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 as Second Non-Final Office Action
This is the second non-final Office action in this application that examines the claims. A restriction requirement was also posted. This supplements the Office action posted on 21 July 2026. This Office action adds a requirement under the PTO’s Sequence Rules.
The undersigned left a voice-mail with Joshua Elliott (22 July 2026) that a second non-final action would be posted shortly.
The undersigned apologizes for any inconvenience this may cause.
Minor adjustments were also made to referencing claims were also made.
Election/Restrictions
A restriction requirement was posted on 5 January 2026. Applicant's election without traverse of SEQ ID NO:11 in the reply filed on 5 May 2026 is acknowledged. The requirement is still deemed proper and is therefore made FINAL.
Claims 4 and 18-26 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claims 1-3, 5-17, and 27-30 are examined herein.
Applicant is reminded that upon the cancellation of claims to a non-elected invention, the inventorship must be amended in compliance with 37 CFR 1.48(b) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. Any amendment of inventorship must be accompanied by a request under 37 CFR 1.48(b) and by the fee required under 37 CFR 1.17(i).
Sequence Rules
Specific deficiency under the Sequence Rules of MPEP § 2422 (citing to 37 C.F.R. 1.821). – Amino acid sequences appearing in at least Claim 1 are not identified by sequence identifiers in accordance with 37 CFR 1.821(d).
See, for example, the claims in the parent application (16/468,036) submitted 9 March 2020. The SEQ ID NOs are also in the specification on pages 3-4.
Full compliance in with the sequence rules is required in response to this Office action. Applicant can either give each sequence present within the drawings, specification and/or tables a unique identifier number, or specify them as a range with respect to an already identified sequence. A complete response to this Office action must include both compliance with the sequence rules and a response to the issues set forth herein. Failure to fully comply with both of these requirements in the time period set forth in this Office action will be held to be non-responsive.
Examiner’s Notes & Claim Interpretation
2. Citations to Applicant’s specification are abbreviated herein “Spec.”
Occasionally, “SIN” may be used as an abbreviation “SEQ ID NO:” herein.
In the alignment below SEQ ID NO:1 is compared with SEQ ID NO:11
Alignment of SEQ ID NO:1 versus SEQ ID NO:11 using NCBI’s BLAST® website:
QUERY is SEQ ID NO:1 is “Query” and SEQ ID NO:11 is “Sbjct”. Some of the “MOTIFS” are underlined.
Query 31 MGNISEREEPTSAKRVAVVGAGVSGLAAAYKLKSHGLSVTLFEADSRAGGKLKTVKKDGF 90
M + + + P S KRVAVVGAGVSGLAAAYKLKSHGL VT+FEA+ RAGG+L++V +DG
SIN 11 MASSATDDNPRSVKRVAVVGAGVSGLAAAYKLKSHGLDVTVFEAEGRAGGRLRSVSQDGL 60
Query 91 IWDEGANTMTESEAEVSSLIDDLGLREKQQLPISQNKRYIARDGLPVLLPSNPAALLTSN 150
IWDEGANTMTESE EV LID LGL+EKQQ PISQ+KRYI ++G P+L+P+NPAALL S
Sbjct 61 IWDEGANTMTESEIEVKGLIDALGLQEKQQFPISQHKRYIVKNGAPLLVPTNPAALLKSK 120
Query 151 ILSAKSKLQIMLEPFLWRKHNATELSDEHVQESVGEFFERHFGKEFVDYVIDPFVAGTCG 210
+LSA+SK+ ++ EPF+W++ + + + DE+ ESVG FFERHFGKE VDY+IDPFV GT
Sbjct 121 LLSAQSKIHLIFEPFMWKRSDPSNVCDENSVESVGRFFERHFGKEVVDYLIDPFVGGTSA 180
Query 211 GDPQSLSMHHTFPEVWNIEKRFGSVFAGLIQSTLLSKKEKGGENASI--KKPRVRGSFSF 268
DP+SLSM H+FPE+WN+EKRFGS+ AG +QS L +K+EK GEN + K RGSFSF
Sbjct 181 ADPESLSMRHSFPELWNLEKRFGSIIAGALQSKLFAKREKTGENRTALRKNKHKRGSFSF 240
Query 269 QGGMQTLVDTMCKQLGEDELKLQCEVLSLSYNQKGIPSLGNWSVSSMSNNTSEDQSYDAV 328
QGGMQTL DT+CK+LG+D+LKL +VL+L+Y G S NWS++S SN +++D DAV
Sbjct 241 QGGMQTLTDTLCKELGKDDLKLNEKVLTLAYGHDGSSSSQNWSITSASNQSTQD--VDAV 298
Query 329 VVTAPIRNVKEMKIMKFGNPFSLDFIPEVTYVPLSVMITAFKKDKVKRPLEGFGVLIPSK 388
++TAP+ NVK++KI K G PF L+F+PEV+YVP+SVMIT FKK+ VKRPLEGFGVL+PSK
