Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
DETAILED ACTION
Application Status
This application is a 371 of PCT/US20/33004, filed on 11/12/2021.
Claims 63, 77-88 and 89 are currently pending in this patent application.
In response to a previous Office action, a Non-Final Rejection Office action (mailed on 07/07/2025), Applicants filed a response and an amendment on January 7, 2026, amending claims 63, 79-88 and 89.
Claims 63, 77-88 and 89 are present for examination.
Applicants' arguments filed on January 7, 2026, have been fully considered and are deemed persuasive to overcome some of the rejections previously applied. Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.
Priority
Acknowledgement is made of applicants claim for priority of US Provisional applications 62/847,904, filed on 05/14/2019, 62/847,928, filed on 05/14/2019, 62/847,936, filed on 05/14/2019, and 62/847,910, filed on 05/14/2019.
Withdrawn-Specification Objection
The previous objection of the Specification for reciting an embedded hyperlink and/or other form of browser-executable code, is withdrawn in view of Applicant’s amendment to the Specification and persuasive arguments. See MPEP § 608.01.
Withdrawn-Claim Rejections - 35 USC § 112(b)
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The previous rejection of Claims 88 and 89 under 35 U.S.C. 112(b), as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention, is withdrawn in view of Applicant’s amendment to the Specification and persuasive arguments.
Withdrawn-Claim Objections
The previous objection of Claim 89 is under 37 CFR 1.75 as being a substantial duplicate of claim 88, is withdrawn in view of Applicant’s amendment to the Specification and persuasive arguments.
Maintained-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 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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
MPEP-2131 Anticipation — Application of 35 U.S.C. 102 [R-08.2017]
A claimed invention may be rejected under 35 U.S.C. 102 when the invention is anticipated (or is "not novel") over a disclosure that is available as prior art. To reject a claim as anticipated by a reference, the disclosure must teach every element required by the claim under its broadest reasonable interpretation. See, e.g., MPEP § 2114, subsections II and IV.
"A claim is anticipated only if each and every element as set forth in the claim is found, either expressly or inherently described, in a single prior art reference." Verdegaal Bros. v. Union Oil Co. of California, 814 F.2d 628, 631, 2 USPQ2d 1051, 1053 (Fed. Cir. 1987). "When a claim covers several structures or compositions, either generically or as alternatives, the claim is deemed anticipated if any of the structures or compositions within the scope of the claim is known in the prior art." Brown v. 3M, 265 F.3d 1349, 1351, 60 USPQ2d 1375, 1376 (Fed. Cir. 2001) Note that, in some circumstances, it is permissible to use multiple references in a 35 U.S.C. 102 rejection. See MPEP § 2131.01.
MPEP-2131.01 Multiple Reference 35 U.S.C. 102 Rejections [R-11.2013]
Normally, only one reference should be used in making a rejection under 35 U.S.C. 102. However, a 35 U.S.C. 102 rejection over multiple references has been held to be proper when the extra references are cited to:
(A) Prove the primary reference contains an "enabled disclosure;"
(B) Explain the meaning of a term used in the primary reference; or
(C) Show that a characteristic not disclosed in the reference is inherent.
The previous rejection of Claims 63, 77-86 and 87d under 35 U.S.C. 102(a)(1/2) based upon a public use or sale or other public availability of the invention as anticipated by Soll et al.(Compositions and methods for making selenocysteine containing polypeptides. US 2018/0105854 A1, publication 04/19/2018, priority date 10/04/2017), is maintained. This rejection has been discussed at length in the previous Office Action, and the rejection is maintained as discussed previously and for the following reasons.
The Broadest Reasonable Interpretation (BRI) of claim 63, which is drawn to a method of producing a plasmid, the method comprising culturing a population of genetically engineered released bacteria under conditions such that a plasmid comprising the at least one exogenous nucleic acid sequence is produced, wherein the genetically engineered released bacteria comprises (i) at least one genetically engineered codon, wherein, the at least one genetically engineered codon comprises a sense codon, (ii) at last one deletion of a nucleic acid sequence, encoding a transfer RNA (tRNA) cognate to the sense codon, and (iii) at least one exogenous nucleic acid sequence encoding a therapeutic polypeptide or portion thereof, wherein the at least one exogenous nucleic acid sequence comprises the at least one genetically engineered codon.
