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
The amended claim set filed 27 Feb 2026 is acknowledged. Claims 20-25 and 27-40 are currently pending. Of those, claims 20-25, 27-28, 33, and 36-39 are currently amended, and no claims are new. Claims 30-40 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim.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 telephonic election of 26 Nov 2025 and were acknowledged in the Remarks filed 27 Feb 2026. Claims 1-19, and 26 are cancelled. Claims 20-25 and 27-29 will be examined on the merits herein.
For clarity of the record, references to the specification in this action will use paragraph numbers from the Pre-Grant Publication, US-20240271084-A1 (PTO-892).
Response to Arguments
The Applicants’ arguments filed 27 Feb 2026 are acknowledged. For clarity, in this action, said arguments will be referred to as “Remarks” and the Non-Final Office Action mailed 16 Dec 2025 will be referred to as “NFOA.”
Objection(s) and Rejection(s) Withdrawn
The objection to the drawings (NFOA par. 21-22) is withdrawn in view of the updated drawings.
The objection to claim 21 (NFOA par. 24) is withdrawn in view of the claim amendments.
The rejection of claims 26-28 under 35 U.S.C. 112(b) (NFOA par. 27-28) is withdrawn in view of the claim amendments and arguments.
The rejections of claims 20-22, 25 and 29 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Crannenburgh et al. (NFOA par. 29-32) and claims 20-25 and 29 are rejected under 35 U.S.C. 103 as being unpatentable over Crannenburgh et al. in view of Hägg et al. (NFOA par. 33-38) are withdrawn in view of the claim amendment to move subject matter from claim 26 in claim 20 and arguments pointing out that claim 26 was not previously rejected.
Rejection(s) Maintained
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim Rejections - 35 USC § 112(d)
Claim 25 remains rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, 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. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Regarding claim 25, the claim reads “The recombinant bacterial cell of claim 20, wherein the bacterial genome lacks any gene being capable of functionally complementing the at least one essential gene in the absence of the inducer molecule.” However, claim 20 states that the inactivated gene is “at least one endogenous essential gene”, and the specification defines this term as a gene “which is required for proper function of the bacterial cell” [0023]. If the essential gene is required for the function, it appears that the genome must necessarily lack any gene that is capable of “functionally complementing the at least one essential gene” (i.e. that can also perform the same function), other than the introduced copy of the essential gene, which is defined in claim 20 as having expression “dependent on the presence of said inducer molecule” so it cannot “functionally [complement] … in the absence of the inducer molecule”. Therefore, it appears that claim 25 does not limit claim 20 because it merely recites an inherent outcome from claim 20’s limitation that the at least one essential gene is modified to be expressed in an inducer-dependent manner. If applicant disagrees with this interpretation and feels that claim 25 does limit claim 20, clarification is requested.
Response to Argument
Applicant argues (Remarks pg. 7) that “Genes are often only essential under certain growth conditions, e.g., when specific carbohydrates, amino acids, or other essential growth components are unavailable and they cannot be synthesized. In this regard, some genes are conditionally essential, depending on growth conditions or the genetic background of the cell. By way of example, L-lysine auxotrophic bacteria are unable to synthesize lysine, which is produced from L-aspartate via nine enzymatic steps. If neither lysine nor any of its intermediates are present in the growth medium, each of the nine genes involved may be essential. However, if the gene encoding the first enzyme is mutated and the intermediate B-aspartyl-phosphate is supplied exogenously, the remaining genes can complement the deficiency.
Based on this understanding: within the scope of claim 20, the presence of further genes that may complement the deficiency of the essential gene under certain growth conditions is not excluded; whereas claim 25 explicitly excludes such conditionally essential genes.”
This argument has been carefully considered but is not found persuasive. This argument relies on the understanding of “essential gene” that is commonly used in the field, that essential genes are those that are required for cell growth and/or viability. However, as stated in the NFOA (par. 23) the specification defines the term in a broader way based off of any generic function in the cell: “the specification states “The term “endogenous essential gene” as used herein refers to a gene which is naturally occurring in the genome [(i.e. endogenous)] of the bacterial cell and which is required for proper function of the bacterial cell [(i.e. essential)]” [0023]. This definition is broader than the typical meaning of “essential gene” in the art, which is typically limited to genes that are required for cell growth and/or viability. The specification’s special definition will be used when interpreting the recitation of “at least one endogenous essential gene” in claim 20; the gene(s) is not required to be essential for viability, the gene(s) could be required for any function of the cell.”
