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 .
Claim Objections
Claims 14, 15, and 16 are objected to under 37 CFR 1.75 as being a substantial duplicate of claims 11,12, and 13. See MPEP § 608.01(m).
Claim Rejections - 35 USC § 112
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 8 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 claims 5, 8, 9, the limitation “improving” renders the scope of the claim unclear and is a relative term which renders the claim indefinite. The term is not defined by the claim nor is a baseline given, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. See MPEP 2173.05(b).
Regarding claim 8, the limitation “improving” and “significantly” renders the scope of the claim unclear and is a relative term which renders the claim indefinite. The term is not defined by the claim, the specification does not provide a standard for ascertaining the requisite degree, and one of ordinary skill in the art would not be reasonably apprised of the scope of the invention. See MPEP 2173.05(b).
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.
Claims 1-4 are rejected under 35 U.S.C. 103 as being unpatentable over Bekkala, A. et al., Evaluation of Reproductive, Developmental, and Genetic Toxicities of Cyclophosphamide and Eugenol. U.S. Food and Drug Administration. (Abstract; published 12-08-2021 and Xiong, H. et al., An enhanced C. elegans based platform for toxicity assessment. Scientific Reports. 2017.(7:9839). pp 1-11. .
Regarding claims 1-4, Bekkala et al., teaches the use of C. elegans treated with cyclophosphamide (CTX) as a toxicity model, notably for reproductive toxicity “by assessing fecundity, brood size, and hatchability” which coincide with “growth rate, body size, and life span”; along with genome-wide sequence analysis to assess for mutations following CTX treatment—the method is evaluated as a tool to examine “developmental, reproductive, and genetic toxicity” (Abstract).
However, Bekkala et al., does not describe the concentrations of CTX tested (claim 1). Bekkala et al., also does not explicitly reveal L1-stage (claim 3) and wild type N2 C. elegans (claim 4), that are obtained following a sodium hypochlorite process (claim 2).
However, regarding claims 1 and 3, Xiong, H. et al et al., teaches methods for a toxicity assays using L1 stage of Celegans, for chemical sensitivity testing to assess reproductivity toxicity, as further determined in wild type N2 (page 3, paragraph 2); the assay examined pharmaceutical applications according to toxicity databases for pharmaceuticals, these databases provide ranges for therapeutic concentrations of CTX (page 5, Table 1). . Regarding claim 2, L1 worms were obtained after a sodium hypochlorite treatment (page9, paragraph7).
It would have been obvious to one of ordinary skill in the art at the effective date of filing, to use the claimed CTX concentrations so as to optimize the concentrations and reported ranges of CTX for an assay to measure reproductive toxicity in the C. elegans model. The concentrations of CTX tested by Bekkala et al., for purposes of drug toxicity testing would have been standardized to the claimed ranges to provide efficacious therapeutic ranges, used to treat patients while measuring for drug safety for said reproductive toxicity model. As such, optimizing the ranges of efficacy of performance would provide result effective outcome (see In re Aller 220 F.2d 454, 456, 105 USPQ 233, 235 (CCPA 1955); see MPEP 2144.05). Likewise, it would have been obvious to assess toxicity of wild type N2 C. elegans strains following the sodium hypochlorite process to examine L1 stage larvae that are synchronized in developmental stage to measure fecundity, growth, and additional traits of reproductive toxicity.
The ordinary artisan would have been motivated to perform a reproductive toxicity assay and characterize the methods, of: stage of growth (L1), relative to wild type status (N2), preparation treatment for larvae synchronization (sodium hypochlorite process), and concentrations of CTX tested as to simply define the optimized test conditions and/or procedures for continuity of method(s). Accordingly, the claimed invention and the combined prior art of Bekkala, A. et al., and Xiong, H. et al. et al., as a whole, is obvious and the ordinary artisan would have had reasonable expectation of success to fine-tune the prior art, to arrive at the claimed invention because both perform the same methods and arrive at the same shared objective for the assay, as the instant application, and therefore should reasonably expect to successfully produce the same outcome.
