DETAILED CORRESPONDENCE
Status of the Application
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Claims 34-46, 48-57, 59, 60, and 62-71 are pending in the application.
Applicant’s amendment to the claims, filed June 10, 2026, is acknowledged. This listing of the claims replaces all prior versions and listings of the claims.
Applicant’s remarks filed June 10, 2026 in response to the non-final rejection filed March 23, 2026 have been fully considered.
Claims 47 and 61 have been canceled by applicant’s amendment filed June 10, 2026 and any objection and rejection previously applied to claims 47 and 61 is/are withdrawn.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Restriction/Election
In response to a requirement for restriction/election mailed May 14, 2025, applicant elected with traverse the invention of Group II, pending claims 46, 48-52, 55, 59, 60, and 62-71, and species (E6), the at least one mutated gene is a gene involved in Lpp functionality and consists of the complete deletion of the ybiS gene, in the reply filed on July 11, 2025. The requirement was deemed proper and made FINAL in the non-final rejection mailed August 1, 2025.
Claims 34-45, 53, 54, 56, and 57 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim.
Claims 49, 51, 52, 55, 59, 62, 63, and 66-69 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to nonelected species, there being no allowable generic or linking claim.
Claims 46, 48, 50, 60, 64, 65, 70, and 71 are being examined on the merits only to the extent the claims read on the elected subject matter.
Claim Objections
The objections to claims 46 and 60 are withdrawn in view of applicant’s amendment to claim 46 to recite “envelope” and applicant’s amendment to claim 60 to recite “said at least one amplified extra-genomic nucleic acid molecule.”
Claims 60 and 70 are objected to because of the following informalities:
Claim 60 is objected to in the recitation of "the at least extra-genomic nucleic acid molecule" in the last line of step a) and in the interest of improving claim form, it is suggested that the term "one" be inserted between "least" and "extra-genomic."
Claim 70 is objected to in the recitation of “wherein the step of lysing the bacteria comprises subjecting said bacteria to an osmotic shock,” which is redundant to claim 46, which also recites “wherein the step of lysing the bacteria comprises subjecting said bacteria to an osmotic shock.” In the interest of improving claim form, it is suggested that claim 70 be amended to recite “The method of claim 46, wherein said osmotic shock corresponds to a decrease in osmotic concentration of at least about 10%.”
Claim Rejections - 35 USC § 112(b)
The rejection of claims 46, 48, 50, 60, 64, and 65 under 35 U.S.C. 112(b) is withdrawn in view of applicant’s amendment to claim 46 to recite “as compared to an E. coli bacterium that has not been genetically modified to mutate or delete the ybiS gene,” and applicant’s amendment to claim 50 to recite “wherein the genetically modified E. coli bacteria comprises a complete deletion of the ybiS gene.”
Claim Rejections - 35 USC § 103
The rejection of claims 46, 48, 50, 64, and 65 under 35 U.S.C. 103 as being unpatentable over Chen et al. (Microbial Biotechnology 7:360-370, 2014; cited on the IDS filed September 2, 2022; hereafter “Chen”) in view of Sanders (Microbiology 159:1842-1852, 2013; cited on Form PTO-892 mailed August 1, 2025; hereafter “Sanders”) and Yu et al. (Nucleic Acids Research 36:e84, 2008, 8 pages; cited on Form PTO-892 mailed August 1, 2025; hereafter “Yu”) is withdrawn in view of applicant’s amendment to claim 46 to recite “wherein the step of lysing the bacteria comprises subjecting the bacteria to an osmotic shock.” The combination of Chen, Sanders, and Yu does not teach or suggest osmotic shock.
Claims 46, 48, 50, 64, 65, and 70 are rejected under 35 U.S.C. 103 as being unpatentable over Chen in view of Sanders, Yu, Peterson et al. (U.S. Patent No. 3,589,982; cited on the attached Form PTO-892; hereafter “Peterson”), and Chen et al. (Biochem. Engineer. J. 19:211-215, 2004; cited on the attached Form PTO-892; hereafter “Chen-2”).
As amended, the claims are drawn to a method for the production and the purification of at least one polypeptide comprising the steps of:
a) culturing genetically modified E. coli bacteria comprising at least one mutated or deleted ybiS gene, said bacteria having an altered envelope integrity and being oversensitive to bacterial lysis as compared to an E. coli bacterium that has not been genetically modified to mutate or delete the ybiS gene, said bacteria comprising a nucleic acid molecule encoding the at least one polypeptide, so as to amplify the at least one polypeptide;
b) lysing the bacteria obtained at step a) so as to obtain a lysis mixture; and
c) purifying said at least one polypeptide from the lysis mixture obtained at step b),
wherein the step of lysing the bacteria comprises subjecting said bacteria to an osmotic shock.
