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 .
Notice of Pre-AIA or AIA Status
This action is written in response to applicant’s correspondence received 15 June 2026. Claims 1-20 are currently pending. Accordingly, claims 1-20 are examined herein.
Any rejection or objection not reiterated herein has been overcome by amendment.
Applicant' s amendments have been thoroughly reviewed, but are not persuasive to place the
claims in condition for allowance for the reasons that follow.
Claim Interpretation
Regarding claims 2-3 and 15-16, it is noted that the instant specification describes “a variant” of a sequence as being directed towards a sequence that has at least 50% identity to a particular nucleic acid sequence of interest (Instant specification; pg. 18). Accordingly, the claims are interpreted as claiming sequences that have at least 50% identity with the claimed SEQ ID NOs.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1, 3-13, and 17-18 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Rondon (“Transcriptional programming using engineered systems of transcription factors and genetic architectures” Nature Communications 10.1 (2019): 4784).
Regarding claim 1, it is noted that the newly amended claim limitations require that the one or more DNA operator elements is a tandem operator-promoter that is “capable” of series parallel operator function. Applicant has noted that support for the newly filed claim limitations is found at the instant specification at FIGs. 9A-9B and page 52 lines 19-25 (Remarks; pg. 1). Page 25 lines 19-25 of the instant specification defines the newly recited structure as follows: “The general design of the in-tandem operator-promoter was composed of two DNA operators, one intercalated between the -33 and -7 hexamer and the other proximal to the TSS (Figures 8 and 9). In principle, this design maintains the ability to concurrently direct the binding of one or more cognate transcription factors while preserving orthogonal DNA binding. NOTE: The general form of this genetic architecture has been designated as a series-parallel (SE-PA) operator function” (pg. 52, lines 19-25).
Rondon is directed towards a study concerned with biological programming structure that leverages a system of engineered transcription factors and complementary genetic architectures (Abstract). Rondon teaches the use of regulatory protein templates that comprise a dimeric transcription factor alongside its corresponding ligand and cognate DNA operator (pg. 2; see Fig. 1). Rondon teaches that the transcription factor comprises a regulatory core domain and an alternate DNA recognition unit (i.e., a DNA binding domain) (pg. 2; see Fig. 1). Rondon teaches that the DNA recognition unit is linked to the regulatory core domain (pg. 2; see Fig. 1). Rondon teaches that the DNA recognition unit recognizes the DNA operator element such that, in the presence or absence of a specific inducer molecule, gene expression can be modulated as desired (pg. 2; see Fig. 1). Rondon teaches that two or more regulatory protein templates (i.e., two or more regulatory core domains) can be utilized together to create Boolean logical AND and OR gates (pg. 5-7; see Fig. 5). Rondon further teaches that the transcription factors may be encoded on a vector in order to express the Boolean logic gates in a bacterial cell (pg. 11).
Regarding the newly recited limitations, Rondon teaches the use of an architecture of operators termed “Series architecture” and teaches that “In the series architecture (SERI), two operators are employed, each acted on by a transcription factor with a different ADR unit. The first operator (pOP1) lies within the promoter element, flanked by the −35 and −10 hexamers in the core position, while the second operator (OP2), lies downstream in the proximal position” (pg. 5; see Fig. 4).
Accordingly, Rondon appears to teach the exact same structure of tandem operator-promoters that is currently being claimed and defined in the instant specification. As taught by MPEP 2112, “when the structure recited in the reference is substantially identical to that of the claims, claimed properties or functions are presumed to be inherent.” Accordingly, the function of being “capable of series parallel operator function” is inherently anticipated by the structure of Rondon.
Regarding claim 3, Rondon teaches the use of a vector encoding a LacI YQR that comprises 100% identity to the claimed SEQ ID NO: 1 (pg. 11; see attached sequence alignment). Rondon teaches the use of a promoter that comprises 99.9% identity to the claimed SEQ ID NO: 2 (pg. 11; see attached sequence alignment). Rondon teaches that the DNA operators are located downstream of a promoter element such that they can be expressed in a target cell of interest (pg. 3).
Regarding claims 4-5, Rondon teaches that the AND gate can be constructed via the use of two engineered regulatory protein templates that comprise repressor regulatory core domains (i.e., both regulatory core domains may comprise a repressor) (pg. 6-7; see Fig. 5b).
