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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 3/10/2026 has been entered.
Application Status
This action is written in response to applicant’s correspondence received on 3/10/2026. Claims 1-6 are pending. Claims 1, 3, and 5 have been amended. All pending claims are currently under examination.
Claim Rejections - 35 USC § 112 – New Rejection Necessitated by Amendment
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 following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 6 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Regarding claim 6, claim 6 is directed to a method of regulating the expression of a synthesis pathway gene in E. coli by introducing the system of claim 3 into an E. coli cell, where the system dynamically regulates the synthesis pathway gene in response to cell density via AI-2. Claim 6 depends from claim 3, which is directed to a system that comprises a dCpf1 expression vector, a reporter vector comprising GFP and mCherry coding sequences, and crRNAs targeting one of GFP and mCherry. Claim 3 is therefore a reporter system which is not directed to any synthesis pathway gene. Claim 3 is therefore directed to the regulation of a reporter gene using specific crRNAs for said reporter gene. It is therefore unclear how the system of claim 3 would be involved in a method of dynamically regulating a synthesis pathway because the crRNAs in claim 3 are directed to reporter genes such as GFP and mCherry, and not synthesis pathway genes.
Claim Rejections - 35 USC § 112 – New Rejection After Amendment
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.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
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 of carrying out his invention.
Claims 1-6 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, 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, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
MPEP 2163.II.A.3.(a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention”.
For claims drawn to a genus, MPEP § 2163 states the written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice, reduction to drawings, or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. See Regents of the University of California v. Eli Lilly & Co, 119 F.3d at 1568, 43 USPQ2d at 1406.
Regarding claim 1, claim 1 is drawn to an autioinducer-2 (AI-2) molecular response element consisting of SEQ ID NO: 1, where the AI-2 element is recited to be a cell-density dependent starting element, where the AI-2 element is recited with the functional language of being responsive to AI-2 signaling molecules to regulate gene expression in a cell-density dependent manner. Thus, claim 1 is reciting the broad genus of “cell,: where the AI-2 element is recited with structural-functional relationships of being capable of acting in response to AI-2 in a “cell” density dependent manner. This claim language is problematic because as discussed further below, a given cell type will not necessarily respond to AI-2 induction in a cell-density dependent manner.
Regarding the guidance provided in the specification, the Applicant has constructed an AI-2 response element (i.e., promoter), and tested the response element in E. coli cells of the specific strain MG1655 (e.g., paragraph 18). The Applicant has tested the response in reporter assays, where dCpf1 targeting mCherry and GFP was tested using specific crRNAs to target such reporter constructs (Figures 4-6). The Applicant has described how to construct such AI-2 response element promoters and reporter construct vectors (Examples 1-4). However, the Applicant has not tested such constructs in other “cell-density” dependent expression backgrounds with the exception of testing in the E. coli strain MG1655.
Regarding the present state of the art, it is known in the art that AI-2 induction systems rely on quorum sensing receptors which require complete LSR operons. For instance, Brito (Brito PH et al. Genome Biol Evol. 2013;5(1):16-30) is a research article which focuses on the diversity of AI-2 quorum sensing operons present across E. coli strains (Title, Abstract, and throughout). Brito teaches that:
“We show that all natural strains possess the signal emitter (the luxS gene), but many lack a functional signal receptor (complete lsr operon) and the ability to regulate extracellular signal concentrations,” (Abstract).
Brito further teaches that:
“A recent study showed that the ability to bind and internalize AI-2 signal via Lsr is not ubiquitous among E. coli strains. Two E. coli strains were shown to lack many genes in the operon, and phenotypic assays confirmed lack of function. The finding of this unexpected polymorphism leads us to investigate the genetic diversity of the AI-2 system among E. coli natural populations,” (page 17, right column final paragraph to page 18 first paragraph).
Thus, Brito teaches that not all E. coli cells comprise fully functional Lsr components necessary for cell-density dependent responses to AI-2 quorum sensing because they lack full Lsr operons, and furthermore teach that this finding is “unexpected” and therefore speaks to the uncharacterized and unpredictable nature of the genus of E. coli and AI-2 cell-density dependent response promoters.
Brito further teaches Figure 2, which shows that cells such as Shigella species and E. coli species lack complete Lsr operons and therefore do not respond in cell-density dependent manner to quorum sensing using AI-2 start elements.
Furthermore, Brito teaches that quorum sensing, such as AI-2 quorum sensing, is a phenomenon found in bacterial cells (Abstract). Thus, the recited response element is not functional as a starting element responsive to AI-2 molecules in a cell-density dependent manner within other cell types such as eukaryotes, which lack quorum sensing cellular machinery per Brito (Abstract).
The Applicant has not shown possession of the genus of cells which respond in a “cell-density dependent manner,” which broadly encompasses any cell type, where the AI-2 response element recited is recited with functional limitations to be required to be responsive to AI-2 molecules in a cell-density dependent manner. The art teaches, according to Brito, that a response element such as SEQ ID NO: 1 which is an AI-2 responsive promoter is unpredictable with regards to whether or not it will function in a cell-density dependent manner dependent upon the cell type it is in owing to the fact that not all cells have complete Lsr operons which would allow them to uptake AI-2. Furthermore, SEQ ID NO: 1 was not shown to be a cell-density dependent starting element in cells such as eukaryotes, which do not comprise bacterial quorum sensing machinery.
