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 .
Application Status
In response to Non-Final Office Action mailed on 12/31/2025, applicants' response, arguments and amendments filed on dated 05/29/2026 is acknowledged; in said response applicants’ have amended claims 1-3, 6-7 and 35 and canceled claims 5, 9 and 41. Thus, amended claims 1-3, 6-8 and 10-40 are pending and are now under consideration; elected Group I, claims 1-3, 6-8, 10-12 and 33-40 of the elected invention is now under consideration for examination; and the non-elected Groups’ II-IV, claims 13-32 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected invention, there being no allowable generic or linking claim. Applicant timely traversed the restriction (election) requirement in the reply filed on 12/11/2025. Rejections and/or objections not reiterated from previous office action are hereby withdrawn.
Withdrawn-Claim Rejections: 35 USC § 112(b)
Previous rejections:I. Claims 5 (claim 6 depending therefrom) and 7 rejected under 35 U.S.C. 112(b); and II. Claim 35 is rejected under 35 U.S.C. 112(b), is being withdrawn due to claim amendments.
Withdrawn-Claim Rejections: 35 USC § 102 (AIA )
Previous rejection of claims 1-3, 5-9, 12, 33-34, 36-37 and 39-40 rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by North et al., (US 2024/0060037 A1; priority 03/25/2021), is being withdrawn due to claim amendments.
Withdrawn-Claim Rejections: 35 USC § 103
Previous rejection of claims 1-3, 5-12 and 33-41 rejected under 35 U.S.C. 103(a) as being unpatentable over North et al., (US 2024/0060037 A1; priority 03/25/2021) as applied to claims 1-3, 5-9, 12, 33-34, 36-37 and 39-40 (see 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) rejection above) and further in view of Voight et al., (US 9,040,266 B2), Wood et al., (US 2020/0337314 A1) and Begmatov et al., (Microorganisms, 2021, Vol. 9,2362, pages 1-21), is being withdrawn due to claim amendments.
New-Claim Objections
Claim 1 and 2-3, 6-8, 10-12 and 33-40 depending therefrom are objected to for the following informality: Claim 1 recites "MarBHDK"; examiner suggests the following amendment claim 1 to recite "methylthio-alkane reductase obtained from Rhodospirillum rubrum (MarBHDK).
Maintained-Claim Rejections: 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(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 1-3, 6-8, 10-12 and 33-40 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
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. For a broad generic claim, the specification must provide adequate written description to identify the genus of the claim.
“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 biomolecule, it is "not sufficient characteristic for written description purposes, even when accompanied by a method of obtaining the claimed biomolecule.”
“The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice . . ., reduction to drawings . . ., or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus.” MPEP 2163.
Furthermore, a “‘representative number of species’ means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. The disclosure of only one species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure ‘indicates that the patentee has invented species sufficient to constitute the gen[us].’ See Enzo Biochem, 323 F.3d at 966, 63 USPQ2d at 1615; Noelle v. Lederman, 355 F.3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004) (Fed. Cir. 2004) (‘[A] patentee of a biotechnological invention cannot necessarily claim a genus after only describing a limited number of species because there may be unpredictability in the results obtained from species other than those specifically enumerated.’). ‘A patentee will not be deemed to have invented species sufficient to constitute the genus by virtue of having disclosed a single species when … the evidence indicates ordinary artisans could not predict the operability in the invention of any species other than the one disclosed.’ In re Curtis, 354 F.3d 1347, 1358, 69 USPQ2d 1274, 1282 (Fed. Cir. 2004).” MPEP 2163.
The claims recite the following broadly claimed genera:
Claims 1-3, 6-8, 10-12 and 33-40 recite a genera of host cells/genera of cellular context selected from Saccharomyces cerevisiae, Nitrospiraceae family and Nitrobacteraceae family (fermenting organisms producing C2-4 alkene from C2-4 alkanol; as in claims 1-3, 6-8, 10-12 and 33-40); comprising a cellular machinery able to produce any C2-4 alkene from any C2-4 alkanol (genera of products and substrates; as in claims 1-3, 6-8, 10-12 and 33-37) and comprising any undefined genetic modification i.e., wherein the engineered host cell comprises S-Adenosyl-L-methionine (SAM) pathway enzymes, selected from the group consisting of any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase including variants, mutants and homologs of undefined and unlimited structures and any non-native enzyme of undefined and unlimited structures catalysing the conversion of C2-4 alkanol (as in claims 1-3, 6-8, 10-12 and 33-40; also see claims objections for claims interpretation).
