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 1-20 are pending.
Election/Restrictions
Applicant's election with traverse of Group I, claims 1-6, in the reply filed on 09/08/2026 is acknowledged. The traversal is on the ground(s) that the lactic acid bacterium described in Quintana et al. does not fall under the definition of the claims of "a lactic acid bacterium in which a function of a kup gene is suppressed and acid tolerance is improved” because the strain that Quintana et al. disclose (i.e., L. lactis MG1363) possesses two copies of the kup genes, kupA and kupB, and that the presence of one single Kup protein (i.e., KupB) is sufficient for potassium uptake and for satisfying the vital needs of the cell concerning cell turgor, proton motive force, and pH homeostasis.
This is not found persuasive because, as explained in the Requirement for Restriction Office Correspondence mailed on 07/15/2026, the technical feature required by Groups I-V is a lactic acid bacterium with an inhibited functional gene or kup gene. This technical feature is not a special technical feature as it does not make a contribution over the prior art in view of Quintana because Quintana teaches Lactobacillus lactis strain with a mutation in the kupA gene resulting in a nonfunctional KupA (i.e. inhibited function of a kup gene). The requirement is still deemed proper and is therefore made FINAL.
Claims 7-20 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to nonelected inventions, there being no allowable generic or linking claim.
Information Disclosure Statement
The information disclosure statements (IDS) filed on 08/13/2024 and 06/05/2026 are acknowledged and have been considered.
Claim Rejections - 35 USC § 112
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 claims contain 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 claims are drawn to a method comprising inhibiting a function of a kup gene of a lactic acid bacterium. The claims are drawn to a large and variant genus of inhibition mechanisms of a function of a kup gene in any lactic acid bacterium. The genus is large and variant because inhibition of a gene encompasses transcriptional repression, post-transcriptional silencing, permanent genetic knockout, different mutations, growth conditions, repressors, proteins, chemicals, etc. Furthermore, the genus of lactic acid bacteria is large and variant. Suzuki ("Taxonomy of lactic acid bacteria: historical background and prospects." (2024): 15-22) reports that the order of Lactobacillales includes 70 genera (Abstract). The specification discloses examples of inhibition include amino acid mutation such as substitution, deletion, insertion, and/or addition of one or more amino acids (page 15 lines 5-8), and discloses in Tables 2, 4, and 6 a substitution and a frameshift mutation in kup gene of L. delbrueckii subsp. bulgaricus OLL205405 and L. delbrueckii subsp. bulgaricus OLL205406 strains. The specification does not disclose other inhibition mechanisms, nor does it show that the inhibition of a function of a kup gene in other species of lactic acid bacteria results in improving acid tolerance. Prior art Quintana and Pham (cited in 102 rejection) disclose that c-di-AMP binds and inhibits Kup proteins in Lactococcus lactis (Abstract, page 6 para. 2) but are silent on the strain’s acid tolerance. Pham also teaches that sixty-one species, mainly lactic acid bacteria, within the Firmicutes contain Kup homologs. Prior art Bowman ("New insights into the cyclic di-adenosine monophosphate (c-di-AMP) degradation pathway and the requirement of the cyclic dinucleotide for acid stress resistance in Staphylococcus aureus." Journal of Biological Chemistry 291.53 (2016): 26970-26986) teaches that c-di-AMP levels regulate potassium transport and impact acid tolerance in Staphylococcus aureus (Abstract, page 26976 para “c-di-AMP Levels Increase in WT as well as ybbR Mutant S. aureus Strains upon Exposure to Acid Stress). The prior art’s disclosure of 1 species of inhibitor of Kup protein or homologs has not established a strong correlation between structure and function. The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species. The strains described in Quintana, Pham and Bowman references are not representative of the entire genus when there is substantial variation within the genus. One of skill in the art would not have recognized that the inventor was in possession of the necessary common attributes or features possessed by the species of the genus in view of the species disclosed by Quintana and Pham.
For inventions in an unpredictable art, adequate written description of a genus which embraces widely variant species cannot be achieved by disclosing one species within the genus.
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 1-6 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 4 recite the limitation “artificially inhibiting”. The term artificially is subjective and broad and does not inform one of ordinary skill in the art of the metes and bounds of the claim. The limits of what makes a step artificial, or the degree of human intervention is not defined. It is not clear if a mutation caused by UV, for example, is considered artificial since it is caused by an outside source, with or without human intervention.
Claims 2-3 and 5-6 do not cure the indefiniteness and are also rejected.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-6 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception of laws of nature, natural phenomena, and products of nature (a law of nature and natural phenomenon) without significantly more.
