69, 70, 72, 73, 75, 76, 78, 79, 81, or 82;
encoding a polypeptide comprising a sequence having at least 80% sequence identity to any one of the amino acid sequences of SEQ ID NOs: 71,74, 77, 80, or 83;
comprising a nucleotide sequence having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs: 84-87, 88-91, 92-95, 96-108 or 109-112;
and/or encoding an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 113.
Claim 7 is drawn to a method for editing a specific site in the genome of a plant cell, the method comprising introducing a gene editing system into the plant cell, the gene editing system comprising a CRISPR-Cas effector protein in association with a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to an endogenous Phytochrome Interacting Factor(PIF) gene and the CRISPR-Cas effector protein cleaving, in a site-specific manner, a target site within the endogenous PIF gene in the plant cell, the endogenous PIF gene:
(a) comprising a sequence having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:69, 70, 72, 73, 75, 76, 78, 79, 81, or 82;
(b) comprising a region having at least 80% sequence identity to any one of the nucleotide sequences of SEQ ID NOs:84-87, 88-91, 92-95, 96-108 or 109-112;
(c) encoding a polypeptide comprising a sequence having at least 80% sequence identity to any one of the amino acid sequences of SEQ ID NOs:71, 74, 77, 80,or 83; and/or
(d) encoding a region having at least 80% sequence identity to the amino acid sequence of SEQ ID NO:113, thereby generating an edit in the endogenous PIF gene of the plant cell.
Claim 9 is drawn to the method of claim 7, wherein the edit results in a mutation in the basic Helix Loop Helix (bHLH) domain of the PIF polypeptide encoded by the endogenous PIF gene.
Claim 10 is drawn to the method of claim 7, further comprising regenerating a plant from the plant cell comprising the edit in the endogenous PIF gene to produce a plant comprising the edit in its endogenous PIF gene.
Claim 11 is drawn to the method of claim 10, wherein the plant comprising the edit in its endogenous PIF gene has an attenuated Shade Avoidance Response compared to a control plant that is devoid of the edit.
Regarding claim 1, Wu discloses generating ZmPIF knockout transgenic lines using sgRNA/ CRISPR mediated targeted deletions (p. 801, section titled Generation and Mutation Analysis of CRISPR/Cas9 Knockout Lines in Maize, ¶1). Wu discloses the Zmpif4.1 and Zmpif4.2 double knockout mutants (p. 796, section titled Knockout of ZmPIFs by CRISPR/Cas9 Causes Short Mesocotyls in Maize under Darkness) comprised mutations to sequences of Zmpif4.1 (GRMZM5G86596) and Zmpif4.2 (GRMZM2G165042). GRMZM2G165042 has an amino acid sequence that is 99% identical to instant SEQ ID NO: 80 as evidenced by maizeGDB (see attached reference and alignment below). Therefore, the instantly claimed gRNA that binds to a target site within an endogenous gene encoding a Phytochrome Interacting Factor (PIF) transcription factor, wherein the endogenous gene encodes a polypeptide comprising a sequence that has at least 80% sequence identity to SEQ ID NO: 80 is anticipated by the disclosure of Wu.
Regarding claim 7, Wu discloses transforming maize cells with a CRISPR/Cas9 gene-editing system comprising dual sgRNAs that target endogenous ZmPIF genes for targeted deletion and confirms editing success (p. 801, section titled Generation and Mutation Analysis of CRISPR/Cas9 Knockout Lines in Maize, ¶1, Supplementary data Fig. S12). Wu discloses the Zmpif4.1 and Zmpif4.2 double knockout mutants (p. 796, section titled Knockout of ZmPIFs by CRISPR/Cas9 Causes Short Mesocotyls in Maize under Darkness) comprised mutations to sequences of Zmpif4.1 (GRMZM5G86596) and Zmpif4.2 (GRMZM2G165042). GRMZM2G165042 has an amino acid sequence that is 99% identical to instant SEQ ID NO: 80 as evidenced by maizeGDB (see attached reference and alignment below). Therefore, the instantly claimed method of introducing a gene editing system into the plant cell, the gene editing system comprising a CRISPR-Cas effector protein in association with a guide nucleic acid, wherein the guide nucleic acid comprises a spacer sequence that binds to an endogenous Phytochrome Interacting Factor(PIF) gene and the CRISPR-Cas effector protein cleaving, in a site-specific manner, a target site within the endogenous PIF gene in the plant cell, the endogenous PIF gene having at least 80% sequence identity to SEQ ID NO: 80 is anticipated by Wu.
