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
Applicant’s response dated 07/06/2026 is duly acknowledged.
Claims 2 and 25 were previously canceled by applicants per amendment dated 06/14/2024.
Claims 1, 3-24 and 26-31 as currently amended/presented are pending in this application.
Election/Restrictions
Applicant's election with traverse of Group I (claims 1 and 3-23; directed to “A system…”, taken herein as a product) in the reply filed on 07/06/2026 (see REM, p.2) is acknowledged. The traversal is mainly on the ground(s) that “Overall, neither document suggests modifying a microorganism so that ATP can be generated both through a light-dependent ion pump and a redox-dependent ion pump while reducing equivalents are supplied independently, as required by the claims” (see REM, p. 2). This is not found persuasive because as currently presented, instant claims are not drawn to “a microorganism” per se, they are specifically directed to “a system” comprising components (i)-(iii), i.e. the product and/or a kit with assembly of components, the components of which would be obvious to an artisan in the art for intended purposes of generating ATP (for instance in vitro), given the disclosure/suggestions from the cited prior art references of Poehlein et al when taken with the disclosure from Gong et al, as discussed in the CTRS dated 05/06/2026, pages 4-5. Moreover, it is to be noted that instant claim 1 does not require both types of “ion pumps” (see recitation of “and/or” in the wherein clause of claim 1, as presented) for generating ATP as argued by the applicants.
The requirement is still deemed proper and is therefore made FINAL.
Claims 24 and 26-31 (non-elected inventions of Groups II-V) have been withdrawn from further considerations.
Claims 1 and 3-23 (elected invention of Group I, taken as election with traverse; directed to “A system…”, taken herein as a product/kit) have been examined on their merits in this action hereinafter.
Priority
This application is a 371 of PCT/EP2022/086989 (filed on 12/20/2022), which claims foreign priority from European applications EP 21217564.0 (filed on 12/23/2021), and EP 21217703.4 (filed on 12/24/2021).
Objection to Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (see SPEC, p. 32, line 2). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Objections
1. Claim 9 (as presented) is objected to because of the following informalities: claim 9 has been reproduced herein below:
“9. (Original) The system according to claim 8, wherein the biotic and/or abiotic components comprise one or more of: electron bifurcating hydrogenase, oxygen tolerant hydrogenase, formate dehydrogenase, carbon monoxide dehydrogenase, inorganic semiconducting material, redox mediator, protein nanowire.”
As recited, claim 9 does not provide for any conjunction before the last component, for instance “redox mediator, and protein nanowire”, which is suggested to clarify the invention. In the alternative, applicants are advised to recite in the form of a proper Markush group of “selected from the group consisting of A, B, C, and a combination thereof”, if desired. Appropriate correction is suggested.
2. Claim 17 is objected to because of the following informalities: claim 17 recites limitations “Rnf or Ech” as abbreviations, which need to be fully recited in the claims (with the abbreviated limitations in parenthesis, if desired), at least the first time they appear in a claim or a claim set.
Appropriate correction is required.
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 1 and 3-23 (as presented) 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 1 recites the following:
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Claim limitation “components necessary for” (the term “necessary for” has been taken herein as a generic place holder for “means for”) has been evaluated under the three-prong test set forth in MPEP § 2181, subsection I, but the result is inconclusive. Thus, it is unclear whether this limitation should be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, because- though the claim recites the term “necessary for” the “biochemical conversion of an inorganic carbon source into acetyl CoA”, this generic place holder has not been modified with sufficient structural features for performing the claimed function, per se. However, the components recited in sections (i)-(iii) have been presented as generic means in order to obtain the intended results of generating “electrochemical ion gradient” that is ”utilized to generate ATP”. None of the components as recited provide specific structural features to define the “source of reducing equivalents”, “light-dependent ion pump”, or the “redox-dependent ion pump”, and therefore, it is unclear if applicants want to invoke the claims so as to be interpreted under 35 USC 112(f). The boundaries of this claim limitation are ambiguous; therefore, the claim is indefinite and is rejected under 35 U.S.C. 112(b) or pre-AIA 35 U.S.C. 112, second paragraph.
In response to this rejection, applicant must clarify whether this limitation should be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. Mere assertion regarding applicant’s intent to invoke or not invoke 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph is insufficient. Applicant may:
(a) Amend the claim to clearly invoke 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, by reciting “means” or a generic placeholder for means, or by reciting “step.” The “means,” generic placeholder, or “step” must be modified by functional language, and must not be modified by sufficient structure, material, or acts for performing the claimed function;
(b) Present a sufficient showing that 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, should apply because the claim limitation recites a function to be performed and does not recite sufficient structure, material, or acts to perform that function;
(c) Amend the claim to clearly avoid invoking 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, by deleting the function or by reciting sufficient structure, material or acts to perform the recited function; or
(d) Present a sufficient showing that 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, does not apply because the limitation does not recite a function or does recite a function along with sufficient structure, material or acts to perform that function.
Appropriate correction and/or explanation is required.
