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 .
This office action is in response to the amendment filed on November 17, 2025. Claims 1-7, 9, and 13-16 have been cancelled. New claims 17-19 have been added. Claims 8, 10-12, and 17-19 are currently pending and are under examination.
Any objections or rejections not reiterated below are hereby withdrawn.
Withdrawal of Rejections
The rejection of claims 1-3 and 5-7, 9, and 13-16 under 35 U.S.C. 101 as claiming the same invention as that of claims 1-12 of prior U.S. Patent No. 11,041,217 B2 (11/7/2024 IDS, Patent document #1) is withdrawn based on the cancellation of the claims.
The rejection of claim 4 on the ground of nonstatutory double patenting as being unpatentable over claim 2 of U.S. Patent No. 11, 041,217 B2 (11/7/2024 IDS, Patent document #1) is withdrawn based on the cancellation of the claim.
The rejection of claim(s) 1, 2, 14, and 15 under 35 U.S.C. 102(a)(1) as being anticipated by Moscoso et al. (Virulence 9(1): 604-620; Jan. 1, 2018; 11/7/2024 IDS, NPL doc# 2) is withdrawn based on the cancellation of the claims.
The rejection of claims 1, 2, 3, 4, and 5 under 35 U.S.C. 103 as being unpatentable over Moscoso et al. (Virulence 9(1): 604-620; 11/7/2024 IDS, NPL doc# 2) and Cabral et al. (Nature Communications 8: 15480 doi: 10.1038/ncomms15480 (2017); 11/7/2024 IDS, NPL doc # 1) is withdrawn based on the cancellation of the claims.
The rejection of claims 1, 2, 3, 4, and 5 under 35 U.S.C. 103 as being unpatentable over Moscoso et al. (Virulence 9(1): 604-620; 11/7/2024 IDS, NPL doc# 2), Cabral et al. (Nature Communications 8: 15480 doi: 10.1038/ncomms15480 (2017); 11/7/2024 IDS, NPL doc # 1), and Zhang et al. (Molecular Microbiology 49(6): 1577-1593 (2003); 11/7/2024 IDS, NPL doc #6) is withdrawn based on the cancellation of the claims.
The rejection of claims 8 and 10 under 35 U.S.C. 103 as being unpatentable over Moscoso et al. (Virulence 9(1): 604-620; 11/7/2024 IDS, NPL doc# 2) is withdrawn based on a new analysis presented in a new below rejection based on reference to a target environment claim limitation.
The rejection of claim 9 under 35 U.S.C. 103 as being unpatentable over Moscoso et al. (Virulence 9(1): 604-620; 11/7/2024 IDS, NPL doc# 2) is withdrawn based on the cancellation of the claim.
Pending Rejections
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.
Claims 8, 10-12, and 17-19 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.
Claim 8 refers to a method of making a recombinant Staphylococcus bacterium, but the steps end with a different end process result. It is unclear if the claim is drawn to a method of making a recombinant bacterium or a method of introducing a recombinant Staphylococcus bacterium into a target environment? Clarification is requested as to the method being claimed. Claims dependent on the rejected claim fail to cure the indefiniteness.
Claim 18 is rejected for depending on itself.
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.
Claim 17 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 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 MPEP states that the purpose of the written description requirement is to ensure that the inventor had possession, at the time the invention was made, of the specific subject matter claimed. The courts have stated:
"To fulfill the written description requirement, a patent specification must describe an invention and do so in sufficient detail that one skilled in the art can clearly conclude that "the inventor invented the claimed invention." Lockwood v. American Airlines, Inc., 107 F.3d 1565, 1572, 41 USPQ2d 1961, 1966 (Fed. Cir. 1997); In re Gostelli, 872 F.2d 1008, 1012, 10 USPQ2d 1614, 1618 (Fed. Cir. 1989) ("[T]he description must clearly allow persons of ordinary skill in the art to recognize that [the inventor] invented what is claimed."). Thus, an applicant complies with the written description requirement "by describing the invention, with all its claimed limitations, not that which makes it obvious," and by using "such descriptive means as words, structures, figures, diagrams, formulas, etc., that set forth the claimed invention." Lockwood, 107 F.3d at 1572, 41 USPQ2d at 1966." Regents of the University of California v. Eli Lilly & Co., 43 USPQ2d 1398.
