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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 11/14/2025 has been entered.
Status of claims
Claims 1, 5, 9-11, 16, 19, 20, 25, 29-35, 37 and 39 as amended on 11/14/2025 are pending.
Claims 19, 20, 25, 29-35, 37 and 39 were withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to nonelected inventions. Election was made without traverse in the reply filed on 10/18/2024.
Claims 1, 5, 9-11 and 16 as amended on 11/14/2025 are under examination in the instant office action.
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.
Claims 1 and 5 are rejected under 35 U.S.C. 102 (a) (1) as being anticipated by US 7,090,998 (Ishikawa et al) in the light of evidence by Kifle et al (Frontiers in Plant Science. 2016, Vol. 6, article 1225, pages 1-8).
The cited US 7,090,998 (Ishikawa et al) discloses a strain in which an arcA protein does not function normally as result of disruption (see abstract) such as deletion of a gene arcA gene or its fragment or its promoter (col. 8, lines 44-51). The mutant strain, in which functional arcA is no longer produced, is or can be also obtained by mutagenesis (col. 9, lines 15-19). Therefore, the document teaches a genetically engineered non-intergeneric bacterium comprising a genetic modification introduced into a gene arcA within the broadest reasonable meaning of the claim 1.
As applied to claim 5: the bacteria belong to Pantoea (col. 3, lines 33-39) including Pantoea ananatis (example 4, col. 16-21) that are diazotrophic bacteria as evidenced by Kifle (see abstract and see table 3).
Thus, the cited document anticipated the claimed bacteria.
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, 5, 9-11 and 16 are rejected under 35 U.S.C. 103 as being unpatentable over US 7,090,998 (Ishikawa et al) in view of Kifle et al (Frontiers in Plant Science. 2016, Vol. 6, article 1225, pages 1-8), US 5,077,209 (O’Gara), Mus et al (Applied and Environmental Microbiology. 2016, Vol. 82, No. 13, pages 3698-3710) and US 2018/0002243 (Temme et al).
The cited US 7,090,998 (Ishikawa et al) discloses a bacterial strain in which an arcA protein does not function normally as result of disruption (see abstract) such as deletion of a gene arcA gene or its fragment or its promoter (col. 8, lines 44-51). The mutant strain, in which functional arcA is no longer produced, is/can be also obtained by mutagenesis (col. 9, lines 15-19). In particular, the modified bacteria bacteria belong to Pantoea (col. 3, lines 33-39) including Pantoea ananatis (example 4, col. 16-21) that are diazotrophic bacteria as evidenced by Kifle (see abstract and see table 3).
Further, the cited US 7,090,998 (Ishikawa et al) explicitly recognizes that in the genetically modified strain, comprising non-functional arcA, the inhibition of TCA genes is canceled (col. 9, lines 33-35) and a production of glutamine is increased (col. 21, lines 13-15).
It is well knonw that functional TCA and production of glutamine are directly linked to nitrogen fixation network (see figures 2-3 of reference by Mus) and that functional TCA is necessary to support and to improve nitrogen fixation in diazotrophic bacteria (see US 5,077,209 (O’Gara) at col. 2, liners 15-16).
Thus, it would be obvious or one having ordinary skill in the art at the time the claimed invention was filed would reasonably recognize that a diazotrophic bacteria with non-functional or genetically modified gene acrA of the cited US 7,090,998 (Ishikawa et al) would be characterized by improved or increased nitrogen fixation or “further comprise modification in a nitrogen fixation network” as encompassed by the claim 9.
It is well knonw that nitrogen fixation genetic network include genes of Nif cluster such as NifA, NifL, NifH; for example: see US 2018/0002243 (Temme et al) at par. 0013 and 0028. The cited US 2018/0002243 (Temme et al) also teaches that enhanced nitrogen fixation resulting from genetic modification of bacteria include increased expression of NifA, decreased expression of NifL, decreased activity of GlnE (par. 0028); that genetic variation can result of random mutation (0028) in “non-intergeneric bacteria” (0015).
Thus, it would be obvious or one having ordinary skill in the art at the time the claimed invention was filed would reasonably recognize that a diazotrophic bacteria with non-functional or genetically modified gene acrA of the cited US 7,090,998 (Ishikawa et al) would be characterized by improved or increased nitrogen fixation or “further comprise modification in a nitrogen fixation network” that include increased expression of NifA, decreased expression of NifL, decreased activity of GlnE (par. 0028) as encompassed by the claims 10, 11 and 16.
Thus, the claimed invention as a whole was clearly prima facie obvious, especially in the absence of evidence to the contrary.
The claimed subject matter fails to patentably distinguish over the state art as represented be the cited references. Therefore, the claims are properly rejected under 35 USC § 103.