Regarding claims 63, 77-86 and 87, Soll et al. teach a engineered plasmid pSecUAG-A used for Sec (selenocysteine) insertion in a genetically engineered E. coli host cell genome using UAG stop codon to convert amino acid cysteine to selenocysteine using seryl-tRNA synthetase (SerRS), comprising genetically modified microorganism, wherein the modified microorganism capable of producing selenocysteine, a non-natural amino acid, containing protein, which is expressed in a system that has been modified or mutated to reduce or eliminate expression of one or more translation release factors genes, wherein the release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon in a mRNA sequence, and deletion of release factor gene results in incorporation of non-natural amino acid by reading termination codon UAG, like selenocysteine. Soll et al. also teach prokaryotic release factors include RF1, RF2 and RF3; and eukaryotic release factors include eRF1 and eRF3, and deletion of one or more release factors may result in "read-through" of the intended stop codon. Soll et al. further teach non-naturally occurring tRNASec, wherein the non-naturally occurring tRNASec can be recognized by seryl-tRNA synthetase (SerRS), and by EF-Tu, and when aminoacylated with serine the Ser-tRNA can (1) be a substrate for an exogenous SelA, a L-seryl-tRNA (Sec) selenium transferase enzyme or a variant thereof; or (2) be a substrate for PSTK and when aminoacylated with phosphorylated serine the Sep-tRNA can serve as a substrate for SepSecS or a variant thereof, wherein the anticodon of the non-naturally occurring tRNASec hybridizes to a stop codon, wherein the tRNASec comprises an acceptor stem 9 base pairs a T-stem comprising 3 base pairs, wherein the SerRS, the EF-Tu, or both are from E. coli, wherein the SelA is not wildtype E. coli SelA, wherein the SelA is from Sulfurimonas honglongensis, Aeromonas salmonicida, or Rubrobacter xylanophilus, wherein the anticodon of the tRNASec recognizes a stop codon, wherein the nucleic acid is DNA or RNA, wherein the nucleic acid further comprising a heterologous expression control sequence, and the tRNASec formed by said nucleic acid, where a host cell comprising said nucleic acid, wherein the host cell is a prokaryote, archaeon, or eukaryote, wherein the prokaryote is E. coli, wherein the nucleic acid is incorporated into the genome of the cell, wherein the host cell is a genetically recoded organism (GRO), wherein the recoded organism comprises suppressor tRNA (para 26-27, 38), wherein GRO allows the reintroduction of UAG codons in a heterologous mRNA, along with orthogonal translation machinery system (OTS) comprising aminoacyl-tRNA synthetase (aaRS), tRNAs to permit efficient and site specific incorporation of non-standard amino acids into protein encoded by the recoded gene of interest (para 271, 272-273). Soll et al. further teach a method of making a recombinant selenocysteine containing protein comprising co-expressing a nucleic acid encoding a tRNASec, wherein the tRNASec is recognized by SerRS and by EF-Tu, or variants thereof, and when aminoacylated with serine the Ser-tRNA is a substrate for SelA or a variant thereof in a host cell also expressing SerRS, EF-Tu, SelA, or PSTK and SepSecS, with a polynucleotide comprising a codon that hybridizes with the anticodon of the tRNASec, wherein the E. coli host cell is genetically recoded organism (see, abstract, (see, the whole document in particular, abstract, para 14, 68, 28, 29, 31, 32-33, 56, 73-74, 89-95, 97, 99-100, 110-117, 121, 168, 265, 270-271, 290, 291, Fig. 9, 11, 12, 15, and claims 1-20). Therefore, Soll et al. anticipate claims 63, 77-86 and 87 of the instant application as written.