Chen is related to the construction of leaky strains and extracellular production of exogenous proteins in recombinant Escherichia coli (see title). Chen teaches that while fermentation conditions have been explored to achieve extracellular production of recombinant proteins in E. coli, there is a disadvantage in that fermentation conditions vary greatly with different target proteins and to overcome the uncertainty of the fermentation conditions, the construction of leaky strains will become a main alternative to transport periplasmic-directed recombinant proteins into media (p. 361, column 1, middle). Chen teaches further studies to improve the extracellular production of the target proteins have become inevitable (p. 361, column 1, bottom) and teaches construction of leaky strains of E. coli by knocking out genes related to the biosynthesis of cell wall and membrane, especially of the outer membrane genes such as lpp encoding Braun’s lipoprotein (p. 361, column 1, middle). Chen teaches expression and analysis of recombinant proteins expressed in the leaky strains, including a determination of the secretory efficiency by comparing the intracellular and extracellular protein levels of the recombinant proteins (p. 365, column 1, top; p. 367, paragraph bridging columns 1-2).
Regarding claim 46, step a) and claims 50, 64, and 65, Chen teaches E. coli JM109 (DE3) is a popular host for the expression of recombinant proteins (p. 361, column 1, last paragraph). Chen teaches that in theory, the disruption of mrcA and mrcB genes encoding peptidoglycan synthetase or the disruption of pal gene encoding the peptidoglycan-associated outer membrane lipoprotein may cause the deficiencies in the structures of cell walls and outer membranes (p. 361, column 2, second full paragraph). Chen teaches E. coli JM109 (DE3) with single or double deletion of genes mrcA, mrcB, pal, and lpp (p. 361, column 2, third paragraph). Chen teaches the E. coli mutants were transformed with an expression vector for reteplase (rPA) (p. 364, column 1) and cultured in TB medium for expression of rPA in the cytoplasm (p. 365, column 1, top). Chen teaches the results suggested that double deletion of peptidoglycan synthetase genes and outer membrane genes may increase the outer membrane permeability enough for the leakage of periplasmic protein without affecting the growth of these strains significantly in complex media (p. 366, column 1, top).
Regarding claim 46, step b), Chen teaches preparing samples for analysis of recombinant proteins including a step of ultrasonication (p. 367, column 2, top). Chen’s step of ultrasonication is considered to be encompassed by step b) of claim 46 because one of ordinary skill in the art would have recognized that ultrasonication results in cell lysis.
Regarding claim 46, step c), Chen teaches centrifugation of the sonicate and collecting a supernatant fraction and a pellet/precipitate fraction (p. 367, column 2, top). Chen’s step of centrifuging the sonicate and collecting a supernatant fraction is considered to be encompassed by step c) of claim 46 because the cytoplasmic rPA within the sonicate is separated from the cellular debris by centrifugation and collecting of the supernatant fraction, which resulted in at least some level of purification of the cytoplasmic rPA as compared to the whole cell sonicate.
Regarding claim 48, as stated above, Chen teaches the E. coli mutants harboring an expression vector (i.e., plasmid) for rPA were cultured in TB medium for expression of rPA in the cytoplasm (p. 365, column 1, top).
The differences between the claimed method and the method of Chen is that Chen does not teach or suggest:
a mutated or deleted ybiS gene as recited in claims 46, 50, 64, and 65; and
while Chen teaches cell lysis by ultrasonication, Chen does not teach cell lysis by osmotic shock as recited in claims 46 and 70.
Regarding difference 1), Sanders teaches ErfK, YbiS, and Ycfs enzymes function by covalently attaching Braun’s lipoprotein to peptidoglycan (p. 1843, column 1, bottom) and are responsible for the attachment of Braun’s lipoprotein to the cell wall (p. 1848, column 1). Sanders teaches an E. coli mutant with deletion of ybiS, erfK, and ycfS genes (referred to as Δldt3), which leaked periplasmic proteins into a culture supernatant (p. 1842, abstract; p. 1846, column 1, bottom).
Yu teaches a method for gene deletion in E. coli (see whole document).
