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
1. Claims 1-2, 4-9, 11, 13-14, 30, 37-38, 73, 88, 91, 100, 102, and 122 are currently pending.
Election/Restrictions
2. Applicant’s election of Group I in the reply filed on January 5, 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 Claims 88, 91, 102 and 122 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 January 5, 2026.
Claims 1-2, 4-9, 11, 13-14, 30, 37-38, 73, and 100 are currently under examination.
Information Disclosure Statement
3. The information disclosure statement (IDS) submitted on February 12, 2024 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner. An initialed copy is attached hereto.
Claim Objections
4. Claim 13 is objected to because of the following informalities: said claim depends upon a rejected based claim. Appropriate correction is required.
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.
5. Claim 2, 30 and 73 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 2 is rendered vague and indefinite by the use of the phrase “wherein: (a) the microbial cell cannot grow in the defined medium and/or the complex medium without the nucleic acid construct”. It is unclear what is meant by said phrase, as it is not explicitly defined in the specification. First, the ‘(a)’ implies there are more options to follow, yet no other subsequent options are labeled. Secondly, it is unclear how “the complex medium without the nucleic acid construct” adds to or fits into the claim. As written, it is impossible to determine the metes and bounds of the claimed invention.
Claim 30 is rendered vague and indefinite by the use of the phrase “a sequence of interest” as well as “a RNA product, peptide product, or a protein product”. It is unclear what is meant by said term, as it is not explicitly defined in the specification. What constitutes a “a sequence of interest”? Further, what constitutes a RNA product, peptide product, or a protein product? What core features/structures must be maintained? As written, it is impossible to determine the metes and bounds of the claimed invention.
Claim 73 is rendered vague and indefinite by the use of the phrase “sequence of interest”. It is unclear what is meant by said phrase, as it is not explicitly defined in the specification. What constitutes a “sequence of interest”? What core features/structures must be maintained? As written, it is impossible to determine the metes and bounds of the claimed invention.
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.
6. Claim(s) 1-2, 4-7, 11, , 38, 73 and 100 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Seta et al., Journal of Bacteriology, 1997; 179(16): 5218-5221 (provided by on IDS).
Independent claim 1 is drawn to a microbial cell lacking or having decreased expression of an endogenous glycolytic gene that encodes a glycolytic enzyme, wherein the microbial cell comprises a nucleic acid construct comprising an expression cassette that encodes a recombinant glycolytic enzyme, and wherein the microbial cell can grow in a defined medium and/or a complex medium.
Seta discloses that glycolysis is a common pathway for glucose breakdown in most living organisms. The phosphorylating glyceraldehyde-3-phosphate dehydrogenase (GAPDH) occupies a pivotal role in glycolysis, converting glyceraldehyde-3-phosphate into 1,3-bi-phosphoglycerate. The gapA gene of Escherichia coli was initially identified by mutations preventing cell growth on glucose (meets claim 11). No GAPDHase activity was observed in the resulting DF221 strain. However, this strain was shown to revert at high levels on glucose-containing media. Many of the revertant were reported to display a GAPDHase activity (12). gapB, a putative GAPDH gene, was identified by sequence identity with the bacterial GAPDHs. gapB is positioned within a gene cluster, where it is found immediately upstream of the pgk and fda glycolysis genes (see page 5218; meets claims 4 and 6).
Moreover, Seta discloses that infection by phage P1 of theBJ5183 cells with gapB deleted (DS109) was quite efficient, as seen by the yield of phage (109 PFU/ml), compared with that of the DgapA strain (DS108), which could not be infected. The transformed DS108 (DgapA) strain with plasmids over expressing the GAPDH encoded either by the E. coli gapA gene(plasmid pBS::EcogapA) or the Bacillus stearothermophilus gapA gene (plasmid B1b). Infection by phage P1 was re-stored in both transformed strains, and the latter was chosen for the phage P1 infection. Lending to a potential role of GAPDH, encoded by the gapA gene, for phage infection, which may suggest another biological function for the GAPDH. In this respect, it is worth noting that GAPDH has been found to associate with membranes of both gram-positive bacteria and eukaryotes (see page 5218; meets claims 4-5, 7 and 38).
Further, Seta discloses that they transformed the DS108 (DgapA) strain with plasmids overexpressing the GAPDH encoded either by the E. coli gapA gene(plasmid pBS::EcogapA) or the Bacillus stearothermophilus gapA gene (plasmid B1b). Strains with deletions of the gapA gene (DS112) or both gapA and gapB genes (DS113) could grow on M63 medium supplemented with a combination of succinate and glycerol, but not on glucose or glycerol alone and, to that extent, behaved like the DF221 strain described previously (12). This data indicated that endogenous gapB-encoded protein, which is produced at a low level and displays very low GAPDHase activity (see page 5219; meeting claims 1-2 and 8) was not sufficient to complement a gapA deletion and thus played no relevant role in glycolysis. Expression of gapA gene in the DS113 strain totally restored the ability of this strain to grow on glucose (data not shown), confirming the essential role of gapA for glycolysis. The DgapA (DS112) and DgapA DgapB (DS113) strains did not give rise to revertant on glucose, in contrast to the DF221 strain (12), indicating that the DgapA phenotype was not suppressed by mutations in gapB or by other genetic events (see page 5220; meeting claims 2 and 73).