Further, for a broad generic claim, the specification must provide adequate written description to identify the genus of the claim. In Regents of the University of California v. Eli Lilly & Co. the court stated:
"A written description of an invention involving a chemical genus, like a description of a chemical species, 'requires a precise definition, such as by structure, formula, [or] chemical name,' of the claimed subject matter sufficient to distinguish it from other materials." Fiers, 984 F.2d at 1171, 25 USPQ2d 1601; In re Smythe, 480 F.2d 1376, 1383, 178 USPQ 279, 284985 (CCPA 1973) ("In other cases, particularly but not necessarily, chemical cases, where there is unpredictability in performance of certain species or subcombinations other than those specifically enumerated, one skilled in the art may be found not to have been placed in possession of a genus ...") Regents of the University of California v. Eli Lilly & Co., 43 USPQ2d 1398.
MPEP § 2163 further states that if a biomolecule is described only by a functional characteristic, without any disclosed correlation between function and structure of the sequence, it is "not sufficient characteristic for written description purposes, even when accompanied by a method of obtaining the claimed sequence." MPEP § 2163 does state that for a generic claim the genus can be adequately described if the disclosure presents a sufficient number of representative species that encompass the genus. If the genus has a substantial variance, the disclosure must describe a sufficient variety of species to reflect the variation within that genus. See MPEP § 2163. Although the MPEP does not define what constitute a sufficient number of representative species, the courts have indicated what do not constitute a representative number of species to adequately describe a broad generic. In Gostelli, the courts determined that the disclosure of two chemical compounds within a subgenus did not describe that subgenus. In re Gostelli, 872, F.2d at 1012, 10 USPQ2d at 1618.
As stated supra, the MPEP states that written description for a genus can be achieved by a representative number of species within a broad genus. Claim 17 is a broadly generic to all possible therapeutic polypeptides or any fragment thereof encompassed by the claims. The possible variations are enormous to any class of polypeptides. Since the MPEP states that if a biomolecule is described only by a functional characteristic, without any disclosed correlation between function and structure, it is "not sufficient characteristic for written description purposes, even when accompanied by a method of obtaining the claimed sequence." MPEP § 2163. Here, though the claims may recite some functional characteristics, the claims lack written description because there is no disclosure of a correlation between function and structure for a genus of any therapeutic polypeptide or any fragments thereof. Moreover, the specification lacks sufficient variety of species to reflect this variance in the genus.
The description requirement of the patent statue requires a description of an invention, not an indication of a result that one might achieve if one made that invention. See In re Wilder, 736, F.2d 1516, 1521, 222 USPQ 369, 372-73 (Fed. Cir. 1984) (affirming rejection because the specification does "little more than outlin[e] goals appellants hope the claimed invention achieves and the problems the invention will hopefully ameliorate.") Accordingly, it is deemed that the specification fails to provide adequate written description for the genus of the claims and does not reasonably convey to one skilled in the relevant art that the inventor(s), at the time the application was filed, had possession of the entire scope of the claimed invention.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
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 as of the effective filing date of the claimed invention(s) 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 as of the effective filing date of the later invention 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 8, 10, 11, and 19 are rejected under 35 U.S.C. 103 as being unpatentable over Moscoso et al. (Virulence 9(1): 604-620; 11/7/2024 IDS, NPL doc# 2; previously cited), Cabral et al. (Nature Communications 8: 15480 doi: 10.1038/ncomms15480 (2017); 11/7/2024 IDS, NPL doc # 1; previously cited), and Zhang et al. (Molecular Microbiology 49(6): 1577-1593 (2003); 11/7/2024 IDS, NPL doc #6; previously cited).
