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, 3-4, 10-12, 14-15, 17-18, 20, 22, 30-31, 33, 35-36, 38-39 and 44 are pending. Claims 1, 11, 20, 31, and 39 are currently amended. Claims 1, 3-4, 10-12, 14-15, 17-18, 20, 22, 30-31, 33, 35-36, 38-39 and 44 are examined on the merits.
Response to Amendment
The rejection of Claims 11, 20, 22, 30, 31, 33, 35, 36, 38, and 44 under 35 U.S.C. 112(b) are withdrawn in view of amendment to the claims.
The rejection of Claims 1, 3, 4, 12, 14, 17, 18, 20, 22, 35, 36, 38, 39, and 44 under 35 USC § 102(a)(1) under Anand is maintained and modified in view of amendments to the claims.
The rejection of Claims 1, 10-11, 20 and 30-31 under 35 USC § 102(a)(1) under Sun is withdrawn in view of amendment to the claims. However, claims 10-11 and 30-31 are newly rejected under 35 U.S.C. §103 for the reasons set forth below.
The rejection of Claims 15 and 33 under 35 U.S.C. §103 is maintained and modified in view of amendment to the claims.
Claim Rejections - 35 USC § 102
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, 3, 4, 12, 14, 17, 18, 20, 22, 35, 36, 38, 39, and 44 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Anand (Ajith Anand et. al., US 20170121722A1, Application 2016-08-26, Publication 2017-05-04)
Claim 1 (BRI): Under BRI consistent with the specification, claim 1 is drawn to a method of producing a regenerable plant structure comprising: introducing into maize plant cell a polynucleotide encoding a polypeptide that has at least 90% sequence identity across the entire length of any one of the recited reference polypeptides (including SEQ ID NO: 30 and 31); and culturing the maize plant cell to produce the regenerable plant structure.
"introduced" means providing a nucleic acid (e.g., expression construct) or protein into a cell. Introduced includes reference to the incorporation of a nucleic acid into a eukaryotic or prokaryotic cell where the nucleic acid may be incorporated into the genome of the cell and includes reference to the transient provision of a nucleic acid or protein to the cell. Introduced includes reference to stable or transient transformation methods. Thus, "introduced" in the context of inserting a nucleic acid fragment (e.g., a recombinant DNA construct/expression construct) into a cell, means "transfection" or "transformation" or "transduction" and includes reference to the incorporation of a nucleic acid fragment into a eukaryotic or prokaryotic cell where the nucleic acid fragment may be incorporated into the genome of the cell (e.g., nuclear chromosome, plasmid, plastid, chloroplast, or mitochondrial DNA), converted into an autonomous replicon, or transiently expressed (e.g., transfected mRNA) (paragraph 0022).
Thus, claim 1 does not require any particular transformation method, promoter, or genomic integration. A “regenerable plant structure” reasonably includes callus, somatic embryos, shoots, or any plant tissue capable of regeneration.
Anand discloses transforming plant cells, including maize plant cells, by introducing a recombinant polynucleotide into the cells (claim 1).
Anand discloses a polynucleotide encoding a polypeptide set forth as SEQ ID NO:6, which shares 93.64% sequence identity across the entire length of SEQ ID NO: 30, and shares 91.04% sequence identity across the entire length of SEQ ID NO: 31 for the present application. This satisfies the claimed requirement of a polypeptide having at least 90% sequence identity to a recited SEQ ID NO (claim 11, and alignment below).
Anand also discloses culturing transformed maize cells and regenerating plants from the transformed cells. Regeneration of a plant from a transformed cell necessarily requires production of regenerable plant structures during tissue culture (claim 1-3).
Accordingly, Anand discloses each limitation of claim 1.
Claim 3 depends from claim 1 and recites the method, wherein the polynucleotide is operably linked to a heterologous promoter functional in a plant cell.
Anand discloses a recombinant expression cassette in which the introduced polynucleotide is operably linked to a promoter functional in a plant cell to express the encoded polypeptide (claim 5). Such a promoter in an introduced recombinant construct is a heterologous promoter (claim 8).