Arguments: Applicants argue that Soll does not anticipate the claimed invention because Soll discloses a genetically engineered bacterial organism comprising, inter alia, a modified or variant nucleic acid sequence encoding tRNAe", which is cognate to the recoded UGA codon, i.e., Soll discloses a modified tRNA that is cognate to a recoded stop codon, and does not include at least one deletion of a nucleic acid sequence encoding a tRNA cognate to a recoded sense codon, as required by the current claims. For at least this reason, the current claims are not anticipated by Soll.
Response: Applicants arguments have been fully considered, but are not deemed persuasive to overcome the rejection on anticipation issues because Soll et al. indeed teach the deletion of the sequence of tRNA and anti-determinant sequence (see, para 13, 93, 143, and Fig. 5), which is important for the interaction between tRNA and its binding partners (such as aminoacyl-tRNA synthetases or the ribosome) is governed by a balance of positive recognition elements and negative "anti-determinant" sequences, and furthermore, deletion or mutation of these sequences alters tRNA functionality, either by enabling new interactions for incorporating non-natural amino acids, or by destroying existing ones.
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Therefore, the rejection is maintained.
Maintained-Claim Rejections - 35 U.S.C. § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied 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.
According to MPEP 2143:
“Exemplary rationales that may support a conclusion of obviousness include:
(A) Combining prior art elements according to known methods to yield
predictable results;
(B) Simple substitution of one known element for another to obtain predictable
results;
(C) Use of known technique to improve similar devices (methods, or products)
in the same way;
(D) Applying a known technique to a known device (method, or product) ready
for improvement to yield predictable results;
(E) “ Obvious to try ” – choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success;
(F) Known work in one field of endeavor may prompt variations of it for use in
either the same field or a different one based on design incentives or other market
forces if the variations are predictable to one of ordinary skill in the art;
(G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art
reference teachings to arrive at the claimed invention.
Note that the list of rationales provided is not intended to be an all-inclusive list. Other rationales to support a conclusion of obviousness may be relied upon by Office personnel.”
The previous rejection of Claims 63, 77-86 and 87-89 under 35 U.S.C. 103 as being unpatentable over Soll et al.(Compositions and methods for making selenocysteine containing polypeptides. US 2018/0105854 A1, publication 04/19/2018, priority date 10/04/2017) as applied to claims 63, 77-86 and 87 above, and further in view of Zahn et al. (Surveillance and elimination of bacteriophage contamination in an industrial fermentation process. Bacteriophages- Biology and applications (2018), Book Chapter, page 1-18, see IDS), is maintained. This rejection has been discussed at length in the previous Office Action, and the rejection is maintained as discussed previously and for the following reasons.
The Broadest Reasonable Interpretation (BRI) of claim 63, which is drawn to a method of producing a plasmid, the method comprising culturing a population of genetically engineered released bacteria under conditions such that a plasmid comprising the at least one exogenous nucleic acid sequence is produced, wherein genetically engineered released bacterial organism comprises (i) at least one genetically engineered codon, (ii) at last one modification to or deletion of: (a) a first nucleic acid sequence, encoding a transfer RNA cognate to the genetically engineered codon, (b) a second nucleic acid sequence encoding a release factor cognate to second genetically engineered second codon, or (c) both.