Claim Rejections - 35 USC § 112 – Written Description
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 and 3-23 (as presented) 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 entire scope of the claimed invention. Claims 1 and 18-21 as presented as reproduced below:
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The product as claimed, i.e. “a system for the generation of acetyl-Coenzyme A…” as currently presented (see instant claim 1 and dependent claims 18-21) encompasses both in vitro as well as in vivo products; wherein the in vivo product encompasses any type of microorganism, recombinant or otherwise. The BRI of the claimed product presented as “a system” is not limited to any particular microorganism (bacteria, fungi, protists, etc.), which are known in the prior art to have a variety of different biochemical pathways for carbon fixation that may or may not be amenable to the required components of the instantly claimed system that can be utilized for ATP generation, per se (see for instance, applicant’s own disclosure on p. 3-4). Moreover, the disclosure of record fails to provide sufficient guidance for any in vitro system with the required components that are necessary to generate ATP via acetyl-CoA production as required by claim 1. Although, the disclosure states generically the intended purpose, wherein the “components required for the independent generation of ATP and reducing equivalents may be assembled in both in vitro and cellular systems” (see p. 7, lines 17-19; see also p. 24, last full paragraph, for instance), no such disclosure for an in vitro system has been provided on record for a reasonable guidance to an artisan in the art. Secondly, the claimed product encompasses the in vivo system that comprises any microorganism, such as a recombinant microorganism that may encompass any bacterial species, fungi, protists, etc., or variants thereof. In fact, the dependent claims 19 and 20 recited two different broad physiological classes of bacteria, such as an acetogen and a purple non-sulfur bacterium. However, the only disclosure and/or guidance provided on record by the applicants pertains to a specific acetogen Acetobacterium woodii that has been modified to introduce a light-dependent ion pump such as a specific bacteriorhodopsin BR2 from Krokinobacter eikastus that requires all-trans retinal to be functionally active (ATR, the component which is not required by the instant claims; see SPEC, Examples 1-2, starting on p. 29). There is no disclosure for any other type of microorganism, or in vivo system comprising any other type of bacterial species/strain, fungi, protist, or any other microbe, which would provide a reasonable guidance for making and using the system as claimed.
Thus, it appears that applicants fail to provide sufficient written description for the claimed subject matter, which has 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 entire scope of the claimed invention.
Appropriate correction and/or explanation is required.
NOTE: 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.
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.
1. Claims 1 and 3-23 (as presented) are rejected under 35 U.S.C. 103 as being unpatentable over Poehlein et al (2012; NPL cited in IDS dated 06/14/2024, citation no. 2) taken with Devroe et al (US 2009/0191599 A1; US-PGPUB cited as ref [A] on PTO 892 form), and Petushkova et al (July 2021; NPL cited as ref. [U] on PTO 892 form).
Claim 1 has been reproduced as follows:
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See limitations of dependent claims 3-23 as currently presented.
Poehlein et al (2012), while teaching an ancient pathway combining carbon dioxide fixation with the generation and utilization of a sodium ion gradient for ATP synthesis (see Title, Abstract), disclose the fact that anaerobic acetogenic bacterium Acetobacterium woodii employs ancient version of carbon dioxide (CO2; i.e. an inorganic carbon source) fixation pathway (Wood-Ljungdahl pathway, WLP) in biosynthesis of acetate from CO₂ and molecular hydrogen (see Title, Abstract, Fig. 1), wherein it combines enzymatic CO₂ fixation into acetyl-CoA with the production of ATP via an energized cell membrane gradient (i.e. electrochemical ion gradient) produced by a sodium-motive ferredoxin:NAD oxidoreductase (Rnf; as a sodium ion pump), and employs metabolic pathway enzymes designed to produce reduced ferredoxin and overcome energetic barriers by virtue of electron-bifurcating, soluble enzymes (i.e. “biotic” component; see p. 5, section “Energy conservation during autotrophic growth: a quantitative model”, 1st paragraph; and Figs. 3 and 5, in particular); wherein they disclose that “[A]cetate formation from hydrogen and carbon dioxide by the Wood-Ljungdahl pathway is catalyzed by cytoplasmic, soluble enzymes. Energy conservation is via a chemiosmotic mechanism of the simplest type with just two enzyme complexes: the ATP synthase and the Rnf complex. The Rnf complex couples oxidation of reduced ferredoxin with reduction of NAD+ and concomittant export of Na+ from the cells” (see p. 6, entire “Conclusions”); and wherein “[T]he metabolism is optimized to (i) get as much as possible reduced ferredoxin to fuel the Rnf complex and (ii) not to use the sodium motive force to overcome energy barriers but the soluble electron bifurcating [FeFe]-hydrogenase and methylene-THF reductase and a hydrogen-coupled formate dehydrogenase. Altogether, this allows for the synthesis of about to 0.5–1 mol ATP per mol of acetate produced” (see p. 7, left column, 1st paragraph).