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Regarding claim 9, Wu discloses a 322 bp deletion and a single nucleotide deletion (Supplementary Fig. 12, ZmPIF4.2-KO, MT sequence, single nucleotide deletion is represented by a single red dash). Using the cDNA sequence of GRMZM2G165042 from maize GDB (beginning at the start codon) which is the sequence in the maize knockout line of Zmpif4s#65 (ZmPIF4.2-KO, MT in Supplementary Fig. 12), and deleting the exact 322 basepairs and the 1 nucleotide as disclosed by Wu in the Supplementary Figure, the resulting nucleotide sequence translates to a polypeptide sequence with multiple early stop codons as shown directly below. Additionally, the bHLH domain (which is approximately positions 333-394 of SEQ ID NO: 80) also has mutations induced by the edit disclosed by Wu. For example, “EKMRALQELI” is at positions 351-360 within the bHLH domain of SEQ ID NO: 80/ GRMZM2G165042. However, the mutation caused by the gene editing as disclosed by Wu alters this polypeptide sequence, and is evidenced by the sequence below lacking the “EKMRALQELI” sequence. Thus, Wu discloses wherein the gene edit results in a mutation in the bHLH domain of the PIF polypeptide encoded by the endogenous PIF gene. Asterisks represent stop codons.
MNQFVPDWSNTSRAAGTSQSQQRTTGAAAAGRARCRRGTRAT*CRLPSRRPRPAPGSRRR
*AWPTAATMPEGTCRASSVRGRRPARRRC*ARSGPASAGATRSWCSARRARRGARPRPAP
EPPAATGPGPPRCRRRWAARTRTPWAAAGATRRPRRGGPTTAASAPPPPQPQPPPRSPRA
PATGAASASGSTPRTRRVPARTRSRGPPRCWRASRRRR*RRRGGAAPPKCTTCRSGGDET
G*TRR*EPCVALSTSLSLSSQHSSSSRL*RVEEARSSHRGLQQPSALSIEAALCSLLSAL
PR*AGFQASSAECEL*LNTK*LAASHRSMVVLCWPSER*TSSSLIGATWETPPGRSAKKT
TSSSCYGATAMSSCRARATGRCRRGRRRRRQWRLHQPPRPCRRKTRAACGSPSRWPTRWT
RTSSRSSSARHRRRHRRRRMRRRRPLVVEPAPKPAASRAAGTSQSQQRTTGAAAAGRARC
RRGTRAT*CRLPSRRPRPAPGSRRR*AWPTAATMPEGTCRASSVRGRRPARRRC*ARSGP
ASAGATRSWCSARRARRGARPRPAPEPPAATGPGPPRCRRRWAARTRTPWAAAGATRRPR
RGGPTTAASAPPPPQPQPPPRSPRAPATGAASASGSTPRTRRVPARTRSRGPPRCWRASR
RRR*RRRGGAAPPKCTTCRSGGDETG*TRR*EPCKSSYLTATRRTRRQCLTRRSSTSSRC
SCKCR*CGWAAPASRRRRR*CSPAYTSTCLGWASGWARQRRRRCRPCRGCRSWPRNRWCP
ARR*AWARCRPTGATCPRWASRSRTGTTSASTTCSRRRRHRRSRA*ATTRRRWGRRRRPC
SRLQSFTTCRGPAAASCPPAPHPECCSRRARKAEGQVRCHALRPSHPPLQFLGYKWEHYD
Regarding claim 10, Wu discloses constructs were introduced into the strain EHA105 and transformed into the immature embryo of a recipient maize inbred line ZC01 using the conventional A. tumefaciens-mediated approach (p. 801, section titled Generation and Mutation Analysis of CRISPR/Cas9 Knockout Lines in Maize, ¶1). Wu then discloses analyzing the CRISPR-mediated knockout mutant plants for shade avoidance response (p. 798, Fig. 8 and right column). Because a knockout plant was tested, it is reasonably interpreted that Wu must also disclose regenerating a plant from the plant cell comprising the edit in the endogenous PIF gene to produce a plant comprising the edit in its endogenous PIF gene.
Regarding claim 11, Wu discloses the pif4 double knockout lines had reduced shade avoidance response compared to wild-type plants (p. 797, ¶2, and Fig. 8 C-D).
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.
