Prosecution Insights
Last updated: October 01, 2026
Application No. 17/774,437

COMPOSITIONS AND METHODS FOR ENHANCED PROTEIN PRODUCTION IN BACILLUS CELLS

Final Rejection §112
Filed
May 04, 2022
Priority
Nov 11, 2019 — provisional 62/933,536 +1 more
Examiner
BREEN, KIMBERLY CATHERINE
Art Unit
1657
Tech Center
1600 — Biotechnology & Organic Chemistry
Assignee
Danisco US Inc.
OA Round
4 (Final)
24%
Grant Probability
At Risk
5-6
OA Rounds
0m
Est. Remaining
81%
With Interview

Examiner Intelligence

Grants only 24% of cases
24%
Career Allowance Rate
19 granted / 80 resolved
-36.2% vs TC avg
Strong +57% interview lift
Without
With
+56.9%
Interview Lift
resolved cases with interview
Typical timeline
3y 5m
Avg Prosecution
41 currently pending
Career history
137
Total Applications
across all art units

Statute-Specific Performance

§101
9.3%
-30.7% vs TC avg
§103
36.2%
-3.8% vs TC avg
§102
8.9%
-31.1% vs TC avg
§112
31.0%
-9.0% vs TC avg
Black line = Tech Center average estimate • Based on career data from 80 resolved cases