However, the system (i.e. the product/kit as claimed in claim 1) comprising a microorganism such as a recombinant acetogen, or a purple non-sulfur bacterium (instant claims 14, 18-21) having a second ion pump that is light-dependent and that generates an electrochemical ion gradient independently of the generation of reducing equivalents (such as rhodopsin; see instant claims 15-16), has not been disclosed by the cited prior art of Poehlein et al, as discussed above.
Devroe et al (2009) while teaching engineered light-harvesting microorganisms (see title, Abstract, and claims), disclose engineered cell or microorganism capable of efficient conversion of carbon dioxide (CO2) and light into biomass and carbon-based products; wherein the microbial cell (such as acetogen Clostridium ljungdahlii) is light-dependent and fixes carbon (see claims 1-7, 28, for instance); wherein the light capturing component is a nucleic acid encoding a rhodopsin such as proteorhodopsin (see claims 15-16, for instance). Although Devroe et al do not specifically exemplify the specific recombinant acetogen, they nevertheless disclose the fact that such light-dependent proton pump can be functionally incorporated into variety of bacterial cells for use in converting carbon dioxide into carbon-based valuable products (see [0081], for instance), including cells having CO2 assimilation pathway enzymes via reductive acetyl-CoA pathway such as Wood-Ljungdahl Pathway (WJP; see Fig. 11, [0024], [0191]. and claim 28, for instance).
Petushkova et al (2021) disclose the fact that purple non-sulfur bacterium (PNSB) are anoxygenic photosynthetic bacteria that can harness simple organic acids as electron donors, produce valuable carbon-based compounds, and they are highly promising producers of molecular hydrogen, and can be cultivated using organic waste waters containing acetic acid (see Abstract). They also disclose the fact that PNSB, due to presence of various enzymatic pathways for carbon assimilation and metabolism, are highly adoptive to several environmental stress including photo/light stress and acetate assimilation (see p.30, 5th paragraph).
Thus, to an artisan of ordinary skill in the art, it would have been obvious to incorporate light-dependent ion pump such as a proteorhodopsin into the recombinant acetogen (such as A. woodii disclosed by Poehlein et al, as discussed above), as taught specifically by Devroe et al such that it increases the potential for generating acetyl-CoA and ultimately generating ATP yield (see Devroe et al, [0054]). In addition, given the benefits of photo-resistance of purple non-sulfur bacterium and being promising producers of reducing equivalents such as molecular hydrogen (see teachings from Petushkova et al, above), an artisan of ordinary skill in the art would have been motivated to include such purple non-sulfur bacterium in the system (or the product) as claimed, especially owing to its stress adoptability, flexibility and presence of various carbon-assimilation pathways, which can be successfully modified to incorporate the light-dependent ion pump as well as WJP-based carbon fixation pathways. Since Devroe et al already disclose the benefits of incorporating the light-dependent ion pump into variety of bacterial cells including acetogens for producing carbon-based valuable products (see teachings above), the limitations of instant claims 22 and 23 would have been obvious and/or fully contemplated by an artisan of ordinary skill in the art, unless evidence/data provided on record to the contrary. In addition, given the detailed disclosure for the enzymatic pathways and specific enzymes involved in carbon dioxide fixation including the recited cell membrane-based ion pumps, as discussed above, it would have been obvious to assemble the recited components in vitro in order to make a kit and/or product as currently claimed for generating acetyl-CoA that can be further utilized for producing ATP, unless evidence/data provided on record to the contrary (which is currently lacking on record; see instant SPEC, Examples 1-2).
It is also noted to applicants that the scope of the showing must be commensurate with the scope of claims to consider evidence probative of unexpected results, for example. In re Dill, 202 USPQ 805 (CCPA, 1979), In re Lindner 173 USPQ 356 (CCPA 1972), In re Hyson, 172 USPQ 399 (CCPA 1972), In re Boesch, 205 USPQ 215, (CCPA 1980), In re Grasselli, 218 USPQ 769 (Fed. Cir. 1983), In re Clemens, 206 USPQ 289 (CCPA 1980). It should be clear that the probative value of the data provided by applicants is not commensurate in scope with the degree of protection sought by the claims (see instant claim 1, in particular).
Thus, the claim as a whole would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the invention as claimed.
As per MPEP 2111.01, during examination, the claims must be interpreted as broadly as their terms reasonably allow. In re American Academy of Science Tech Center, F.3d, 2004 WL 1067528 (Fed. Cir. May 13, 2004)(The USPTO uses a different standard for construing claims than that used by district courts; during examination the USPTO must give claims their broadest reasonable interpretation.). This means that the words of the claim must be given their plain meaning unless applicant has provided a clear definition in the specification. In re Zletz, 893 F.2d 319, 321, 13 USPQ2d 1320, 1322 (Fed. Cir. 1989).
Conclusion
NO claims are currently allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SATYENDRA K. SINGH whose telephone number is (571)272-8790. The examiner can normally be reached M-F 8:00- 5:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, LOUISE W HUMPHREY can be reached at 571-272-5543. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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SATYENDRA K. SINGH
Primary Examiner
Art Unit 1657
/SATYENDRA K SINGH/Primary Examiner, Art Unit 1657
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