DETAILED ACTION
Notice of 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 .
Election/Restrictions
Applicant's election with traverse of Group I-11 in the reply filed on 03 March 2026 is acknowledged. The traversal is on the ground(s) that the prior art of Carlson et al. (Nat. Comm., 2019 – cited IDS 07/21/2023) does not teach the special technical feature requiring the post translational mechanism of claim 1 because they do not teach both part (a) and part (b) of claim 1. This is not found persuasive because as noted in the restriction itself, the special technical feature is part (a) and/OR part (b) because claim 23 (and dependents therefrom) does not require both parts. Thus, the special technical feature of all the claims is either part (a) or part (b) OR both parts (a) and (b) of claim 1. To this end, Carlson et al. does teach at least part (a) of claim 1; and hence the polynucleotide as required in claim 23 and this then breaks unity of invention.
The requirement is still deemed proper and is therefore made FINAL.
Status of Application
Claims 1-12, 15-16, 23-25, 33-35 are pending; Claims 12, 15-16, 23-25, 33-35 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected subject matter, there being no allowable generic or linking claim. Thus, claims 1-11 are subject to examination on the merits.
Priority
The instant application is a 371 of PCT/US2021/024006 filed 24 March 2021 which claims benefit of Provisional application 62/993,860 filed 24 March 2020 is acknowledged. Said document has been received.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on 30 May 2024, 21 July 2023 and 21 July 2023 have been considered by the examiner. See initialed and signed PTO/SB/08’s.
Drawings
The drawings are objected to because the details are not of sufficient quality to decipher what is being shown. Specifically, Figures 4a and 4d (the 23S rRNA figure), Figure 6b, 6c, Figure 9a, Figures 12b, 12c, Figure 16a, Figure 16c, Figure 17, Figure 20, .
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Figures 1-25 should be designated by a legend such as --Prior Art-- because only that which is old is illustrated. See MPEP § 608.02(g).
Said Drawings were first published in the NPL reference 1 cited on the IDS 05/30/2024 (Aleksashin PhD thesis); and in Aledkashin et al. (Nat. Comm. February 2019,) cited as NPL document 1 in the IDS of 07/21/2023.
Corrected drawings in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. The replacement sheet(s) should be labeled “Replacement Sheet” in the page header (as per 37 CFR 1.84(c)) so as not to obstruct any portion of the drawing figures. If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Compliance with Sequence Rules
The sequence listing, filed in computer readable form (.txt) on 26 September 2022, has been received and entered. This application contains sequence disclosures that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 C.F.R. § 1.821(a)(1) and (a)(2). However, this application fails to fully comply with the requirements of 37 C.F.R. § 1.821 through 1.825.
The following Figures/parts of the specification contain sequences that contain four or more specifically defined amino acids or ten or more specifically defined nucleotides without any corresponding SEQ ID NO: and/or no reference to any SEQ ID NO: in the Brief Description of the Drawings.
In Figure 2b, the two primer sequences each require a sequence identifier.
In Figure 4d, the 23S rRNA requires a sequence identifier.
In Figure 7b, the two primer sequences each require a sequence identifier.
In Figure 19, all of the primers in the table require a sequence identifier.
Figure 21, all of the primers in the table require a sequence identifier.
* If the noted sequences are in the sequence listing as filed, Applicants must amend the specification to identify the sequences appropriately by SEQ ID NO:. If the noted sequences are not in the sequence listing as filed, Applicants must provide (1) an updated copy of the sequence listing containing the requisite sequences in computer readable form (.txt), (2) an amendment directing its entry into the specification, (3) a statement that no new matter has been added and (4) an amendment to the specification to identify the identified sequences by SEQ ID NO:, which can be in the Brief Description of the Drawings section of the specification (For Figures only) and (5) an updated incorporation by reference statement with the new date of creation, sequence file name and size. – See also MPEP 2422.
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.
Claims 1-11 are rejected under 35 U.S.C. 112(b) as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor regards as the invention.