Office Action

§112
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 Claims 2, 4-7, 10-21 and 23 are canceled. Claims 1, 3, 8-9, 22 and 24 are pending. Claims 8-9 are withdrawn from consideration as being drawn to a nonelected invention. Claims 1, 3, 22 and 24 are under consideration in this action. Priority The instant claims are entitled to an effective filing date of 11/11/2019. 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. 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, 3, 22 and 24 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. The amendment filed on 03/20/2026 has introduced new matter into the claims. Claim 1 as filed on 03/20/2026 recites a method for producing an increased amount of a protease in a modified Bacillus subtilis cell comprising: obtaining an isogenic reference Bacillus subtilis cell having a yitMOP operon encoding YitM, YitO and YitP polypeptides each having at least 99% identity to SEQ ID NO: 2, SEQ ID NO: 4 and SEQ ID NO: 6 respectively and further comprising an expression construct encoding the protease operably linked to a Bacillus secretion signal peptide, deleting the yitMOP operon to produce the modified B. subtilis cell, and fermenting the modified cell under suitable conditions for the production of the protease, wherein the modified cell produces an increased amount of the protease relative to the isogenic reference B. subtilis cell comprising the expression construct but lacking the yitMOP deletion when fermented under the same conditions. Claim 3 as filed on 03/20/2026 recites a method for producing an increased amount of a protease in a modified Bacillus subtilis cell comprising: obtaining an isogenic reference Bacillus subtilis cell having a yitM gene encoding YitM polypeptide having at least 99% identity to SEQ ID NO: 2 and further comprising an expression construct encoding the protease operably linked to a Bacillus secretion signal peptide, deleting the yitM gene to produce the modified B. subtilis cell, and fermenting the modified cell under suitable conditions for the production of the protease, wherein the modified cell produces an increased amount of the protease relative to the isogenic reference B. subtilis cell comprising the expression construct but lacking the yitM gene deletion when fermented under the same conditions. Applicant's amendment, filed 03/20/2026, directs to support to the entirety of the application and the claims as originally filed, and asserts that no new matter has been added. See p. 5 of the remarks paragraph 3. However, the specification as filed does not provide sufficient written description of the above underlined limitations. Claims 1, 3, 22 and 24 contain new matter because of the isogenic reference Bacillus subtilis; and because of the expression construct encoding a protease that is operably linked to a Bacillus secretion signal peptide. The disclosure as filed and the original claims do not provide support for an isogenic reference Bacillus subtilis. The specification and the original claims do not recite the term isogenic. The specification teaches “genetically modified Bacillus sp. cells derived (obtained) from parental Bacillus sp. cells (e.g., such as parental Bacillus cells expressing/producing a protein of interest)”. See [0006]. The specification teaches comparing the expression and/or production of a protein of interest in an unmodified parental cell to a modified daughter cell. See [0066]. The original claims filed 05/04/2022 teach obtaining a parental Bacillus sp. cell producing a protein of interest (POI), and the original claims provide support for a modified cell that produces an increased amount of the POI relative to the parental cell when fermented under the same conditions. See claim 1 filed 05/04/2022. However, the specification does not provide support for obtaining an isogenic reference B. subtilis cell, nor does the specification provide support for producing increased amounts of a protease relative to the isogenic reference B. subtilis cell. The disclosure as filed and the original claims do not provide support for an expression construct encoding a protease operably linked to a Bacillus secretion signal peptide. The specification teaches a B. subtilis strain named ZM207 comprising an introduced expression cassette encoding a ME-3 protease. The introduced expression cassette comprises a promoter sequence positioned upstream and operably linked to an open reading frame (ORF) encoding the ME-3 protease which is upstream and operably linked to an ORF encoding alanine racemase. See [0086]. The specification teaches a parental B. subtilis strain named CB24-12 comprising an introduced expression cassette encoding the V42 protease. The introduced expression cassette comprises a promoter sequence positioned upstream and operably linked to an ORF encoding the V42 protease which is upstream and operably linked to an ORF encoding the alanine racemase. See [0092]. Thus, the specification teaches expression cassettes encoding ME-3 or V42 proteases. However, the specification and original claims not explicitly teach a “Bacillus secretion signal peptide”, or an expression construct encoding a protease operably linked to a Bacillus secretion signal peptide. Such limitations recited in instant claims 1 and 3, and required by dependent claims 22 and 