Regarding claims 6 and 8, Rondon teaches that the two regulatory core domains in the Boolean logic gates are each specifically recognized by a first and second agent (pg. 6-7; see Fig. 5).
Regarding claims 7 and 9, Rondon teaches the use of an asymmetric parallel system, denoted AND[PARA]HAND, that required the use of two regulatory core domains that could recognize a first IPTG input and a second D-ribose input (pg. 9; see Fig. 7b).
Regarding claims 10-11, Rondon teaches the use of regulatory core domains that can be linked to the same, or different, DNA binding domains and function within the Boolean logic gates (pg. 4, 8; see Figs. 2 and 6).
Regarding claim 12, Rondon teaches the use of an asymmetric parallel system, denoted AND[PARA]HAND, that required the use of two sets of two regulatory core domains (i.e., I+YQR, E+TAN, R+HQN, and R+HQN) that could be linked to one of three DNA binding domains (i.e., YQR, TAN, and HQN) that could be recognized by three different DNA operator elements (pg. 9; see Fig. 7b).
Regarding claim 13, Rondon teaches that the Boolean logic gate can be operably connected to a GFP reporter protein (pg. 6; see Fig. 5).
Regarding claims 17-18, Rondon teaches that the Boolean logic gates may be utilized in an E. coli K12 strain that had the LacI and lac operon deleted (pg. 11).
Response to Arguments
Applicant's arguments filed 15 June 2026 have been fully considered but they are not persuasive.
Applicant alleges that Rondon only discusses multiple DNA operators as being configured “in parallel or in series”, not a tandem operator-promoter, capable of series parallel (SE-PA) operator function as the claims currently recite (Remarks; pg. 2).
This argument is not found persuasive because the structure of the claimed tandem operator-promoter disclosed in the specification appears to be identical to the structure of the SERI architecture described in Rondon. As discussed above, because the structure of the SERI architecture of Rondon is substantially identical to the tandem operator-promoter of the claims, claimed properties or functions are presumed to be inherent as taught by MPEP 2112.
Applicant alleges that the previously cited Huang reference is the inventors’ own work less than one year before the effective filing date of the claimed invention and that a Declaration under 37 C.F.R. 1.130 accompanies the response (Remarks; pg. 2).
The Declaration under 37 C.F.R. 1.130 is accepted and is sufficient to overcome the previously cited Huang reference. Accordingly, the previously pending 35 USC 102 rejection over the Huang reference has been withdrawn.
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) 2, 14, and 19-20 is/are rejected under 35 U.S.C. 103 as being unpatentable over Rondon (“Transcriptional programming using engineered systems of transcription factors and genetic architectures” Nature Communications 10.1 (2019): 4784) as applied to claims 1, 3-13, and 17-18 above, and further in view of Lu (PG Pub No. US 2018/0163216 A1).
Regarding claims 2, 14, and 19-20, Rondon anticipates claims 1, 3-13, and 17-18 as described above. Rondon further teaches that the transcription factors may be encoded on a vector in order to express the Boolean logic gates in a bacterial cell (pg. 11).
Rondon does not teach or suggest that the construct further comprises a variant of SEQ ID NO: 34 (Claim 2). Rondon does not teach or suggest that the construct further comprises a nucleic acid sequence encoding a dCas9 and a sgRNA (Claim 14). Rondon does not teach or suggest that the bacterial cell is B. thetaiotaomicron (Claim 19). Rondon does not teach or suggest that the construct could be utilized in a method of modifying a gastrointestinal tract microbiome in a subject (Claim 20).
However, one of ordinary skill in the art would have considered the teachings of Lu as both references are common fields of endeavor pertaining to the use of transcription factors and their expression within cells of interest.