Claims 2 and 8 are rejected under 35 U.S.C. 103 as being unpatentable over Wu as applied to claims 1 and 7 above, and further in view of Li (Li, J., Li, Y., & Ma, L. (2019). CRISPR/Cas9‐based genome editing and its applications for functional genomic analyses in plants. Small Methods, 3(3), 1800473.) and GenBank accession No. DAA50359 (GenBank accession No. DAA50359, putative HLH DNA-binding domain superfamily protein, published online 10/24/2013).
Claim 2 is drawn to the guide nucleic acid of claim 1, wherein the guide nucleic acid comprises a spacer having the nucleotide sequence of any one of SEQ ID NOs:114-119.
Claim 8 is drawn to the method of claim 7, wherein the spacer sequence comprises a nucleotide sequence of any one of SEQ ID NOs:114-119.
Regarding claims 2 and 8, Wu teaches the limitations of claims 1 and 7 as set forth in the previous anticipation rejection. The teachings of Wu as they are applied to claims 1 and 7 are set forth previously herein and are incorporated by reference. Specifically, Wu teaches generating PIF4 double knockout in maize plants (p. 796) that display reduced shade avoidance response as compared to WT control plants (abstract, p. 797 ¶2, Fig. 8, C and D). One of the PIF4 sequences, GRMZM2G165042 which encodes a polypeptide sequence that is over 99% identical to instant SEQ ID NO: 80, is knocked out by inducing two mutations: one being a 322 bp deletion and the other a single nucleotide deletion (Supplementary Fig. 12, Zmpif4s#65, ZmPIF4.2-KO, MT sequence) in the sequence of GRMZM2G165042 in maize plants (p. 796 and 801). Additionally, Wu teaches PIFs are bHLH transctiption factors with highly conserved bHLH domains (p. 790 ¶2, p. 791 entire page, and p. 792 ¶2).
However, Wu does not explicitly teach the limitations of claims 2 and 8 as recited above.
It is noted that the spacer sequence of SEQ ID NO: 119 is the reverse complement of (i.e. would bind at) positions 1005-1027 in SEQ ID NO: 79, which corresponds to approximately positions 315-323 of SEQ ID NO: 80.
In analogous art, Li teaches CRISPR/Cas9 has been widely used to create various mutants and become a routine tool in plant laboratories around the world (p. 8) including knockouts and fragment deletions (Fig. 7). Furthermore, the polypeptide sequence of GRMZM2G165042 is linked in the maizeGDB database as GenBank accession No. DAA50359 which identifies amino acid residues 333 to 394 as the bHLH domain.
Because Wu teaches knockout of a protein that has 99% sequence identity to instant SEQ ID NO: 80 results in reduce shade avoidance response, and methods of knocking out and deleting fragments from genes/ proteins are routine and known in the art, it would be prima facie obvious to design a spacer of a gRNA to target any sequence of the known gene/protein to knockout the gene for the purpose of reducing shade avoidance response and in turn increasing yield as taught by Wu (abstract). This is especially true for the known amino acid residues that make up the bHLH domain as identified by GenBank Accession No. DAA50359. Therefore, it would be prima facie obvious to design a guide RNA wherein the spacer binds near the known, conserved bHLH domain, thus arriving at instantly claimed SEQ ID NO: 119 as the spacer sequence, for the purpose of inducing a mutation in the bHLH domain to knock out the function of the bHLH transcription factor (PIF4) and reduce shade avoidance response/ increase yield as taught by Wu (abstract). Additionally, one of ordinary skill in the art would have a reasonable expectation of success because generating knockouts via various methods is well understood and routine in the art, and one of ordinary skill in the art would expect that designing the spacer upstream and nearby the bHLH domain could reasonably be expected to create mutations within the bHLH domain and knockout the gene and encoded protein.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 7 and 9-11 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 55, 64, and 71 of copending Application No. 18442164 (reference application).
Although the claims at issue are not identical, they are not patentably distinct from each other.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 8 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 55, 64, and 71 of copending Application No. 18442164 (reference application) in view of Wu (Wu, G., Zhao, Y., Shen, R., Wang, B., Xie, Y., Ma, X., ... & Wang, H. (2019). Characterization of maize phytochrome-interacting factors in light signaling and photomorphogenesis. Plant physiology, 181(2), 789-803.), Li (Li, J., Li, Y., & Ma, L. (2019). CRISPR/Cas9‐based genome editing and its applications for functional genomic analyses in plants. Small Methods, 3(3), 1800473.) and GenBank accession No. DAA50359 (GenBank accession No. DAA50359, putative HLH DNA-binding domain superfamily protein, published online 10/24/2013).