In applicant’s example, the mutant lacking the first enzyme in the lysine pathway may be conditionally essential in the manner the term is typically used in; i.e. the cell can grow in certain conditions. However, the term “conditionally essential” is not present in the claim. Instead, “functional complementation” would mean the function is restored; i.e. the cell can catalyze the first reaction in the lysine pathway again. The remaining genes do not complement the deficiency because the mutated protein’s enzymatic function is not regained in different growth conditions.
The examiner agrees that applicant’s description of claim 25 as excluding conditionally essential genes that are only required for growth in certain growth conditions would further limit a claim 20 that includes all essential genes; however, this is not the scope of current claim 25. Applicant may wish to amend the claim, while avoiding introducing new matter, in order to better reflect the intended subject matter.
Claim Rejections - 35 USC § 103
Claims 20-22, 25, and 27-29 remain rejected under 35 U.S.C. 103 as being unpatentable over Crannenburgh et al. (2001; hereafter Crannenburgh; made of record in IDS filed 14 Feb 2024) in view of Papadakis et al. (US-20180371001-A1; hereafter Papadakis; PTO-892).
Regarding claims 20-21, Cranenburgh teaches “two novel Escherichia coli strains (DH1lacdapD and DH1lacP2dapD) that … contain the essential chromosomal gene, dapD, under the control of the lac operator/promoter.” (Abstract). Cranenburgh also discloses that the bacteria contain a deletion of dapD (pg. 2 col. 1 par. 4, pg. 2 col. 2 par. 1 see genotype) and that the lac-controlled dapD gene is inserted into the chromosome/genome of the bacteria (pg. 2 col. 1 par. 5).
Crannenburgh also teaches that the purpose of creating the strain is to “allow antibiotic-free plasmid selection and maintenance” (Title) and “No antibiotic resistance genes or other protein expressing sequences are required on the plasmid, and antibiotics are not necessary for plasmid selection, making these strains a valuable tool for therapeutic DNA and recombinant protein production.” (Abstract). Crannenburgh teaches overcoming this growth defect because “when the strains are transformed with a multicopy plasmid containing the lac operator, the operator competitively titrates the LacI repressor and allows expression of dapD from the lac promoter. Thus transformants can be isolated and propagated simply by their ability to grow on any medium by repressor titration selection.” (Abstract).
Regarding claim 22, 25, Crannenburgh teaches that “dapD encodes tetrahydrodipicolinate Nsuccinyltransferase… DAP cross-links peptidoglycan in the bacterial cell wall (23) and is a precursor for lysine biosynthesis (24). Mutants with disrupted dapD are therefore DAP and lysine auxotrophs. As lysine is present in the rich media often used to grow E.coli (such as LB broth) and DAP is not, dapD mutants will undergo cell lysis unless DAP is added to the medium (25).” (pg. 3 par. bridging cols). The gene is required for cell growth and viability in rich media, and the genome lacks a gene capable of functionally complementing dapD and preventing cell lysis.
Regarding claim 29, the strains use lac or lacP promoters, which are induced by IPTG (pg. 3 col. 2 par. 2 to par. bridging pg. 3-4).
Crannenburgh does not teach the bacteria comprises an expression plasmid which comprises at least one plasmid copy of the at least one essential gene, wherein said plasmid copy is under the control of an expression control sequence that is endogenous to said bacterial cell, as in claim 20, that the plasmid copy is controlled by the native expression control sequence, as in claims 27, or that the expression plasmid further comprises at least one further nucleic acid of interest which is required for recombinant manufacture of a compound of interest in the cell, as in claim 28.