Lu is directed towards a study concerned with methods, compositions and nucleic acids for building genetic circuits in Bacteroides and Parabacteroides bacteria (Abstract). Lu teaches the use of vectors that can be used to manipulate gene expression in a variety of Bacteroides and Parabacteroides species ([0004]). Lu teaches that B. thetaiotaomicron cells are candidates for modulating the gut ecosystem and that utilizing genetic circuits to control gene expression in B. thetaiotaomicron cells would allow for the therapeutic delivery of the cells to the human microbiome ([0004]). Lu teaches the use of a nucleic acid encoding a dCas9 and sgRNA that could repress endogenous genes of interest in B. thetaiotaomicron cells ([0026]-[0027]). Lu teaches that genetic inducible systems, CRISPRi, and genetic memory switches were validated in B. thetaiotaomicron cells colonizing the mouse gut ([0004]). Lu teaches the use of a pNBU1 vector that comprises a sequence that has 70.9% identity to the claimed SEQ ID NO: 34 ([0098]; see SEQ ID NO: 209 in attached sequence alignment). Lu teaches that the pNBU1 vector was created to introduce recombinant DNA into a wide range of Bacteroides species ([0097]). Lu teaches that the pNBU1 vector showed a greater host range and efficiency relative to a pNBU2 plasmid and that the pNBU1 vector was capable of facilitating recombinant gene expression in multiple Bacteroides species, including B. thetaiotaomicron, B. fragilis, B. ovatus, B. vulgatus, B. caccae, B. eggerthii and Parabacteroides distasonis ([0097]).
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 bacterial cell and vector of Rondon for a B. thetaiotaomicron cell and a pNBU1 vector comprising a sequence that has 70.9% identity to the claimed SEQ ID NO: 34, as described by Lu. A person of ordinary skill in the art would have been motivated to utilize the pNBU1 vector in order to have the ability to insert the bacterial genetic logic gate described by Rondon into a B. thetaiotaomicron cell in order to therapeutically deliver the cells to the human microbiome. A person of ordinary skill in the art would have had a reasonable expectation of success because Rondon teaches the use of a genetic circuit that can control the expression of genes within a bacterial cell while Lu teaches the use of a vector that can insert recombinant DNA into a B. thetaiotaomicron cell.
It would have also been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to further utilize a nucleic acid encoding a dCas9 and an sgRNA, and modify the gastrointestinal tract microbiome of a subject, as described by Lu. A person of ordinary skill in the art would have been motivated to do so in order to repress endogenous genes within the B. thetaiotaomicron cell in order to therapeutically deliver the modified cells to a gastrointestinal tract microbiome of a subject. A person of ordinary skill in the art would have had a reasonable expectation of success because Rondon teaches the use of a genetic circuit that can control the expression of genes within a bacterial cell while Lu teaches that dCas9 and sgRNAs can be utilized alongside genetic circuits to provide further control over the endogenous expression of target genes of interest within B. thetaiotaomicron cells.
Claim(s) 15 is/are rejected under 35 U.S.C. 103 as being unpatentable over Rondon (“Transcriptional programming using engineered systems of transcription factors and genetic architectures” Nature Communications 10.1 (2019): 4784) as applied to claims 1, 3-13, and 17-18 above, and further in view of Mimee ("Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota." Cell systems 1.1 (2015): 62-71), Lu (PG Pub No. WO 2016/201174 A2), and Boitano (PG Pub No. US 2019/0010495 A1).
Regarding claim 15, Rondon anticipates claims 1, 3-13, and 17-18 as described above. Rondon further teaches that the transcription factors may be encoded on a vector in order to express the Boolean logic gates in a cell of interest to express a nucleic acid of interest (pg. 11).
Rondon does not teach or suggest that the construct comprises a combination of variants of SEQ ID NOs: 6 and 16 (Claim 15).
However, one of ordinary skill in the art would have considered the teachings of Mimee, Boitano and Marco as both references are common fields of endeavor pertaining to the use of nucleic acids that can be expressed in cells of interest.
Mimee is drawn towards a study concerned with synthetic genetic circuits that are operably linked to a dCas9 and an sgRNA to alter the metabolic capacity of B. thetaiotaomicron and its resistance to antimicrobial peptides (Abstract). Mimee teaches the use of a vector encoding a dCas9 and an sgRNA that are operably linked to a synthetic genetic circuit that can alter the expression of a NanoLuc luciferase reporter (pg. 63-64). Mimee teaches the use of a 20 nucleotide RNA guide sequence that comprises 100% identity to the first 20 nucleotides of the claimed SEQ ID NO: 16 and can target a NanoLuc reporter sequence (see “NL4” in Supplementary Table S5). Mimee teaches that the NanoLuc reporter was able to be knocked down by the IPTG induction of the dCas9 in order to determine if the genetic gate was functional in a B. thetaiotaomicron cell (pg. 67).