In view of the combined teachings of Chen, Sanders, and Yu, it would have been obvious to one of ordinary skill in the art before the effective filing date to completely delete ybiS, erfK, and ycfS genes in an E. coli JM109 (DE3) host cell and determine the resulting secretory efficiency according to Chen. One would have been motivated to do this because Chen taught the inevitability of further studies to improve the extracellular production of target proteins and taught constructing leaky strains by knocking out genes related to the biosynthesis of cell wall and membrane will become a main alternative to transport periplasmic-directed recombinant proteins into media, and Sanders taught knocking out ybiS, erfK, and ycfS genes, which are related to the biosynthesis of cell wall, had the effect of leaking periplasmic proteins. Given that the sequences for each of ErfK, YbiS, and Ycfs enzymes are taught by Sanders (p. 1845, Figure 1), Yu taught a method for gene deletion in E. coli, and Chen taught a method for determining secretory efficiency of a leaky strain, one would have expected success to completely delete ybiS, erfK, and ycfS genes in a E. coli JM109 (DE3) host and determine its secretory efficiency of a recombinantly-expressed protein.
Regarding the limitation “said bacteria…being oversensitive to bacterial lysis” in step a) of claim 46, the phrase “oversensitive to bacterial lysis” is interpreted as meaning any level or amount of increased sensitivity to bacterial lysis as compared to a bacterium with unaltered envelop integrity. The combination of Chen, Sanders, and Yu does not explicitly teach an E. coli JM109 (DE3) host cell with deletion of ybiS, erfK, and ycfS genes is “oversensitive to bacterial lysis.” However, given that an E. coli JM109 (DE3) host cell with deletion of ybiS, erfK, and ycfS genes has a cell wall deficiency and leaked periplasmic proteins into a culture supernatant, it is presumed that an E. coli JM109 (DE3) host cell with deletion of ybiS, erfK, and ycfS genes has the property of being “oversensitive to bacterial lysis” as recited in step a) of claim 1.
Regarding difference 2), decades before the effective filing date, osmotic shock as a method for cell lysis was well-known in the prior art. For example, Peterson teaches “various known procedures” for extracting a protein produced by a bacterial cell including ultra-sonic energy (sonication), i.e., ultrasonication, or osmotic shock for cell lysis (column 2, lines 45-52).
Chen-2 teaches that in a standard osmotic shock, cells are first suspended in a solution of 20% sucrose supplemented with EDTA and following centrifugation, the cells are resuspended in cold water (p. 211, column 2, top; p. 212, column 1, bottom). The “standard osmotic shock” of Chen-2 corresponds to a 20% decrease in osmotic concentration of sucrose.
In view of the combined teachings of Chen, Peterson, and Chen-2, it would have been obvious to one of ordinary skill in the art before the effective filing date to substitute Chen’s ultrasonication with osmotic shock for cell lysis. One of ordinary skill would have expected success and could have substituted Chen’s ultrasonication with osmotic shock for cell lysis because Peterson taught “various known procedures” for extracting a protein produced by a bacterial cell including osmotic shock for cell lysis, and Chen-2 taught a procedure for a “standard osmotic shock.” One of ordinary skill would have found it obvious to make the substitution because, based on the relevant teachings of Peterson, an ordinarily skilled artisan would have predicted that osmotic shock is an alternative to ultrasonication for cell lysis.
Therefore, the invention of claims 46, 48, 50, 64, 65, and 70 would have been obvious to one of ordinary skill in the art before the effective filing date.
RESPONSE TO REMARKS: Applicant argues that by amendment to claim 46 to recite “wherein the step of lysing the bacteria comprises subjecting said bacteria to an osmotic shock,” applicant’s superior and unexpected results are now commensurate in scope with the claimed invention.
Applicant’s arguments and allegation of unexpected results are not found persuasive. According to MPEP 716.02(e), applicant’s results must be compared with the closest prior art, which is Chen or Sanders. However, applicant’s results are not a comparison with the deletion mutants of Chen and/or Sanders. Also, according to MPEP 716.02(d), applicant’s results must be commensurate in scope with the claimed invention. In this case, applicant’s results are based on the effects of deleting the entire ybiS gene, however, with the exception of claim 50, the claims do not require a deletion of the entire ybiS gene. Rather, the claims recite a “mutated” or “deleted” ybis gene, which encompasses any mutations and/or partial deletions of a ybiS gene and while nonobviousness of a broader claimed range can be supported by evidence based on unexpected results from testing a narrower range (MPEP 716.02(d).I), there is no evidence of record or line of reasoning to support the position that applicant’s results due to deleting the entire ybiS gene would be expected to extend to all mutations and/or partial deletions of a ybiS gene.