The copending application does not explicitly claim wherein the spacer sequence comprises a nucleotide sequence of any one of SEQ ID NO: 114-119.
Wu teaches a nearly identical method to that instantly claimed, including generating PIF4 double knockout in maize plants (p. 796) that display reduced shade avoidance response as compared to WT control plants (abstract, p. 797 ¶2, Fig. 8, C and D). One of the PIF4 sequences, GRMZM2G165042 which encodes a polypeptide sequence that is over 99% identical to instant SEQ ID NO: 80, is knocked out by inducing two mutations: one being a 322 bp deletion and the other a single nucleotide deletion (Supplementary Fig. 12, Zmpif4s#65, ZmPIF4.2-KO, MT sequence) in the sequence of GRMZM2G165042 in maize plants (p. 796 and 801). Additionally, Wu teaches PIFs are bHLH transctiption factors with highly conserved bHLH domains (p. 790 ¶2, p. 791 entire page, and p. 792 ¶2).
It is noted that the spacer sequence of SEQ ID NO: 119 is the reverse complement of (i.e. would bind at) positions 1005-1027 in SEQ ID NO: 79, which corresponds to approximately positions 315-323 of SEQ ID NO: 80.
In analogous art, Li teaches CRISPR/Cas9 has been widely used to create various mutants and become a routine tool in plant laboratories around the world (p. 8) including knockouts and fragment deletions (Fig. 7). Furthermore, the polypeptide sequence of GRMZM2G165042 is linked in the maizeGDB database as GenBank accession No. DAA50359 which identifies amino acid residues 333 to 394 as the bHLH domain.
Because Wu teaches knockout of a protein that has 99% sequence identity to instant SEQ ID NO: 80 results in reduce shade avoidance response, and methods of knocking out and deleting fragments from genes/ proteins are routine and known in the art, it would be prima facie obvious to design a spacer of a gRNA to target any sequence of the known gene/protein to knockout the gene for the purpose of reducing shade avoidance response and in turn increasing yield as taught by Wu (abstract). This is especially true for the known amino acid residues that make up the bHLH domain as identified by GenBank Accession No. DAA50359. Therefore, it would be prima facie obvious to design a guide RNA wherein the spacer binds near the known, conserved bHLH domain, thus arriving at instantly claimed SEQ ID NO: 119 as the spacer sequence, for the purpose of inducing a mutation in the bHLH domain to knock out the function of the bHLH transcription factor (PIF4) and reduce shade avoidance response/ increase yield as taught by Wu (abstract). Additionally, one of ordinary skill in the art would have a reasonable expectation of success because generating knockouts via various methods is well understood and routine in the art, and one of ordinary skill in the art would expect that designing the spacer upstream and nearby the bHLH domain could reasonably be expected to create mutations within the bHLH domain and knockout the gene and encoded protein.
This is a provisional nonstatutory double patenting rejection.
Claim 1 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 55, 64, and 71 of copending Application No. 18442164 (reference application) in view of Wu (Wu, G., Zhao, Y., Shen, R., Wang, B., Xie, Y., Ma, X., ... & Wang, H. (2019). Characterization of maize phytochrome-interacting factors in light signaling and photomorphogenesis. Plant physiology, 181(2), 789-803.).
The copending application does not explicitly claim a guide nucleic acid that binds to a target site within the endogenous gene encoding the PIF transcription factor.
In analogous art, Wu teaches generating ZmPIF knockout transgenic lines using sgRNA/ CRISPR mediated targeted deletions (p. 801, section titled Generation and Mutation Analysis of CRISPR/Cas9 Knockout Lines in Maize, ¶1). Wu discloses the Zmpif4.1 and Zmpif4.2 double knockout mutants (p. 796, section titled Knockout of ZmPIFs by CRISPR/Cas9 Causes Short Mesocotyls in Maize under Darkness) comprised mutations to sequences of Zmpif4.1 (GRMZM5G86596) and Zmpif4.2 (GRMZM2G165042). GRMZM2G165042 has an amino acid sequence that is 99% identical to instant SEQ ID NO: 80 as evidenced by maizeGDB (see attached reference and alignment below).