Boitano is directed towards an invention concerned with genome editing systems, reagents and methods for the treatment of hemoglobinopathies (Abstract). Boitano teaches the use of a nucleic acid molecule encoding multiple guide RNAs and a CRISPR/Cas9 molecule ([0030]). Boitano teaches that promoters for the Cas9 and guide RNAs can be inducible (i.e., the expression of the Cas9 and guide RNA may be inducible) ([0489]). Boitano teaches the use of a guide RNA that comprises 87.1% identity to the claimed SEQ ID NO: 16 and comprises an RNA scaffold sequence that has 100% identity to nucleotides 21-100 of the claimed SEQ ID NO: 16 ([0098]; see SEQ ID NO: 1772 in attached sequence alignment).
Lu is directed towards an invention concerned with building genetic circuits in Bacteroides bacteria (Abstract). Lu teaches the use of a dCas9 that has 99.9% sequence identity to the claimed SEQ ID NO: 6 (pg. 4; see SEQ ID NO: 157 in attached sequence alignment).
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 Rondon such that it controlled the transcription of a dCas9 molecule having 99.9% sequence identity to the claimed SEQ ID NO: 6, as described by Lu, and a guide RNA that comprises a guide sequence that has 100% identity to the first 20 nucleotides of the claimed SEQ ID NO: 16 and a scaffold sequence that has 100% identity to nucleotides 21-100 of the claimed SEQ ID NO: 16 in order to arrive at a Cas9 guide RNA that comprises 100% identity to the claimed SEQ ID NO: 16, as described by Mimee and Boitano. A person of ordinary skill in the art would have been motivated to do so in order to target knockdown of a reporter protein in order to validate if the genetic logic gate is functional in Bacteroides bacteria. A person of ordinary skill in the art would have had a reasonable expectation of success because Rondon teaches that the construct can be utilized to modulate the transcription of a downstream nucleic acids while Mimee teaches that utilizing genetic logic gates to modulate the expression of a dCas9 and an sgRNA can control the expression of a reporter protein. Further, both Mimee and Boitano teach that the claimed SEQ ID NO: 16 is a combination of a known Cas9 guide RNA sequence and a known Cas9 guide RNA scaffold sequence.
Claim(s) 16 is/are rejected under 35 U.S.C. 103 as being unpatentable over Rondon (“Transcriptional programming using engineered systems of transcription factors and genetic architectures” Nature Communications 10.1 (2019): 4784) as applied to claims 1, 3-13, and 17-18 above, and further in view of Needham (PG Pub No. US 2019/0374588 A1).
Regarding claim 16, Rondon anticipates claims 1, 3-13, and 17-18 as described above. Rondon further teaches that the transcription factors may be encoded on a vector in order to express the Boolean logic gates in a cell of interest to express a nucleic acid of interest (pg. 11).
Rondon does not teach or suggest that the construct comprises a variant of the claimed SEQ ID NO: 70 (Claim 16).
However, one of ordinary skill in the art would have considered the teachings of Needham as both references are common fields of endeavor pertaining to the use of nucleic acids that can be expressed in cells of interest.
Needham is drawn towards an invention concerned with genetically engineered bacterial strains for modulation of 4EP and 4EPS (Abstract). Needham teaches the use of a pNBU2 plasmid that can comprise a recombinant gene encoding a native B. ovatus BACOCA_01194 gene and a recombinant gene encoding a Bacillus subtilis PAD enzyme that can be chromosomally inserted into a mutant B. ovatus bacteria in order to confer erythromycin resistance to the mutant strain (i.e., the pNBU2 plasmid may be utilized to insert recombinant DNA into the chromosome of a mutant B. ovatus strain) ([0063]-[0064]). Needham teaches that the pNBU2 vector comprises a sequence that has 52.5% identity to the claimed SEQ ID NO: 70 ([0063]; see SEQ ID NO: 3 in attached sequence alignment).
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 of Rondon for a vector comprising a variant of the claimed SEQ ID NO: 70, as described by Needham. A person of ordinary skill in the art would have had a reasonable expectation of success because both Rondon and Needham teach the use of vectors that can be delivered to bacterial cells of interest in order to express recombinant DNA from the cell’s chromosomes.
Claim(s) 16 is/are rejected under 35 U.S.C. 103 as being unpatentable over Rondon (“Transcriptional programming using engineered systems of transcription factors and genetic architectures” Nature Communications 10.1 (2019): 4784) as applied to claims 1, 3-13, and 17-18 above, and further in view of Mimee ("Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota." Cell systems 1.1 (2015): 62-71), and Lu (PG Pub No. WO 2016/201174 A2), Boitano (PG Pub No. US 2019/0010495 A1).