Claim 4 depends from claim 1 and recites the method, wherein the polynucleotide is stably incorporated into the genome of the maize plant cell, or wherein the polynucleotide is transiently expressed in the maize plant cell.
Anand discloses stable transformation of plant cells, including maize plant cells, in which an introduced polynucleotide is an incorporated into the genome (paragraph 0249). Anand also discloses transient expression of introduced polynucleotides in plant cell without genomic integration (paragraph 0208).
Claim 12 depends from claim 1 and recites the regenerable plant structure comprises a somatic embryo, embryogenic callus, somatic meristem, organocallus, a shoot, or a shoot further comprising roots.
Anand discloses culturing transformed maize cells to regenerated plants, which necessarily includes production of at least one regenerable plant structure selected from a shoot and/or a shoot compressing roots during regeneration (paragraph 0058).
Claim 14 is drawn to the method of claim 1, wherein expression of the polypeptide results in an increased somatic embryo induction frequency or increased embryo productivity relative to a control maize plant cell lacking the polynucleotide encoding the polypeptide.
Anand discloses that expression of the disclosed polypeptide increases somatic embryo response/induction frequency across a population of infected immature cotyledons relative to a control (paragraph 0304 and fig 17A).
Claim 17 is drawn from claim 1 and further recites introducing a genome editing system in the maize plant cell.
Anand discloses that the disclosed methods and compositions are used to introduce into plants polynucleotides useful to target a specific site for modification in the genome, including by TALENs, meganuclease, zinc finger nucleuses, and CRISPR-Cas, and discloses introducing a CRISPR-Cas system into plants for genome modification of a target sequence in a plant or plant cell (paragraph 0166).
Claim 18 is drawn to the method of claim 17, wherein the genome editing system comprises a CRISPR-based system, wherein the CRISPR-based system comprises (i) an RNA-guided nuclease or a polynucleotide encoding the RNA-guided nuclease; and (ii) a guide RNA or a polynucleotide encoding the gRNA under BRI.
Anand discloses a RISPR/Cas genome editing system in which short RNA (crRNA and tracrRNA, or a single guide RNA) directs a Cas endonuclease to a DNA target to cleave the target (paragraph 0181, 0184, 0185).
Anand further discloses that a guide nucleotide/guide polynucleotide forms a complex with a Cas endonuclease and enables the Cas endonuclease to recognize and optionally cleave a DNA target site, including as a single guide molecule comprising targeting and Cas-recognition domains (paragraph 0182-0185).
Therefore, Anand discloses all of the limitations of claim 18.
Accordingly, claims 1, 3, 4, 12, 14, 17, and 18 are rejected as being anticipated by Anand for the reasons set forth above.
Claim 20 is drawn to a maize plant cell comprising a polynucleotide encoding a polypeptide (i. e., SEQ ID NO:30 or SEQ ID NO:31) having at least 90% - 99.5% sequence identity across the entire length of one of the listed polypeptides, wherein callus growth, somatic embryogenesis, and/or regeneration capacity of the maize plant cell is increased relative to a control maize plant cell lacking the polynucleotide encoding the polypeptide under the same culture conditions.
Anand discloses a polynucleotide encoding a polypeptide set forth as SEQ ID NO:6, which shares 93.64% sequence identity across the entire length of SEQ ID NO: 30, and shares 91.04% sequence identity across the entire length of SEQ ID NO: 31 for the present application for the present application as mentioned in claim 1. Anand further discloses that expression of WUS/WOX morphogenic regulators increases somatic embryo induction frequency relative to a control (paragraph 0304; fig 17A) and supports regeneration of transformed maize plants from transformed maize cells (paragraph 0245-0247; paragraph 0281), thereby disclosing increased somatic embryogenesis and/or regeneration capacity as recited in claim 20.
Claim 22 is drawn to the maize plant cell of claim 20, wherein the polynucleotide is operably linked to a heterologous promoter functional in a plant cell, which is the same promoter limitation recites in claim 3
Claim 35 depends from claim 20 and further recites the maize plant cell comprising a genome editing system, which corresponds to the same genome-editing system limitation recited in claim 17.