For these reasons, it is the examiner's position that the applicant's results fail to rebut a prima facie case of obviousness and the claimed invention would have been obvious to one of ordinary skill in the art before the effective filing date.
Claim 60 is rejected under 35 U.S.C. 103 as being unpatentable over Chen in view of Sanders and Yu.
As amended, claim 60 is drawn to a method for the production and the purification of at least one extra-genomic nucleic acid molecule, comprising the steps of:
a) culturing genetically modified E. coli bacteria comprising at least one mutated or deleted ybiS gene, said bacteria having an altered envelop integrity and being oversensitive to bacterial lysis as compared to an E. coli bacterium that has not been genetically modified to mutate or delete the ybiS gene, said bacteria comprising the at least one extra-genomic nucleic acid molecule so as to amplify the at least extra-genomic nucleic acid molecule;
b) lysing the bacteria obtained at step a) so as to obtain a lysis mixture; and
c) purifying said at least one amplified extra-genomic nucleic acid molecule from the lysis mixture obtained at step b).
Chen is related to the construction of leaky strains and extracellular production of exogenous proteins in recombinant Escherichia coli (see title). Chen teaches that while fermentation conditions have been explored to achieve extracellular production of recombinant proteins in E. coli, there is a disadvantage in that fermentation conditions vary greatly with different target proteins and to overcome the uncertainty of the fermentation conditions, the construction of leaky strains will become a main alternative to transport periplasmic-directed recombinant proteins into media (p. 361, column 1, middle). Chen teaches further studies to improve the extracellular production of the target proteins have become inevitable (p. 361, column 1, bottom) and teaches construction of leaky strains of E. coli by knocking out genes related to the biosynthesis of cell wall and membrane, especially of the outer membrane genes such as lpp encoding Braun’s lipoprotein (p. 361, column 1, middle). Chen teaches expression and analysis of recombinant proteins expressed in the leaky strains, including a determination of the secretory efficiency by comparing the intracellular and extracellular protein levels of the recombinant proteins (p. 365, column 1, top; p. 367, paragraph bridging columns 1-2).
Regarding claim 60, step a), Chen teaches E. coli JM109 (DE3) is a popular host for the expression of recombinant proteins (p. 361, column 1, last paragraph). Chen teaches that in theory, the disruption of mrcA and mrcB genes encoding peptidoglycan synthetase or the disruption of pal gene encoding the peptidoglycan-associated outer membrane lipoprotein may cause the deficiencies in the structures of cell walls and outer membranes (p. 361, column 2, second full paragraph). Chen teaches E. coli JM109 (DE3) with single or double deletion of genes mrcA, mrcB, pal, and lpp (p. 361, column 2, third paragraph). Chen teaches the E. coli mutants were transformed with an expression vector for reteplase (rPA) (p. 364, column 1) and cultured in TB medium for expression of rPA in the cytoplasm (p. 365, column 1, top). Chen’s expression vector for rPA is considered to be encompassed by “extra-genomic nucleic acid molecule” in claim 60. Chen teaches the results suggested that double deletion of peptidoglycan synthetase genes and outer membrane genes may increase the outer membrane permeability enough for the leakage of periplasmic protein without affecting the growth of these strains significantly in complex media (p. 366, column 1, top).
Regarding claim 60, step b), Chen teaches preparing samples for analysis of recombinant proteins including a step of ultrasonication (p. 367, column 2, top). Chen’s step of ultrasonication is considered to be encompassed by step b) of claim 60 because one of ordinary skill in the art would have recognized that ultrasonication results in cell lysis.
Regarding claim 60, step c), Chen teaches centrifugation of the sonicate and collecting a supernatant fraction and a pellet/precipitate fraction (p. 367, column 2, top). Chen’s step of centrifuging the sonicate and collecting separate supernatant and pellet/precipitate fractions is considered to be encompassed by step c) of claim 60 because the expression vector for rPA within the sonicate is separated by centrifugation into the supernatant fraction and/or pellet/precipitate fraction and the supernatant fraction and pellet/precipitate fraction are each collected, which resulted in at least some level of purification of the expression vector for rPA as compared to the whole cell sonicate.