Regarding claim 16, it is noted that the claimed SEQ ID NO: 70 is directed towards a pNBU2 vector utilized for LacI-controlled sgRNA for NanoLuc knockdown and comprises LacI(YQR) as defined by SEQ ID NO: 1 (pg. 60-61), CFXA promoters as defined by SEQ ID NO: 7 (pg. 65), and nano4sgRNA as defined by SEQ ID NO: 16 (pg. 65) (see pg. 59).
Rondon anticipates claims 1, 3-13, and 17-18 as described above. Rondon further teaches that the transcription factors may be encoded on a vector in order to express the Boolean logic gates in a cell of interest to express a nucleic acid of interest (pg. 11).
Rondon does not teach or suggest that the construct comprises a variant of the claimed SEQ ID NO: 70 (Claim 16).
However, as discussed above, Rondon teaches the use of a vector encoding a LacI(YQR) that comprises 100% identity to the claimed SEQ ID NO: 1 (pg. 11; see attached sequence alignment).
Further, as discussed above, Mimee and Boitano render obvious the use of an sgRNA that comprises 100% sequence identity to the claimed SEQ ID NO: 16.
Additionally, Lu further teaches the use of a PcfxA promoter that comprises 100% identity to the claimed SEQ ID NO: 7 (pg. 2; see SEQ ID NO: 151 in attached sequence alignment). Lu also teaches the use of a pNBU2 integration vector that was able to encode the promoters and genetic circuits of the invention and insert the elements into a B. thetaiotaomicron chromosome (pg. 21).
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 Rondon such that it comprised LacI(YQR) as defined by SEQ ID NO: 1, CFXA promoters as defined by SEQ ID NO: 7, and a nano4sgRNA as defined by SEQ ID NO: 16 within a pNBU2 insertion vector, as described by Mimee, Boitano, and Lu. A person of ordinary skill in the art would have been motivated to do so in order to insert and test the genetic logic gate within a B. thetaiotaomicron host cell and test the functionality of the genetic logic gate via the use of a known reporter that can be knocked down by dCas9 and an sgRNA targeting NanoLuc. A person of ordinary skill in the art would have had a reasonable expectation of success because the claimed SEQ ID NO: 70 comprises known a LacI(YQR) sequence, known CFXA promoter sequences, and a known nano4sgRNA sequence within a well-known insertion vector.
Response to Arguments
Applicant's arguments filed 15 June 2026 have been fully considered but they are not persuasive.
Applicant alleges that the additionally cited references do not teach the newly recited claim limitations (Remarks; pg. 2-5).
This argument is not found persuasive because Rondon anticipates the newly recited claim limitations as discussed above in the recited 35 USC 102 rejection of record.
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 § 2146 et seq. 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 filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual 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/apply/applying-online/eterminal-disclaimer.
Claims 1, 3-13, and 17-18 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claim 1 of copending Application No. 18/790,573 (reference application) in view of Rondon (“Transcriptional programming using engineered systems of transcription factors and genetic architectures” Nature Communications 10.1 (2019): 4784).
This is a provisional nonstatutory double patenting rejection.
Regarding claim 1, copending claim 1 claims a synthetic memory system, comprising: a recombinase; a modified transcription factor (i.e., a DNA binding domain); and a first nucleic acid comprising a first attachment site (i.e., a first group of one regulatory core domain), a second attachment site (i.e., a second group of one regulatory core domain), and a target gene between said first attachment site and said second attachment site; wherein at least one of the first attachment site and the second attachment site comprises a modified DNA operator to which the modified transcription factor can reversibly bind; and wherein, when the modified transcription factor is bound to the modified DNA operator, the recombinase is blocked from binding to the attachment site comprising said modified DNA operator (see copending claim 1).
Copending claim 1 does not teach or suggest that the one or more DNA operators is a tandem operator-promoter, capable of SE-PA operator functions (Claim 1).
The applicable teachings of Rondon are discussed above as applied to claim 1.
Therefore, it would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted the copending operator for the tandem operator-promoter because it would have merely amounted to a simple substitution of one known element for another to obtain predictable results. Because both the copending claims and Rondon teach the use of operators that could be bound to one or more DNA binding domains in order to control transcription of a nucleic acid of interest, one would have expected that both the copending operator and the tandem operator-promoter of Rondon to have performed the same function of controlling the interaction a DNA binding protein has with a nucleic acid of interest. Therefore, the substitution would have predictably resulted in in the successful generation of the claimed construct because both operators are utilized for the same function to control the same activity of a DNA binding protein..
