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 .
Election/Restrictions
Applicant’s election without traverse of Group I, claims 1-10, in the reply filed on 20 October 2025 is acknowledged. Further, Mr. Barkley was contacted via a phone call on 6 November 2025 requesting a response to the species election requirement mailed 18 July 2025. Applicant elected claim 7 and claim 9. For the purposes of examination, claims 2-6 and 8 have been rejoined into examination.
Claims 11-23 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 20 October 2025 and the interview conducted 6 November 2025.
Applicant is reminded that upon the cancelation of claims to a non-elected invention, the inventorship must be corrected in compliance with 37 CFR 1.48(a) if one or more of the currently named inventors is no longer an inventor of at least one claim remaining in the application. A request to correct inventorship under 37 CFR 1.48(a) must be accompanied by an application data sheet in accordance with 37 CFR 1.76 that identifies each inventor by his or her legal name and by the processing fee required under 37 CFR 1.17(i).
Claim Objections
Claims 1, 7, and 9-10 are objected to because of the following informalities: MPEP 608.01(m) states, “Each claim begins with a capital letter and ends with a period. Periods may not be used elsewhere in the claims except for abbreviations.” In the current case, the claims recite the phrase “Cupriavidus sp.”. Examiner suggests amending the phrase to recite “Cupriavidus sp[[.]]ecies”. Appropriate correction is required.
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 1-10 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.
Regarding claim 1, the claim is drawn towards a non-naturally occurring Cupriavidus species that comprises at least one genetic deletion that improves the organism’s growth on formate by at least 24 percent over a naturally occurring Cupriavidus species. Accordingly, the claim is interpreted as reciting a genus of genetic deletions within a genus of Cupriavidus species that possess the claimed function.
The MPEP lists factors that can be used to determine if sufficient evidence of possession has been furnished in the disclosure of the application. These include "level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention. Disclosure of any combination of such identifying characteristics that distinguish the claimed invention from other materials and would leave one of skill in the art to the conclusion that the applicant was in possession of the claimed species is sufficient." MPEP 2163. A claimed genus may be satisfied through sufficient descriptions of a representative number of species or disclosure of relevant, identifying characteristics such as functional characteristics coupled with known or disclosed correlation between function and structure. MPEP 2163(3)a(II). The number of species that describe the genus must be adequate to describe the entire genus; if there is substantial variability, a large number of species must be described.
The analysis for adequate written description considers (a) actual reduction to practice, (b) disclosure of drawings or structural chemical formulas, (c) sufficient relevant identifying characteristics in the way of complete/partial structure or physical and/or chemical properties or functional characteristics when coupled with known or disclosed correlation with structure, and (d) representative number of samples.
As the claims currently recite, as described above, the claim is directed towards a genus of genetic deletions that are capable of improving a Cupriavidus species’ growth rate on formate. While claiming a structure by a function is not prohibited, there must be sufficient structure-function relationship described in the specification such that the claimed genus was represented by a representative number of species or the teachings of the specification, or, the prior art can be used support a well-known structure-function relationship.
In the instant case, the instant specification does not support the claimed structure-function relationship that any [emphasis added] genetic deletion within any [emphasis added] Cupriavidus species would predictably result in an improved growth rate on formate by at least 24 percent over a naturally occurring Cupriavidus species. Further, the prior art does not support a clear, well-defined, and predictable structure-function relationship between all genetic deletions within a Cupriavidus species and having the function of improving its growth rate on formate by at least 24 percent over a naturally occurring Cupriavidus species.
Prior Art
Prior to the effective filing date of the claimed invention, the prior art provides evidence for at least one species within the claimed genus of genetic deletions that does not possess the claimed function.
Claassens (Metabolic Engineering 62 (2020): 30-41) is drawn towards a study concerned with engineering Cupriavidus necator H16 (i.e., a Cupriavidus species) via the deletion and replacement of the ATP-inefficient Calvin cycle with a synthetic reductive glycine pathway and determining the organism’s growth rate on formate (i.e., the Cupriavidus necator comprises at least one genetic deletion) (Abstract, pg. 37). Claassens teaches that introducing plasmids encoding a synthetic reductive glycine pathway allowed for the strain to grow on formate (pg. 34-35). However. Claassens teaches that the final growth yield that was achieved with the synthetic reductive glycine pathway nearly matched that of the WT strain using the Calvin Cycle (i.e., the genetic deletions described in Claassens did not improve growth of the C. necator by at least 24 percent over a naturally occurring C. necator) (Abstract).
Thus, the closet prior art teaches that it was neither predictable nor well-known that any species within the claimed genus of genetic deletions possessed the function of improving any Cupriavidus species’ growth rate on formate by at least 24 percent over a naturally occurring Cupriavidus species. Rather, the closet prior art shows that at least one species within the claimed genus does not possess the claimed function. Therefore, the prior art does not support a clear, well-defined, and predictable structure-function relationship between any [emphasis added] genetic deletion within any [emphasis added] Cupriavidus species and the function of improving its growth rate on formate by at least 24 percent over a naturally occurring Cupriavidus species.
