DETAILED ACTION
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
The amendment filed April 8, 2026, has been received and entered.
Claims 1-36, 38-44, and 46-190 are cancelled. Claim 210 is new.
Claims 37, 45, and 191-210 are examined on the merits.
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 45 and 191-204 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 45, 191-195, and 197 are indefinite as being both incomplete, by their dependence on a cancelled claim; and for lack of antecedent basis for its limitation (“The microbial composition…”) which is not present in cancelled base claim 38. Since claim 195 is indefinite, then its dependent claim, claim 196, is rendered indefinite. Also, since claim 197 is indefinite, then its dependent claims, claims 198-204, are rendered indefinite. Therefore, claims 45 and 191-204 are rejected under 35 U.S.C. 112(b).
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 37, 191-195, 197-201, 203, and 205-210 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.
Claims 37 and 205-210 require the broad genus of one or more engineered gram-positive diazotrophic bacteria capable of fixing nitrogen irrespective of exogenous nitrogen levels at a rate at least equivalent to a rate of nitrogen fixation in a wild-type gram-positive diazotrophic bacterium in the absence of exogenous nitrogen, wherein the one or more engineered gram-positive diazotrophic bacteria comprise a heterologous promoter operably linked to a nif operon and/or a mutant GlnR protein. However, the specification as filed does not provide a representative number of species of the claimed genus to adequately describe the claimed genus, nor would one of skill in the art be able to visualize or recognize the identity of the members of the claimed genus.
Additionally, Applicant describes the heterologous promoter linked to a nif operon at least in Figure 9 and paragraph [0091] (in particular, a heterologous promoter comprising a nucleic acid sequence selected from any one of SEQ ID NOs: 1-11). Applicant also describes the mutant GlnR protein at paragraph [0094] (in particular, a GlnR protein comprising an amino acid sequence selected from the group consisting of SEQ ID NO: 17-19). The bacteria engineered to comprise the heterologous promoter and mutant GlnR protein as described in paragraphs [0091] and [0094] are shown in Figure 10.
However, Applicant does not describe the structures that are required for obtaining the claimed function of fixing nitrogen irrespective of exogenous nitrogen levels at a rate at least equivalent to a rate of nitrogen fixation in a wild-type gram-positive diazotrophic bacterium in the absence of exogenous nitrogen. As such, one of ordinary skill in the art would not recognize engineered gram-positive diazotrophic bacteria that can perform the recited function from other gram-positive diazotrophic bacteria that would not, based upon their structural composition.
In view of these teachings, Applicant appears to be claiming the invention on the basis of function alone. “A definition by function alone "does not suffice" to sufficiently describe a coding sequence "because it is only an indication of what the gene does, rather than what it is." Eli Lilly, 119 F.3 at 1568, 43 USPQ2d at 1406. See also Fiers, 984 F.2d at 1169-71, 25 USPQ2d at 1605-06 (discussing Amgen Inc. v. Chugai Pharma. Co., 927 F.2d 1200, 18 USPQ2d 1016 (Fed. Cir. 1991)). (MPEP 2163).
The limited number of species described by Applicant are insufficient to describe the recited genus by virtue of example.
Response to Arguments
Applicant’s arguments, filed April 8, 2026, with respect to the objections to claims 199-201 and 206, and the rejection under 35 U.S.C. 112(b) of claims 197-204 have been fully considered and are persuasive. The objections have been overcome by the amendments to claims 199-201 and 206. The rejection under 35 U.S.C. 112(b) has been overcome by the amendments to claims 197-201. Therefore, these objections and this rejection have been withdrawn.
However, Applicant’s arguments are unpersuasive with respect to the rejection under 35 U.S.C. 112(a). The amendment to claim 37 is not sufficient for overcoming the rejection. Applicant also cites paragraphs [0084] and [0106] of the specification for description of diazotrophs and primers designed for the nifH gene that can be used to identify diazotrophs. Applicant states that in view of these paragraphs of the specification and examples (e.g., paragraph [0008]), then “gram-positive diazotrophic bacteria” are gram-positive bacteria that can fix nitrogen gas and can be identified by expression of the nifH gene. However, the claims do not limit the gram-positive diazotrophic bacteria as being identified by expression of the nifH gene, so the scope is broader than argued by Applicant.