Sbjct 299 IMTAPLYNVKDIKITKRGTPFPLNFLPEVSYVPISVMITTFKKENVKRPLEGFGVLVPSK 358
Query 389 EQHNGLKTLGTLFSSMMFPDRAPSDMCLFTTFVGGSRNRKLANASTDELKQIVSSDLQQL 448
EQ NGLKTLGTLFSSMMFPDRAPSD+ L+TTF+GG++NR+LA ASTDEL++IV+SDL++L
Sbjct 359 EQKNGLKTLGTLFSSMMFPDRAPSDLYLYTTFIGGTQNRELAQASTDELRKIVTSDLRKL 418
Query 449 LGTEDEPSFVNHLFWSNAFPLYGHNYDSVLRAIDKMEKDLPGFFYAGNHKGGLSVGKAMA 508
LG E EP+FVNH +WS FPLYG NY SVL+AIDK+EKDLPGFF+AGN+KGGLSVGKA+A
Sbjct 419 LGAEGEPTFVNHFYWSKGFPLYGRNYGSVLQAIDKIEKDLPGFFFAGNYKGGLSVGKAIA 478
Query 509 SGCKAAELVISYLDS 523
SGCKAA+LVISYL+S
Sbjct 479 SGCKAADLVISYLNS 493n
Specification
The Office requires that prophetic examples must be clearly distinguished. “Properly Presenting Prophetic and Working Examples in a Patent Application,” Fed. Reg. 86(124):35074-75 (Jul. 2021).
Thus, in Example 1: “design mutants are synthesized by.” Spec. p. 141, l. 10.
All or most of the examples are written in present tense suggesting that they are prophetic. Example 5 does mention transgenic plants. Id., p. 153, l. 11.
However the figures are largely pictures of transgenic plants. And the Description of the Drawing section (pp. 11-13) confirms they are transgenic plants.
So the Examples appear to be non-prophetic.
Claim Objections
Claims 7-12, 14-16, 26 and 27 are objected to because of the following informalities.
Claims 7, 8, 9, 10, 11, 12, 14, 15, 16, 26 and 27 are objected to because they recite the limitation “as defined in” which raises a question of whether Applicant is attempting to establish a definition – Applicant is entitled to be their own lexicographer – is that the intent here?
Appropriate correction is requested.
Improper Markush Group
Claims 5, 17, and 26 and 27 are rejected on the basis that they or their base claim contain 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 groupings in claims 5, 17 and 28 are 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.
Claim 17, part (a), for example, reads on a Markush group of approximately 118 proteins.
When the elected SEQ ID NO:11, for example, was compared with SEQ ID NO:1 above, they are only approximately 83% identical.
Further, when SEQ ID NO:1 was compared with SEQ ID NO:30 in the Office action of 7 September 2021 in application serial number 16/468,036 (of which this application is a continuation) (alignment on pages 5-6)
the sequences were only 59% identical. (NCBI’s BLAST®, website accessed 26 August 2021 ).
Applicant presents no teachings that such a diverse group of sequences will function equivalently with the same activity in the instant invention. In fact much of Applicant’s teachings focus on minor variations in amino acid sequence from the wild0type sequences.
Therefore the species of the Markush group lack both a substantial structural feature and a common use that flows from the substantial structural feature. Therefore, one of ordinary skill in the art would not perceive a substantial structural feature and/or a common use that flows from the substantial structural feature in the members of the Markush group given the focus of Applicant’s invention.
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.
Claims depending on the claims reciting an improper Markush group are included in this rejection.
Claim Rejections - 35 USC § 112(b)
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 1-3, 5-17 and 27-30 are 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 pre-AIA the applicant regards as the invention.
Claim 1 is rejected because of antecedent basis problems. Thus it recites a “polynucleotide encoding a mutated PPO polypeptide” in lines 1-2 and then “the corresponding wildtype sequence” in at least part 1 and other places. Given that Applicant’s specification emphasizes how many similar polypeptide sequences there are – for example the top of page 7, “the corresponding wildtype sequence” is indefinite.
