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 .
Election/Restrictions
Applicant’s election without traverse of Group V, claims 23 and 25 in the reply filed on 06/12/2026 is acknowledged.
Claim 1-3, 5-13, 15-20, 22 and 27 withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected inventions, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 06/12/2026.
Priority
The instant application claims benefit to PCT/FI2022/050495 and FI20215805 and is acknowledged. The instant claims herein are examined using the effective filing date of 07/14/2021 for the basis of any prior art rejections.
Information Disclosure Statement
The information disclosure statement(s) (IDS) submitted on 01/12/2024 was properly filed in compliance with 37 CFR 1.97. Accordingly, the information disclosure statement(s) was considered.
Specification
The disclosure is objected to because of the following informalities: the specification refers to the drawings as “Figure” instead of “FIG.”
Appropriate correction is required.
Drawings
The drawings are objected to because the drawings recite “Figure instead of “FIG.”
Furthermore, figures 4-6 depict amino acid sequences containing 4 or more specifically defined amino acids not referenced by sequence identifiers (37 CFR 1.831.b; 37 CFR 1.831.c; 37 CFR 1.832.a).
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Objections
Claim 25 objected to because of the following informalities: claim 25 recites “PHA syntethase” and should be corrected to recite “PHA synthase”. Appropriate correction is required.
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 23 and 25 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 applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 23 recites “A method of producing hydroxy fatty acids, diacids and/or polyhydroxyalkanoate (PHA) from enzymatic degradation products of hydrocarbons by the enzyme of claim 2 or by a micro-organism and/or host cell comprising the enzyme as substrates to a hydroxy fatty acids, diacids and/or polyhydroxyalkanoate (PHA) producing enzyme, or to a micro-organism and/or a host cell comprising the hydroxy fatty acids, diacids and/or polyhydroxyalkanoate (PHA) producing enzyme”. As written, claim 23 does not recite any active steps to perform the claimed method. For illustrative purposes, the examiner points Applicant to MPEP 2173.05(q): Attempts to claim a process without setting forth any steps involved in the process generally raises an issue of indefiniteness under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph. For example, a claim which read: "[a] process for using monoclonal antibodies of claim 4 to isolate and purify human fibroblast interferon" was held to be indefinite because it merely recites a use without any active, positive steps delimiting how this use is actually practiced. Ex parte Erlich, 3 USPQ2d 1011 (Bd. Pat. App. & Inter. 1986). While the claim at issue does not explicitly recite a “use”, there are no active, positively recited steps required to practice the claimed method. At most, the claim merely requires the enzyme of claim 2 or a microorganism or host cell comprising the enzyme of claim 2 for the production of hydroxy fatty acids, diacids, and/or PHA. Please note that although a claim should be interpreted in light of the specification disclosure, it is generally considered improper to read limitations contained in the specification into the claims. See In re Prater, 415 F.2d 1393, 162 USPQ 541 (CCPA 1969) and In re Winkhaus, 527 F.2d 637, 188 USPQ 129 (CCPA 1975), which discuss the premise that one cannot rely on the specification to impart limitations to the claim that are not recited in the claim. As such, for the purposes of compact patent prosecution, the examiner is interpreting the claimed method to require the production of hydroxy fatty acids, diacids, and/or PHA from hydrocarbons by contacting the hydrocarbons with the enzyme of claim 2 or a microorganism or host cell comprising the enzyme. Please note that dependent claim 25 is also indefinite due to dependency on indefinite claim 23.
Further regarding claim 23, claim 23 refers back to independent claim 2, which recites “an isolated enzyme or a fragment thereof comprising the amino acids His31, Tyr35, Glu167, His168, and Tyr171 corresponding to the amino acid positions presented in SEQ ID NO: 2, and optionally at least one of the amino acids selected from the group comprising the amino acids His 27, His32, Asn40 and Trp166 corresponding to the amino acid positions presented in SEQ ID NO: 2, wherein said enzyme or fragment thereof is capable of degrading a hydrocarbon chain, and wherein the enzyme is optionally genetically modified” (emphasis added). The phrase “presented in SEQ ID NO: 2” renders the claim indefinite because the phrase could be interpreted to be “as shown in SEQ ID NO: 2”, which is considered exemplary claim language that renders the scope of the claim indefinite (see MPEP 2173.05(d)).
It is noted any interpretation of the claims set forth above does not relieve Applicant of the responsibility of responding to this rejection. If the actual interpretation of the claims is different than that posited by the Examiner, additional rejections and art may be readily applied in a subsequent final Office action.
Claim Rejections - 35 USC § 112(a)
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 23 and 25 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.