Claims 1-6 recite a method (Step 1: YES) comprising a step of artificially inhibiting a function of a kup gene of a lactic acid bacterium. Prior art Quintana (cited in 102 rejection) teaches Lactococcus lactis strain with a spontaneous mutation in the kupA gene resulting in a nonfunctional KupA and teaches that the activity of KupA and KupB proteins of L. lactis IL1403 are inhibited by c-di-AMP (i.e., law of nature and natural phenomenon). Prior art Pham (cited in 102 rejection) teaches c-di-AMP naturally binds and inhibits KupB (Abstract, page 6 para. 2). Claims 2-3 and 5-6 limit the lactic acid bacteria to the genus of Lactobacillus, which are natural products. Where a process claim reciting a nature-based product is drafted in such a way that there is no difference in substance from a product claim, the claim is subject to the markedly different analysis for the recited nature-based product. These types of claims are drafted in a way that focuses on the product rather than the process steps. See MPEP 2106.04(c).I.C. The claims recite the step of inhibiting a function of a kup gene. Under the broadest reasonable interpretation, this claim is focused on the inhibited function of the kup gene which is a nature-based product as discussed above. There is no indication in the specification that artificially introducing a mutation in the kup gene would structurally/functionally be different compared to the spontaneous mutation found in nature. The specification discloses that L. delbrueckii subsp. bulgaricus OLL205405 strain and L. delbrueckii subsp. bulgaricus OLL205406 strains have mutations in the kup gene (frameshift and nonsense mutation) and were subcultured to reverse these mutations. Thus, it is understood that these strains are natural mutant strains with an inhibited function of a kup gene (page 4, page 26, page 50, Table 2). The recited step and composition do not have markedly different characteristics from their naturally occurring counterparts (Step 2A prong 1: YES). The instant claims do not introduce any additional limitations which transform or improve on the judicial exceptions recited in claims 1 and 4 (Step 2A prong 2: NO). Claims 1-6 are directed to a judicial exception and do not qualify as eligible subject matter under 35 U.S.C. § 101.
Claim Rejections - 35 USC § 102
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.
Claims 1 and 4 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Quintana (Journal of bacteriology 201.10 (2019): 10-1128, of record in IDS).
Regarding claims 1 and 4, Quintana teaches Lactococcus lactis strain (i.e., lactic acid bacterium) with a spontaneous mutation in the kupA gene resulting in a nonfunctional KupA and teaches the activity of KupA and KupB proteins of L. lactis IL1403 are inhibited by c-di-AMP (i.e., inhibiting the function of a kup gene) (Abstract, page 4 para.2, page 9 first para). Regarding the limitations “improving acid tolerance of a lactic acid bacterium” and “a lactic acid bacterium with improved acid tolerance”, MPEP 2111.02(II) states that if the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.
Claims 1 and 4 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Pham (PLoS genetics 14.8 (2018): e1007574, of record in IDS).
Regarding claims 1 and 4, Pham teaches a high cyclic-di-AMP Lactococcus lactis mutant and teaches that c-di-AMP binds KupB, a K+ importer, and inhibits K+ uptake (i.e., the function of KupB) (Title, page 6 para 2). Regarding the limitations “improving acid tolerance of a lactic acid bacterium” and “a lactic acid bacterium with improved acid tolerance”, MPEP 2111.02(II) states that if the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.
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 for establishing a background for determining obviousness under 35 U.S.C. 103 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.
Claims 1-6 are rejected under 35 U.S.C. 103 as being unpatentable over Quintana (Journal of bacteriology 201.10 (2019): 10-1128, of record in IDS).
Regarding claims 1-6, Quintana teaches Lactococcus lactis strain (i.e., lactic acid bacterium) with a spontaneous mutation in the kupA gene resulting in a nonfunctional KupA and teaches that the activity of Kup potassium transporters is inhibited by c-di-AMP (i.e., artificially inhibiting the function of a kup gene) (Abstract, page 4 para.2, page 9 first para). Quintana teaches that the Kup transporters are widespread in numerous species of Lactobacillus (page 8 para 2).
Regarding the limitations “improving acid tolerance of a lactic acid bacterium” and “a lactic acid bacterium with improved acid tolerance”, MPEP 2111.02(II) states that if the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.
Claims 1-6 are rejected under 35 U.S.C. 103 as being unpatentable over Pham (PLoS genetics 14.8 (2018): e1007574, of record in IDS).
Regarding claims 1-6, Pham teaches a high cyclic-di-AMP Lactococcus lactis mutant and teaches that c-di-AMP binds KupB, a K+transporter, and inhibits K+ uptake (i.e., the function of KupB) (Title, page 6 para 2). Pham teaches that KupB is also found in Lactobacillus reuteri (Fig. 2, page 7 para. 3).
Regarding the limitations “improving acid tolerance of a lactic acid bacterium” and “a lactic acid bacterium with improved acid tolerance”, MPEP 2111.02(II) states that if the body of a claim fully and intrinsically sets forth all of the limitations of the claimed invention, and the preamble merely states, for example, the purpose or intended use of the invention, rather than any distinct definition of any of the claimed invention’s limitations, then the preamble is not considered a limitation and is of no significance to claim construction.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MARY A CRUM whose telephone number is (571)272-1661. The examiner can normally be reached M-F 8:00-5:00 CT with alternate Fridays off.
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/MARY A CRUM/ Examiner, Art Unit 1657
/THANE UNDERDAHL/ Primary Examiner, Art Unit 1699
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