Claim 1 does not end in a period. Rather it ends with “and/or” which suggests other elements of the claim are missing. This renders the claim indefinite as the scope of the claim cannot be determined. Dependent claims 2-11 are included in the rejection as they do not remedy the noted deficiency.
Claim 8 is further rejected as being indefinite because it recites specific nucleotide residues which result in a change of function mutation in a large ribosome subunit rRNA. However, it is unclear what sequence these residues actually correspond to as there are numerous large ribosomal sequences. For example, the claims are not limited as to whether the large ribosomes are eukaryotic (e.g. a 60S subunit which contains 28S, 5.8S and 5S rRNA) or prokaryotic (which possess 50S subunits having 23S and 5S RNA); and even if they were, each sequence will differ from species to species. It is suggested to insert a specific sequence (SEQ ID NO:) to which the nucleotide residues correspond.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
Claims 1-11 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor at the time the application was filed, had possession of the claimed invention.
Regarding the instant claims, the MPEP in section 2163(I) states that the purpose of the written description requirement is to ensure that the inventor had possession, at the time the invention was made/filed, of the specific subject matter claimed:
To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonable conclude the inventor had possession of the claimed invention. See, e.g., Moba, B.V. v. Diamond Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed. Cir. 2003); Vas-Cath, Inc. v. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116. However, a showing of possession alone does not cure the lack of a written description. Enzo Biochem, Inc. v. Gen-Probe, Inc., 323 F.3d 956, 969-70, 63 USPQ2d 1609, 1617 (Fed. Cir. 2002). For example, it is now well accepted that a satisfactory description may be found in originally-filed claims or any other portion of the originally-filed specification. See In re Koller, 613 F.2d 819, 204 USPQ 702 (CCPA 1980); In re Gardner, 475 F.2d 1389, 177 USPQ 396 (CCPA 1973); In re Wertheim, 541 F.2d 257, 191 USPQ 90 (CCPA 1976). However, that does not mean that all originally-filed claims have adequate written support. The specification must still be examined to assess whether an originally-filed claim has adequate support in the written disclosure and/or the drawings.
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An applicant shows that the inventor was in possession of the claimed invention by describing the claimed invention with all of its limitations using such descriptive means as words, structures, figures, diagrams, and formulas that fully set forth the claimed invention. Lockwood v. Amer. Airlines, Inc., 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997)"
Further, for a broad generic claim, the specification must provide adequate written description to identify the entire genus of the claim. In Regents of the University of California v. Eli Lilly & Co. the court stated:
"A written description of an invention involving a chemical genus, like a description of a chemical species, 'requires a precise definition, such as by structure, formula, [or] chemical name,' of the claimed subject matter sufficient to distinguish it from other materials." Fiers, 984 F.2d at 1171, 25 USPQ2d 1601; In re Smythe, 480 F.2d 1376, 1383, 178 USPQ 279, 284985 (CCPA 1973) ("In other cases, particularly but not necessarily, chemical cases, where there is unpredictability in performance of certain species or subcombinations other than those specifically enumerated, one skilled in the art may be found not to have been placed in possession of a genus ...") Regents of the University of California v. Eli Lilly & Co., 43 USPQ2d 1398 (Fed. Circ. 1997).
MPEP § 2163 further states that if a biomolecule is described only by a functional characteristic, without any disclosed correlation between function and structure of the sequence, it is "not sufficient characteristic for written description purposes, even when accompanied by a method of obtaining the claimed sequence." Furthermore, the courts have also held that possession may not be shown by merely describing how to obtain possession of members of the claimed genus or how to identify their common structural features. See University of Rochester, 358 F.3d at 927, 69 USPQ2d at 1895.