24, which did not appear in the specification or original claims, as filed, introduce new concepts and violate the description requirement of the first paragraph of 35 U.S.C 112. Applicant is required to provide sufficient written support for the limitations recited in the instant claims. Applicant can remove the new matter limitations from the claims to obviate this rejection. Scope of Enablement Claims 1, 3, 22 and 24 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for: a method for producing an increased amount of a ME-3 protease in a modified Bacillus subtilis ZM207 cell comprising: obtaining a B. subtilis ZM207 cell having a yitMOP operon encoding YitM, YitO and YitP polypeptides having SEQ ID NO: 2, SEQ ID NO: 4 and SEQ ID NO: 6, respectively, introducing an expression construct encoding the ME-3 protease into the B. subtilis ZM207 cell, modifying the B. subtilis ZM207 cell by deleting the yitMOP operon or by deleting the yitM gene encoding SEQ ID NO: 2, and fermenting the modified cell under suitable conditions for the production of the ME-3 protease, wherein the modified cell produces an increased amount of ME-3 protease relative to a B. subtilis ZM207 cell prior to the deletion when fermented under the same conditions; the specification does not reasonably provide enablement for: producing an increased amount of a protease in a modified Bacillus subtilis cell comprising: obtaining an isogenic reference Bacillus subtilis cell having a yitMOP operon encoding YitM, YitO and YitP polypeptides each having at least 99% identity to SEQ ID NO: 2, SEQ ID NO: 4 and SEQ ID NO: 6 respectively and further comprising an expression construct encoding the protease operably linked to a Bacillus secretion signal peptide, deleting the yitMOP operon to produce the modified B. subtilis cell, and fermenting the modified cell under suitable conditions for the production of the protease, wherein the modified cell produces an increased amount of the protease relative to the isogenic reference B. subtilis cell comprising the expression construct but lacking the yitMOP deletion when fermented under the same conditions (relevant to instant claim 1); or producing an increased amount of a protease in a modified Bacillus subtilis cell comprising: obtaining an isogenic reference Bacillus subtilis cell having a yitM gene encoding YitM polypeptide having at least 99% identity to SEQ ID NO: 2 and further comprising an expression construct encoding the protease operably linked to a Bacillus secretion signal peptide, deleting the yitM gene to produce the modified B. subtilis cell, and fermenting the modified cell under suitable conditions for the production of the protease, wherein the modified cell produces an increased amount of the protease relative to the isogenic reference B. subtilis cell comprising the expression construct but lacking the yitM gene deletion when fermented under the same conditions (relevant to instant claim 3). The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims. The factors to be considered in determining whether a disclosure would require undue experimentation include: A) The breadth of the claims; (B) The nature of the invention; (C) The state of the prior art; (D) The level of one of ordinary skill; (E) The level of predictability in the art; (F) The amount of direction provided by the inventor; (G) The existence of working examples; and (H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. In re Wands, 8 USPQ2d, 1400 (CAFC 1988) and MPEP 2164.01. The breadth of the claims and the nature of the invention: Claim 1 entails a correlation between the structure of a modified B. subtilis cell with a protease expression construct and a deleted yitMOP operon, and the function of increasing protease production; wherein the deleted yitMOP operon encodes YitM, YitO and YitP polypeptides having at least 99% identity to SEQ ID NO: 2, SEQ ID NO: 4 and SEQ ID NO: 6 respectively. The introduced protease expression construct is required to encode any protease operably linked to any Bacillus secretion signal peptide. The specification discloses that the genus Bacillus includes all species within the genus, including species that have been reclassified. See [0064]. Therefore, the claimed Bacillus secretion signal peptide encompasses any secretion signal peptide from any current or former Bacillus species. Claim 22 depends from claim 1 and requires the cell to further comprise a deletion of the sdpABC operon, wherein the sdpABC operon encodes SdpA, SdpB and SdpC polypeptides having at least 99% identity to SEQ ID NO: 43, 45 and 47 respectively. Claim 22 attributes the structure of the deleted sdpABC operon to further increases in the amount of the protease. Claim 3 entails a correlation between the structure of a modified B. subtilis cell with a protease expression construct and a deleted yitM gene, and the function of increasing protease production; wherein the deleted yitM gene encodes YitM polypeptide having at least 99% identity to SEQ ID NO: 2. Claim 24 depends from claim 1 and requires the cell to further comprise a deletion of the sdpABC operon, wherein the sdpABC operon encodes SdpA, SdpB and SdpC polypeptides having at least 99% identity to SEQ ID NO: 43, 45 and 47 respectively. Claim 24 attributes the structure of the deleted sdpABC operon to further