The difference between the claimed method and the method of Chen is that Chen does not teach or suggest a mutated or deleted ybiS gene.
Sanders teaches ErfK, YbiS, and Ycfs enzymes function by covalently attaching Braun’s lipoprotein to peptidoglycan (p. 1843, column 1, bottom) and are responsible for the attachment of Braun’s lipoprotein to the cell wall (p. 1848, column 1). Sanders teaches an E. coli mutant with deletion of ybiS, erfK, and ycfS genes (referred to as Δldt3), which leaked periplasmic proteins into a culture supernatant (p. 1842, abstract; p. 1846, column 1, bottom).
Yu teaches a method for gene deletion in E. coli (see whole document).
In view of Chen, Sanders, and Yu, it would have been obvious to one of ordinary skill in the art before the effective filing date to completely delete ybiS, erfK, and ycfS genes in an E. coli JM109 (DE3) host cell and determine the resulting secretory efficiency according to Chen. One would have been motivated to do this because Chen taught the inevitability of further studies to improve the extracellular production of target proteins and taught constructing leaky strains by knocking out genes related to the biosynthesis of cell wall and membrane will become a main alternative to transport periplasmic-directed recombinant proteins into media, and Sanders taught knocking out ybiS, erfK, and ycfS genes, which are related to the biosynthesis of cell wall, had the effect of leaking periplasmic proteins. Given that the sequences for each of ErfK, YbiS, and Ycfs enzymes are taught by Sanders (p. 1845, Figure 1), Yu taught a method for gene deletion in E. coli, and Chen taught a method for determining secretory efficiency of a leaky strain, one would have expected success to completely delete ybiS, erfK, and ycfS genes in a E. coli JM109 (DE3) host and determine its secretory efficiency of a recombinantly-expressed protein.
Regarding the limitation “said bacteria…being oversensitive to bacterial lysis” in step a) of claim 60, the phrase “oversensitive to bacterial lysis” is interpreted as meaning any level or amount of increased sensitivity to bacterial lysis as compared to a bacterium with unaltered envelop integrity. The combination of Chen, Sanders, and Yu does not explicitly teach an E. coli JM109 (DE3) host cell with deletion of ybiS, erfK, and ycfS genes is “oversensitive to bacterial lysis.” However, given that an E. coli JM109 (DE3) host cell with deletion of ybiS, erfK, and ycfS genes has a cell wall deficiency and leaked periplasmic proteins into a culture supernatant as taught by Sanders, it is presumed that an E. coli JM109 (DE3) host cell with deletion of ybiS, erfK, and ycfS genes has the property of being “oversensitive to bacterial lysis” as recited in step a) of claim 60.
Therefore, the invention of claim 60 would have been obvious to one of ordinary skill in the art before the effective filing date.
RESPONSE TO REMARKS: Applicant argues the obviousness rationale is directed to a method for producing and purifying proteins, however, claim 60 is directed to production and purification of at least one extra-genomic nucleic acid molecule and thus, according to applicant, the rejection does not establish a prima facie case of obviousness. Applicant argues the combination of cited prior art fails to teach or suggest purification of nucleic acids from a lysis mixture because while Chen describes expression vectors, the “pellet” fraction disclosed in Chen is not a lysis mixture and there is no teaching or suggestion that cell lysis has occurred. Applicant argues that even if cell lysis has occurred, there is no teaching or suggestion of obtaining pure or substantially pure nucleic acids from the sonicated mixture.
Applicant’s arguments are not found persuasive. For the reasons set forth above, Chen’s method of determining secretory efficiency using an E. coli JM109 (DE3) host cell modified to completely delete ybiS, erfK, and ycfS genes is encompassed by claim 60. As stated above, regarding claim 60, step b), Chen teaches preparing samples for analysis of recombinant proteins including a step of ultrasonication (p. 367, column 2, top). Chen’s step of ultrasonication is considered to be encompassed by step b) of claim 60 because one of ordinary skill in the art would have recognized that ultrasonication results in cell lysis, and regarding claim 60, step c), Chen teaches centrifugation of the sonicate and collecting a supernatant fraction and a pellet/precipitate fraction (p. 367, column 2, top). Chen’s step of centrifuging the sonicate and collecting separate supernatant and pellet/precipitate fractions is considered to be encompassed by step c) of claim 60 because one of ordinary skill in the art would have recognized that the expression vector for rPA is within the sonicate, and the expression vector for rPA within the sonicate is separated by centrifugation into the collected supernatant fraction and/or pellet/precipitate fraction, which resulted in at least some level of purification of the expression vector for rPA as compared to the whole cell sonicate. While applicant argues the cited prior art does not teach pure or substantially pure nucleic acids from the sonicated mixture, the claims do not require any particular level of purification and do not require obtaining pure or substantially pure nucleic acids.