Regarding claims 63, 77-86 and 87, Soll et al. teach a engineered plasmid pSecUAG-A used for Sec (selenocysteine) insertion in a genetically engineered E. coli host cell genome using UAG stop codon to convert amino acid cysteine to selenocysteine using seryl-tRNA synthetase (SerRS), comprising genetically modified microorganism, wherein the modified microorganism capable of producing selenocysteine, a non-natural amino acid, containing protein, which is expressed in a system that has been modified or mutated to reduce or eliminate expression of one or more translation release factors genes, wherein the release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon in a mRNA sequence, and deletion of release factor gene results in incorporation of non-natural amino acid by reading termination codon UAG, like selenocysteine. Soll et al. also teach prokaryotic release factors include RF1, RF2 and RF3; and eukaryotic release factors include eRF1 and eRF3, and deletion of one or more release factors may result in "read-through" of the intended stop codon. Soll et al. further teach non-naturally occurring tRNASec, wherein the non-naturally occurring tRNASec can be recognized by seryl-tRNA synthetase (SerRS), and by EF-Tu, and when aminoacylated with serine the Ser-tRNA can (1) be a substrate for an exogenous SelA, a L-seryl-tRNA (Sec) selenium transferase enzyme or a variant thereof; or (2) be a substrate for PSTK and when aminoacylated with phosphorylated serine the Sep-tRNA can serve as a substrate for SepSecS or a variant thereof, wherein the anticodon of the non-naturally occurring tRNASec hybridizes to a stop codon, wherein the tRNASec comprises an acceptor stem 9 base pairs a T-stem comprising 3 base pairs, wherein the SerRS, the EF-Tu, or both are from E. coli, wherein the SelA is not wildtype E. coli SelA, wherein the SelA is from Sulfurimonas honglongensis, Aeromonas salmonicida, or Rubrobacter xylanophilus, wherein the anticodon of the tRNASec recognizes a stop codon, wherein the nucleic acid is DNA or RNA, wherein the nucleic acid further comprising a heterologous expression control sequence, and the tRNASec formed by said nucleic acid, where a host cell comprising said nucleic acid, wherein the host cell is a prokaryote, archaeon, or eukaryote, wherein the prokaryote is E. coli, wherein the nucleic acid is incorporated into the genome of the cell, wherein the host cell is a genetically recoded organism (GRO), wherein the recoded organism comprises suppressor tRNA (para 26-27, 38), wherein GRO allows the reintroduction of UAG codons in a heterologous mRNA, along with orthogonal translation machinery system (OTS) comprising aminoacyl-tRNA synthetase (aaRS), tRNAs to permit efficient and site specific incorporation of non-standard amino acids into protein encoded by the recoded gene of interest (para 271, 272-273). Soll et al. further teach a method of making a recombinant selenocysteine containing protein comprising co-expressing a nucleic acid encoding a tRNASec, wherein the tRNASec is recognized by SerRS and by EF-Tu, or variants thereof, and when aminoacylated with serine the Ser-tRNA is a substrate for SelA or a variant thereof in a host cell also expressing SerRS, EF-Tu, SelA, or PSTK and SepSecS, with a polynucleotide comprising a codon that hybridizes with the anticodon of the tRNASec, wherein the E. coli host cell is genetically recoded organism (see, abstract, (see, the whole document in particular, abstract, para 14, 68, 28, 29, 31, 32-33, 56, 73-74, 89-95, 97, 99-100, 110-117, 121, 168, 265, 270-271, 290, 291, Fig. 9, 11, 12, 15, and claims 1-20).
Soll et al. do not teach recoded organism comprises phage receptor gene or portion thereof (for claims 88-89).
However, Zahn et al. teach elimination of bacteriophage contamination in an industrial fermentation process, and phage contamination happens by infecting bacteria used in the fermentation process, where the bacteriophage infect bacteria including E. coli through page receptor, and deletion mutation of said phage receptor fermenting bacteria enable the fermentation process resistant to phage contamination of the fermenting bacterial cell E. Coli (see, title, abstract, page 3-4, 9 (para 4), Fig. 7).
Zahn et al. clearly teach elimination of phage receptor, and further teach bacteriophage contamination in an industrial fermentation process, and phage contamination happens by infecting bacteria used in the fermentation process, where the bacteriophage infect bacteria including E. coli through page receptor, and deletion mutation of said phage receptor fermenting bacteria enable the fermentation process resistant to phage contamination of the fermenting bacterial cell E. Coli.
Therefore, before the effective filing date, it would have been obvious to one of ordinary skill in the art to arrive at the claimed invention as a whole by combining the teachings of Soll et al. and Zahn et al. to use E. coli bacterial cell that comprises phage receptor and deletion mutation of said phage receptor fermenting bacteria enable the fermentation process resistant to phage contamination of the fermenting bacterial cell E. Coli as taught by Zahn et al. to be used in the method of Soll et al. and modify Soll et al. in view of the teachings of Zahn et al. in making genetically recoded microbial organism E. coli devoid of phage receptor to arrive the claimed invention.