increases in the amount of the protease. The state of the prior art and the level of predictability in the art: With respect to the state of the art on Bacillus strains containing the yitMOP operon, Kobayashi (PLoS Genetics, 2019, 15(10), e1008232) teaches an undomesticated B. subtilis strain NCIB3610, referred to as the wild-type strain or 3610, that encodes yitPOM (e.g. parental Bacillus). See the first 2 lines of the results section. The yitPOM operon is a paralog of the sdpABC operon; however, these operons are under different control and play distinct roles. See the first 2 lines in the second paragraph of the discussion section on page 20. According to table S1 of Kobayashi, not all B. subtilis strains have a yitPOM operon. See the paragraph spanning pages 18-19 and table S1. For example, table S1 of Kobayashi indicates that B. subtilis Bs916 does not have yitPOM. Yet, B. subtilis Bs916 is a wild-type strain, as evidenced by Zhou (PLoS One, 11(5), e0156247, 2016). See table 1 of Zhou. Thus, the state of the art indicates that the yitPOM operon is not ubiquitous to all Bacillus strains. With respect to the state of the art of on deleting the yitMOP operon or yitM gene, Kobayashi teaches derivatives of wild-type B. subtilis strain NCIB3610, such as N1263 with ΔyitR-yitM::tet and N1290 with a ΔnprB-yitM. See table 1 and the first paragraph of the materials and methods section. As shown in figure 2C, the deleted regions in both ΔyitR-yitM and ΔnprB-yitM include the operon yitPOM. Kobayashi teaches maintaining B. subtilis strain NCIB3610 and derivatives (e.g. NCIB3610 and N1263) in LB and growing the B. subtilis strains on LB plates overnight. See the first paragraph in the materials and methods section. Thus, Kobayashi teaches genetically modifying a parental NCIB3610 B. subtilis cell by deleting the yitMOP operon, which includes the yitM gene, and fermenting the modified cells. However, Kobayashi is silent regarding an increased production of an enzyme. Fu (CN118406709, published 07-30-2024), a past filing date reference, teaches a method for enhancing the secretory expression of B. subtilis characterized by silencing the genes ytxE, ytrF, trpP, gabP, fliP, thiT, yyaD, motB-2, fliQ, flhA, yvcS, sipV, yitP, ecsB, fliR, fliF, ceA, yvrO,oxaAB, and flhB in the originating bacteria; or overexpressing the genes yxdM, secDF, cydD, sdpB,pomA, skfF, yvbW, motA, crh, spoiIIQ, comEA, and ytnA. See claim 1. Thus, Fu indicates that silencing the yitP gene or overexpressing the sdpB gene in B. subtilis may contribute to enhancing secretory expression, but Fu is silent regarding the way in which secretory expression would be affected by deleting the yitMOP operon, deleting the yitMOP promoter, deleting the yitM gene, or deleting the sdpABC operon. The amount of direction provided by the inventor and the existence of working examples: Example 3 describes the production of a protease ME-3 in B. subtilis cells. A parental ZM207 cell and modified cells are fermented under identical conditions in Grants II medium at 42˚C for forty hours. See paragraph [0272]. The parental ZM207 cell comprises a deleted alanine racemase gene (ΔalrA) and an introduced expression cassette encoding a ME-3 protease. See [0086]. The modified cells include the following ZM207 daughter strains: ZM336 comprising ΔyitMOP, ZM268 comprising ME-3 protease +ΔsdpABC +ΔyitMOP, and ZM434 comprising ΔyitM. See paragraph [0272] and table 14 and 15. Subsequently, fermentation supernatants are taken and ME-3 protease activity is determined. The parental ZM207 strain produces a ME-3 protease titer of 46.2 ± 1.7 mOD/min, while the ZM336 daughter strain (ΔyitMOP) has a titer of 68.4± 0.3, the ZM268 daughter strain (ME-3 protease +ΔsdpABC +ΔyitMOP) has a titer of 74.2± 0.8 and the ZM434 daughter strain (ΔyitM) had a titer of 78.7 ± 0.3. See paragraph [0273] and table 15. Thus, the instant disclosure teaches B. subtilis cells lacking the yitMOP operon (i.e. the ZM336 and ZM268 strains) and a genetically modified B. subtilis cell lacking yitM (i.e. ZM434) that are able to produce increased amount of a heterologous ME-3 protease, as compared to the ZM207 parental strain. Example 4 describes the production of heterologous protease (V42) in parental and modified B. subtilis cells under large scale fermentation conditions. A B. subtilis strain named “JL77” comprises an introduced expression cassette encoding a V42 protease and a combined deletion of the yitMOP operon and the sdpABC operon (ΔyitMOP +ΔsdpABC). As shown in figure 2, the JL77 produces more heterologous V42 protease as compared to CB24-12 parental strain. See [0277]. The CB24-12 strain comprises a deleted alanine racemase gene and an introduced expression cassette encoding the V42 protease. See [0092]. Thus, the instant specification indicates that a daughter strain lacking both yitMOP and sdpABC (i.e. the JL77 strain) is capable of producing increased amounts of a V42 protease, as compared to a parental cell. Yet, the specification does not indicate whether the ΔyitMOP structure alone, i.e. without the ΔsdpABC, is solely responsible for the increased production of V42 protease. In summation, the specification provides guidance for producing one enzyme, ME-3 protease, at increased amounts by genetically modifying B. subtilis ZM207 cells comprising a deleted alanine