Further, the elected SEQ ID NO:11 does not appear to have either Motif 1 or Motif 3. How to interpret the requirement for motifs is indefinite.
Claim 17 is rejected because it recites, as a limitation, "stringent conditions.” The metes and bounds of the claimed invention are unclear because Applicant fails to precisely define the conditions used either in the claim or in the specification. The specification does not discuss stringent conditions. The examiner is aware that the nucleic acid hybridization is a function of kinetics and conditions (see, e.g., Wahl et al. (1987) Meth Enzymol 152:399, entire article) with the detection of a signal in, for example, a Southern blot, representing the most stable hybrid formed between the immobilized nucleic acid and the probe, but other hybrids can and do form. Therefore, Applicant has failed to provide an adequate definition of stringent conditions as it applies to the claim limitation and thus the claim is indefinite.
Claim 17 also is rejected because it recites a long list of SEQ ID NOs but adds “variant, paralogue, orthologue or homolog” of any.
Thus the relative term “mutated” in relation to the recited sequences, but the limitation “mutated” also applies to the variants, paralogues, orthologues and homologs. Thus a “variant” of a mutant of SEQ ID NO:11 appears to include the wild-type sequence.
The recitation of “differs from the wildtype sequence” in about the middle of part (d) does not obviate this rejection given the current scope of the claim.
Claims 17-18 are rejected because they recite the limitation “that positions” in the last line. The limitation has the antecedent basis of “one or more positions” and additionally “positions” is in the plural form in contrast to “that.”
Dependent claims are included in this rejection because none provide limitations obviating this rejection.
Claim Rejections - 35 USC § 112(a)
The following is a quotation 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 35 U.S.C. 112 (pre-AIA ), first paragraph:
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 1-3, 5-17, and 27-30 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 claims contain 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 17 encompasses a vast genus of mutated PPO polypeptides even just considering only SEQ ID NO:11. Not only does claim 17 include the claimed mutants of SEQ ID NO:11 it includes all variants, paralogues, orthologues and homologs thereof. The sensitivity of PPO polypeptides to amino acid sequence changes is well established in the art. Further, the claimed genus includes polypeptide sequences encoded by DNA sequences that hybridize to a DNA sequence encoding SEQ ID NO:11 even if that limitation results in a rejection under 35 USC 112(b).
The Federal Circuit held that a written description of an invention "’requires a precise definition, such as by structure, formula [or] chemical name,’ of the claimed subject matter sufficient to distinguish it from other materials." Regents of the Univ. of Cal. v. Eli Lilly & Co., 119 F.3d 1559, 1568, 43 USPQ2d 1398, 1405 (Fed. Cir. 1997) (quoting Fiers v. Revel, 984 F.2d 1164, 1171, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993)). The court also stated "naming a type of material generally known to exist, in the absence of knowledge as to what that material consists of is not a description of that material." Id., 119 F.3d at 1568, 43 USPQ2d at 1406. The court held that “[a] description of a genus of cDNAs may be achieved by means of a recitation of a representative number of cDNAs, defined by nucleotide sequence, falling within the scope of the genus or of a recitation of structural features common to members of the genus, which features constitute a substantial portion of the genus.” Id., 119 F. 3d at 1569, 43 USPQ2d at 1406.
The art regarding PPO mutants is well-developed. E.g. Li & Nicholl (2005) Pest Manag Sci 61:277-85 & Aponte et al., WO 2015/092706 A1 (25 June 2015).
Applicant describes the enzyme activity of several amino-acid-substituted PPOs: SEQ ID NO:1 and SEQ ID NO:2. Spec., pp. 143-152.
Applicant describes creating transgenic plants. Id., pp. 152-154. Pictures of such plants appear in the figures.
Applicant fails to satisfy the written description requirement because Applicant fails to describe a representative number of species of polypeptides in comparison to the size of the claimed genus around the elected species of SEQ ID NO:11. Applicant also fails to describe the structural elements of this polypeptide that are necessary and/or sufficient for activity in the instant invention. Therefore Applicant has not demonstrated to one skilled in the art possession of the broad genus of claimed polypeptides. Since the specification fails to provide an adequate written description to support the breadth of the claims, one of skill in the art would not believe Applicant to be in possession of the invention as broadly as claimed at the time of filing.