The copending claims do not teach or suggest that the plurality of nucleic acid sequence comprises a combination of variants of SEQ ID NOs: 1 and 2 (Claim 3). The copending claims do not teach or suggest that the first group or second group of regulatory core domains comprise a repressor (Claims 4-5). The copending claims do not teach or suggest that the first group of regulatory core domains is recognized by IPTG (Claims 6-7). The copending claims do not teach or suggest that the second group of regulatory core domains is recognized by D-ribose (Claims 8-9). The copending claims do not teach or suggest that the first and second group of regulatory core domains are linked to the same or different DNA binding domains (Claims 10-11). The copending claims do not teach or suggest the use of three DNA binding domains as claimed in claim 12 (Claim 12). The copending claims do not teach or suggest that the construct further comprises a nucleic acid encoding a reporter (Claim 13). The copending claims do not teach or suggest a cell comprising the construct (Claim 17), selected from a bacterial cell (Claim 18).
However, one of ordinary skill in the art would have considered the teachings of Rondon as both references are common fields of endeavor pertaining to the use of constructs comprising DNA regulatory core domains and DNA binding domains.
The applicable teachings of Rondon are discussed above as applied to claims 3-13 and 17-18.
Therefore, it would have been obvious to modify the copending claims in order to arrive at instant claims 3-13 and 17-18. A person of ordinary skill in the art would have been motivated to do so in order to utilize known DNA binding domains, DNA operators, and DNA regulatory domains that can be recognized by a first and second agents in a cell, as described by Rondon. A person of ordinary skill in the art would have had a reasonable expectation of success because both the copending claims and Rondon teach the use of constructs comprising regulatory core domains, DNA binding domains, and DNA operator elements that can be utilized to modulate the transcription of a target nucleic acid of interest.
Claim(s) 2, 14, and 19-20 is/are rejected under 35 U.S.C. 103 as being unpatentable over claim 1 of copending Application No. 18/790,573 (reference application) in view of Rondon (“Transcriptional programming using engineered systems of transcription factors and genetic architectures” Nature Communications 10.1 (2019): 4784) as applied to claims 1, 3-13, and 17-18 above, and further in view of Lu (PG Pub No. US 2018/0163216 A1).
Regarding claims 2, 14, and 19-20, copending claim 1 in view of Rondon renders obvious claims 1, 3-13, and 17-18 as described above. Rondon further teaches that the transcription factors may be encoded on a vector in order to express the Boolean logic gates in a bacterial cell (pg. 11).
Copending claim 1 in view of Rondon does not teach or suggest that the construct further comprises a variant of SEQ ID NO: 34 (Claim 2). Copending claim 1 in view of Rondon does not teach or suggest that the construct further comprises a nucleic acid sequence encoding a dCas9 and a sgRNA (Claim 14). Copending claim 1 in view of Rondon does not teach or suggest that the bacterial cell is B. thetaiotaomicron (Claim 19). Copending claim 1 in view of Rondon does not teach or suggest that the construct could be utilized in a method of modifying a gastrointestinal tract microbiome in a subject (Claim 20).
Lu is directed towards a study concerned with methods, compositions and nucleic acids for building genetic circuits in Bacteroides and Parabacteroides bacteria (Abstract). Lu teaches the use of vectors that can be used to manipulate gene expression in a variety of Bacteroides and Parabacteroides species ([0004]). Lu teaches that B. thetaiotaomicron cells are candidates for modulating the gut ecosystem and that utilizing genetic circuits to control gene expression in B. thetaiotaomicron cells would allow for the therapeutic delivery of the cells to the human microbiome ([0004]). Lu teaches the use of a nucleic acid encoding a dCas9 and sgRNA that could repress endogenous genes of interest in B. thetaiotaomicron cells ([0026]-[0027]). Lu teaches that genetic inducible systems, CRISPRi, and genetic memory switches were validated in B. thetaiotaomicron cells colonizing the mouse gut ([0004]). Lu teaches the use of a pNBU1 vector that comprises a sequence that has 70.9% identity to the claimed SEQ ID NO: 34 ([0098]; see SEQ ID NO: 209 in attached sequence alignment). Lu teaches that the pNBU1 vector was created to introduce recombinant DNA into a wide range of Bacteroides species ([0097]). Lu teaches that the pNBU1 vector showed a greater host range and efficiency relative to a pNBU2 plasmid and that the pNBU1 vector was capable of facilitating recombinant gene expression in multiple Bacteroides species, including B. thetaiotaomicron, B. fragilis, B. ovatus, B. vulgatus, B. caccae, B. eggerthii and Parabacteroides distasonis ([0097]).