Papadakis teaches a genetically modified cell where a chromosomal (native) gene essential for the growth of said cell is substantially inactivated or deleted, and where the cell comprises an expression plasmid comprising the gene and DNA sequences necessary for the gene’s expression (i.e. an expression plasmid which comprises at least one plasmid copy of the at least one essential gene, wherein said plasmid copy is under the control of the expression control sequence which is biologically active in said bacterial cell) as well as at least one recombinant gene necessary to produce the oligosaccharide product (i.e. said expression plasmid comprises at least one further nucleic acid of interest, which is required for the recombinant manufacture of a compound of interest in said recombinant bacterial cell) [0008-11, 0045-0049]. Papadakis teaches that dapD is an example of an essential gene that can be used in the invention [0023], and is used in a “preferred embodiment” [0026]. Papadakis teaches that the DNA sequence necessary for the gene’s expression can be the native promoter, or “any suitable equivalent DNA sequence that is able to initiate the transcription”, but that a preferred embodiment uses the native promoter (“the whole locus including the upstream and the downstream is inserted in the plasmid to ensure that gene regulatory events are not defected”) [0052]. Papadakis teaches that this has the benefit of producing “an efficient, safe and easily up-scalable process for producing oligosaccharides can be obtained that even fulfils the more and more strict regulatory requirements with regard to the antibiotic-based production systems” [0036].
One of ordinary skill in the art at the time of filing would consider it prima facie obvious to improve the Crannenburgh bacterial cell for recombinant protein production that lacks dapD activity in the typical rich media used to grow cells by adding a plasmid with a copy of dapD and recombinant proteins of interest as taught by Papadakis, thereby arriving at the claimed invention, because Papadakis teaches that use of a plasmid comprising the native gene to overcome an inactivated chromosomal gene is “efficient, safe and easily up-scalable” [0052]. Therefore the combination would be desirable because this expressing an active copy of the gene is known to produce a beneficial recombinant bacterial strain. See MPEP 2144(II): “The strongest rationale for combining references is a recognition, expressly or impliedly in the prior art … that some advantage or expected beneficial result would have been produced by their combination.” This modification can be performed with a reasonable expectation of success because Papadakis specifically teaches that their method can be used to replace an inactive chromosomal dapD (such as in Cranenburgh’s bacteria in typical rich media) with an active plasmid version of the gene, and the molecular biology techniques to generate the plasmid and transform it into the bacteria were within the level of ordinary skill at the time of filing as demonstrated by both references’ use of these techniques.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that applying a known technique to a known device, method or product ready for improvement is obvious because a particular known technique is recognized as part of the ordinary capabilities of one skilled in the art. In the instant case, Crannenburgh contains a “base” product of a E. coli strain with a dapD gene that is inactive in rich media; and Papadakis contains a similar E. coli strain where the dapD gene has been inactivated or deleted wherein the technique of expressing an active copy of dapD on an expression plasmid as a selectable marker instead of using an antibiotic resistance gene is taught as advantageous. Thus, one of ordinary skill in the art would have recognized that applying the known technique taught by Papadakis would have yielded predictable results (i.e. the same advantages) and an improved system. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Alternately, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that the simple substitution of one known element for another to obtain predictable results is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that "the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results". In the instant case, the prior art (Crannenburgh) teaches a product that only differs from the claimed invention by the substitution of a single component (i.e. substitution of the plasmid used to overcome the dapD inactivation and express a recombinant gene used); the substituted element (i.e. the plasmid comprising a recombinant gene and a copy of dapD that is expressed and active in the cell) was already known and already shown to function as a plasmid that can be used to express a recombinant gene and overcome the dapD inactivation, therefore no change in the function of the substituted element occurred; and one of ordinary skill in the art would be capable of substituting one plasmid or plasmid component (the lac operator of Crannenburgh for the active dapD gene of Papadakis) for another with a reasonable expectation of success (i.e. the substitution of the element would lead to predictable results). Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Response to Argument
Applicant argues (Remarks pg. 9) that “Cranenburgh does not teach or suggest that the introduced copy of the at least one essential gene is operatively linked to a heterologous expression control sequence inducible by an inducer molecule. The lac operator/promoter employed by Cranenburgh to control dapD is endogenous to E. coli itself. There is no teaching or suggestion in Cranenburgh to use a heterologous expression control sequence to control the expression of the essential gene copy.”
