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 .
DETAILED ACTION
Claims 1-13 are under examination. Claims 14-15 are withdrawn.
Election/Restrictions
Applicant’s election of Group I: claims 1-13 in the reply filed on July 9, 2026 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claims 14-15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on July 9, 2026.
Claims 14-15 are not in compliance with 37 CFR 1.121(c), which states: the status of every claim must be indicated after its claim number by using one of the following identifiers in a parenthetical expression: (Original), (Currently amended), (Canceled), (Withdrawn), (Previously presented), (New), and (Not entered). Claims 14 and 15 should be identified as (withdrawn) for being directed to a non-elected invention.
Claims 1-13 are under examination herein.
Priority
This application, filed on 7/16/2024, is a 371 of PCT/EP2023/051537 filed on 1/23/2023, which claims benefit of EUROPEAN PATENT OFFICE (EPO) 22152702.1 filed on 1/21/2022. The effective filing date of the instant application is January 21, 2022.
Information Disclosure Statement
The information disclosure statement filed on 1/14/2025 complies with 37 CFR 1.98(a)(2), which requires a legible copy of each cited foreign patent document; each non-patent literature publication or that portion which caused it to be listed; and all other information or that portion which caused it to be listed. All references were considered.
Drawings
The drawings are objected to because the figures are not properly labeled, figure 1 is a photograph, and the quality of figure 1 makes it difficult to identify the arrows referred to in the specification.
37 CFR 1.84 (u)(1) states “The different views must be numbered in consecutive Arabic numerals, starting with 1, independent of the numbering of the sheets and, if possible, in the order in which they appear on the drawing sheet(s). Partial views intended to form one complete view, on one or several sheets, must be identified by the same number followed by a capital letter. View numbers must be preceded by the abbreviation "FIG." Where only a single view is used in an application to illustrate the claimed invention, it must not be numbered and the abbreviation "FIG." must not appear.”
In the instant case, the view numbers for Figures 1-11 are preceded by the word "Figure" instead of the abbreviation "FIG.". Figures 2-3 and 5 have two different figures, which should be labeled individually as “FIG. 2A” and “FIG. 2B”; “FIG. 3A” and “FIG. 3B”, and “FIG. 5A” and “FIG. 5B”. The specification should also be updated to reflect these changes.
As per 37 C.F.R. 1.84(b)(1), photographs, including photocopies of photographs, are not ordinarily permitted in utility and design patent applications. The Office will accept photographs in utility and design patent applications, however, if photographs are the only practicable medium for illustrating the claimed invention. For example, photographs or photomicrographs of: electrophoresis gels, blots (e.g., immunological, western, Southern, and northern), auto- radiographs, cell cultures (stained and unstained), histological tissue cross sections (stained and unstained), animals, plants, in vivo imaging, thin layer chromatography plates, crystalline structures, and, in a design patent application, ornamental effects, are acceptable. If the subject matter of the application admits of illustration by a drawing, the examiner may require a drawing in place of the photograph. The photographs must be of sufficient quality so that all details in the photographs are reproducible in the printed patent. Figure 1 is a black and white photograph, however the quality of the images does not allow all the details to be visualized.
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 Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 2 and 12-13 are rejected under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 2 recites “the bacterium according to claim 1, which has been modified to have a decreased expression of an endogenous polypeptide having polyphosphate kinase activity compared to an otherwise identical bacterium that does not carry said modification”. Claim 2 depends from claim 1, which recites “a genetically engineered bacterium which has been modified to have a decreased expression and/or activity of an endogenous polypeptide having polyphosphate kinase activity compared to an otherwise identical bacterium that does not carry said modification.” Thus, by requiring the exact same limitation as claim 1, claim 2 does not further narrow claim 1 from which it depends, and therefore is an improper dependent claim.