It would therefore be obvious to combine the teachings to arrive at the instantly claimed guide nucleic acid with a reasonable expectation of success because Wu teaches an identical method and also provides guide nucleic acids to perform the method, and incorporation of the guide nucleic acids could be achieved by one of ordinary skill in the art without encountering any special technical difficulties. One of ordinary skill in the art would have been motivated to combine the teachings because, as stated above, Wu teaches an identical method to that instantly claimed, and further provides the guide nucleic acids to achieve the method. Therefore, it would be prima facie obvious to arrive at the instantly claimed guide nucleic acid for the same purpose that is to perform the method of editing the PIF gene.
This is a provisional nonstatutory double patenting rejection.
Claim 2 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 55, 64, and 71 of copending Application No. 18442164 (reference application) and Wu (Wu, G., Zhao, Y., Shen, R., Wang, B., Xie, Y., Ma, X., ... & Wang, H. (2019). Characterization of maize phytochrome-interacting factors in light signaling and photomorphogenesis. Plant physiology, 181(2), 789-803.) as applied to claim 1, and further in view of Li (Li, J., Li, Y., & Ma, L. (2019). CRISPR/Cas9‐based genome editing and its applications for functional genomic analyses in plants. Small Methods, 3(3), 1800473.) and GenBank accession No. DAA50359 (GenBank accession No. DAA50359, putative HLH DNA-binding domain superfamily protein, published online 10/24/2013).
As described in the previous provisional DP rejection, Wu teaches generating PIF4 double knockout in maize plants (p. 796) that display reduced shade avoidance response as compared to WT control plants (abstract, p. 797 ¶2, Fig. 8, C and D). One of the PIF4 sequences, GRMZM2G165042 which encodes a polypeptide sequence that is over 99% identical to instant SEQ ID NO: 80, is knocked out by inducing two mutations: one being a 322 bp deletion and the other a single nucleotide deletion (Supplementary Fig. 12, Zmpif4s#65, ZmPIF4.2-KO, MT sequence) in the sequence of GRMZM2G165042 in maize plants (p. 796 and 801). Additionally, Wu teaches PIFs are bHLH transctiption factors with highly conserved bHLH domains (p. 790 ¶2, p. 791 entire page, and p. 792 ¶2).
However, the copending application and Wu do not explicitly teach the guide nucleic acid comprises a spacer having a nucleotide sequence of any one of SEQ ID NOs: 114-119.
It is noted that the spacer sequence of SEQ ID NO: 119 is the reverse complement of (i.e. would bind at) positions 1005-1027 in SEQ ID NO: 79, which corresponds to approximately positions 315-323 of SEQ ID NO: 80.
In analogous art, Li teaches CRISPR/Cas9 has been widely used to create various mutants and become a routine tool in plant laboratories around the world (p. 8) including knockouts and fragment deletions (Fig. 7). Furthermore, the polypeptide sequence of GRMZM2G165042 is linked in the maizeGDB database as GenBank accession No. DAA50359 which identifies amino acid residues 333 to 394 as the bHLH domain.
Because Wu teaches knockout of a protein that has 99% sequence identity to instant SEQ ID NO: 80 results in reduce shade avoidance response, and methods of knocking out and deleting fragments from genes/ proteins are routine and known in the art, it would be prima facie obvious to design a spacer of a gRNA to target any sequence of the known gene/protein to knockout the gene for the purpose of reducing shade avoidance response and in turn increasing yield as taught by Wu (abstract). This is especially true for the known amino acid residues that make up the bHLH domain as identified by GenBank Accession No. DAA50359. Therefore, it would be prima facie obvious to design a guide RNA wherein the spacer binds near the known, conserved bHLH domain, thus arriving at instantly claimed SEQ ID NO: 119 as the spacer sequence, for the purpose of inducing a mutation in the bHLH domain to knock out the function of the bHLH transcription factor (PIF4) and reduce shade avoidance response/ increase yield as taught by Wu (abstract). Additionally, one of ordinary skill in the art would have a reasonable expectation of success because generating knockouts via various methods is well understood and routine in the art, and one of ordinary skill in the art would expect that designing the spacer upstream and nearby the bHLH domain could reasonably be expected to create mutations within the bHLH domain and knockout the gene and encoded protein.
Conclusion
No claims are allowed.
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JESSICA N. STOCKDALE
Examiner
Art Unit 1663
/JESSICA NICOLE STOCKDALE/Examiner, Art Unit 1663
/CHARLES LOGSDON/Primary Examiner, Art Unit 1662
Prosecution Insights