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 bacterial cell and vector of copending claim 1 in view of Rondon for a B. thetaiotaomicron cell and a pNBU1 vector comprising a sequence that has 70.9% identity to the claimed SEQ ID NO: 34, as described by Lu. A person of ordinary skill in the art would have been motivated to utilize the pNBU1 vector in order to have the ability to insert the bacterial genetic logic gate described by copending claim 1 in view of Rondon into a B. thetaiotaomicron cell in order to therapeutically deliver the cells to the human microbiome. A person of ordinary skill in the art would have had a reasonable expectation of success because Copending claim 1 in view of Rondon teaches the use of a genetic circuit that can control the expression of genes within a bacterial cell while Lu teaches the use of a vector that can insert recombinant DNA into a B. thetaiotaomicron cell.
It would have also been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to further utilize a nucleic acid encoding a dCas9 and an sgRNA, and modify the gastrointestinal tract microbiome of a subject, as described by Lu. A person of ordinary skill in the art would have been motivated to do so in order to repress endogenous genes within the B. thetaiotaomicron cell in order to therapeutically deliver the modified cells to a gastrointestinal tract microbiome of a subject. A person of ordinary skill in the art would have had a reasonable expectation of success because Copending claim 1 in view of Rondon teaches the use of a genetic circuit that can control the expression of genes within a bacterial cell while Lu teaches that dCas9 and sgRNAs can be utilized alongside genetic circuits to provide further control over the endogenous expression of target genes of interest within B. thetaiotaomicron cells.
Claim(s) 15 is/are rejected under 35 U.S.C. 103 as being unpatentable over claim 1 of copending Application No. 18/790,573 (reference application) in view of Rondon (“Transcriptional programming using engineered systems of transcription factors and genetic architectures” Nature Communications 10.1 (2019): 4784) as applied to claims 1, 3-13, and 17-18 above, and further in view of Mimee ("Programming a human commensal bacterium, Bacteroides thetaiotaomicron, to sense and respond to stimuli in the murine gut microbiota." Cell systems 1.1 (2015): 62-71), Lu (PG Pub No. WO 2016/201174 A2), and Boitano (PG Pub No. US 2019/0010495 A1).
Regarding claim 15, copending claim 1 in view of Rondon renders obvious claims 1, 3-13, and 17-18 as described above. Rondon further teaches that the transcription factors may be encoded on a vector in order to express the Boolean logic gates in a cell of interest to express a nucleic acid of interest (pg. 11).
Copending claim 1 in view of Rondon does not teach or suggest that the construct comprises a combination of variants of SEQ ID NOs: 6 and 16 (Claim 15).
However, one of ordinary skill in the art would have considered the teachings of Mimee, Boitano and Marco as both references are common fields of endeavor pertaining to the use of nucleic acids that can be expressed in cells of interest.
Mimee is drawn towards a study concerned with synthetic genetic circuits that are operably linked to a dCas9 and an sgRNA to alter the metabolic capacity of B. thetaiotaomicron and its resistance to antimicrobial peptides (Abstract). Mimee teaches the use of a vector encoding a dCas9 and an sgRNA that are operably linked to a synthetic genetic circuit that can alter the expression of a NanoLuc luciferase reporter (pg. 63-64). Mimee teaches the use of a 20 nucleotide RNA guide sequence that comprises 100% identity to the first 20 nucleotides of the claimed SEQ ID NO: 16 and can target a NanoLuc reporter sequence (see “NL4” in Supplementary Table S5). Mimee teaches that the NanoLuc reporter was able to be knocked down by the IPTG induction of the dCas9 in order to determine if the genetic gate was functional in a B. thetaiotaomicron cell (pg. 67).