One of ordinary skilled in the art would have been motivated to use a phage receptor negative genetically recoded microbial organism E. coli, which can be a valuable tool for using in Research and Development, which is commercially, industrially and financially beneficial. One of ordinary skilled in the art would have a reasonable expectation of success because Soll et al. could successfully make a genetically recoded microbial organism E. coli cell lacking phage receptor. Thus, the above references render the claims prima facie obvious to one of ordinary skill in the art.
Arguments: Applicants argue that Soll does not obvious to a skilled artisan to arrive the claimed invention because Soll discloses a genetically engineered bacterial organism comprising, inter alia, a modified or variant nucleic acid sequence encoding tRNALeu", which is cognate to the recoded UGA codon, i.e., Soll discloses a modified tRNA that is cognate to a recoded stop codon, and does not include at least one deletion of a nucleic acid sequence encoding a tRNA cognate to a recoded sense codon, as required by the current claims. Applicants also argue that Soll does not teach or suggest "at least one deletion of a nucleic acid sequence encoding a transfer RNA (tRNA) cognate to the sense codon," as required by the claims, and Zahn does not remedy this deficiency. Applicants further argue that Zahn teaches "surveillance and elimination of bacteriophage contamination in an industrial fermentation process. The Office Action does not even allege that Zahn teaches or suggests "at least one deletion of a nucleic acid sequence encoding a transfer RNA (tRNA) cognate to the sense codon," as required by the claims. Thus, neither Soll nor Zahn, alone or in combination, renders the currently claimed invention obvious. For at least these reasons, Applicant respectfully requests reconsideration and withdrawal of this rejection.
Response: Applicants arguments have been fully considered, but are not deemed persuasive to overcome the rejection on obviousness issues because Soll et al. indeed teach the deletion of the sequence of tRNA and anti-determinant sequence (see, para 13, 93, 143, and Fig. 5), which is important for the interaction between tRNA and its binding partners (such as aminoacyl-tRNA synthetases or the ribosome) is governed by a balance of positive recognition elements and negative "anti-determinant" sequences, and furthermore, deletion or mutation of these sequences alters tRNA functionality, either by enabling new interactions for incorporating non-natural amino acids, or by destroying existing ones.
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As discussed previously, Soll et al. indeed teach a engineered plasmid pSecUAG-A used for Sec (selenocysteine) insertion in a genetically engineered E. coli host cell genome using UAG stop codon to convert amino acid cysteine to selenocysteine using seryl-tRNA synthetase (SerRS), comprising genetically modified microorganism, wherein the modified microorganism capable of producing selenocysteine, a non-natural amino acid, containing protein, which is expressed in a system that has been modified or mutated to reduce or eliminate expression of one or more translation release factors genes, wherein the release factor is a protein that allows for the termination of translation by recognizing the termination codon or stop codon in a mRNA sequence, and deletion of release factor gene results in incorporation of non-natural amino acid by reading termination codon UAG, like selenocysteine. Soll et al. also teach prokaryotic release factors include RF1, RF2 and RF3; and eukaryotic release factors include eRF1 and eRF3, and deletion of one or more release factors may result in "read-through" of the intended stop codon. Soll et al. further teach non-naturally occurring tRNASec, wherein the non-naturally occurring tRNASec can be recognized by seryl-tRNA synthetase (SerRS), and by EF-Tu, and when aminoacylated with serine the Ser-tRNA can (1) be a substrate for an exogenous SelA, a L-seryl-tRNA (Sec) selenium transferase enzyme or a variant thereof; or (2) be a substrate for PSTK and when aminoacylated with phosphorylated serine the Sep-tRNA can serve as a substrate for SepSecS or a variant thereof, wherein the anticodon of the non-naturally occurring tRNASec hybridizes to a stop codon, wherein the tRNASec comprises an acceptor stem 9 base pairs a T-stem comprising 3 base pairs, wherein the SerRS, the EF-Tu, or both are from E. coli, wherein the SelA is not wildtype E. coli SelA, wherein the SelA is from Sulfurimonas