This argument has been carefully considered but is not found persuasive. The instant specification states: “The term “heterologous expression control sequence being inducible by an inducer molecule” as referred to herein relates to a nucleic acid sequence which is capable when being operatively linked to a coding nucleic acid sequence of a gene to govern the expression of said coding nucleic acid sequence of the gene. …Moreover, the inducible expression control sequence referred to herein shall be heterologous with respect to the wild type, i.e. naturally occurring, bacterial cell, i.e. it shall be an expression control sequence which does not naturally occur in the recombinant bacterial cell or which is not natively associated with the endogenous essential gene in the said bacterial cell.” [0028, emphasis added]. The lac operator/promoter is not natively associated with the endogenous essential gene (dapD), so it is heterologous as defined in the instant specification.
Applicant argues (Remarks pg. 9) that “Cranenburgh's expression control system functions in a fundamentally different manner than the claimed invention. Cranenburgh's expression system functions such that in the presence of the plasmid containing the lac operator, the operator competitively titrates the Lacl repressor and allows expression of dapD from the lac promoter; thus, transformants can be isolated and propagated simply by their ability to grow on any medium by repressor titration selection. Therefore, Cranenburgh's expression system functions via a titrated de-repression of the lac promoter leading to cell viability in the presence of the plasmid. In contrast, in the expression system of the claimed invention, it is the repression of the promoter (via omission of the inducer from the growth medium) that leads to cell viability in the presence of the plasmid. This system enables maintenance of the recombinant bacterial strain in the absence of any plasmid without the need for any antibiotics, antitoxins, repressor titration, auxotrophic complementation, etc., as commonly employed in the prior art. For these reasons, a person of ordinary skill in the art would not have recognized Cranenburgh's expression system as functionally equivalent to that of the claimed invention.”
This argument has been carefully considered but is not found persuasive. In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., promoter repression leading to cell viability) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). Instead, claim 20 states “the expression of said endogenous essential gene in the recombinant bacterial cell is dependent on the presence of said inducer molecule”. In both situations laid out by the applicant’s arguments, the expression of the gene varies in a way that depends on the presence of the inducer molecule, so the claimed limitation is taught by the art.
Applicant argues (Remarks pg. 9-10) that “Cranenburgh discloses that all repressor-titration strains retain the chromosomal kan gene used to replace the deleted dapD gene. They posit next steps to create a derivative deletion strain for kan as well as dapD, and which therefore contains no antibiotic resistance gene. See Cranenburgh at p. 6, last paragraph of Discussion. Therefore, the header of the article and the disclosure in the abstract is misleading with respect to the lack of antibiotic resistance genes.”
This argument has been carefully considered but is not found persuasive. In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., a lack of antibiotic resistance genes) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). The rejection does not assert or rely on bacteria that actually lack antibiotic resistance genes because this is not a claimed feature. Instead, the rejection noted Cranenburgh teaches benefits to their technique/strategy. Applicant has not provided any reason to believe that one of ordinary skill in the art at the time of filing would have doubted that Cranenburgh’s asserted benefit that the antibiotic resistance gene is not required.
Applicant argues (Remarks pg. 9-10) that the teachings of Crannenburgh should be considered “Notwithstanding Papadakis' alleged disclosure of the expression plasmid according to the claimed invention,” and concludes that “Neither Hagg nor Papadakis cure the deficiency of Cranenburgh with respect to the expression system and use of a heterologous expression control sequence according to the claimed invention.”
This argument has been carefully considered but is not found persuasive. The arguments of deficiencies in Cranenbugh’s teachings are not persuasive, as discussed above. So, Hagg and Papadakis are not required to cure the alleged deficiencies.
Double Patenting
Claims 20-25 and 27-29 remain provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 5, 16-17, and 20 of copending Application No. 18/842,950 in view of Cranenburgh et al. (2001; hereafter Cranenburgh; made of record in IDS filed 14 Feb 2024). This is a provisional nonstatutory double patenting rejection.
Regarding instant claims 20 and 25, ‘950 claim 1 (and its dependent claims) teaches “A recombinant bacterial cell comprising in its genome at least one essential gene the endogenous promoter of which has been replaced by a heterologous expression control sequence that is being inducible by an inducer molecule such that the expression of said essential gene in the recombinant bacterial cell is dependent on the presence of said inducer molecule and comprises an expression plasmid containing at least one plasmid copy of the at least one essential gene, wherein said plasmid copy is under the control of the expression control sequence that is biologically active in said bacterial cell.”