Claim 1 is included because of its indefiniteness.
Dependent claims are included in this rejection because none provide further limitations obviating this rejection.
Claims 1-3, 5-17, and 27-30 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for SEQ ID NO:1 with from one to four of the amino acid sequence changes described by Motifs 1-4, does not reasonably provide enablement for all variants, paralogues, orthologs and homologs. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
The Federal Circuit in In re Wands lists eight considerations for determining whether or not undue experimentation would be necessary to practice an invention. In re Wands, 858 F2d 731, 8 USPQ2d 1400, 1406 (Fed. Cir. 1988). These factors are: the quantity of experimentation necessary, the amount of direction or guidance presented, the presence or absence of working examples of the invention, the nature of the invention, the state of the prior art, the relative skill of those in the art, the predictability or unpredictability of the art, and the breadth of the claims. Id.
Claim 17 encompasses a vast genus of mutated PPO polypeptides even just considering only SEQ ID NO:11. Not only does claim 17 include the claimed mutants of SEQ ID NO:11, it includes all variants, paralogues, orthologues and homologs thereof. The sensitivity of PPO polypeptides to amino acid sequence changes is well established in the art. Further, the claimed genus includes polypeptides encoded by DNA sequences that hybridize to a DNA sequence encoding SEQ ID NO:11.
The art regarding PPO mutants is well-developed. E.g. Li & Nicholl (2005) Pest Manag Sci 61:277-85 & Aponte et al., WO 2015/092706 A1 (25 June 2015).
Applicant teaches the enzyme activity of several amino-acid-substituted PPOs: SEQ ID NO:1 and SEQ ID NO:2 as discussed above. Applicant teaches creating transgenic plants. Id., pp. 150-152. Pictures of such plants appear in the figures.
One of skill in the art, after reading the specification, would be uncertain as to both how to make and how to use the genus as broadly as claimed to function within the instant invention. One of skill in the art would find it difficult to predict which of the claimed sequence, e.g. orthologs, could be used in the instant invention, and which could not. Although testing individual sequences can be routine, Applicant has provided no guidance as to how to proceed.
Given the claim breadth regarding variant sequences, combined with the unpredictability in the art, and lack of guidance as discussed above, undue experimentation is required to practice Applicant’s invention. Therefore one skilled in the art would be forced to make and test numerous embodiments with no guidance as to which ones could be used in the instant invention. Thus Applicant’s claimed invention would require undue trial and error experimentation with no reasonable expectation of success.
Furthermore, claim 17 is merely drawn nucleic acid with an arguably defined sequence of nucleotides and/or amino acids. Unless the, e.g. isolated nucleic acid molecule, provides a useful and functional product, Applicant fails to teach how to use the instant invention. No functional limitation is recited.
Therefore the invention is not enabled throughout the broad scope of the claims. Dependent claims are included in this rejection because none provide further limitations obviating this rejection.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 17 and 26-27 are rejected under 35 U.S.C. 101 because the claims read on, for example, (a) a nucleic acid molecule encoding SEQ ID NO:1 or a variant thereof and (d) a nucleic acid molecule that hybridizes with a molecule encoding SEQ ID NO:11. Give the broad scope, the wild-type protein could be regarded as a variant thereof, and the coding sequence of the wild-type gene would hybridize to the gene encoding SEQ ID NO:11.
In any case, naturally-occurring mutants are known to exist. E.g., Li & Nicholl (2005) Pest Manag Sci 61:277-85.
Therefore the claimed invention is directed to non-statutory subject matter because the claimed invention is directed to a naturally-occurring nucleic acid or fragment thereof, whether isolated or not, that is not patent-eligible pursuant to the Supreme Court decision in Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576, 133 S.Ct. 2107, 186 L.Ed.2d 124, 106 USPQ2d 1972 (2013). Thus the claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception.
Claims 26 and 27 are included in this rejection because neither provides limitations obviating this rejection. Claim 26 requires an expression cassette but Applicant only defines an ‘expression cassette’ as requiring a plant promoter (Spec., p. 9, first full paragraph) but that reads on the native gene. Such a gene could also be used as a transformation vector in, e.g. calcium phosphate precipitation.
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to RUSSELL T BOGGS whose telephone number is (571)272-2805. The examiner can normally be reached Monday - Friday, 0800 to 1830 Mtn.
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/RUSSELL T BOGGS/Examiner, Art Unit 1663
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