racemase gene (ΔalrA) and a deleted yitMOP operon or a deleted yitM gene, where the deleted yitMOP operon encodes YitM protein (SEQ ID NO: 2), YitO (SEQ ID NO: 4) and YitP (SEQ ID NO: 6) and the deleted yitM gene encodes YitM protein (SEQ ID NO: 2). See paragraph [0257] of the specification. As such, the specification does not reduce to practice deleting a yitMOP operon that encodes YitM, YitO, and YitP polypeptides having less than 100% identity to SEQ ID NOs: 2, 4 and 6 respectively, nor does the specification reduce to practice deleting a yitM gene that encodes a polypeptide that has less than 100% identity to SEQ ID NO: 2. The quantity of experimentation needed to make or use the invention: In view of the nature of the invention, the breadth of the claims, the guidance and working examples in the specification, and the level of predictability within the art, as evidenced above, one skilled in the art could not use the disclosed method to increase the production of any protease in any B. subtilis strain, without undue experimentation. Prior to the effective filing date of the instantly claimed invention, it was well known that not all wild-type B. subtilis strains encode the yitPOM operon as evidenced by Kobayashi and Zhou. The working examples in the instant specification demonstrate increasing ME-3 protease production by deleting the yitMOP operon or the yitM gene in the parental B. subtilis ZM207 strain. Although the instant specification also demonstrates increasing the production of heterologous protease (V42), the increased production is the result of the combined deletion of the yitMOP operon and the sdpABC operon (ΔyitMOP +ΔsdpABC) in the B. subtilis JL77 strain. Consequently, there is no indication that deleting the yitMOP operon or the yitM gene in other B. subtilis strains besides B. subtilis ZM207 will result in an increased amount of any protein besides ME-3 protease relative to a parental strain. Furthermore, there is no indication that deleting any yitMOP operon that encodes polypeptides YitM, YitO, and YitP having at least 99% identity to SEQ ID NOs: 2, 4 and 6 respectively (relevant to instant claim 1), or deleting any yitM gene that encodes a YitM polypeptide that has at least 99% identity to SEQ ID NO: 2 (relevant to instant claim 3) will result in an increased production any and all proteases. Accordingly, the claims are enabled for a method for producing an increased amount of ME-3 protease in a modified Bacillus subtilis ZM207 cell comprising: obtaining a Bacillus subtilis ZM207 cell having a yitMOP operon encoding YitM, YitO and YitP polypeptides having SEQ ID NO: 2, SEQ ID NO: 4 and SEQ ID NO: 6 respectively, introducing an expression construct encoding ME-3 protease into the B. subtilis ZM207 cell, modifying the B. subtilis ZM207 cell by deleting the yitMOP operon or by deleting the yitM gene encoding SEQ ID NO: 2, and fermenting the modified cell under suitable conditions for the production of ME-3 protease, wherein the modified cell produces an increased amount of the ME-3 protease relative to the unmodified B. subtilis ZM207 cell when fermented under the same conditions. Response to Arguments Applicant's arguments filed 03/20/2026 have been fully considered but they are not persuasive. §112(a) enablement rejection Applicant argues that the amended claims are limited to proteases and to Bacillus hosts having a yitMOP operon encoding YitM, YitO, YitP each ≥99% identical to SEQ ID NOs: 2, 4 and 6, or a yitM gene with YitM ≥99% to SEQ ID NO: 2, and require an isogenic reference comparator. Applicant asserts that the specification and record provide multiple working examples demonstrating that deletion of yitMOP or yitM increases secreted serine proteases in Bacillus under matched conditions: (i) T. cellulosilytica ME-3 proteases in ZM207 with ΔyitMOP and ΔyitM (ii) a B. amyloliquefaciens V42 serine protease in JL77 with ΔyitMOP+ΔsdpABC; and (iii) a B gibsonii serine protease where the ΔyitMOP effect is isolated in an isogenic ΔsdpABC background. See p. 6 of the remarks paragraph 5. This argument is not persuasive because the examples pointed to by Applicant are not commensurate in scope with the instant claims. Applicant argues that there are multiple working examples demonstrating that the deletion of yitMOP or yitM increases secreted serine proteases in Bacillus under matched conditions. However, the instant claims do not limit the protease to serine proteases. Applicant argues that the working examples show isolating the effect of the ΔyitMOP operon using isogenic ΔsdpABC background. However, the claimed “isogenic reference Bacillus subtilis” does not require a ΔsdpABC background. Rather, the isogenic reference Bacillus subtilis is only required to have two elements 1) an expression construct encoding a protease operably linked to any Bacillus secretion signal peptide; and 2) either a yitMOP encoding YitM, YitO, YitP each having at least 99% identity to SEQ ID NOs: 2, 4 and 6 respectively or a yitM encoding YitM that has at least 99% identity to SEQ ID NO 2; the specification is silent regarding expression constructs encoding a protease operably linked to a Bacillus secretion signal peptide. Applicant argues that causation is established in isogenic designs across multiple serine proteases. In example 3, an isogenic B. subtilis