Additionally, Applicant points out that the specification describes GlnR including types of bacteria that have GlnR as well as GlnR’s structure and function, e.g., paragraph [0085]. However, the description, such as in paragraph [0085] of the specification does not explain the mutations required for a GlnR protein to promote expression of the nif operon irrespective of exogenous nitrogen levels, thus resulting in the bacteria being capable of fixing nitrogen irrespective of exogenous nitrogen levels at a rate at least equivalent to a rate of nitrogen fixation in a wild-type gram-positive diazotrophic bacterium in the absence of exogenous nitrogen. Applicant argues that the specification also provides a multiple sequence alignment of GlnR relative to Paenibacillus polymyxa strain CI41 across Paenibacillus, citing Figure 7 and SEQ ID NOs: 16 and 35-46. However, the claims do not limit the bacteria to Paenibacillus or the residues of Figure 7 that allow ammonium tolerance of GlnR, and it is unclear which mutation(s) are necessary such that the bacteria have the functional properties claimed (capable of fixing nitrogen irrespective of exogenous nitrogen levels at a rate at least equivalent to a rate of nitrogen fixation in a wild-type gram-positive diazotrophic bacterium in the absence of exogenous nitrogen). There is insufficient description for the skilled artisan to recognize the necessary mutations, including mutations other than those shown in Figure 7, that are required in the GlnR protein of a gram-positive diazotrophic bacteria to obtain the claimed functions (including promoting expression of the nif operon irrespective of exogenous nitrogen levels).
Applicant further asserts that the specification provides examples of making and identifying mutant GlnR proteins that promote expression of the nif operon irrespective of exogenous nitrogen levels as well as examples of making and identifying mutants having a heterologous promoter operably linked to a nif operon, where the heterologous promoter replaces at least a portion of the nif operon endogenous promoter and promotes expression of the nif operon irrespective of exogenous nitrogen levels. These examples include methods for generating GlnR mutants that may be ammonium resistant and then identifying GlnR mutants that can activate transcription of the nif gene cluster even in the presence of ammonium as described in paragraphs [0303]-[0304] of Example 1, and Figure 3; methods for isolating GlnR mutants and evaluating the nitrogenase of the GlnR mutants in the presence of ammonium as described in paragraphs [0305]-[0311] of Example 1; Figures 4-6 for GlnR mutants having nifB promoter activity even in the presence of ammonium, e.g., paragraph [0307] referring to Figure 5. However, the scope of the claims is broader than Example 1, and the skilled artisan would not have recognized how to apply the example to bacteria other than Paenibacillus or to arrive at other glnR mutants.
Furthermore, Applicant cites methods for generating bacteria having a heterologous promoter operably linked to a nif operon in Example 2, which refers to Figures 8-10 and promoters 1, 2, 4, 5, 8, and 13 of Figures 11 and 12. However, the scope of the claims is broader than Example 2, and the skilled artisan would not have recognized how to apply the examples to bacteria other than Paenibacillus or to arrive at other nif promoter mutants.
Moreover, the arguments do not address the absence of description of the structures that are required for obtaining the claimed function of fixing nitrogen irrespective of exogenous nitrogen levels at a rate at least equivalent to a rate of nitrogen fixation in a wild-type gram-positive diazotrophic bacterium in the absence of exogenous nitrogen.
Additionally, the amendment necessitated a new rejection under 35 U.S.C. 112(b).
Conclusion
No claims are allowed.
Claims 45, 196, 202, and 204 would be allowable if rewritten to overcome the rejection(s) under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), 2nd paragraph, set forth in this Office action and to include all of the limitations of the base claim and any intervening claims.
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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Sef
/SUSAN E. FERNANDEZ/Examiner, Art Unit 1651
/DAVID W BERKE-SCHLESSEL/Primary Examiner, Art Unit 1651
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