For these reasons, it is the examiner’s position that the claimed invention would have been prima facie obviousness to one of ordinary skill in the art before the effective filing date.
Claims 60 and 71 are rejected under 35 U.S.C. 103 as being unpatentable over Cooke et al. (J. Biotechnol. 85:297304, 2001; cited on the attached Form PTO-892; hereafter “Cooke”) in view of Chen and Sanders.
Cooke teaches processes based on recombinant DNA technology require extensive characterization in order to meet international regulatory agency requirements for biotherapeutics, concerning both product- and process-derived impurities and contaminants (p. 298, column 1, top). Cooke teaches RNA contamination of plasmid biotherapeutics must be minimized (p. 298, column 1, bottom) and discloses a method for enhancing large-scale purification of essentially RNA-free plasmid DNA by producing the plasmid DNA using an E. coli modified with a chromosomal RNase A expression cassette (p. 299, column 1, top). Cooke teaches the expressed RNase is translocated to the periplasm of the E. coli and is released during plasmid extraction by alkaline lysis (p. 297, Abstract).
Regarding claim 60, step a), Cooke teaches construction of a modified E. coli JM107 plasmid host with an RNase expression cassette integrated into the host chromosome, referred to as JMRNase A (p. 297, Abstract; p. 300, section 2.3). Cooke teaches growth of JMRNase A transformed with a test plasmid (p. 300, column 2; p. 301, Figure 2).
Regarding claim 60, steps b) and c) and claim 71, Cooke teaches isolating and purifying plasmid DNA from E. coli cells by alkaline lysis followed by isopropanol precipitation (p. 299, column 2, middle).
The difference between claims 60 and 71 and the method of Cooke is that Cooke does not teach or suggest a mutated or deleted ybiS gene.
Chen teaches the extracellular secretion of target proteins can offer a better environment for protein folding and reduce the risk of intracellular enzyme degradation (p. 360, column 2, bottom). Chen teaches the construction of leaky strains will become a main alternative to transport periplasmic-directed recombinant proteins into media and teaches leaky strains are constructed by knocking out genes related to biosynthesis of cell wall and membrane, especially of the outer membrane genes such as lpp encoding Braun’s lipoprotein (p. 361, column 1, middle).
Sanders teaches ErfK, YbiS, and Ycfs enzymes function by covalently attaching Braun’s lipoprotein to peptidoglycan (p. 1843, column 1, bottom) and are responsible for the attachment of Braun’s lipoprotein to the cell wall (p. 1848, column 1). Sanders teaches an E. coli mutant with deletion of ybiS, erfK, and ycfS genes (referred to as Δldt3), which leaked periplasmic proteins into a culture supernatant (p. 1842, abstract; p. 1846, column 1, bottom).
In view of the combined teachings of Cooke, Chen, and Sanders, it would have been obvious to one of ordinary skill in the art before the effective filing date to modify the JMRNase A of Cooke’s method by knocking out ybiS, erfK, and ycfS genes. One would have been motivated to do this because Cooke taught the expressed RNase is directed to the periplasm, Chen taught constructing leaky strains by knocking out genes related to the biosynthesis of cell wall and membrane will become a main alternative to transport periplasmic-directed recombinant proteins into media, and Sanders taught knocking out ybiS, erfK, and ycfS genes, which are related to the biosynthesis of cell wall, had the effect of leaking periplasmic proteins.
Regarding the limitation “said bacteria…being oversensitive to bacterial lysis” in step a) of claim 60, the phrase “oversensitive to bacterial lysis” is interpreted as meaning any level or amount of increased sensitivity to bacterial lysis as compared to a bacterium with unaltered envelop integrity. The combination of Cooke, Chen, and Sanders does not explicitly teach the JMRNase A of Cooke’s method modified by knocking out ybiS, erfK, and ycfS genes is “oversensitive to bacterial lysis.” However, given that Sanders taught an E. coli JM109 (DE3) host cell with deletion of ybiS, erfK, and ycfS genes has a cell wall deficiency and leaked periplasmic proteins into a culture supernatant, it is presumed that the JMRNase A of Cooke’s method modified by knocking out ybiS, erfK, and ycfS genes has the property of being “oversensitive to bacterial lysis” as recited in step a) of claim 60.
