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, 3-4, 10-12, 14-15, 17-18, 20, 22, 30-31, 33, 35-36, 38-39 and 44 are examined on the merits.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 11, 20, 22, 30, 31, 33, 35, 36, 38, and 44 rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claims 11 and 31 are rejected as indefinite for the recitation “…. the maize plant cell comprises a regeneration-recalcitrant germplasm…”. The term “regeneration-recalcitrant germplasm” renders the scope of the claims unclear, because it is a relative, functional descriptor and the specification provides no definition, objective criteria, or test for determine whether a given maize germplasm is “regeneration-recalcitrant”. In particular, (1) no objective boundary or threshold. the claims do not specify any measurable criterion on numerical threshold that distinguishes “regeneration-recalcitrant” germplasm from non-recalcitrant germplasm. (2) Dependence on conditions makes scope uncertain. whether a maize genotype is “recalcitrant” varies with genotype, explant type and developmental stage, media composition and plant growth regulator, selection regime, light/dark conditions, temperature, culture duration, and transformation method. Because the claims do not identify the baseline protocol or conditions under which “recalcitrance” is assessed, a person of ordinary skill in the art cannot determine with reasonable certainty which germplasm is included within the scope of the claims.
Claim 20 is rejected as indefinite for the recitation “where in expression of the polypeptide increases …..”. While “increases” can often be interpreted related to a non-transgenic control, the claim here ties the “polypeptide” to sequence that are maize proteins (e.g., SEQ ID NO: 22-24 and 31-33), which maize cells may already endogenously express. In that circumstance, it is unclear what the default comparison baseline is, e.g., (1) a wild-type maize plant cell expressing the endogenous protein at native levels, (2) non-transformed cell under the same culture conditions, (3) a cell lacking expression of the protein, or (4) a cell expressing a different allele/variant. Because the claim does not specify the control condition, the scope of “increases” is uncertain, and it is unclear when the functional limitation is satisfied.
Furthermore, claim 20 is rejected as indefinite for the recitation “…expression of the polypeptide increases proliferation,…..”. the limitation “proliferation” renders the scope of claim 20 unclear because it is a relative, functional result that lacks objective boundaries, and the claim does not specify (1) what “proliferation” refers to (e.g., cell division rate, biomass accumulation, callus growth, increase in cell number, or increased culture expansion); (2) the conditions or assay under which proliferation is measured.
Dependent claims 22, 30, 31, 33, 35, 36, 38, and 44 are included in this rejection because they do not include additional limitations to resolve the ambiguity.
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: 24); 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:10, which shares 95.99% sequence identity across the entire length of SEQ ID NO: 24 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:24) having at least 90% - 99.5% sequence identity across the entire length of one of the listed polypeptides, wherein expression of the polypeptide increases proliferation, somatic embryogenesis, and/or regeneration capacity of the maize plant cell.
Anand discloses a polynucleotide encoding a polypeptide set forth as SEQ ID NO:10, which shares 95.99% sequence identity across the entire length of SEQ ID NO: 24 for the present application as mentioned in claim 1.
Anand discloses that expression of WUS leads to adventitious shoot proliferation (i. e., increased proliferation) (paragraph 0120), and discloses biologically active variants retaining WUS/WOX activity (paragraph 0136-0139).
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: 24), 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:10) 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.
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Claims 1, 10-11, 20, and 30-31 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Sun (Yuejin Sun et. al., WO2021030242A1, Application filed 2020-08-10, Published 2021-02-18).
Claim 1 is drawn to a method of producing a regenerable plant structure by (1) introducing a polynucleotide into a maize plant cell encoding a polypeptide having at least 90-99.5 % sequence identity across the entire length of one of the listed polypeptides (including SEQ ID NO: 1); and culturing the maize plant cell to produce the regenerable plant structure.