Regarding instant claim 21, ‘950 claim 3 teaches the bacterial cell can be from the genus Escherichia.
Regarding instant claim 22, ‘950 claim 2 teaches the at least one essential gene can be one(s) that is/are required for proper cell growth, proliferation and/or survival. Also, ‘950 claim 3 teaches that at least one essential gene can be a gene required for cell growth and/or viability.
Regarding instant claims 23-24, ‘950 claim 3 teaches that the essential gene can be selected from the group consisting of: infA, infC/IF-3, dnai, dnaK, era, frr, ftsL, ftsN, ftsZ, grpE, mopA, mopB, msbA, nusG, parC, rpsB, secY and trmA.
Regarding claim 28, ‘950 claim 5 teaches said expression plasmid can comprise at least one further nucleic acid of interest that is required for the recombinant manufacture of a compound of interest in said recombinant bacterial cell.
Regarding claim 29, ‘950 claim 16 teaches that the heterologous expression control sequence can include AraC/PBAD promoter, RhaR-RhaS/rhaBAD promoter, XylS/Pm promoter, NitR/PnitA promoter, ChnR/Pb inducer/promoter, a tetracycline-inducible promoter (tetON/OFF), a lac//IPTG promoter, an ethanol-inducible promoter (AlcA/AlcR), a steroid- inducible promoter (LexA/XVE), and a vanillate-inducible promoter. Also, ‘950 claims 17 and 20 teach that said inducer molecule can be selected from the group consisting of: arabinose, rhamnose, xylose, sucrose, tetracycline, anhydrotetracycline and IPTG.
The claims of ‘950 do not teach that (i) at least one endogenous essential gene which is inactivated, and (ii) the copy of the said at least one essential gene is an introduced copy of the essential gene, as in claim 20. The claims of ‘950 do not teach that said expression control sequence which is biologically active is the expression control sequence which is natively associated with the at least one endogenous essential gene, as in claim 27.
Regarding claims 20-21, Cranenburgh teaches “two novel Escherichia coli strains (DH1lacdapD and DH1lacP2dapD) that … contain the essential chromosomal gene, dapD, under the control of the lac operator/promoter.” (Abstract). Cranenburgh also discloses that the bacteria contain a deletion of dapD (pg. 2 col. 1 par. 4, pg. 2 col. 2 par. 1 see genotype) and that the lac-controlled dapD gene is inserted into the chromosome/genome of the bacteria (pg. 2 col. 1 par. 5). Cranenburgh teaches that this location was chosen because “there are no genes within 35 kb upstream which could cause transcriptional readthrough and thus dapD expression in the absence of induction or repressor titration” (pg. 3 col. 2 par. 2). Regarding claim 22, 25, Crannenburgh teaches that “dapD encodes tetrahydrodipicolinate Nsuccinyltransferase… DAP cross-links peptidoglycan in the bacterial cell wall (23) and is a precursor for lysine biosynthesis (24). Mutants with disrupted dapD are therefore DAP and lysine auxotrophs. As lysine is present in the rich media often used to grow E.coli (such as LB broth) and DAP is not, dapD mutants will undergo cell lysis unless DAP is added to the medium (25).” (pg. 3 par. bridging cols). The gene is required for cell growth and viability in rich media, and the genome lacks a gene capable of functionally complementing dapD and preventing cell lysis. Regarding claim 29, the strains use lac or lacP promoters, which are induced by IPTG (pg. 3 col. 2 par. 2 to par. bridging pg. 3-4).
Regarding claims 20 and 25-27, Papadakis teaches a genetically modified cell where a chromosomal (native) gene essential for the growth of said cell is substantially inactivated or deleted, and where the cell comprises an expression plasmid comprising the gene and DNA sequences necessary for the gene’s expression (i.e. an expression plasmid which comprises at least one plasmid copy of the at least one essential gene, wherein said plasmid copy is under the control of the expression control sequence which is biologically active in said bacterial cell) as well as at least one recombinant gene necessary to produce the oligosaccharide product (i.e. said expression plasmid comprises at least one further nucleic acid of interest, which is required for the recombinant manufacture of a compound of interest in said recombinant bacterial cell) [0008-11, 0045-0049]. Papadakis teaches that the DNA sequence necessary for the gene’s expression can be the native promoter, or “any suitable equivalent DNA sequence that is able to initiate the transcription”, but that a preferred embodiment uses the native promoter (“the whole locus including the upstream and the downstream is inserted in the plasmid to ensure that gene regulatory events are not defected”) [0052]. Papadakis teaches that this has the benefit of producing “an efficient, safe and easily up-scalable process for producing oligosaccharides can be obtained that even fulfils the more and more strict regulatory requirements with regard to the antibiotic-based production systems” [0036].