The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the inventor was in possession of the claimed genus. See, e.g., Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1340, 94 USPQ2d 1161, 1167 (Fed. Cir. 2010); University of California v. Eli Lilly & Co., 119 F.3d 1559, 43 USPQ2d 1398 (Fed. Cir. 1997) at 1406; Juno Therapeutics, Inc. v. Kite Pharma, Inc., 10 F.4th 1330, 1337, 2021 USPQ2d 893 (Fed. Cir. 2021) ("[T]he written description must lead a person of ordinary skill in the art to understand that the inventor possessed the entire scope of the claimed invention. Ariad, 598 F.3d at 1353–54 ('[T]he purpose of the written description requirement is to ensure that the scope of the right to exclude, as set forth in the claims, does not overreach the scope of the inventor's contribution to the field of art as described in the patent specification.' (internal quotation marks omitted).").
A "representative number of species" means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. See AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300, 111 USPQ2d 1780, 1790 (Fed. Cir. 2014). The issue is whether the skilled artisan would understand inventor to have invented, and been in possession of, the invention as claimed.
Independent claim 23 (and thus the dependent claims) A method of producing hydroxy fatty acids, diacids and/or polyhydroxyalkanoate (PHA) from enzymatic degradation products of hydrocarbons by the enzyme of claim 2 or by a micro-organism and/or host cell comprising the enzyme as substrates to a hydroxy fatty acids, diacids and/or polyhydroxyalkanoate (PHA) producing enzyme, or to a micro-organism and/or a host cell comprising the hydroxy fatty acids, diacids and/or polyhydroxyalkanoate (PHA) producing enzyme”. Claim 2 recites “an isolated enzyme or a fragment thereof comprising the amino acids His31, Tyr35, Glu167, His168, and Tyr171 corresponding to the amino acid positions presented in SEQ ID NO: 2, and optionally at least one of the amino acids selected from the group comprising the amino acids His 27, His32, Asn40 and Trp166 corresponding to the amino acid positions presented in SEQ ID NO: 2, wherein said enzyme or fragment thereof is capable of degrading a hydrocarbon chain, and wherein the enzyme is optionally genetically modified. The enzyme of SEQ ID NO: 2 in question is a superoxide dismutase enzyme from B. licheniformis (see example 1).
The specification defines “fragment” as part of that sequence, e.g. a sequence that has been truncated at the N- and/or C-terminal end (see pg. 42). Thus, the examiner has interpreted the claim to require any fragment of the enzyme that must retain functional capacity to degrade a hydrocarbon. This is problematic because the specification fails to teach an art-recognized correlation between structure and function.
In support of the claimed genus of enzymes, the specification discloses the use of full length superoxide dismutase from Bacillus licheniformis, Bacillus cereus, Bacillus flexus, Bacillus subtilis and Rhodococcus ruber that was expressed in Escherichia coli before subsequent PHA production during co-cultivation of Yarrowia lipolytica yeast expressing a Bacillus flexus superoxide dismutase, Yarrowia lipolytica yeast expressing Bacillus cereus chloroperoxidase and with Pseudomonas putida bacterium (see Table 1; Example 1-8). Applicant further discloses that plastic (i.e., hydrocarbons) degradation carried out with superoxide dismutase was enhanced by chloroperoxidase to produce degradation products that were then used to produce PHA from P. putida bacterium (see example 8). There is no disclosure in the specification that demonstrates the use of any fragments of superoxide dismutase for the degradation of hydrocarbons for subsequent production of PHA. The use of full length superoxide dismutases cannot reasonably be extrapolated and applied to support possession of the entire claimed genus of enzyme fragments useful for hydrocarbon degradation, because no one species, combination, or variant accounts for the variability amongst the claimed genus. As in Ariad, merely drawing a fence around the outer limits of a purported genus is not an adequate substitute for describing a variety of materials constituting the genus and showing that one has invented a genus and not just a species
There is also no disclosure as to what structure(s) must be present or retained on the fragment of superoxide dismutase that would result in a functional fragment for hydrocarbon degradation. Applicant has not has not provided any information or steps as to how one of ordinary skill would obtain a functional fragment of superoxide dismutase, or any sufficient distinguishing structure-function relationship with respect to the broad genus as claimed. This data cannot be extrapolated to any and all possible fragments of the enzyme. Even with knowledge in the art regarding modification of genes, one of ordinary skill would not reasonably know, based on the disclosure provided, what structures or functions are required for the outcome of creating a functional fragment of superoxide dismutase without a recognized correlation between structure and function.
The specification, then, is considered devoid of sufficiently detailed, relevant, identifying characteristics demonstrating that Applicant was in possession of the claimed genus of superoxide dismutase enzyme fragments, i.e., additional complete or partial structures, other physical and/or chemical properties, functional characteristics coupled with a known or disclosed correlation between function and structure, or some combination thereof demonstrating possession of the claimed genus.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim 23 is rejected under 35 U.S.C. 103 as being unpatentable over Guzik et al. (Conversion of post consumer polyethylene to the biodegradable polymer polyhydroxyalkanoate. Appl Microbiol Biotechnol 98, 4223–4232 (2014); hereinafter “Guzik”) in view of Uniprot A0AAW6KKF0_9BACI superoxide dismutase from B. licheniformis (see search results 03/23/2026) and Zhang et al. (Alleviation of reactive oxygen species enhances PUFA accumulation in Schizochytrium sp. through regulating genes involved in lipid metabolism. Metab Eng Commun. 2018 Mar 27;6:39-48; hereinafter “Zhang”).