Sun discloses methods and compositions for improving plant transformation efficiency using WOX-family morphogenic regulators and their corresponding coding sequences (claim 1). Sun’s “Brief Description of the Sequences and Table 1” identifies SEQ ID NO:41 as the Sobic.003G350900.1.p WOX protein from Sorghum bicolor and identifies the corresponding coding sequence at SEQ ID NO:40, and Sun explains that these “Example WOX proteins and … proteins, and corresponding coding sequences” described in the sequence listing are used in the disclosed methods/compositions for improving transformation efficiency (page 34, line 5-10).
Sun discloses introducing/transforming plant cells (including monocots such as corn/maize) with a nucleic acid encoding a WOX morphogenic regulator (e.g., WO2021030242A1 SEQ ID NO:40 encoding SEQ ID NO:41) to improve transformation efficiency (including regeneration-related outcomes such as callus formation/redifferentiation) (page 3, line 5-10). Further, Sun discloses recovering/regenerating transformed plant material through tissue culture steps as part of the transformation workflow, which necessarily includes culturing transformed cells to obtain regenerable plant structures (page 50, line 15-28).
As sequence analysis, SEQ ID NO:1 of the instant application is 100% identical to a WOX gene disclosed in Sun (e.g., WO2021030242A1 WOX example sequences, including SEQ ID NO:41, Sobic.003G350900.1.p) (below), such that the WOX polypeptide taught in Sun meets the limitation of “at least 90%....99.5 % sequence identity across the entire length of SEQ ID NO: 1). Therefore, Sun anticipates introducing a polynucleotide encoding a polypeptide meeting the claimed identity requirement into a maize plant cell and culturing the maize plant cell to produce a regenerable plant structure, as recited in claim 1.
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.
Sun discloses 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 discloses 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 11 depends from claim 1 and further recites the maize plant cell comprises a regeneration-recalcitrant germplasm.
Sun discloses that a WOX-family morphogenic regulator improves transformation efficiency in recalcitrant corn. Specifically, Sun discloses that BdWOX5 was shown to improve recalcitrant corn AA3676 transformation (vector 25072) when under the control of strong constitutive maize ubiquitin 1 promoter (prZmUbi1) (page 51, line 3-10). Thus, Sun expressly discloses performing the disclosed transformation/regeneration-improvement method in a recalcitrant maize germplasm, meeting the additional limitation of claim 11.
Accordingly, claims 1, and 10-11 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 having at least 90% - 99.5% sequence identity across the entire length of one of the listed polypeptides (including the WOX polypeptides exemplified in WO2021030242A1), wherein expression of the polypeptide increases proliferation, somatic embryogenesis, and/or regeneration capacity of the maize plant cell.
As set forth above for claim 1, Sun disclose that expression of such morphogenic regulators improves transformation efficiency. Sun further expressly discloses regeneration of transformed maize tissues, stating that “healthy transformed calli” are transferred to regeneration media “to produce shoots”, and that regenerated shoots are transferred to a rooting medium “to establish well rooted plantlets”(page 50, line 3-11), thereby disclosing increased regeneration capacity as recited in claim 20.
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.
Claim 31 depends from claim 20 and further recites the maize plant cell comprises a regeneration-recalcitrant germplasm, which corresponds to the same recalcitrant germplasm limitation recited in claim 11.
Accordingly, claims 20, and 30-31 are rejected as being anticipated by Sun for the reasons set forth above.
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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 15, and 33 are rejected under 35 U.S.C. §103 as being unpatentable over Anand (2017) as applied claim 14 and 20, in view of Lowe (Keith Lowe et. al., The Plant Cell (2016) Vol. 28: 1998–2015).
Claims 14 and 20 as the teaching of Anand is discussed above.
Claim 15 is interpreted as depend of claim 14.
Claim 33 is interpreted as depend of claim 20.
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.
Conclusion
No claims are allowed.
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/YANXIN SHEN/ Examiner, Art Unit 1663
/WEIHUA FAN/ Primary Examiner, Art Unit 1663