One of ordinary skill in the art at the time of filing would consider it prima facie obvious to generate the bacteria of ‘950 by using the method of Crannenburgh to delete the native essential gene and also add an inducible version of the gene, thereby arriving at the claimed invention for all except claim 27, because Crannenburgh teaches that the use of the second location is beneficial to prevent potential transcriptional readthrough that would cause the essential gene to be expressed in the absence of induction. See MPEP 2144(II): “The strongest rationale for combining references is a recognition, expressly or impliedly in the prior art … that some advantage or expected beneficial result would have been produced by their combination.” This modification could be performed with a reasonable expectation of success because Crannenburgh teaches how to perform the modifications, and the resulting inactivated gene falls within the scope of the claims of ‘950.
Also, one of ordinary skill in the art at the time of filing would consider it prima facie obvious to generate the bacteria of ‘950 by using a native promoter as the “expression control sequence which is biologically active in said bacterial cell”, thereby arriving at the claimed invention, because Papadakis teaches that the promoter used for expressing an essential gene is not limited and can be “any suitable equivalent DNA sequence that is able to initiate the transcription”, but that use of a native promoter is beneficial to ensure correct gene expression [0052].. See MPEP 2144(II): “The strongest rationale for combining references is a recognition, expressly or impliedly in the prior art … that some advantage or expected beneficial result would have been produced by their combination.” The modification could be performed with a reasonable expectation of success because Papadakis specifically teaches that any promoter can be used, and the ‘950 claims also recite the same scope of promoters that must only be “biologically active in said bacterial cell”.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that combining prior art elements according to known methods to yield predictable results, is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. In the instant case all elements (i.e. the cell of the claims of ‘950, the method/strategy of generating an inactivated essential gene of Crannenburgh, and the use of a native promoter of Papadakis) were known in the art. In addition, combining these elements yields a method/composition wherein each element merely performs the same function as it does separately; thus the results of the combination would be recognized as predictable to one of ordinary skill in the art. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Response to Arguments
Applicant argues (Remarks pg. 10) that “Applicant respectfully submits that the instant application is an earlier-filed, earlier-expiring application than US'950, and as such does not extend a period of exclusivity on the claimed subject matter beyond the expiration date of US'950. The MPEP provides that "[i]f a provisional nonstatutory double patenting rejection is the only rejection remaining in an application having the earlier patent term filing date, the examiner should withdraw the rejection in the application having the earlier patent term filing date and permit that application to issue as a patent." MPEP at § 804(1)(B)(1)(b)(i).”
This argument has been carefully considered but is not found persuasive because the instant rejection is not the only rejection remaining.
New Rejection(s)
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 20-25 and 27-29 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 20 recites the limitation "said plasmid copy". There is insufficient antecedent basis for this limitation in the claim because the claim has been amended to read “at least one additional copy of the at least one endogenous essential gene” rather than “at least one plasmid copy of the at least one endogenous essential gene” as in the previous claim set’s claim 26. Claims 21-25 and 27-29 are also rejected because they depend from claim 20 and do not obviate this issue. As a suggestion, the claim could be amended to read “said plasmid copy of the at least one endogenous essential gene”, or the like, in order to clearly convey the intent from former claim 26.
Claim Rejections - 35 USC § 103
Claims 20-25 and 27-29 are newly rejected under 35 U.S.C. 103 as being unpatentable over Crannenburgh et al. (2001; hereafter Crannenburgh; made of record in IDS filed 14 Feb 2024) in view of Papadakis et al. (US-20180371001-A1; hereafter Papadakis; PTO-892) as applied to claims 20-22 and 25-29 above, and further in view of Hägg et al. (2004; hereafter Hagg; made of record in IDS filed 14 Feb 2024).