As it pertains to claim 100, the claimed composition is substantially identical to that of Serta, it inherently possess the same properties as that of kit, absent evidence to the contrary. Since the Office does not have the facilities for examining and comparing applicants’ composition with the composition of the prior art, the burden is on applicant to show a novel or unobvious difference between the claimed product and the prior art. See In re Best, 562 F.2d 1252, 195 USPQ 430 (CCPA 1977) and In re Fitzgerald et al., 205 USPQ 594.
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.
7. Claim(s) 14 is rejected under 35 U.S.C. 103 as being unpatentable over Seta et al., Journal of Bacteriology, 1997; 179(16): 5218-5221, as applied to claims 1-2, 4-7, 11, 13, 38, 73 and 100 above, and further in view of Lessard, Chapter 11, Methods in Enzymology; 533:181-189.
Independent claim 1 is drawn to a microbial cell lacking or having decreased expression of an endogenous glycolytic gene that encodes a glycolytic enzyme, wherein the microbial cell comprises a nucleic acid construct comprising an expression cassette that encodes a recombinant glycolytic enzyme, and wherein the microbial cell can grow in a defined medium and/or a complex medium.
Dependent claim 14 is drawn to the microbial cell of claim 1, wherein: (a) the complex medium is Luria Broth (LB), Terrific Broth, Super Optimal broth with Catabolite repression (SOC media), or any derivative thereof; and/or (b) the defined medium is Korz broth, M9 minimal media, or any derivative thereof.
Seta teaches the limitations as set forth above.
Lessard teaches growth media for E. coli. Liquid growth media are used to recover bacteria immediately following the transformation step as well as to increase the number of bacteria from a colony or a glycerol stock. All E. coli require some basic nutrients for survival. These include vitamins and minerals (provided by yeast extract), as well as a source of nitrogen to aid in nucleic acid and amino acid production (provided by tryptone). Variations in the growth medium allow scientists to optimize the growth rate, plasmid yield, and transformation efficiency depending on the application and the bacterial strain used. Four important E. coli growth media are described:
1.1. LB: ‘Lysogeny’ or Luria broth (LB) is the most commonly used growth medium for E. coli. It promotes fast growth and provides good plasmid yields, making it an excellent choice for most applications, especially small-scale plasmid preps.
1.2. TB: ‘Terrific broth’ is richer than LB and includes glycerol as an energy source, leading to faster growth and consequently a higher yield of bacteria per volume. It also contains potassium phosphates to lower the chance of cell death due to a drop in pH. TB is a good choice for the growth of larger cultures or bacteria carrying low copy number plasmids. Check the manufacturer’s recommendations before using it with plasmid prep kits as it may promote the growth of too many bacteria, which can overload the purification columns (see Explanatory Chapter: How Plasmid Preparation Kits Work).
1.3. 2 YT: 2 YT is richer than LB, but very similar in its composition. It is especially useful for culturing phage-infected bacteria.
1.4. SOC: ‘Super optimal broth with catabolite repression’ is primarily used for the recovery step following transformation. A combination of salt, magnesium, and glucose stabilizes the bacteria and promotes plasmid uptake, thereby increasing transformation efficiency (see pages 181-182).
It would have been obvious before the effective filing date of the presently claimed invention to employ complex mediums as a source of vitamins and minerals, as well as a source of nitrogen for E. coli with a reasonable expectation of success. This modification may be viewed as the substitution of a particular medium which was known and suggested in the art for their use in E. coli growth media generally suggested by the combined teachings of Lessard. The skilled artisan would have been motivated to make this modification because variations in the growth medium allow scientists to optimize the growth rate, plasmid yield, and transformation efficiency. Additionally, Luria broth (LB), for instance, is the most commonly used growth medium for E. coli as it promotes fast growth and provides good plasmid yields, making it an excellent choice for most applications, especially small-scale plasmid preps.
The skilled artisan would have had a reasonable expectation of success because the substitution of one known element for another would have yielded predictable results to one of ordinary skill in the art at the time of the invention. See the recent Board decision Ex parte Smith,--USPQ2d--, slip op. at 20, (Bd. Pat. App. & Interf. June 25, 2007) (citing KSR, 82 USPQ2d at 1396). Accordingly, the subject matter of claim 14 would have been prima facie obvious to one of ordinary skill in the art before the effective filing date of the presently claimed invention, absent evidence to the contrary.
Conclusion
8. No claim is allowed.
9. The prior art made of record and not relied upon is considered pertinent to applicant's disclosure. Burke et al., WO 2007/103389.
10. Any inquiry concerning this communication or earlier communications from the examiner should be directed to LAKIA J JACKSON-TONGUE whose telephone number is (571)272-2921. The examiner can normally be reached Monday-Friday 930AM-530PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Daniel Kolker can be reached at (571) 272-3181. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/LAKIA J JACKSON-TONGUE/ Examiner, Art Unit 1645 March 6, 2026
/BRIAN GANGLE/ Primary Examiner, Art Unit 1645