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 .
Reissue: Final Office Action
Procedural Posture
On 8/14/2018: US Patent 10,047,405 issued to Kotula et al. with claims 1-20.
On 10/29/2021: Applicants filed US Reissue Patent Application No. 17/514,733 for US Patent 10,047,405 with claims 1-20.
On 12/1/2023: A non-final Office Action (OA) was mailed rejecting claims 1-20.
On 4/18/2025: After several improper responses, applicants filed a proper response to the 12/1/23 OA with arguments and amendments.
Status of the Claims
The amendments and arguments filed 4/18/2025 are acknowledged and have been fully considered. Claims 6-24 are now pending and are now under consideration. Claims 1-5 are cancelled; claims 6, 11, 12, and 20 are amended; claims 21-24 have been added.
Second Non-Final Office Action
This Office action is non-final because two claims (18 and 20) are now rejected that were previously not rejected.
OBJECTIONS/REJECTIONS WITHDRAWN
The objections and rejections of claims 1-5 under are moot in light of the claim cancellations.
The objections to claims 11, 12, 15, and 16 are withdrawn in light of the claim amendments.
The rejection of claims 12-14 and 16-17 under 35 U.S.C. 102(a)(1) is withdrawn in light of the claim amendments.
The double patenting rejection of record has been withdrawn in light of the terminal disclaimer filed and approved on 3/27/24.
REJECTIONS MAINTAINED
The rejection of claims 15 and 19 under 35 U.S.C. 103 is maintained as discussed below.
Claim Objections (New)
A. Claims 6-24 are objected to because they are not accompanied by, on a separate sheet of paper, an explanation of the support in the disclosure of the patent for the changes made to the claims. See 37 CFR 1.173(c). Pursuant to 37 CFR 1.173(c), each claim amendment must be accompanied by an explanation of the support in the disclosure of the patent for the amendment (i.e., support for all changes made in the claim(s), whether insertions or deletions). See also MPEP 1453(II).
Applicants’ single sentence on page 5 of the 4/18/25 response generally asserting support for amended claims 6, 11, 12, and 20 “can be found, for example, through the originally filed specification or claims” and alleging the absence of new matter is insufficient.
B. Claim 12 is objected to for the following informalities: The claim recites the limitation "wherein the antagonistic transcription factors are cI and Cro" in the last line of the claim with the terms "cI" and "Cro" italicized. Convention in the art is to refer to gene names with italics to distinguish them over the proteins (e.g., transcription factors) that the genes encode, which are not italicized. Since the portion of claim 12 in question clearly refers to transcription factors, it is clear that the italicized terms are intended to refer to the proteins encoded by the respective genes. Thus, this issue is raised as an objection and not a rejection under 112(b), however the terms in question should be amended to the non-italicized form to conform to standard nomenclature in the art and for consistency with claim 15, which correctly refers to these factors without italics.
Statement Under 37 CFR 3.73(c) (Maintained)
This application is objected to under 37 CFR 1.172(a) as lacking the written consent of all assignees owning an undivided interest in the patent. The proof of Ownership of the assignee must be in compliance with 37 CFR 1.172. See MPEP § 1410.02.II.
In particular, in the Statement under CFR 3.73(c), filed 10/29/2021, box 4B (a chain of title from the inventors(s) of the patent) should be checked.
A proper consent of the assignee in compliance with 37 CFR 1.172 and 3.73 is required in reply to this Office action.
Response to Arguments: Objection Under 37 CFR 1.172(a)
Applicants do not appear to have addressed this objection, which was raised in the prior non-final Office action (see the objection bridging pgs. 2-3 in the OA dated 12/1/2023). None of the responses filed since the 12/1/2023 OA mention this objection at all, and no new 3.73(c) statement has been filed.
Claim Rejections - 35 USC § 112(a)
The following is a quotation 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.