Boitano is directed towards an invention concerned with genome editing systems, reagents and methods for the treatment of hemoglobinopathies (Abstract). Boitano teaches the use of a nucleic acid molecule encoding multiple guide RNAs and a CRISPR/Cas9 molecule ([0030]). Boitano teaches that promoters for the Cas9 and guide RNAs can be inducible (i.e., the expression of the Cas9 and guide RNA may be inducible) ([0489]). Boitano teaches the use of a guide RNA that comprises 87.1% identity to the claimed SEQ ID NO: 16 and comprises an RNA scaffold sequence that has 100% identity to nucleotides 21-100 of the claimed SEQ ID NO: 16 ([0098]; see SEQ ID NO: 1772 in attached sequence alignment).
Lu is directed towards an invention concerned with building genetic circuits in Bacteroides bacteria (Abstract). Lu teaches the use of a dCas9 that has 99.9% sequence identity to the claimed SEQ ID NO: 6 (pg. 4; see SEQ ID NO: 157 in attached sequence alignment).
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 copending claim 1 in view of Rondon such that it controlled the transcription of a dCas9 molecule having 99.9% sequence identity to the claimed SEQ ID NO: 6, as described by Lu, and a guide RNA that comprises a guide sequence that has 100% identity to the first 20 nucleotides of the claimed SEQ ID NO: 16 and a scaffold sequence that has 100% identity to nucleotides 21-100 of the claimed SEQ ID NO: 16 in order to arrive at a Cas9 guide RNA that comprises 100% identity to the claimed SEQ ID NO: 16, as described by Mimee and Boitano. A person of ordinary skill in the art would have been motivated to do so in order to target knockdown of a reporter protein in order to validate if the genetic logic gate is functional in Bacteroides bacteria. A person of ordinary skill in the art would have had a reasonable expectation of success because copending claim 1 in view of Rondon teaches that the construct can be utilized to modulate the transcription of a downstream nucleic acids while Mimee teaches that utilizing genetic logic gates to modulate the expression of a dCas9 and an sgRNA can control the expression of a reporter protein. Further, both Mimee and Boitano teach that the claimed SEQ ID NO: 16 is a combination of a known Cas9 guide RNA sequence and a known Cas9 guide RNA scaffold sequence.
Claim(s) 16 is/are rejected under 35 U.S.C. 103 as being unpatentable over claim 1 of copending Application No. 18/790,573 (reference application) in view of Rondon (“Transcriptional programming using engineered systems of transcription factors and genetic architectures” Nature Communications 10.1 (2019): 4784) as applied to claims 1, 3-13, and 17-18 above, and further in view of Needham (PG Pub No. US 2019/0374588 A1).
Regarding claim 16, Copending claim 1 in view of Rondon renders obvious claims 1, 3-13, and 17-18 as described above. Rondon further teaches that the transcription factors may be encoded on a vector in order to express the Boolean logic gates in a cell of interest to express a nucleic acid of interest (pg. 11).
Copending claim 1 in view of Rondon does not teach or suggest that the construct comprises a variant of the claimed SEQ ID NO: 70 (Claim 16).
Needham is drawn towards an invention concerned with genetically engineered bacterial strains for modulation of 4EP and 4EPS (Abstract). Needham teaches the use of a pNBU2 plasmid that can comprise a recombinant gene encoding a native B. ovatus BACOCA_01194 gene and a recombinant gene encoding a Bacillus subtilis PAD enzyme that can be chromosomally inserted into a mutant B. ovatus bacteria in order to confer erythromycin resistance to the mutant strain (i.e., the pNBU2 plasmid may be utilized to insert recombinant DNA into the chromosome of a mutant B. ovatus strain) ([0063]-[0064]). Needham teaches that the pNBU2 vector comprises a sequence that has 52.5% identity to the claimed SEQ ID NO: 70 ([0063]; see SEQ ID NO: 3 in attached sequence alignment).
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 of Copending claim 1 in view of Rondon for a vector comprising a variant of the claimed SEQ ID NO: 70, as described by Needham. A person of ordinary skill in the art would have had a reasonable expectation of success because both Rondon and Needham teach the use of vectors that can be delivered to bacterial cells of interest in order to express recombinant DNA from the cell’s chromosomes.
Response to Arguments
Applicant's arguments filed 15 June 2026 have been fully considered but they are not persuasive.
Applicant alleges that a terminal disclaimer will be filed once allowable subject matter is obtained in one of the applications 9Remarks; pg. 5).
This argument is not found persuasive because a terminal disclaimer has not been filed. Accordingly, the previously present double patenting rejections of record are maintained.
Conclusion
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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/KYLE T REGA/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636
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