honglongensis, Aeromonas salmonicida, or Rubrobacter xylanophilus, wherein the anticodon of the tRNASec recognizes a stop codon, wherein the nucleic acid is DNA or RNA, wherein the nucleic acid further comprising a heterologous expression control sequence, and the tRNASec formed by said nucleic acid, where a host cell comprising said nucleic acid, wherein the host cell is a prokaryote, archaeon, or eukaryote, wherein the prokaryote is E. coli, wherein the nucleic acid is incorporated into the genome of the cell, wherein the host cell is a genetically recoded organism (GRO), wherein the recoded organism comprises suppressor tRNA (para 26-27, 38), wherein GRO allows the reintroduction of UAG codons in a heterologous mRNA, along with orthogonal translation machinery system (OTS) comprising aminoacyl-tRNA synthetase (aaRS), tRNAs to permit efficient and site specific incorporation of non-standard amino acids into protein encoded by the recoded gene of interest (para 271, 272-273). Soll et al. further teach a method of making a recombinant selenocysteine containing protein comprising co-expressing a nucleic acid encoding a tRNASec, wherein the tRNASec is recognized by SerRS and by EF-Tu, or variants thereof, and when aminoacylated with serine the Ser-tRNA is a substrate for SelA or a variant thereof in a host cell also expressing SerRS, EF-Tu, SelA, or PSTK and SepSecS, with a polynucleotide comprising a codon that hybridizes with the anticodon of the tRNASec, wherein the E. coli host cell is genetically recoded organism (see, abstract, (see, the whole document in particular, abstract, para 14, 68, 28, 29, 31, 32-33, 56, 73-74, 89-95, 97, 99-100, 110-117, 121, 168, 265, 270-271, 290, 291, Fig. 9, 11, 12, 15, and claims 1-20). Soll et al. do not teach recoded organism comprises phage receptor gene or portion thereof (for claims 88-89). However, Zahn et al. teach elimination of bacteriophage contamination in an industrial fermentation process, and phage contamination happens by infecting bacteria used in the fermentation process, where the bacteriophage infect bacteria including E. coli through page receptor, and deletion mutation of said phage receptor fermenting bacteria enable the fermentation process resistant to phage contamination of the fermenting bacterial cell E. Coli (see, title, abstract, page 3-4, 9 (para 4), Fig. 7).
Therefore, before the effective filing date, it would have been obvious to one of ordinary skill in the art to arrive at the claimed invention as a whole by combining the teachings of Soll et al. and Zahn et al. to use E. coli bacterial cell that comprises phage receptor and deletion mutation of said phage receptor fermenting bacteria enable the fermentation process resistant to phage contamination of the fermenting bacterial cell E. Coli as taught by Zahn et al. to be used in the method of Soll et al. and modify Soll et al. in view of the teachings of Zahn et al. in making genetically recoded microbial organism E. coli devoid of phage receptor to arrive the claimed invention. One of ordinary skilled in the art would have been motivated to use a phage receptor negative genetically recoded microbial organism E. coli, which can be a valuable tool for using in Research and Development, which is commercially, industrially and financially beneficial. One of ordinary skilled in the art would have a reasonable expectation of success because Soll et al. could successfully make a genetically recoded microbial organism E. coli cell lacking phage receptor. Thus, the above references render the claims prima facie obvious to one of ordinary skill in the art. Therefore, the rejection is maintained.
Maintained-Double Patenting Rejections (Provisional)
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 obviousness-type 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); and 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 a nonstatutory double patenting ground provided the conflicting application or patent either is shown to be commonly owned with this application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement.
Effective January 1, 1994, a registered attorney or agent of record may sign a terminal disclaimer. A terminal disclaimer signed by the assignee must fully comply with 37 CFR 3.73(b
Claims 63, 77-88 and 89 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-8, 15, 18-19, 34-38 and 39 copending Application No. 17/611,010 (published as US 2022/0282263A1). Although the claims at issue are not identical, they are not patentably distinct from each other because the claims are of overlapping scope.