Written Description
Claim 24 is rejected under 35 U.S.C. 112(a), as failing to comply with the written description requirement. The claim 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(s), at the time the application was filed, had possession of the claimed invention. Specifically, claim 24 recites, "… wherein the inducible promoter is responsive to tetracycline, tetrathionate, reactive oxygen species, sdiA and hydrogen sulfite gas (H2S)". Thus, the claim does not recite a Markush group of alternatives, but rather requires that the inducible promoter be responsive to all five recited species (note the use of the word "and" at the end of the list).
Nowhere in the instant specification do applicants describe an inducible promoter that is responsive to all five of the recited species. At col. 20, lines 43-58 and col. 40, lines 38-46, the application teaches an inducible promoter that can sense a trigger element selected from the group consisting of the species recited in instant claim 24 (i.e., a single member, not all of the species). Further, at col. 22, lines 30-42, the specification teaches that sensing the different species recited in claim 24 is necessary for different diagnoses. In fact, at col. 22, lines 43-61, col. 23, lines 17-26, and col. 25, lines 1-11, the specification teaches the use of different inducible promoters for different stimulus species (e.g., hydrogen peroxide (a reactive oxygen species), hydrogen sulfide, tetrathionate). Applicants fail to describe a single inducible promoter that is responsive to more than one of the species recited in claim 24.
Applicants are alerted that "a sufficient description of a genus ... requires the disclosure of either a representative number of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can ‘visualize or recognize’ the members of the genus." AriadPharms., Inc. v. EliLilly & Co., 598 F.3d 1336, 1350 (Fed. Cir. 2010). A "generic claim may define the boundaries of a vast genus of chemical compounds, and yet the question may still remain whether the specification, including original claim language, demonstrates that the applicant has invented species sufficient to support a claim to a genus." Id. at 1349. “[M]erely drawing a fence around a perceived genus is not a description of the genus.” AbbVie Deutschland GmbH & Co., KG v. Janssen Biotech, Inc., 759 F.3d 1285, 1300 (Fed. Cir. 2014). “One needs to show that one has truly invented the genus, i.e., that one has conceived and described sufficient representative species encompassing the breadth of the genus.” Id. “Otherwise, one has only a research plan, leaving it to others to explore the unknown contours of the claimed genus.” Id.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 15 is rejected under 35 U.S.C. 112(d) as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends. Specifically, claim 15 recites the limitation "wherein the antagonistic transcription factors are cI and Cro". This limitation is already present in claim 12, from which claim 15 depends. Applicants are required to cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 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(a) 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 at the time any inventions covered therein were effectively filed 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 at the time a later invention was effectively filed 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.
Claims 12-20 are rejected under 35 U.S.C. 103 as being unpatentable over KOBAYASHI (Kobayashi, H, et al., PNAS (2004), 101(22); 8414-8419) in view of HASTY (Hasty, J., et al. Nature (2002), 420; 224-230; on IDS).
Introduction: Instant claim 12 and claims dependent thereon are drawn to an engineered unicellular organism comprising a cI/Cro-reporter gene-based toggle switch and an inducible trigger element that can respond to a stimulus.
Kobayashi teaches engineered Escherichia coli strains that can be constructed to have programmable behaviors (abstract). The cells are transformed with plasmids containing a genetic toggle switch interfaced with a biosensor module; the genetic toggle switch “endows these strains with binary response dynamics and an epigenetic inheritance that supports a persistent phenotypic alteration in response to transient signals” (abstract; Fig. 1). In other words, the engineered cells contain a memory element integrated into the genome of the organism (i.e., a persistent phenotypic alteration; binary response elements) and an inducible gene regulatory factor trigger element (i.e., a biosensor that is responsive to biological signals) as in claim 12.