Working Examples
With regard to working examples, the specification provides little evidence on the possession of a sufficient number of species which are encompassed by the claimed genus and possess the claimed function. The claimed genus of any single genetic deletion within any Cupriavidus species is extraordinarily large because the genus encompasses any deletion anywhere in the genome of any Cupriavidus species.
The instant specification identifies 8 different non-naturally occurring strains of Cupriavidus necator that each comprised different genetic deletions, selected from 10 total genetic deletions, that resulted in the non-naturally occurring strains of Cupriavidus necator species having improved growth on formate by at least 24 percent when compared to a naturally occurring Cupriavidus necator (pg. 8-9, 32, 34; see Tables 1, 6, and 8). The 10 disclosed genetic deletions are structurally and functionally different from one another because there is no common structure shared by the deletions, as each deletion refers to a different gene that has a different function when compared to a different disclosed gene. Further, there is no structure-function correlation described in the specification with regard to the entirety of the claimed genus. The 10 disclosed genetic deletions are not representative of the genus as a whole because the genus, as discussed above, claims any deletion anywhere in the genome of any Cupriavidus species. Thus, there is a massive degree of structural variation in the members of the claimed genus that is not adequately described by 10 genetic deletions. The specification only provides a single working example of a species of Cupriavidus, Cupriavidus necator, that can comprise at least one genetic deletion in order to improve its growth on formate by at least 24 percent when compared to a naturally occurring Cupriavidus species. Further, the instant specification only identifies 10 different genetic deletions that could be within a non-naturally occurring Cupriavidus necator strain that would result in the claimed function. Therefore, a person of ordinary skill in the art would interpret the working examples as providing support only for specific mutations within a non-naturally occurring Cupriavidus necator strain that resulted in the claimed function.
Thus, the instant specification does not provide written description for the entirety of the claimed genus of genetic deletions or the entirety of the claimed genus of Cupriavidus species as recited in claim 1.
Conclusion
The specification does not identify a structure-function relationship between any [emphasis added] genetic deletion within any [emphasis added] non-naturally occurring Cupriavidus species and the function of improving its growth on formate by at least 24 percent when compared to a naturally occurring Cupriavidus species sufficient to show the applicant was in possession of the claimed genus. Further, the closet prior art shows that prior to the effective filing date of the claimed invention there was at least one genetic deletion within a Cupriavidus necator (i.e., a Cupriavidus species) that did not possess the function of improving its growth on formate by at least 24 percent when compared to a naturally occurring Cupriavidus species.
Thus, claim 1 is rejected under 35 U.S.C. 112(a).
Regarding claim 7, although the claim does recite a specific genetic deletion that is present within a Cupriavidus necator strain, the claim is nonetheless drawn towards that genetic deletion being present in a large genus of Cupriavidus species, as described above in claim 1. Accordingly, the claim does not rectify the written description rejection described above, the claims are also rejected under U.S.C. 112(a).
Regarding claim 9, as the claim is ultimately dependent on claim 1 and does not rectify the written description rejection described above, the claim is also rejected under U.S.C. 112(a).
Regarding claim 10, although the claim does recite that the Cupriavidus species is Cupriavidus necator, the claim is nonetheless drawn towards a strain of Cupriavidus necator that comprises a large genus of genetic deletions that is not supported by the specification, as described above and applied to claim 1. Accordingly, the claim does not rectify the written description rejection described above, the claims are also rejected under U.S.C. 112(a).
Closest Prior Art
Regarding claims 1, 7, and 9-10, the closest prior art is Claassens (Metabolic Engineering 62 (2020): 30-41). Claassens is drawn towards a study concerned with engineering Cupriavidus necator H16 (i.e., a Cupriavidus species) via the deletion and replacement of the ATP-inefficient Calvin cycle with a synthetic reductive glycine pathway and determining the organism’s growth rate on formate (Abstract, pg. 37). Claassens teaches that introducing plasmids encoding a synthetic reductive glycine pathway allowed for the strain to grow on formate (pg. 34-35). However. Claassens teaches that the final growth yield that was achieved with the synthetic reductive glycine pathway nearly matched that of the WT strain using the Calvin Cycle (i.e., the genetic deletions described in Claassens did not improve growth of the C. necator by at least 24 percent over a naturally occurring C. necator) (Abstract).
Therefore, the prior art does not teach or suggest the use of at least one genetic deletion in a non-naturally occurring Cupriavidus species that improved its growth on formate by up to 24 percent over a naturally occurring Cupriavidus species (Claim 1).
Accordingly, if all the outstanding claim rejections and objections are overcome, the claims would be placed in conditions for allowance.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KYLE T REGA whose telephone number is (571)272-2073. The examiner can normally be reached M-R 8:30-4:30, every other F 8:30-4:30 (EDT/EST).
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Neil Hammell can be reached at 571-270-5919. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/KYLE T REGA/Examiner, Art Unit 1636
/NEIL P HAMMELL/Supervisory Patent Examiner, Art Unit 1636