Moscoso et al. disclose a mutant Staphylococcus bacterium that lacks genes involved in D-alanine biosynthesis. The mutant does not have genes, alanine racemase (alr1 and alr2), and D-alanine aminotransferase (dat). The mutant requires exogenous addition of D-alanine for growth. The D-alanine auxotroph has the ability to induce protective immunity against staphylococcal infection.
Cabral et al. disclose a Staphylococcus mutant that also can function as auxotrophic vaccines with a gene inactivation similar to the bacterium disclosed by Moscoso et al. The glutamate racemase (MurI) enzyme converts L-glutamate to D-Glu for synthesis of peptidoglycan. Cabral et al. produce an auxotrophic strain with inactivation of genes required for peptidoglycan synthesis, both glutamate racemase (MurI) and D-alanine amino acid transaminase (dat) (see entire document, e.g. abstract). The auxotrophic strain generates antibody-mediated immune responses (see page 5, Generation of antibody-mediated immune responses section).
Cabral et al. disclose that vaccination with D-Glu auxotrophic strain elicited IgG cross-reactivity with a variety of coagulase-negative Staphylococci species (see page 5, second to last paragraph in right hand column). The Staphylococcus epidermidis is a coagulase-negative bacterium. Therefore it would have been obvious to also make an auxotrophic vaccine with alanine auxotrophs as disclosed by Moscoso, since the immune response was shown with D-Glu auxotrophic bacteria in Cabral et al.
Vaccine development to Staphylococcus bacterium provides the motivation to make the gene inactivations as currently claimed. Antibiotic resistant strains of Staphylococcus bacterium are known in the art. It would have been obvious to the person having ordinary skill in the art to manufacture the Staphylococcus bacterium as currently claimed with mutations comprising gene inactivation for alr1, alr2, dat, and MurI, because all of the genes are involved in peptidoglycan synthesis and auxotrophs of the bacterium has been shown to function as auxotrophic attenuated vaccines.
Moscoso et al. does teach a Staphylococcus strain in which both alr1 and alr2 genes are inactivated and the main reason for making such a strain is to provide a strain to make a vaccine against pathogenic Staphylococcus strains. The reference of Cabral et al. provides supplemental teachings. In fact, Moscoso et al. reference by itself teaches in detail the roles of the two genes alr1 and 2 as well as the dat gene (see page 605 left column last para through right column first paragraph). This reference by itself teaches why all three genes alr1 and alr2 as well as dat gene needs to be inactivated to develop a strain of Staphylococcus strain that becomes dependent on D-alalnine for growth. Basically such a strain becomes attenuated for these genes and does not grow in the absence of D-alanine, a good candidate for developing a vaccine for Staphylococcus. This is also taught by Moscoso reference. The only missing teaching was why one of skill in the art would limit such a strain to S.epidermidis. That could have been remedied by using the reference of Zhang et al. Molecluar Microbilogy (2003); 49(6)-1577-1593 “Genome-based analysis of virulence genes in a non-biofilm-forming Staphylococcus epidermidis strain (ATCC 12228)”) (cited in the specification). The reference teaches S.epidermidis is a facultative anaerobic bacteria, and is part of the normal human flora and that although S. epidermidis is not usually pathogenic, patients with compromised immune systems are at risk of developing infection and these infections are generally hospital-acquired ( see Levinson, W. (2010). Review of Medical Microbiology and Immunology (11th ed.). pp. 94-99,). The reference also teaches S. epidermidis is a particular concern for people with catheters or other surgical implants because it is known to form biofilms that grow on these target environmental devices. Therefore in order to combat such infections caused by S.epidermidis in a target environment, one of skill in the art would be motivated to develop attenuated strain of S.epidermidis in which the alr1 and alr2 genes as well as dat gene are attenuated such that these strain grow only in presence of D-alanine and such strains can be used to develop vaccines against S.epidermidis infection.
Conclusion
No claims are allowed.
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.
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/ANAND U DESAI/Supervisory Patent Examiner, Art Unit 1655