In particular, the circuit components of E. coli strain B1 include: a sensor component comprised of an acyl-homoserine (AHL) inducible plasmid, a regulator component comprising a toggle switch plasmid pTSMb1, and an output comprising polycistronic GFP expression. Kobayashi indicates that the B1 strain detects and retains memory of quorum sensing molecules (Table 1; p. 8415). As shown in Fig. 5A, provided here below, and with respect to claim 12, the B1 strain comprises:
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(a) a memory element comprising sequences of two antagonist transcription factors or gene regulatory factors (i.e., the regulatory unit, lacI and cI857) and a reporter gene (gfp), wherein the factors are arranged in a genetic toggle switch configuration, and wherein the reporter gene is arranged downstream and operably linked to one of the factors (Ptrc and cI857); and
(b) an inducible gene regulatory factor trigger element (the sensor) comprising an inducible promoter (Plux) and a duplicated copy of one of the transcription or gene regulator factors in the memory element (lacI), wherein the duplicated copy of the transcription or gene regulatory factor is operably linked to an inducible promoter (Plux [Wingdings font/0xE0] lacI), wherein the inducible promoter is responsive to a stimulus (AHL), and wherein the memory circuit is integrated into the genome of the organism (Figs. 1, 5; Table 1; p. 8415).
Kobayashi discloses that the regulatory circuit (a genetic toggle switch) is comprised of two genes, lacI and cI, that encode transcriptional regulator proteins (i.e., transcription factors) LacR and CI, respectively (p. 8415; Results section). The lacI gene is repressed by CI protein, and the cI gene is repressed by LacR protein. Thus, the transcription factors are antagonist transcription factors as each inhibits expression of the other’s gene. This design endows cells with two distinct phenotypic states: one where the CI activity is high and the expression of lacI is low, and one where the activity of LacR is high and the expression of cI is low (Fig. 2A). The antagonistic genes used by Kobayashi in the B1 strain were lacI and cI (specifically cI857), wherein lacI is the duplicated gene operably linked to an inducible promoter and cI857 is a temperature-sensitive mutation of the cI gene.
Kobayashi teaches that the stability of the distinct expression states of the B1 strain was confirmed in control experiments where stable expression was observed for up to 50 hours, which corresponds to 50-60 generations (see p. 8418, 1st col., 1st par.), which evidences that the memory circuit is integrated into the genome of the organism, as in claim 12.
Thus, Kobayashi teaches an engineered bacteria (a unicellular organism) comprising a memory circuit, wherein the memory circuit comprises: (a) a memory element comprising sequences of two antagonistic transcription factors/gene regulatory factors, and a reporter gene arranged downstream thereof; and (b) an inducible gene regulatory factor trigger element comprising a duplicated copy of one of the transcription/gene regulatory factors in the memory element, which copy is linked to an inducible promoter responsive to a stimulus, and wherein the memory circuit is integrated into the genome of the organism.
However, Kobayashi does not teach that the gene-based memory element comprises cI and Cro, wherein Cro is the duplicated gene.
Hasty discloses bacteria comprising a memory circuit, wherein the memory circuit comprises the lambda phage sequences of cI and Cro (p. 226, 1st col., 2nd full par.; Fig. 2). Hasty indicates that cI/Cro acts as a natural toggle switch found in the PR/PRM region of lambda phage. These elements act antagonistically to control the lysis/lysogeny decision: Cro, controlled by PR, represses PRM, whereas cI, controlled by PRM, represses PR (p. 226, 1st col., 2nd full par.; Fig. 2a). Hasty discloses that a memory circuit may also comprise a reporter gene such as gfp (green fluorescent protein) (bridging pgs. 226-227 and Figs. 2-3), as well as an inducible promoter, such as a tetracycline-response promoter (Figs. 2-3).
Consistent with the teachings of Kobayashi, Hasty teaches that the networks (i.e., memory circuits) can be inserted into cells, such as E. coli (see Fig. 4), and shows the growth and maintenance of the E. coli without antibiotic selection (bridging pgs. 227-228).