The teachings of Crannenburgh and Papadakis, and the reasoning for combining, were laid out above.
The combination of Crannenburgh and Papadakis does not teach that the at least one endogenous essential gene is selected from the group consisting of: infA, infC/IF-3, dnai, dnaK, era, frr, ftsL, ftsN, ftsZ, grpE, mopA, mopB, msbA, nusG, parC, rpsB, secY and trmA, as in claim 23, or is infA or secY, as in claim 24.
Regarding claims 20-25 and 29, Hagg teaches “an E. coli strain that has been deleted for its chromosomal infA gene” (i.e. the cell has in its genome (i) at least one endogenous essential gene which is inactivated) and also carries a plasmid that “is maintained, since it carries the small essential gene infA (coding for translation initiation factor 1, IF1)” (Abstract). The infA gene is functional when under the control of an IPTG-inducible trc promoter (pg. 23 col. 1 par. 1). Hagg teaches that the infA gene is essential for cell viability (pg. 19 col. 1 par. 2). Hagg teaches that there are benefits to using infA as an essential gene that is chromosomally deleted: “The use of the infA gene for plasmid stabilization does not give any cross-feeding effect, since any IF1-molecules leaking into the media from damaged or lysed cells, cannot be absorbed by plasmid-free cells that may have arisen during cultivation. IF1 is a small protein, consisting of only 71 amino acids (Cummings and Hershey, 1994). This means that the size of any expression vector carrying infA can be maintained small and that the metabolic burden of the plasmid on cellular growth is kept at a minimum. The small size of the vector is an additional advantage of the stability system described here since it allows for insertion of rather large DNA fragments containing any genes desirable for expression.” (pg. 29 col. 1 par. 2). Hagg teaches that the strategy is flexible: “The method described here is not limited to E. coli strains and E. coli based replicons such as the ColE1- replicon derived from pBR322. It can also be used for other bacterial species and/or for other replicons. Appropriate derivatives of plasmids described can be advantageous for use in gene therapy or to serve as DNA vaccines. Furthermore, the stabilization system can be used to modify production systems that are already in use in order to avoid antibiotics and antibiotic resistance genes during large-scale cultivation.” (par. bridging pg. 29-30).
One of ordinary skill in the art at the time of filing would consider it prima facie obvious to improve the bacteria dependent on inducible expression of the essential gene dapD from the combination of Crannenburgh and Papadakis by using infA as an essential gene instead as taught by Hagg, thereby arriving at the claimed invention, because Hagg demonstrates that infA also is functional as an essential gene that can be used for antibiotic-free plasmid selection when expressed in an inducible manner, and because Hagg teaches several benefits of using infA as a knocked out essential gene to maintain plasmids due to its small size, as quoted above. Therefore the combination would be desirable because the art recognizes that infA is a desirable protein to use for antibiotic-free plasmid selection that uses selection pressure from an essential gene. See MPEP 2144(II): “The strongest rationale for combining references is a recognition, expressly or impliedly in the prior art … that some advantage or expected beneficial result would have been produced by their combination.” This modification could be performed with a reasonable expectation of success because Hagg specifically teaches that the infA gene concept is not limited to use in the specific E. coli strains used in their examples and instead can be used to modify production systems that are already in use. This teaches that one of ordinary skill in the art considered the gene manipulations required to make the Crannenburgh gene modification using infA instead of dapD to be within their skill well before the time of filing (note Hagg was published 2004 and the effective filing date is 2021).
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that the simple substitution of one known element for another to obtain predictable results is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that "the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results". In the instant case, the prior art (Crannenburgh) teaches a product that only differs from the claimed invention by the substitution of a single component (i.e. substitution of the essential gene used); the substituted element (i.e. the infA) was already known and already shown to function as an essential gene that can be used to provide selection pressure to maintain a plasmid in the absence of antibiotics, therefore no change in the function of the substituted element occurred; and one of ordinary skill in the art would be capable of substituting one gene sequence for another with a reasonable expectation of success (i.e. the substitution of the element would lead to predictable results). Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Conclusion
No claims are allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/AMELIA NICOLE DICKENS/Examiner, Art Unit 1645
/SAMIRA J JEAN-LOUIS/Supervisory Patent Examiner, Art Unit 1642
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