ZM207 background expressing ME-3 shows that both ΔyitMOP and ΔyitM cause increased extracellular ME-3 activity under identical cassette and fermentation conditions, isolating the effect to the deletion itself. Independently, exhibit A (previously submitted) isolates the ΔyitMOP effect for a B. Gibsonii subtilisin variant by comparing an isogenic pair, 3216 (ΔsdpABC) versus 3230 (ΔsdpABC +ΔyitMOP), thus attributing the increase specifically to ΔyitMOP in that background. See p. 7 of the remarks last passage. This argument is not persuasive because the claimed isogenic reference B. subtilis is not limited to the ZM207 strain, which includes a deletion of an alanine racemase gene (ΔalrA) and an expression cassette encoding a ME-3 protease (see [0086]); nor is the isogenic reference B. subtilis required to have the same ΔsdpABC background as described for strains 3216 or 3230. Exhibit A filed 06/10/2025 is insufficient to overcome the rejection, because the evidence is not commensurate in scope with the instant claims. The yitMOP described in exhibit A is understood to be the yitMOP operon encoding YitM SEQ ID NO:2 , YitO SEQ ID NO: 4 and YitP SEQ ID NO: 6. Furthermore, the sdpABC in exhibit A is understood to be the sdpABC operon encoding SdpA SEQ ID NO: 43, SdpB SEQ ID NO: 45 and SdpC SEQ ID NO: 47. However, the instant claims filed 03/20/2026 do not require 100% identity matches to SEQ ID NOs: 2, 4, 6, 43, 45 or 47. Applicant argues that the paralogs between yitMOP and sdpABC support predictability. Applicant asserts that the loss-of-function at yitMOP will modulate the same stress/cannibalism circuitry relevant to secreted protease production, thereby supporting enablement for the at least 99% identity alleles of YitM/YitO/YitP recited in the claims. See p. 8 of the remarks paragraph 1. This argument is not persuasive because arguments of counsel cannot take the place of factually supported objective evidence (MPEP 2145 or 716.01(c)). Applicant has not pointed to evidence commensurate in scope with the instant claims. 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 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. Claims 1, 3, 22 and 24 are 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. Claims 1 and 3 recite “isogenic reference” in line 3, and again in lines 10-11 of claim 1 or in lines 9-10 of claim 3, such recitation renders the claims indefinite, because there are multiple reasonable interpretations for the limitation. There is no definition for the term “isogenic” in the instant specification. Therefore, in one interpretation “isogenic” is a population with essentially identical genes. See Yokoyama (News-Medical.net, 2020) p. 1 paragraph 2. However, in this interpretation the scope is still unclear for two reasons. The first reason is that the instant claims recite “an isogenic reference Bacillus subtilis cell” in the singular form, which contradicts the definition as a population with essentially identical genes. The second reason is that the definition is ambiguous due to the term essentially. Under an alternative interpretation, “isogenic” means genetically identical (except for sex). Coming from the same individual or from the same inbred strain. See Lefers p. 1 (Northwestern.edu, 2026). As such, the scope encompassed by the claimed isogenic reference B. subtilis cell is unclear. Claims 22 and 24 depend from claim 1 and 3 respectively and are rejected for the reason set forth above. Claims 22 and 24 recite “the modified cell of claim [1 or 3] that lacks the sdpABC operon deletion” in lines 5-6. There is insufficient antecedent basis for this limitation in the claim. Claim 22 and 24 depend from claims 1 and 3 respectively, but claims 1 and 3 do not require the modified cell to include any sdpABC operon. Therefore, it is unclear which modified cell of claim 1 or 3 is being referenced. Conclusion Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a). A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action. Any inquiry concerning this communication or earlier communications from the examiner should be directed to KIMBERLY C BREEN whose telephone number is (571)272-0980. The examiner can normally be reached M-Th 7:30-4:30, F 8:30-1:30 (EDT/EST). Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, LOUISE HUMPHREY can be reached at (571)272-5543. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300. Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000. /LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657 /K.C.B./Examiner, Art Unit 1657
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Prosecution Timeline

Show 1 earlier event
Feb 10, 2025
Non-Final Rejection mailed — §112
Jun 10, 2025
Response Filed
Aug 11, 2025
Final Rejection mailed — §112
Nov 10, 2025
Request for Continued Examination
Nov 12, 2025
Response after Non-Final Action
Nov 24, 2025
Non-Final Rejection mailed — §112
Mar 20, 2026
Response Filed
May 12, 2026
Final Rejection mailed — §112 (current)

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Prosecution Projections

5-6
Expected OA Rounds
24%
Grant Probability
81%
With Interview (+56.9%)
3y 5m (~0m remaining)
Median Time to Grant
High
PTA Risk
Based on 80 resolved cases by this examiner. Grant probability derived from career allowance rate.

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