Accordingly, it would have been obvious to one of ordinary skill in the art at the time of filing to have substituted cI/Cro as taught by Hasty for cI857/lacI as the antagonistic transcription factors in the memory circuit of Kobayashi and thereby arrive at the presently claimed invention. Based upon the teachings of Hasty, the skilled artisan would have recognized that the cI/Cro transcription factors are a natural co-repressive genetic toggle switch from the bacteriophage lambda, and therefore could be used as part of engineered gene circuits to program bacteria as taught by Kobayashi. Kobayashi, in fact, teaches cI in conjunction with lacI as the genetic toggle switch module in engineered bacteria (e.g., Figs. 2-4). Therefore, the substitution cI of for cI857, and Cro for lacI would have been obvious. This is because the artisan has good reason to pursue the known options within his or her technical grasp to obtain predictable results. Such would amount to the simple substitution of one known functionally equivalent element for another to achieve a predictable outcome.
Regarding claim 13, antibiotic selection was not used to maintain the memory circuit in Kobayashi’s E. coli (see p. 8418, 1st col., 1st par.).
Regarding claims 14-15, the memory circuit of Hasty comprises the antagonistic transcription factors Cro and CI (p. 226, 1st col., 2nd full par.; Fig. 2).
Regarding claim 16, the reporter gene gfp, taught by both Kobayashi and Hasty, expresses the fluorescent protein GFP (green fluorescent protein).
Regarding claim 17, both Kobayashi and Hasty teach inducible promoters responsive to environmental cues. Specifically, Kobayashi teaches the inducible promoter Plux is responsive to acyl homoserine lactone (AHL). AHL is an intercellular signaling molecule (i.e., a small molecule) used by bacteria to monitor their population density in quorum-sensing control of gene expression. Similarly, Hasty teaches the use of promoters sensitive to environmental markers such as autoinducer molecules that can diffuse into the extracellular environment and enter receiver cells to stimulate production of a GFP reporter gene (p. 229, 1st col.).
Regarding claim 18, Hasty discloses that a memory circuit may also comprise a reporter gene such as gfp (green fluorescent protein) (p. 224, 2nd col.; bridging pgs. 226-227 and Figs. 2-3), as well as an inducible promoter, such as a tetracycline-response promoter (Figs. 1-4).
Regarding claim 19, this claim only requires that a genomic rearrangement is “detectable” (i.e., that one could detect changes to the genome of the modified organism (e.g., E. coli as taught by Kobayashi) by PCR analysis). The modifications taught by Kobayashi and Hasty meet this requirement, absent evidence to the contrary.
Regarding claim 20, the culture medium in which the bacteria are grown and/or the assay media in which the cells are analyzed (e.g., see Kobayashi at p. 8415, 1st col., teaching that the cells were resuspended in phosphate-buffered saline) meets the limitation of formulation comprising the cells and "a pharmaceutically acceptable ingredient" because such media include water, which is pharmaceutically acceptable.
Response to Arguments: Obviousness Rejection
Applicants' arguments have been fully considered but are not persuasive.
Regarding the rejections under 35 USC § 103, in the responses dated 3/29/24 and 7/23/24, applicants argue claims 1-5, 15, and 19 have been cancelled. However, claims 15 and 19 are still pending and have not been cancelled in the current amendment. No further arguments against this rejection were presented in the responses dated 1/14/25 or 4/18/25.
Summary/Conclusion
Claim 12-20 are rejected; claims 1-5 are cancelled. Claims 6-11 and 21-24 are objected to but would otherwise be allowable if the objections are addressed.
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 extension fee 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 date of this final action.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Kevin S Orwig whose telephone number is (571)270-5869. The examiner can normally be reached Mon.-Fri. 8AM-5PM.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Tim Speer can be reached at (313) 446-4825. The fax phone number for the organization where this application or proceeding is assigned is 571-273-9900.
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/Kevin S Orwig/
Patent Reexamination Specialist
Art Unit 3991
Conferees:
/Lora E Barnhart Driscoll/ Patent Reexamination Specialist, Art Unit 3991
/T.M.S/ Supervisory Patent Examiner, Art Unit 3991