Claim 36 is drawn to the maize plant cell of claim 35, wherein the genome editing system comprises a CRISPR-based system, wherein the CRISPR-based system comprises (i) an RNA-guided nuclease or a polynucleotide encoding the RNA-guided nuclease; and (ii) a guide RNA or a polynucleotide encoding the gRNA under BRI.
Claim 36 recites the same genome-editing system limitation as claim 18, but in the context of a maize plant cell.
Claim 38 recites a maize plant, tissue, organ, callus, or cell culture comprising the maize plant cell of claim 20.
Anand discloses producing transgenic T0 maize plants from Agrobacterium transformed maize immature embryos expressing WUS2 and ODP2, thereby providing a maize plant/tissue/cell culture comprising the transformed maize plant cell (e.g., somatic embryos and regenerated plants) (paragraph 0245-0247, and 0281).
Claim 39 is drawn to a recombinant polynucleotide comprising (a) a polynucleotide encoding a polypeptide having at least 90%, at least 95% - 99.5% sequence identity to one of the listed polypeptides (e.g., SEQ ID NO: 30 or 31), or (b) a polynucleotide having at least 90% - 99.5% sequence identity to one of the listed nucleotide sequence (e. g., SEQ ID NO: 7, 8, 9, 36, or 38); wherein the polynucleotide of (a) or (b) is operably linked to a heterologous promoter functional in a plant cell.
Under the broadest reasonable interpretation, claim 39 is drawn to a recombinant polynucleotide expression construct comprising a polynucleotide encoding a recited morphogenic polypeptide (or a sequence-identity variant thereof) operably linked to a heterologous promoter functional in a plant cell. As set forth above for claims 1 and 3, Anand discloses WOX-family morphogenic regulator coding sequences used for improving transformation efficiency (including the WOX example sequences identified in its sequence listing, e.g., US 20170121722A1 SEQ ID NO:6) in nucleic acid constructs that include a promoter for producing the nucleic acid in a plant cell. Therefore, Anand discloses the recombinant polynucleotide of claim 39.
Claim 44 is drawn to a method for producing a maize plant by regenerating a maize plant from the maize plant cell of any one of claim 20.
As set forth above for claim 20, Anand discloses the recited transformed maize plant cell. Anand further discloses regenerating a whole maize plant from the transformed maize plant cell (plant regeneration from the modified cell), thereby meeting the “regenerating a maize plant from the maize plant cell” limitation (example 1).
Accordingly, claims 20, 22, 35, 36, 38, 39, and 44 are rejected as being anticipated by Anand for the reasons set forth above.
Response to Applicant’s Remarks:
Argument 1: Applicant argues §102 over Anand is overcome because SEQ ID NO:1 and 24 were deleted.
Applicant’s arguments have been considered but are not persuasive. Although claims 1, 20, and 39 were amened to delete SEQ ID NO: 1 and SEQ ID NO: 24, Anand still anticipates because Anand SEQ ID NO: 6 has about 94% identity to instant SEQ ID NO: 30 and about 91% sequence identity to instant SEQ ID NO: 31, which satisfy the claimed “at least 90% sequence identity” limitation. Therefore, the §102 rejection over Anand is maintained and modified.
Argument 2: Applicant argues §102 over Sun is overcome because Sun was based on deleted SEQ ID NO:1.
Applicant’s arguments are persuasive. The §102 rejection over Sun is withdrawn in view of the amendments. However, claims 10-11, and 30-31 are now rejected under §103 for the reasons set forth in the Final Action.
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Claim Rejections - 35 USC § 103
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 10 and 30 are rejected under 35 U.S.C. §103 as being unpatentable over Anand (2017) as applied claims 1 and 20, in view of Sun (Yuejin Sun et. al., WO2021030242A1, Application filed 2020-08-10, Published 2021-02-18).
Claims 1 and 20 as the teaching of Anand is discussed above.
Claim 10 is interpreted as depend of claim 1.
Claim 30 is interpreted as depend of claim 20.