Guzik teaches a process for the conversion of post-consumer (agricultural) polyethylene (PE) waste to the biodegradable polymer medium chain length polyhydroxyalkanoate (PHA; a hydroxy fatty acid polyester) by the thermal treatment of PE in the absence of air (pyrolysis) generated a complex mixture of low molecular weight paraffins with carbon chain lengths from C8 to C32 (PE pyrolysis wax) before using the PE as a substrate for various bacterial strains to grow and produce PHA from the PE pyrolysis wax (a method of producing hydroxy fatty acids/PHA by using enzymatic degradation products of hydrocarbon as a substrate as in claim 23; see abstract, Table 1, Fig. 1-2 and Table 4). Guzik does not explicitly teach the microorganism contains a PHA producing enzyme. However, Guzik teaches the use of various bacterial strains used to produce PHA, including P. putida (see Table 1 reproduced below), which Applicant’s specification evidences is capable of producing PHA (see example 8). Thus, absent evidence to the contrary, the P. putida strain of Guzik (i.e., the same strain as used by Applicant) is a microorganism comprising a PHA producing enzyme (see MPEP 2112.01).
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Guzik does not explicitly teach contacting the hydrocarbons with the enzyme of claim 2.
However, Uniprot A0AAW6KKF0_9BACI explicitly teaches a sequence of superoxide dismutase that has 99.6% identity to SEQ ID NO: 2 that comprise the amino acids His31, Tyr35, Glu167, His168 and Tyr171 (see alignment below). Furthermore, Zhang teaches alleviation of reactive oxygen species during fatty acid accumulation (see title, abstract). Zhang explicitly teaches that reactive oxygen species limits the accumulation of fatty acids like polyunsaturated fatty acids during fatty acid biosynthesis, and further teaches that over expression of superoxide dismutase (SOD1) alleviates reactive oxygen species and oxidative damage to cells (see pg. 44, Fig. 3-5).
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Therefore, it would have been prima facie obvious to one of ordinary skill at the time of filing to modify the method of producing PHA/hydroxy fatty acids as taught by Guzik and include superoxide dismutase as taught by Uniprot and Zhang to arrive at the claimed invention with a reasonable expectation of success. One of ordinary skill would have been motivated to make the modification because Uniprot teaches a suitable superoxide dismutase enzyme that can successfully be used to reduce ROS and oxidative damage to cells during fatty acid production.
Accordingly, the claimed invention was prima facie obvious to one of ordinary skill at the time of filing, especially in the absence of evidence to the contrary.
Second rejection
Claim 25 is rejected under 35 U.S.C. 103 as being unpatentable over Guzik, Uniprot, and Zhang as applied to claim 23 and further in view of Rivas et al (US20150203878 A1; hereinafter “Rivas”).
As discussed above, claim 23 was rendered prima facie obvious in view of the teachings of
Rivas teaches a method of produce polyhydroxyalkanoate (PHA) using a genetically engineered microorganism overexpressing PHA synthase by culturing the microorganism (the host cell is modified to overexpress an enzyme producing PHA as in claim 23; see abstract, claim 1 and 12-13; paragraph 0117). Rivas further teaches that the microorganism is capable of increased production of this compound without a decline in the PHA content over time and is useful in the commercial production of PHAs (see abstract).
Therefore, it would have been prima facie obvious to one of ordinary skill at the time of filing to modify the method of producing PHA/hydroxy fatty acids from polyethylene hydrocarbons as taught by Guzik, Uniprot, and Zhang by overexpressing PHA synthase in a PHA producing microorganism as taught by Rivas to arrive at the claimed invention with a reasonable expectation of success. One of ordinary skill would have been motivated to make the modification because Rivas explicitly teaches microroganisms overexpressing the synthase enzyme is advantageously capable of increased production of this compound without a decline in the PHA content over time and is useful in the commercial production of PHAs.
Accordingly, the claimed invention was prima facie obvious to one of ordinary skill at the time of filing, especially in the absence of evidence to the contrary.
Conclusion
NO CLAIMS ALLOWED.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
Yang S, Li S, Jia X. Production of medium chain length polyhydroxyalkanoate from acetate by engineered Pseudomonas putida KT2440. J Ind Microbiol Biotechnol. 2019 Jun;46(6):793-800. doi: 10.1007/s10295-019-02159-5. Epub 2019 Mar 12.
Mohammed et al. International Journal of Biological Macromolecules 156 (2020) 1064–108
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GEORGIANA C REGLAS whose telephone number is (571)270-0995. The examiner can normally be reached M-Th: 8:00am-2:00pm.
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/G.C.R./Examiner, Art Unit 1651
/THOMAS J. VISONE/Supervisory Patent Examiner, Art Unit 1672
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