DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Application Status
This action is written in response to applicant’s correspondence received 9 July 2025. Claims 1, 109-117, and 118-143 are pending. Claims 116-117 and 122-143 remain withdrawn from consideration as being drawn to a non-elected invention. Accordingly, claims 1, 109-115, and 118-121 are currently under examination.
Applicant’s arguments, filed 9 July 2025 have been fully considered and are deemed persuasive. Therefore, the previously presented rejections of the claims under 35 USC 103 have been withdrawn. Accordingly, this action is NON-FINAL.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claim(s) 1, 109, 111, 119, and 121 is/are rejected under 35 U.S.C. 103 as being unpatentable over Lambert (Applied and environmental microbiology 73.4 (2007): 1126-1135) in view of Campo (Applied and environmental microbiology 68.5 (2002): 2359-2367).
Regarding claim 1, Lambert is drawn towards a study concerned with a Cre-lox based system for multiple gene deletions and selectable marker removal in Lactobacillus plantarum (Abstract). Lambert teaches the use of a circular vector that comprises (a) an erythromycin resistance gene under control of a P32 promoter (i.e., a selectable marker) and (b) rare-cutting blunt-end restriction sites SwaI, PmeI, SrfI, and Ecl136II that allow for direct cloning of blunt-end PCR products (i.e., a multiple cloning site) that are flanked by lox71 and lox66 sites (i.e., a first region flanked on either side by a target site for a site-specific recombinase) (pg. 1130; see FIG. 2). Lambert teaches that a P32-cat gene was present on the vector and not within the first region (pg. 1130; see FIG. 2). Lambert teaches that the P32-cat gene was able to replace target genes of interest via homologous recombination and can later be excised from the genome when desired (pg. 1131; see FIG. 3). Lambert teaches the use of a second vector, pNZ5348, that expresses a Cre recombinase (i.e., a site-specific recombinase) and comprises a replicon sequence (pg. 1130). Lambert teaches that more advanced alternative possibilities could also be employed, including expression of Cre from a plasmid in which Cre or the origin of replication is flanked by lox sites to ensure cessation of Cre activity before construction of additional mutations in the same genetic background (pg. 1134).
Lambert does not teach or suggest that the vector further comprises a sequence encoding a site-specific recombinase operably linked to an inducible promoter, or a replicon sequence, wherein the inducible promoter and replicon sequence are not within first said region (Claim 1).
However, one of ordinary skill in the art would have considered the teachings of Campo as both references are common fields of endeavor pertaining to the use of Cre recombinases.
Campo is drawn towards a study concerned with a Cre-loxP recombination system to generate chromosomal rearrangements in L. lactis (Abstract). Campo teaches the use of a circular vector, termed pGH-Cre, that comprises a Cre recombinase under the control of a nisin-inducible promoter, PnisA, and a thermosensitive repA replicon (i.e., a replicon sequence) (pg. 2360-2362; see Table 1 and Fig. 2B). Campo teaches that, in permissive conditions for pGh-Cre replication and Cre expression, the Cre recombinase catalyzes recombination between two loxP sites (pg. 2363).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the vector sequence not present within the first region of Lambert for a vector sequence encoding a Cre recombinase under control of an inducible promoter and a replicon sequence, as described by Campo. A person of ordinary skill in the art would have been motivated to do so in order to express the Cre recombinase under certain conditions and from a target genomic region of interest within a cell when desired. A person of ordinary skill in the art would have had a reasonable expectation of success because Lambert teaches that the vector sequence not present within the first region may comprise a P32-cat gene that can be integrated into, expressed from, and excised from, a target genomic region of interest when desired and indicates that the expressing of Cre from a construct in which Cre or the origin of replication is flanked by lox sites can ensure cessation of Cre activity before construction of additional mutations in the same genetic background while Campo teaches the use of a vector sequence that encodes a Cre protein and further comprises a replicon sequence.
Regarding claim 109, Lambert teaches the use of an erythromycin resistance gene (pg. 1130; see FIG. 2).
Regarding claim 111, Campo teaches that the recombinase is a Cre recombinase (pg. 2360-2362; see Table 1 and Fig. 2B).
Regarding claim 119, Campo teaches that the inducible promoter is a nisin inducible promoter (pg. 2360-2362; see Table 1 and Fig. 2B)
Regarding claim 121, Lambert teaches that the presence of PmeI, SwaI, SrfI, and Ecl136II rare-cutting blunt-end restriction sites in the vector (i.e., the multiple cloning site) allows for cloning of PCR-amplified homologous DNA fragments (i.e., gene targeting sequences) that are upstream and upstream and downstream of a mutagenesis locus, which is necessary for targeting of the vector to the genomic locus of interest (pg. 1129).
Claim 110 is rejected under 35 U.S.C. 103 as being unpatentable over Lambert (Applied and environmental microbiology 73.4 (2007): 1126-1135) in view of Campo (Applied and environmental microbiology 68.5 (2002): 2359-2367) as applied to claims 1, 109, 111, 119, and 121 above, and further in view of Keravala (Molecular Genetics and Genomics 276 (2006): 135-146).
Regarding claim 110, Lambert in view of Campo renders obvious claims 1, 109, 111, 119, and 121 as described above.
Lambert in view of Campo does not teach or suggest the use of a site-specific serine recombinase (Claim 110).
However, one of ordinary skill in the art would have considered the teachings of Keravala as both references are analogous prior art pertaining to the design of vectors comprising site-specific recombinases.