Regarding claims 2-6, these claims further recite E. coli cells. However, as taught by Brito (above), not all E. coli cells comprise the necessary cellular machinery to respond to AI-2 quorum induction because some E. coli strains lack fully functional Lsr operons and the receptors to respond to such quorum sensing molecules (above, Figure 2 of Brito). The Applicant has only tested their system in the E. coli strain MG1655, and given the unpredictability of the genus of E. coli and the fact that E. coli strains can “unexpectedly” lack Lsr operons, the Applicant has not shown possession of the genus of E. coli with the presently recited functional language of the claims. The Applicant was furthermore not in possession of the genus of “host cell” because Brito teaches that other cell types such as Shigella are known to not comprise fully functional Lsr operons (Figure 2 of Brito).
A suggestion to obviate the above 112(a) written description rejection is to amend the claims so that the scope of the claims is narrowed specifically to E. coli cells comprising the required Lsr operon necessary for the AI-2 response element (promoter) to function. For instance, the amendment to claim 1 could read “wherein the starting element is responsive to AI-2 signaling molecules to regulate gene expression in a cell-density-dependent manner, wherein the starting element is within an E. coli cell comprising a functional Lsr operon.”
Similar amendments to claims 2-6 can be made in order to narrow the cell types to E. coli which express functional Lsr operons. Paragraph 6 of the Applicant’s specification discusses the functional components of the Lsr operon in the context of AI-2 induction; therefore, amendments to the claims to include limitations requiring the Lsr operon would not constitute new matter.
112(a) – Enablement Rejection Necessitated by Amendment
Claim 6 is rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Regarding claim 6, claim 6 is directed to a method of regulating the expression of a synthesis pathway gene in E. coli comprising introducing the system of claim 3 into an E. coli host cell, where the system dynamically regulates the expression of a synthesis pathway gene in response to cell density signaling via AI-2. Claim 6 depends from claim 3, as it recites that the system of claim 3 is introduced into said E. coli cell, with the overall method accomplishing the dynamic regulation of a synthesis pathway gene. Claim 6 is problematic and not enabled by the specification, for the simple reason that claim 3 recites the components of a dCpf1 expression vector, a reporter vector comprising GFP and mCherry coding sequences, and crRNAs targeting one of GFP and/or mCherry. Claim 3 is therefore a reporter system which is not directed to any synthesis pathway gene because the crRNAs are directed against GFP and mCherry (I.e., fluorescent reporter markers). The nature of the recited invention of claim 6, and its broadest reasonable interpretation, is that the elements of claim 3 are capable of regulating a synthesis gene of E. coli when introduced into E. coli, as recited in claim 6. However, the Applicant has not demonstrated in the specification that the introduction of crRNAs and dCpf1 are capable of dynamically regulating a synthesis pathway gene in E. coli.
Regarding the specification, the Applicant has made constructs which express dCpf1 from a Pj23119-LsrR-Plsr promoter, and have furthermore made vector constructs expressing crRNAs and reporter constructs encoding GFP and mCHerry (Examples 1-4). The Applicants have provided Example 4, where their autoinducer promoter was used to target GFP and mCherry using crRNAs directed against GFP and mCherry (Example 4). The Applicants have not use these components to dynamically regulate the expression of a pathway synthesis gene.
Regarding what is known in the art, it is known that E. coli synthesis pathways involve numerous genes. For instance, Emiola (Emiola A et al. PLoS One. 2015 Apr 28;10(4):e0121216) is a research article that focuses on Lipid A biosynthesis in E. coli (Title, Abstract, and throughout). Emiola teaches that the synthesis of Lipid A in E. coli involves nine enzyme-catalyzed steps, including enzymes such as LpxA. Thus, Emiola teaches that it is known in the art that biosynthesis pathways in E. coli involve numerous enzymes which are not reporter constructs such as GFP or mCherry.
The Applicant has not shown that the specification is enabling for a practitioner to dynamically regulate the expression of a synthesis gene in E. coli as the method presently recited in claim 6 only requires crRNAs which target reporter genes such as GFP and mCherry, which are not known to be involved with synthesis pathways in E. coli. The practitioner is therefore not enabled to target synthesis pathway genes using crRNAs directed against reporter genes, as presently recited, to achieve the overall effect recited in claim 6 of dynamic regulation of a pathway synthesis gene. The practitioner is therefore inherently tasked with undue experimental burden to practice the recited method because the present method does not appear to be feasible (i.e., it is not feasible to regulate a synthesis pathway by targeting reporter genes).
Response to Arguments
The Applicant’s arguments filed 3/10/2026 have been considered but are not persuasive. The Applicant’s amendments have prompted a new search and consideration in light of the amended scope of the claims, where the new search and consideration has prompted the new 112(a) written description rejection, above.
Regarding the Applicant’s argument that the amendments obviate the 112(b) rejections, the Applicant’s amendments have rendered claim 6 unclear for the reasons given above in the 112(b) rejection.
Furthermore, the Applicant’s amendments have clarified the components required in claim 6, where the “reporter gene” has been amended to be GFP or mCherry. This amendment has prompted the 112(a) enablement rejection above.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DOUGLAS CHARLES RYAN whose telephone number is (571)272-8406. The examiner can normally be reached M-F 8AM - 5PM.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Ram Shukla can be reached at (571)-272-0735. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/D.C.R./Examiner, Art Unit 1635
/RAM R SHUKLA/Supervisory Patent Examiner, Art Unit 1635
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