Claims 63, 77-88 and 89 of the instant application are drawn to a method of producing a plasmid, the method comprising culturing the a population of genetically engineered released bacteria of any proceeding claim 1, under conditions such that a plasmid comprising at least one exogenous nucleic acid sequence is produced, wherein the genetically engineered released bacterial organism comprises:(i) at least one genetically engineered codon, (ii) at least one modification to or deletion of:(a) a first nucleic acid sequence encoding a transfer RNA cognate to the genetically engineered codon,(b) a second nucleic acid sequence encoding a release factor cognate to a second genetically engineered second codon, or (c) both, wherein the at least one genetically engineered codon of (i) is present within the bacterial genome, wherein the at least one genetically engineered codon of (i) is present outside the bacterial genome, wherein the at least one modification or deletion of (ii) is present within the bacterial genome, wherein the at least one modification or deletion of (ii) is present outside the bacterial genome, wherein the at least one genetically engineered codon comprises at least one recoded stop codon, wherein the recoded codon comprises a stop codon, and wherein the recoded codon is synonymously replaced in the engineered genetic material, wherein the genetically engineered released bacterial organism comprises a plurality of recoded codons, wherein the recoded codons comprise (i) a sense codon and (ii) a stop codon, and wherein at least one of (i) and (ii) is synonymously replaced in the engineered genetic material, wherein the genetically engineered released bacterial organism further comprises at least one orthogonal translation system (OTS) comprising an aminoacyl-tRNA synthetase (aaRS) and cognate tRNA, and wherein the tRNA of the at least one OTS comprises an anticodon complementary to a recoded codon, wherein the genetically engineered released bacterial organism further comprises at least one orthogonal translation system (OTS) comprising an aminoacyl-tRNA synthetase (aaRS) and cognate tRNA, wherein the tRNA of the at least one OTS comprises an anticodon complementary to a recoded codon, and wherein the tRNA charges a synthetic or unnatural amino acid, wherein the genetically engineered released bacterial organism further comprises at least one orthogonal translation system (OTS) comprising an aminoacyl-tRNA synthetase (aaRS) and cognate tRNA, wherein the tRNA of the at least one OTS comprises an anticodon complementary to a recoded codon, and wherein the tRNA charges a natural amino acid, wherein the genetically engineered released bacterial organism further comprises at least one suppressor tRNA, wherein the tRNA of the at least one suppressor tRNA comprises an anticodon complementary to a recoded codon, and wherein the tRNA charges a natural amino acid, wherein the genetically engineered released bacterial organism further comprises a deletion or modification to at least one phage receptor gene or portion thereof.
The claims of the co-pending application are drawn to a genetically engineered bacterial organism comprising engineered genetic material, the material comprising i) at least one genetically engineered codon, (ii)and b) at least one genetically engineered naturally occurring element at least one modification to or deletion of:(a) a first nucleic acid sequence encoding a transfer RNA cognate to the genetically engineered codon,(b) a second nucleic acid sequence encoding a release factor cognate to a second genetically engineered second codon, or (c) both, and[[ii]](iii at least one exogenous nucleic acid sequence encoding a therapeutic polypeptide or portion thereof- wherein the at least one genetically engineered codon comprises at least one recoded codon, and wherein the recoded codon comprises a sense codon, and wherein the recoded codon is synonymously replaced in the engineered genetic material, and wherein the at least one genetically engineered naturally occurring element comprises a modification to or deletion of (a) a first nucleic acid sequence encoding a transfer RNA cognate to the genetically engineered codon and (b) a second nucleic acid sequence encoding a release factor cognate to a second genetically engineered second codon, wherein the at least one genetically engineered codon is present within the bacterial genome, wherein the at least one genetically engineered codon is present outside the bacterial genome, wherein the at least one modification or deletion of (ii) at least one genetically engineered naturally occurring element is present within the bacterial genome, wherein the at least one modification or deletion of (ii) at least one genetically engineered naturally occurring element