In alterative and in view that claims 9 -11 and 16 are broad with regard to whether modifications related to nitrogen fixation are introduced by natural mutagenesis or intentional generic engineering, the cited US 2018/0002243 (Temme et al) teaches that modifications related to nitrogen fixation can be introduced by random natural mutagenesis and by intentional generic engineering (par. 0028, lines bridging col. 1 and col. 2).
Therefore, it would have been obvious to one having ordinary skill in the art at the time the claimed invention was filed to introduce modifications related to nitrogen fixation as based on modification of Nif gene cluster as taught by the cited US 2018/0002243 (Temme et al) to a diazotrophic bacteria with non-functional or genetically modified gene acrA of the cited US 7,090,998 (Ishikawa et al) with a reasonable expectation of success in further modifying and/or increasing nitrogen fixation by diazotrophic bacteria because the cited US 7,090,998 (Ishikawa et al) explicitly recognizes that in the genetically modified strain, comprising non-functional arcA, the inhibition of TCA genes is canceled, thereby, nitrogen fixation is improved and because nitrogen fixation genetic network is improved by genetic modification of genes of Nif cluster including NifA, NifL, NifH and GlnE as taught by US 2018/0002243 (Temme et al).
Thus, the claimed invention as a whole was clearly prima facie obvious, especially in the absence of evidence to the contrary.
The claimed subject matter fails to patentably distinguish over the state art as represented be the cited references. Therefore, the claims are properly rejected under 35 USC § 103.
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, 5, 9-11 and 16 as amended are/remain rejected under 35 U.S.C. 101 because the claimed invention is directed to a product of nature without significantly more.
The claims recite a “genetically engineered” bacterium comprising a modification “introduced” in a gene as result of a substitution of a promoter of the gene or a deletion of the gene. The claimed-recited bacteria is “non-intergeneric” meaning that it contains its native or natural genes.
The claim recited modification is generic and fails to point that the use of recombinant technology. A substitution of a promoter of a gene or a deletion of a gene does not exclude a natural phenomenon as result of spontaneous mutation. In fact, in view of as-filed specification in “some embodiments” modifications are allowed to be natural (see par. 0054 of the published application US 2022/0211048). The modifications can be obtained or “introduced” by random mutagenesis (0132), by enrichment for bacteria that perform nitrogen fixation (0126) and/or by culturing bacteria on selection media (0013) which is a natural event. Moreover, the claim-recited bacteria is “non-intergeneric” meaning that it contains genes that are natural for this bacteria,
Thus, in the lack of specific characteristics as intended the claimed bacteria is considered to be a naturally occurring bacteria regardless phrase “genetically engineered”, “introduced”, “substitution” and “deletion”, because random mutagenesis and culturing of bacteria on enrichment media do not materially and functionally change the natural events and/or features of naturally occurring bacteria.
This judicial exception is not integrated into a practical application because claimed elements in combination do not add a meaningful limitation or extra-solution to the claimed product, and the claimed product as a whole is nothing more than an attempt to generally link the product of nature to a particular technological environment.
The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because when considered separately and in combination, they do not add significantly more (also known as an “inventive concept”) to the exception.
Response to Arguments
Applicant's arguments filed on 11/14/2025 have been fully considered but they are not all found persuasive and mostly moot in view of new grounds of rejection.
The rejection of claims 10, 11 and 16 under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite, has been withdrawn in view of applicants’ argument that antecedent basis of these claims is based on the phrase “further” comprises a modification in a nitrogen fixation genetic network in the preceding claim 9.
The rejection of claims 1, 5 and 9 under 35 U.S.C. 102 (a)(1) as being anticipated by Krishnan et al (“Citrate Synthase Mutants of Sinorhizobium fredii USDA257 Form Ineffective Nodules with Aberrant Ultrastructure”. Applied and Environmental Microbiology, June 2003, Vol. 69, No. 6, pages 3561–3568) has been withdrawn in view of applicants’ argument that the cited mutant contains modification of lacZ gene which is derived from a different genus of bacteria, thus, the final bacteria is not “non-intergeneric” as recited in claim 1.
With regard to claim rejection under 35 U.S.C. 101 Applicants argue that the specification lists specific genetic modification in table 3 and examples 4-10 and the modification are “introduced” by modern biotechnology and not naturally occurring introduction.
Yet, the claim language is broad and modifications can be obtained or “introduced” by random mutagenesis (0132), by enrichment for bacteria that perform nitrogen fixation (0126) and/or by culturing bacteria on selection media (0013) which is a natural event. Moreover, the claim-recited bacteria is “non-intergeneric” meaning that it contains genes that are natural for this bacteria,
No claims are allowed.
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Vera Afremova
April 2, 2026
/VERA AFREMOVA/ Primary Examiner, Art Unit 1653