Claim(s) 5, 8, and 10-16 are rejected under 35 U.S.C. 103 as being unpatentable over Bekkala, A. et al., Evaluation of Reproductive, Developmental, and Genetic Toxicities of Cyclophosphamide and Eugenol. U.S. Food and Drug Administration. (Abstract; published 12-08-2021) andXiong, H. et al., An enhanced C. elegans based platform for toxicity assessment. Scientific Reports. 2017.(7:9839). pp 1-11. and further in view of García-González, A.P. et al., Worms, bugs and drugs: Caenorhabditis elegans as a model for host-microbe-drug interactions. Current Opinion in Systems Biology. 2017. (6), pp 46–50.
The teachings of Bekkala et al., and Xiong, H. et al., are disclosed above.
With regards to claim 5, Bekkala et al., and Xiong, H. et al.., do not teach selecting and feeding E.coli strains capable of improving reproductive capacity(claim 8) . Bekkala et al., and Xiong, H. et al.., also do not teach a method of verification for single gene mutations of E.coli (claim 10).
However, regarding claims 5 and 8, Garcia-Gonzalez et al., teaches a genetically modified E.coli OP50, introduced as food to C. elegans as a model to assess gut microbiota interactions using a genome-wide screen in N2 C. elegans to measure responses to chemotherapeutic drugs, modified by gut microbial metabolism and gut microbiota which effects reproduction, “embryonic lethality, larval arrest, or developmental delay” (page 2, paragraph 2). Regarding claim 10, to identify the microbial genes effecting chemotherapy metabolism and downstream responses in C. elegans, Garcia-Gonzalez et al., introduced knockdown mutations, single-gene deletions, and created ~ 4000 E.coli OP50 strains used in a genetic screen to assess drug efficacy and host sequalae (page 2, paragraphs 3-4).
Therefore, it would have been obvious to one of ordinary skill in the art at the effective date of filing to combine the teachings of Bekkala et al., and Xiong, H. et al., with Garcia-Gonzalez et al., to create single gene knockouts of E.coli when fed to N2 C. elegans to regulate gut microbiota and downstream drug metabolism, effecting the axis between the gut and reproductive tissues and/or markers of fecundity. Since, the combination of the prior art teaches the same method(s), technology, and test outcomes-- (i.e. chemotherapy and/or drug metabolism toxicity resulting in reproductive side effects and mutated E.coli strains that may reduce negative effects).—.
The motivation to combine the teaching of Bekkala et al., with Xiong, H. et al. and Garcia-Gonzalez et al., are to create a N2 C. elegans model, to assess reproductive markers, relative to post-CTX exposure and select mutated strains of E.coli fed to C. elegans which further modulate reproductive toxicity. Incorporating the methods of Garcia-Gonzalez et al., single gene knockout libraries are created in different E.coli strains and support fecundity in C. elegans relative to the gut-testis or gut-ovary axis. Single gene knockout models of microbial strains combined with treatment exposure in C. elegans models to measure genotypic/phenotypic changes are commercially available through many scientific companies specialized in customized C. elegans modelling services. Such services include using E.coli or other bacteria to create libraries of strains, with technologies like CRISPR/Cas9 gene editing platforms for knockout, point mutations, knock-in etc. for precision-based mutation analysis. Accordingly, both the claimed invention and the prior art references, as a whole, would have been obvious to one of ordinary skill in the art at the time of filing. The ordinary artisan would have had a reasonable expectation of success in modifying the prior art references to arrive at the claimed invention because both produce the same assay to examine fecundity in a C. elegans model following CTX treatment.
Regarding claims 11, 12, 13, and 14-16 Bekkala et al. and Xiong, H. et al. previously addressed the same limitations, described in claims 1-4. Accordingly, the combination of the prior art hatches eggs that produce L1-stage C. elegans (claim 12 and 15) following a sodium hypochlorite wash process (claim 11 and 14) and the assays are conducted with wild type N2 C. elegans (claim 13 and 16).