is present outside the bacterial genome, wherein the at least one exogenous nucleic acid sequence is present within the bacterial genome, wherein the at least one exogenous nucleic acid sequence is present outside the bacterial genome, wherein the engineered genetic material comprises further comprising at least one heterologous nucleic acid sequence, wherein the at least one genetically engineered codon comprises at least one recoded stop codon, wherein the at least one recoded codon comprises a stop codon, and wherein the recoded codon is synonymously replaced in the engineered genetic material, wherein the engineered genetic material comprises comprising a plurality of recoded codons, wherein the recoded codons comprise (i) a sense codon and (ii) a stop codon, and wherein at least one of (i) and (ii) is synonymously replaced in the engineered genetic material, wherein the engineered genetic material further comprises further comprising at least one orthogonal translation system (OTS) comprising an aminoacyl-tRNA synthetase (aaRS) and cognate tRNA, and wherein the tRNA of the at least one OTS comprises an anticodon complementary to a recoded codon, wherein the engineered genetic material further comprises further comprising at least one orthogonal translation system (OTS) comprising an aminoacyl-tRNA synthetase (aaRS) and cognate tRNA, wherein the tRNA of the at least one OTS comprises an anticodon complementary to a recoded codon, and wherein the tRNA charges a synthetic or unnatural amino acid, wherein the engineered genetic material further comprises further comprising at least one orthogonal translation system (OTS) comprising an aminoacyl-tRNA synthetase (aaRS) and cognate tRNA, wherein the tRNA of the at least one OTS comprises an anticodon complementary to a recoded codon, and wherein the tRNA charges a natural amino acid, wherein the engineered genetic material further comprises further comprising at least one suppressor tRNA, wherein the tRNA of the at least one suppressor tRNA comprises an anticodon complementary to a recoded codon, and wherein the tRNA charges a natural amino acid, wherein the engineered genetic material further comprises further comprising a deletion or modification to at least one phage receptor gene or portion thereof, wherein the engineered genetic material genetically engineered bacterial organism does not comprise a deletion or modification to at least one phage receptor gene or portion thereof.
Claims of the instant application listed above cannot be considered patentably distinct over claims 1-8, 15, 18-19, 34-38 and 39 of the reference patents when there are specifically recited embodiments that would either anticipate to claims 63, 77-88 and 89 of the instant application or alternatively render them obvious. Alternatively, claims 63, 77-88 and 89 cannot be considered patentably distinct over claims 1-8, 15, 18-19, 34-38 and 39 of the reference co-pending application when there is specifically disclosed embodiment in the reference copending application falls within the scope of claims 63, 77-88 and 89 of the instant application, i.e. there is substantially overlapping scope between the claimed invention and the teachings of the reference. One having ordinary skill in the art would have been motivated to do this because that embodiment is disclosed as being a preferred embodiment within the claims 1-8, 15, 18-19, 34-38 and 39 of copending Application No. 17/610,010. This is a provisional obviousness-type double patenting rejection because the conflicting claims have not in fact been patented.
Maintained DP rejection
Arguments: Applicants argue regarding Provisional Double Rejections that the present double patenting rejections be held in abeyance until notification of allowable subject matter in the present application.
Response: Applicant’s arguments have been fully considered but are not deemed persuasive to overcome the rejection on Provisional Double Rejections because no terminal disclaimer (TD) has yet been filed, and thus, the rejection is maintained.
Conclusion
Status of the claims:
Claims 63, 77-88 and 89 are rejected.
Applicants must respond to the objections/rejections in each of the sections in this Office action to be fully responsive in prosecution. 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).
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to IQBAL H CHOWDHURY whose telephone number is (571)272-8137. The examiner can normally be reached on M-F, at 9:00-5:00 PM.
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Iqbal H. Chowdhury, PhD.
Primary Patent Examiner
Art Unit 1656 (Recombinant Enzymes and Protein Crystallography)
US Patent and Trademark Office (USPTO)
Ph. (571)-272-8137 and Fax (571)-273-8137
/IQBAL H CHOWDHURY/
Primary Examiner, Art Unit 1656