Claim 10 depends from claim 1 and further recites introducing a polynucleotide encoding a polypeptide having at least 90% - 99.5% sequence identity across the entire length of SEQ ID NO: 5 or 6 in the maize plant cell.
Anand teaches the method of claim 1 as set forth above, Anand does not expressly teach the additional polynucleotide encoding a polypeptide having at least 90% sequence identity across the entire length of instant SEQ ID NO: 5 or 6.
Sun teaches improving plant transformation efficiency by transforming plants (including maize) with morphogenic regulator constructs and further discloses embodiments comprising introducing a nucleic acid encoding a BABY BOOM (BBM) polypeptide (page 34, line 5-10), wherein Sun identifies BBM gene sequence including SEQ ID NO:179 (claim 17).
Based on an amino acid sequence alignment, the polypeptide encoded by instant application SEQ ID NO:6 shares 96.71% sequence identity with the polypeptide sequence of Sun’s WO2021030242A1 SEQ ID NO:179 across the entire length (below), which satisfies the limitation “at least 90% - 99.5% sequence identity” to SEQ ID NO:6 as recited in claim 10.
Therefore, Sun teaches introducing into a maize plant cell a polynucleotide encoding a BBM polypeptide meeting the claimed sequence identity requirement to SEQ ID NO:6, as additionally recited in claim 10.
Claim 10 is prima facie obvious over Anand and Sun.
Claim 30 depends from claim 20 and further recites a polynucleotide encoding a polypeptide having at least 90% - 99.5% sequence identity across the entire length of SEQ ID NO: 5 or 6, which is the same additional “SEQ ID NO: 5 or 6” limitation recited in claim 10.
Anand discloses the maize plant cell of claim 20 as set forth above. Sun further teaches use of a BABY BOOM amino acid sequence together with a WOX morphogenic regulator to improve plant transformation/regeneration efficiency. It would have been obvious to include the additional BABY BOOM polynucleotide taught by Sun in Anand’s WUS/WOX-based maize plant cell to improve regeneration and transformation efficiency with a reasonable expectation of success.
Claim 30 is prima facie obvious over Anand and Sun.
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Claims 11, 15, 31, and 33 are rejected under 35 U.S.C. §103 as being unpatentable over Anand (2017) as applied claim 1, 14 and 20, in view of Lowe (Keith Lowe et. al., The Plant Cell (2016) Vol. 28: 1998–2015).
Claims 1, 14 and 20 as the teaching of Anand is discussed above.
Claim 11 is interpreted as depend of claim 1.
Claim 15 is interpreted as depend of claim 14.
Claims 31, and 33 is interpreted as depend of claim 20.
Claim 11 is drawn to the method of claim 1, wherein the maize plant cell is of a germplasm having no somatic embryo induction when lacking the polynucleotide encoding the polypeptide under the same culture conditions. Claim 31 is drawn to the maize plant cell of claim 20, wherein the maize plant cell is of a germplasm having no somatic embryo induction when lacking the polynucleotide encoding the polypeptide under the same culture conditions.
Anand teaches the method of claim 1 and maize plant cell of claim 20 as set forth above. Anand teaches use of WUS/WOX morphogenic regulators in maize transformation and regeneration methods, including production of regenerated maize plants from transformed maize cells. Anand further teaches increased somatic embryo induction frequency relative to a control by expression of the disclosed morphogenic regulator (paragraph 0304; fig 17A).
Lowe teaches that morphogenic regulators, including WUS2 and BBM, are useful for improving transformation and regeneration in previous non-transformable or recalcitrant maize inbred lines. Lowe teaches that several inbreds had very low baseline transformation/callus response, including baseline bevels of 0-2.0%, and that expression of morphogenic regulators increased embryogenic transgenic callus production, for example PHN46 from 1.7% to 34.9%, PH581 from 0.4% to 16.9%, and PHP38 from 2.0% to 51.7% (page 2000, paragraph 2-3; page 2001, fig 2).