Claim 12 recites “the bacterium according to claim 1, which has been modified to have a decreased production of exopolysaccharides (EPS) compared to an otherwise identical bacterium that does not carry said modification.” Claim 12 depends from claim 1, which recites “a genetically engineered bacterium which has been modified to have a decreased expression and/or activity of an endogenous polypeptide having polyphosphate kinase activity compared to an otherwise identical bacterium that does not carry said modification.” Thus, by requiring decreased production of exopolysaccharides, claim 12 does not further narrow claim 1 from which it depends, and therefore is an improper dependent claim.
Claim 13 recites “the bacterium according to claim 12, which has been modified to have a decreased expression and/or activity of at least one endogenous polypeptide involved in the production of exopolysaccharides (EPS) in said bacterium compared to an otherwise identical bacterium that does not carry said modification.” Claim 13 depends from claim 12, which requires “decreased production of exopolysaccharides (EPS) compared to an otherwise identical bacterium that does not carry said modification”. Thus, by requiring a modification that results in decreased expression and/or activity of at least one polypeptide involved in the production of exopolysaccharides, claim 13 does not further narrow claim 12 from which it depends, and therefore is an improper dependent claim.
Applicant may cancel the claims, amend the claims to place the claims in proper dependent form, rewrite the claims in independent form, or present a sufficient showing that the dependent claims complies with the statutory requirements.
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.
Claims 1-3 are rejected under 35 U.S.C. 102(a)(1) as being clearly anticipated by Casey et al. (“The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440”, Environmental Microbiology Reports, 2013, Vol. 5, No. 5, pp.740-746).
Regarding claims 1-3, Casey teaches the primary enzyme involved in polyphosphate (polyP) synthesis, polyP kinase (ppk) has been deleted in Pseudomonas putida KT2440 (abstract).
Claims 1 and 7 are rejected under 35 U.S.C. 102(a)(1) as being clearly anticipated by Nguyen et al. (“Metabolic role of pyrophosphate‑linked phosphofructokinase pfk for C1 assimilation in Methylotuvimicrobium alcaliphilum 20Z”, Microbial Cell Factories, 2020, Vol. 19, Article 131, 14 pages).
Regarding claims 1 and 7, Nguyen teaches methanotrophs use C1 compounds such as methane or methanol as the sole carbon and energy source (p.1, 1st column). Nguyen teaches Methylotuvimicrobium alcaliphilum 20Z, a model obligate methanotroph (p.2, 1st column top paragraph). Nguyen teaches performing gene knockout experiments to create a pyrophosphate-linked phosphofructokinase pfk knockout strain (p.2, 2nd column – 1st paragraph; Fig. 1)
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.
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.
Claims 4-6 are rejected under 35 U.S.C. 103 as being unpatentable over Casey et al. (“The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440”, Environmental Microbiology Reports, 2013, Vol. 5, No. 5, pp.740-746) as applied to claim 1 above, and further in view of Fekete et al. (“Dynamic regulation of N-acyl-homoserine lactone production and degradation in Pseudomonas putida IsoF”, FEMS Microbiology Ecology, 2010, Vol. 72, Issue 1, pp.22-34).
The teachings of Casey et al. are discussed above.
Regarding claims 4-6, Casey does not teach further modifying the bacterium to have decreased expression or inactivation of Acyl-homoserine-lactone (AHL) activity.
However, Fekete teaches regulation of N-acyl-homoserine lactone production and degradation in Pseudomonas putida IsoF (title). Fekete teaches the strain is a known AHL producer with only one quorum-sensing system (abstract). Fekete further teaches an AHL-negative ppuI mutant of IsoF (p.23, 2nd column last paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the Pseudomonas putida strain taught by Casey to further inactivate an AHL gene to create an AHL-negative mutant as taught by Fekete. Each of Casey and Fekete teach genetically engineering Pseudomonas putida to knock out specific genes. One of ordinary skill in the art would reasonably expect that inactivating a polyphosphate kinase gene taught by Case in addition to inactivating an AHL gene taught by Fekete would result in a genetically engineered Pseudomonas putida with inactivated PPK and inactivated AHL, because it would amount to a combination of known elements in a predictable way, and it was known in the art at the time of invention that each of these genes could be inactivated in Pseudomonas putida using genetic modification.