Keravala is drawn to a study concerned with the ability of five serine phage integrases, from phages A118, U153, Bxb1, φFC1, and φRV1, to mediate recombination in mammalian cells (Abstract). Keravala teaches the use of a plasmid comprising a lacZ gene flanked by attP and attB target sites for a serine site-specific recombinase (pg. 137; see Fig. 1). Keravala teaches that φFC1 (i.e., a site-specific serine recombinase) can interact with the attP and attB target sites in order to excise the lacZ gene from the plasmid (pg. 138).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the Cre site-specific recombinase and lox sites of Lambert in view of Campo for a φFC1 serine site-specific recombinase and attP and attB target sites, as described by Keravala. A person of ordinary skill in the art would have had a reasonable expectation of success because both Keravala and Lambert in view of Campo teach the successful use of a site-specific recombinase that can excise a motif of interest from a plasmid via the use of two target sites.
Claim(s) 112-115 and 118 is/are rejected under 35 U.S.C. 103 as being unpatentable over Lambert (Applied and environmental microbiology 73.4 (2007): 1126-1135) in view of Campo (Applied and environmental microbiology 68.5 (2002): 2359-2367) as applied to claims 1, 109, 111, 119, and 121 above, and further in view of Russell (Applied and Environmental Microbiology 67.9 (2001): 4361-4364).
Regarding claims 112-115 and 118, Lambert in view of Campo renders obvious claims 1, 109, 111, 119, and 121 as described above.
Lambert in view of Campo does not specifically teach or suggest that the replicon sequence is a prokaryotic replicon sequence (Claim 112). Lambert in view of Campo does not specifically teach or suggest that the replicon sequence encodes an origin of replication (ori) and replication initiator protein (Rep protein) (Claim 113). Lambert in view of Campo does not specifically teach or suggest that the replicon sequence is a replicon sequence permissive for replication of said vector in a prokaryote host cell (Claim 114), selected from Lactobacilli (Claim 115), or Lactobacillus gasseri (Claim 118).
However, one of ordinary skill in the art would have considered the teachings of Russell as both references are common fields of endeavor pertaining to the use of RepA replicon sequences.
Russell is drawn to a study concerned with an efficient method for the generation of site- specific chromosomal integrations in Lactobacillus acidophilus and Lactobacillus gasseri (Abstract). Russell teaches the use of a plasmid, pTRK669, that comprises an origin of replication and repAC genes (i.e., a replicon sequence) (pg. 4361). Russell teaches that replication of the vector was successfully observed in L. gasseri at 37°C (i.e., Russell is interpreted as teaching the use of a replicon sequence that is permissive for replication in a Lactobacillus gasseri host cell) (pg. 4361).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to substitute the RepA replicon sequence rendered obvious by Lambert in view of Campo for a repAC replicon sequence, as described by Russell. A person of ordinary skill in the art would have had a reasonable expectation of success because Lambert in view of Campo renders obvious the use of a repA replicon sequence that can be utilized to modify bacterial chromosomes and Russell teaches the use of a repAC replicon sequence that can be utilized in bacterial cells.
Claim 120 is rejected under 35 U.S.C. 103 as being unpatentable over Lambert (Applied and environmental microbiology 73.4 (2007): 1126-1135) in view of Campo (Applied and environmental microbiology 68.5 (2002): 2359-2367) as applied to claims 1, 109, 111, 119, and 121 above, and further in view of Cheo (PG Pub No. US 2002/0007051 A1).
Regarding claim 120, Lambert in view of Campo renders obvious claims 1, 109, 111, 119, and 121 as described above.
Lambert in view of Campo does not teach or suggest that the two target sites for said site-specific recombinase are orientated such that the product of site-specific recombination between two target sites for said site-specific recombinase is a first circular DNA product comprising (a) and (b) and a second circular DNA product comprising (c) and (d) (Claim 120).
However, one of ordinary skill in the art would have considered the teachings of Cheo as both references are analogous prior art pertaining to the use of vectors comprising lox sites.
Cheo is drawn to an invention concerned with compositions and methods for recombinational cloning (Abstract). Cheo teaches the use of a single large plasmid comprising motifs that are flanked by loxP sites ([0237]; see FIG. 27A). Cheo teaches that addition of a Cre protein resolves the single large plasmid into two smaller ones (i.e., a first and second plasmid) ([0237]; see FIG. 27A). Cheo teaches that the first plasmid comprises motifs that are located outside of the loxP sites while the second plasmid comprises motifs that are located within the loxP sites ([0237]; see FIG. 27A). Cheo teaches that utilizing Cre and loxP sites in order to split a single plasmid into two different plasmids allows for the loss of undesired motifs present within the loxP sites while simultaneously maintaining desired motifs located outside of the loxP sites ([0237]).
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to modify the vector of Lambert in view of Campo such that the two target sites for said site-specific recombinase are orientated such that the product of site-specific recombination between two target sites for said site-specific recombinase is a first circular DNA product comprising (a) and (b) and a second circular DNA product comprising (c) and (d), as described by Cheo. A person of ordinary skill in the art would have been motivated to do so in order to remove (a) and (b) located within the loxP sites from the plasmid comprising (a)-(e) in order to render the plasmids unable to operate. A person of ordinary skill in the art would have had a reasonable expectation of success because both Cheo and Lambert in view of Campo teach the use of vectors comprising loxP sites that can have motifs present within the loxP sites excised from the vector.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KYLE T REGA whose telephone number is (571)272-2073. The examiner can normally be reached M-R 8:30-4:30, every other F 8:30-4:30 (EDT/EST).
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Neil Hammell can be reached at 571-270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KYLE T REGA/Examiner, Art Unit 1636
/NANCY J LEITH/Primary Examiner, Art Unit 1636