Therefore, the invention of claims 60 and 71 would have been obvious to one of ordinary skill in the art before the effective filing date.
Claim Rejections - Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP §§ 706.02(l)(1) - 706.02(l)(3) for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/process/file/efs/guidance/eTD-info-I.jsp.
The provisional rejection of claims 46, 48, 50, 64, and 65 on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 5, and 8 of co-pending application no. 18/413,543 (reference application) is withdrawn in view of applicant’s amendment to limit claim 46 to a method for the production and purification of a polypeptide while the claims of the reference application are directed to a method for producing a plasmid DNA.
Claim 60 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 5, and 8 of co-pending application no. 18/413,543 (reference application).
Regarding instant claim 60, claim 1 of the reference application recites a method for producing plasmid DNA, comprising the following steps (a) to (c):
(a) a step of preparing E. coli, which has a mutation in a gene region associated with maintaining outer membrane properties and has a desired plasmid;
(b) a step of culturing E. coli of (a); and
(c) a step of recovering a desired plasmid from bacterial cells after culture;
claim 2 of the reference application recites wherein step (c) is a step of recovering the desired plasmid by dissolving the outer membrane of the bacterial cell after culturing;
claim 5 of the reference application recites (in relevant part) wherein the gene region directly associated with maintaining physical and/or mechanical outer membrane properties is ybiS; and
claim 8 of the reference application recites wherein the mutation is a complete disruption.
Regarding the limitation “said bacteria…being oversensitive to bacterial lysis” in step a) of claim 60, the phrase “oversensitive to bacterial lysis” is interpreted as meaning any level or amount of increased sensitivity to bacterial lysis as compared to a bacterium with unaltered envelop integrity. The claims of the reference application do not explicitly teach the recited E. coli with a deletion of ybiS is “oversensitive to bacterial lysis.” However, given that the recited E. coli with a deletion of ybiS, which, as recited in claim 5 of the reference application is a gene associated with maintaining physical and/or mechanical outer membrane properties, it is presumed that the recited E. coli with a deletion of ybiS has the property of being “oversensitive to bacterial lysis” as recited in step a) of claim 60.
Therefore, claim 60 of this application is unpatentable over claims 1, 2, 5, and 8 of the reference application. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Claim 71 is provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 2, 5, and 8 of co-pending application no. 18/413,543 (reference application) in view of Cooke.
Regarding instant claim 71, while claim 1, step (c) of the reference application recites a step of recovering a desired plasmid from bacterial cells after culture, the claims of the reference application do not recite lysing the bacteria by alkaline lysis.
Cooke teaches isolating and purifying plasmid DNA from E. coli cells by alkaline lysis followed by isopropanol precipitation (p. 299, column 2, middle).
In view of the teachings of Cooke, it would have been obvious to one of ordinary skill in the art for step (c) of claim 1 of the reference application to encompass alkaline lysis in the recovery of the desired plasmid. One would have been motivated and would have expected success to apply alkaline lysis in the recovery of the desired plasmid because step (c) of claim 1 of the reference application recites a step of recovering a desired plasmid from bacterial cells after culture, and Cooke taught isolating and purifying plasmid DNA from E. coli cells by alkaline lysis followed by isopropanol precipitation.
Therefore, claim 71 of this application is unpatentable over claims 1, 2, 5, and 8 of the reference application in view of Cooke. This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
RESPONSE TO REMARKS: Applicant requests withdrawal of the provisional rejection in accordance with MPEP 804.I.B.1.(b).(i), however, the provisional rejections are not the only remaining rejections in the application.
Conclusion
Status of the claims:
Claims 34-46, 48-57, 59, 60, and 62-71 are pending.
Claims 34-45, 49, 51-57, 59, 62, 63, and 66-69 are withdrawn from consideration.
Claims 46, 48, 50, 60, 64, 65, 70, and 71 are rejected.
No claim is in condition for allowance.
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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DAVID J STEADMAN whose telephone number is (571)272-0942. The examiner can normally be reached Monday to Friday, 7:30 AM to 4:00 PM.
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/David Steadman/Primary Examiner, Art Unit 1656
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