Claim(s) 7 and 9 are rejected under 35 U.S.C. 103 as being unpatentable over Bekkala, A. et al., Evaluation of Reproductive, Developmental, and Genetic Toxicities of Cyclophosphamide and Eugenol. U.S. Food and Drug Administration. (Abstract; published 12-08-2021) and Xiong, H. et al., An enhanced C. elegans based platform for toxicity assessment. Scientific Reports. 2017.(7:9839). pp 1-11 in view of García-González, A.P. et al., Worms, bugs and drugs: Caenorhabditis elegans as a model for host-microbe-drug interactions. Current Opinion in Systems Biology. 2017, (6), pp 46–50. and further in view of Rosenthal, J.A. et al., Mechanistic Insight into the TH1-Biased Immune Response to Recombinant Subunit Vaccines Delivered by Probiotic Bacteria-Derived Outer Membrane Vesicles. PLOS One. 2014. (9:11), pp. 1-24.
The teachings of Bekkala et al., Xiong, H. et al., and Garcia-Gonzalez, et al., are disclosed above. Specifically, Garcia-Gonzalez et al. does teach single gene knockout mutations in E.coli OP50 and a library of ~4,000 E.coli strains with said mutations wherein select strains provide health improvements in C. elegans, resulting from gut-microbe-drug metabolism and corresponding reduction in therapy toxicity.
Regarding claim 7, Bekkala et al., Xiong, H. et al., and Garcia-Gonzalez et al., do not specify single gene knockout mutations from the Keio library; or claim 9, the use of the probiotic E.coli strain Nissle 1917 for improving reproductive capacity resulting from a homologous gene knockout.
However, regarding claims 7 and 9, Rosenthal, J.A. et al., teaches Keio single gene mutations introduced into the probiotic E.coli Nissle 1917 (page 4, paragraph 1). The Keio single gene knockout mutations were developed in 2006 and made publicly available as a well-defined set of mutations, introduced into E.coli strains to create libraries of mutant strains.
Therefore, it would have been obvious to one of ordinary skill in the art at the effective date of filing to combine the teachings of Bekkala et al., Xiong, H. et al., et al., Garcia-Gonzalez et al., and Rosenthal et al., to create a library of E.coli Nissle 1917 strains that carried single knockout mutations from the Keio collection, resulting in thousands of strains when digested by C. elegans would generate biological changes in fecundity. Accordingly, the simple substitution of E.coli Nissle 1917 for E.coli OP50 along with the well-characterized mutations from the Keio collection, specifically, would have resulted in the same method of analyzing reproductive drug toxicity, as taught by Bekkala et al., combined with Garcia-Gonzalez et al. and using wild type N2 C. elegans from the same L1 stage larvae, using the same sodium hypochlorite wash process methods as described by Xiong, H. et al., The intended use and outcome of the combined methods of prior art would demonstrate reproductive toxicity and/or amelioration and is the same outcome as the instant application.
The motivation for combining the prior art, as previously noted, is the analysis of single gene knockout libraries in E.coli, resulting in changes to host response to chemotherapies, including reproductive health assessment in a C. elegans model. The added motivation to assess the Keio library in strains of probiotic E.coli (Nissle 1917) are to further examine a well-characterized collection of single gene, knock-out mutations with known phenotypic traits, in a probiotic E.coli—to examine how an established probiotic with said mutations effects and/or restores fecundity via the gut-reproductive-tissue axis. The methods and overall assay, of the instant application, are an accepted model for toxicity testing; such that the U.S. FDA supports standard protocols for toxicity testing using said drug screening process with C. elegans models as an accepted in vivo model and alternative to animal testing. Additionally, the screening of E.coli gene knock-out libraries in a C. elegans model is a commercially available method of analysis. Therefore, the technology associated with the method(s) and the resulting architecture for said drug toxicity model and ameliorating toxic effects, is well known and well-established in the art—therefore one would have reasonably expected success with the methods described in the instant application, which prescribe the same combined methods of the prior art.
Correspondence Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ENUSHA KARUNASENA whose telephone number is (571)272-3972. The examiner can normally be reached Monday-Friday 7:30am-5pm.
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/ENUSHA KARUNASENA/Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
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