It would have been obvious to a person of ordinary skill in the art to apply Anand’s WUS/WOX-based maize transformation/regeneration method to maize germplasm having no somatic embryo induction under control conditions, because Lowe teaches that morphogenic regulators are useful for improving embryogenic callus formation and regeneration in recalcitrant maize inbred lines having little or no baseline response. A person of ordinary skill in the art would have had a reasonable expectation of success because embryogenic response in difficult maize germplasm.
Therefore, claims 11 and 31 are prima facie obvious over Anand and Lowe.
Claim 15 is drawn to the method of claim 14, wherein the somatic embryo induction frequency is increased at least about 50% - 95%, optionally wherein the somatic embryo induction frequency is increased at least 2, 5, 10, and 20-fold relative to a control maize plant cell lacking the polynucleotide encoding the polypeptide.
Anand teaches introducing and expressing morphogenic regulators (including WOX-family regulator and BBM) in maize corn plant cells to improve transformation/regeneration outcomes (abstract).
Anand does not teach quantify “somatic embryo induction frequency” or “embryo productivity” relative to a control lacking the polynucleotide.
Lowe teaches that overexpression of maize Bbm and Wus2 (morphogenic regulators) in maize increases recovery of embryogenic/transformed calli and enables regeneration of healthy plants in previously non-transformable or recalcitrant maize inbred lines. “when Ubipro:Bbm plus nospro:Wus2 was used, transgenic callus was produced at a mean frequency of 45.7% (12,851 independent events from 28,120 immature embryos; Figure 2)” and the callus “exhibited...embryogenic callus” morphology (page 2000, second paragraph). Lowe also teaches that a panel of inbreds is “scored for the percentage of embryos that produced transgenic calli”, and give frequency ranges across genotypes (page 2000, third paragraph). Lowe further teaches the added morphogenic genes increased callus transformation rates “with the callus morphology retaining an embryogenic phenotype” (page 2000, paragraph 1).
Lowe further teaches that adding morphogenic regulators (Bbm+/- Wus2) increases the percentage frequency of producing embryogenic transgenic callus from maize immature embryos from baseline levels (0-2.0%) to much higher frequencies (e.g., PHN46 1.7% to 34.9%; PH581 0.4% to 16.9%; PHP38 2.0% to 51.7%), demonstrating ≥50% and multi-fold increases relative to control (page 2001, fig 2).
Claim 33 is drawn to the maize plant cell of claim 20, wherein the somatic embryo induction frequency is increased at least about 50% - 95%, optionally wherein the somatic embryo induction frequency is increased at least 2, 5, 10, and 20-fold relative to a control maize plant cell lacking the polynucleotide encoding the polypeptide.
A person of ordinary skill in the art would have been motivated to practice Anand’s maize transformation/regeneration methods and compositions with a reasonable expectation that expression of the disclosed morphogenic regulators would increase comatic embryogenesis metrics relative to control, and the particular percentage/fold-increase ranges recited in claim 15 and 33 would have been an obvious results of routine optimization of a result-effective variable.
The claimed invention in claims 15 and 33 as a whole is prima facie obvious over the combined teachings of the prior arts above.
The claimed invention in claims 15 and 33 as a whole is prima facie obvious over the combined teachings of the prior arts above.
Response to Applicant’s Remarks:
Argument: Applicant argues §103 over Anand and Lowe is overcome because SEQ ID 24 were deleted.
Applicant’s arguments have been considered but are not persuasive. The deletion of SEQ ID NO: 24 does not overcome the rejection because Anand SEQ ID NO: 6 still meets the amended sequence identity limitation by having about 94% identity to instant SEQ ID NO: 30 and about 91% sequence identity to instant SEQ ID NO: 31. Lowe further teaches quantifying somatic embryo induction frequency/embryo productivity relative to a control. Therefore, the §103 rejection over Anand is maintained and modified.
Conclusion
No claims are allowed.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YANXIN SHEN whose telephone number is (571)272-7538. The examiner can normally be reached Monday-Friday.
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/YANXIN SHEN/Examiner, Art Unit 1663
/WEIHUA FAN/Primary Examiner, Art Unit 1663
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