Claims 8-11 are rejected under 35 U.S.C. 103 as being unpatentable over Casey et al. (“The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440”, Environmental Microbiology Reports, 2013, Vol. 5, No. 5, pp.740-746) as applied to claim 1 above, and further in view of Rao et al. (“Inorganic Polyphosphate: Essential for Growth and Survival”, Annual Review of Biochemistry, 2009, Vol. 78, pp.605-47).
The teachings of Casey et al. are discussed above.
Regarding claims 8-11, Casey does not teach the bacterium belongs to the genus Methylobacillus (claims 8 and 9), or that the bacterium is Methylobacillus flagellatus (claims 10 and 11).
However, Rao teaches bacterial species that express polyphosphate kinase 1 (PPK1) (abstract). Rao teaches Methylobacillus flagellatus as having polyphosphate kinase 1 (Table 1). Rao also teaches ppk knockouts in Salmonella sp.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute Methylobacillus flagellatus taught by Rao for Pseudomonas putida taught by Casey to obtain a Methylobacillus flagellatus with inactivated polyphosphate kinase activity. Each of Casey and Rao teach genetically engineered microorganisms with knockout of polyphosphate kinase. One of ordinary skill in the art would reasonably expect that knocking out the PPK gene in Methylobacillus flagellatus would predictably result in a genetically engineered Methylobacillus flagellatus where polyphosphate kinase activity has been inactivated, because Rao teaches M. flagellatus contains an endogenous PPK gene, and it was known in the art that one could inactivate the PPK gene in microorganisms.
Claims 12-13 are rejected under 35 U.S.C. 103 as being unpatentable over Casey et al. (“The effect of polyphosphate kinase gene deletion on polyhydroxyalkanoate accumulation and carbon metabolism in Pseudomonas putida KT2440”, Environmental Microbiology Reports, 2013, Vol. 5, No. 5, pp.740-746) as applied to claim 1 above, and further in view of Gulez et al. (“Colony morphology and transcriptome profiling of Pseudomonas putida KT2440 and its mutants deficient in alginate or all EPS synthesis under controlled matric potentials”, MicrobiologyOpen, 2014, Vol. 3, Issue 4, pp.457-469).
The teachings of Casey et al. are discussed above.
Regarding claims 12-13, Casey does not teach modifying the bacterium to have decreased production of exopolysaccharides (claim 12) or decreased expression of at least one endogenous polypeptide involved in the production of exopolysaccharides (claim 13).
Gulez teaches Pseudomonas putida produces alginate, an exopolysaccharide (EPS) known to create hydrated environments and alleviate the effect of water limitation (abstract). Gulez further teaches P. putida KT2440 wild type and its mutants deficient in synthesis of either alginate or all known EPS (abstract).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the Pseudomonas putida strain taught by Casey to further inactivate a gene involved in exopolysaccharide production taught by Gulez. Each of Casey and Gulez teach genetically engineering Pseudomonas putida strains to knock out specific genes. One of ordinary skill in the art would reasonably expect that combining inactivation of a polyphosphate kinase gene taught by Casey with inactivating a gene involved in EPS production taught by Gulez would predictably result in a microorganism with reduced polyphosphate kinase activity and reduced EPS production, because it would amount to a combination of known elements in a predictable way, and it was known in the art at the time of invention that each of these activities could be reduced using genetic modification.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DEEPA MISHRA whose telephone number is (571) 272-6464. The examiner can normally be reached Monday - Friday 8:30am - 1:30pm EST.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Louise W. Humphrey can be reached at (571) 272-5543. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/DEEPA MISHRA/Examiner, Art Unit 1657