The instant claims in their broadest are drawn to an engineered cell comprising a first and second protein translation mechanism/system,
the first comprising: a) the first protein translation mechanism comprising a first engineered ribosome, the first engineered ribosome comprising: i) a small subunit comprising ribosomal RNA (rRNA) and protein; ii) a large subunit comprising a ribosomal RNA (rRNA) and protein; and iii) a linking moiety, wherein the linking moiety comprises a polynucleotide sequence and tethers the rRNA of the small subunit with the rRNA of the large subunit;
b) the second protein translation mechanism comprising a second engineered ribosome, the second engineered ribosome comprising: i) a small subunit comprising rRNA and protein; and ii) a large subunit comprising rRNA and protein;
wherein the second engineered ribosome lacks a linking moiety between the large subunit and the small subunit; and
wherein the small subunit of the second engineered ribosome comprises a modified anti-Shine-Dalgarno sequence to permit translation of templates having complementary and/or cognate Shine-Dalgarno sequence different from endogenous cellular mRNAs of the cell.
Thus, the claims are drawn to an extremely large genus of engineered ribosomes, some of which are tethered to one another; others that are not but which possess a modified anti-Shine-Dalgarno (ASD) sequence; wherein said engineered ribosomes further do or can comprise a multitude of mutations resulting in a change of function (dependent claims 7-8, for example, but this says nothing about the other engineered ribosome system/mechanism). However, the specification only describes prokaryotic ribosomes that have been modified, specifically 16S rRNA and 23S rRNA in the first translation, tethered ribosome system; and likewise, 16S rRNA and 23S rRNA for the second ribosome translation system with specific modified ASD’s of 3′-GGUGUU-5′, 3′-UGGUGU-5′, 3′-GGUGUC-5′, 3′-GUUUAG-5′, 3′-UGGAAU-5′, 3′GGAUCU-5′, 3′-UGGAUC-5′, 3′-UGGUAA-5′, and 3′-UGGAUC-5′. And specific change of function point mutations (gain or loss of function, both) in the 23S rRNA large subunit of the second unlinked translation system, wherein only those described in Figure 17 are present. All of these, combined and/or individually, however, do not adequately describe/represent the entire and diverse genus of engineered first and second translation mechanisms which comprise modified small and/or large ribosomal subunits from eukaryotes and prokaryotes, wherein the kinds of modifications (engineered) are unlimited for both large and small ribosome subunits in both translation mechanisms/systems. Thus, it cannot be said that the specification establishes possession of the claimed genus.
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.
(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.
Claim(s) 1-11 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Aleksashin, N., PhD Thesis, Univ. Illinois - Chicago, Published 01 January 2019, which is outside the one-year grace period – cited on IDS 05/30/2024.
Aleksashin teaches: Regarding claims 1-4, an engineered E. coli cell which comprises two translation systems/mechanisms: the first having a small subunit comprising small subunit rRNA and a large subunit rRNA and a linking moiety which tethers the rRNA of the small subunit with the rRNA of the large subunit; and a second translation mechanism comprising a second engineered ribosome which comprises a small subunit comprising rRNA and a large subunit comprising rRNA; wherein said the ribosomal subunit of the second translation system are not linked and wherein the small subunit comprises an anti-Shine-Dalgarno (ASD) sequence; both systems further comprise proteins – See Figures 3.1-3.2 (pp. 74-76) and reproduced herein.
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As noted in the description:
Regarding claim 5, the second engineered ribosome comprises a change of function mutation which is not at the ASD, wherein 120 single-nucleotide mutations were made to the 23S rRNA – See pp. 91-101.
Regarding claim 6, the second engineered ribosome comprises a modified ASD making them dissociable for making orthogonal proteins wherein said modified ASD comprises GUGGUU in the 16S rRNA gene (See Description Figure 3.2);
Regarding claims 8-9, an A2058G mutation is made which introduces an antibiotic resistance function in the large subunit of the large ribosome rRNA; additional mutations in the large ribosome subunit of 23S rRNA, however, are disclosed in Table 3.2, pp. 96-101;
Regarding claim 10, the first engineered large subunit comprises a permutated 16S-23S hybrid (See description above, Figure 3.2);
Regarding claim 11, said the linking moiety employed to tether the subunits in the first system is a polynucleotide linking helices 101 and 44 (See description above, Figure 3.2).
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SUZANNE M NOAKES whose telephone number is (571)272-2924. The examiner can normally be reached M-F (7-4).
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/SUZANNE M NOAKES/Primary Examiner, Art Unit 1656 02 April 2026