The structural elements recited in claims 1-3, 6-8, 10-12 and 33-40 are not sufficient structure to form “any S-Adenosyl-L-methionine (SAM) pathway enzymes… any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase of undefined and unlimited structures catalysing the conversion of C2-4 alkanol” having no specific structural elements of any kind and having associated activity. There in inherent unpredictability in regards to encoding polynucleotides and encodes polypeptides/which amino acid sequences may have the associated function in any undefined cellular context/engineered host cell i.e., “any S-Adenosyl-L-methionine (SAM) pathway enzymes… any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase of undefined and unlimited structures catalysing the conversion of C2-4 alkanol” and possibly fall within the claims and those amino acid sequences that do not have “any S-Adenosyl-L-methionine (SAM) pathway enzymes… any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase of undefined and unlimited structures catalysing the conversion of C2-4 alkanol” activity. As such, claims 1-3, 6-8, 10-12 and 33-40 recite a genera of biomolecules described only by a functional characteristics (i.e., encoding polynucleotides and encodes polypeptides/which amino acid sequences may have the associated function in any undefined cellular context/engineered host cell i.e., “any S-Adenosyl-L-methionine (SAM) pathway enzymes… any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase of undefined and unlimited structures catalysing the conversion of C2-4 alkanol” activity, without any disclosed correlation between function and structure of the biomolecule, it is "not sufficient characteristic for written description purposes, even when accompanied by a method of obtaining the claimed biomolecule.” Further, without any structural limitations for structural features that actually provide for “any S-Adenosyl-L-methionine (SAM) pathway enzymes… any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase of undefined and unlimited structures catalysing the conversion of C2-4 alkanol” activity, claims 1-3, 6-8, 10-12 and 33-40 have no defined outer bounds for the scope of “any S-Adenosyl-L-methionine (SAM) pathway enzymes… any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase of undefined and unlimited structures catalysing the conversion of C2-4 alkanol” activity that fall within the scope of the claims. Due to the literal unlimited structural scope of the claims, it is not possible to provide for a representative number of species that adequately described are representative of the entire genus having no fixed structural outer boundaries. Further, such genera of altered enzymes as recited lack “a precise definition, such as by structure, formula, [or] chemical name, of the claimed subject matter sufficient to distinguish it from other materials” and without any required structure that is sufficient for providing the recited enzyme activity, the recited genera lack disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus. The claims lack adequate written description in the as-filed specification for the reasons stated.
No information, beyond the characterization of specific cellular context/engineered Saccharomyces cerevisiae ATCC 96581 strain comprising specific structures, a Oleate hydratase encoded by the polynucleotide sequence of SEQ ID NO: 1, and a Linalool dehydratase encoded by the polynucleotide sequence of SEQ ID NO: 2, method of making and method of use of said Saccharomyces cerevisiae ATCC 96581 strain for the production of ethanol (see Examples 1-2, ¶ [0068-0076], pages 18-21 of specification) has been provided by the applicants’, which would indicate that they had possession of the genera of host cells/genera of cellular context selected from Saccharomyces cerevisiae, Nitrospiraceae family and Nitrobacteraceae family (fermenting organisms producing C2-4 alkene from C2-4 alkanol; as in claims 1-3, 6-8, 10-12 and 33-40); comprising a cellular machinery able to produce any C2-4 alkene from any C2-4 alkanol (genera of products and substrates; as in claims 1-3, 6-8, 10-12 and 33-37) and comprising any undefined genetic modification i.e., wherein the engineered host cell comprises S-Adenosyl-L-methionine (SAM) pathway enzymes, selected from the group consisting of any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase including variants, mutants and homologs of undefined and unlimited structures and any non-native enzyme of undefined and unlimited structures catalysing the conversion of C2-4 alkanol (as in claims 1-3, 6-8, 10-12 and 33-40; also see claims objections for claims interpretation).
The genus of polynucleotides and encoded polypeptides required in the claimed invention is an extremely large structurally and functionally variable genus in the claimed genera of engineered host cells. While the argument can be made that the recited genus of polypeptides is adequately described by the disclosure of the structures of amino acid sequences and the encoding polynucleotides as disclosed in the characterization of specific cellular context/engineered Saccharomyces cerevisiae ATCC 96581 strain comprising specific structures, a Oleate hydratase encoded by the polynucleotide sequence of SEQ ID NO: 1, and a Linalool dehydratase encoded by the polynucleotide sequence of SEQ ID NO: 2, method of making and method of use of said Saccharomyces cerevisiae ATCC 96581 strain for the production of ethanol (see Examples 1-2, ¶ [0068-0076], pages 18-21 of specification), since one could use structural homology to isolate those polypeptides and the encoding polynucleotides recited in the claims. The art clearly teaches the “Practical Limits of Function Prediction”: (a) Devos et al., (Proteins: Structure, Function and Genetics, 2000, Vol. 41: 98-107), teach that the results obtained by analyzing a significant number of true sequence similarities, derived directly from structural alignments, point to the complexity of function prediction. Different aspects of protein function, including (i) enzymatic function classification, (ii) functional annotations in the form of key words, (iii) classes of cellular function, and (iv) conservation of binding sites can only be reliably transferred between similar sequences to a modest degree. The reason for this difficulty is a combination of the unavoidable database inaccuracies and plasticity of proteins (Abstract, page 98) and the analysis poses interesting questions about the reliability of current function prediction exercises and the intrinsic limitation of protein function prediction (Column 1, paragraph 3, page 99) and conclude that “Despite widespread use of database searching techniques followed by function inference as standard procedures in Bioinformatics, the results presented here illustrate that transfer of function between similar sequences involves more difficulties than commonly believed. Our data show that even true pair-wise sequence relations, identified by their structural similarity, correspond in many cases to different functions (column 2, paragraph 2, page 105).
(b) Whisstock et al., (Quarterly Reviews of Biophysics 2003, Vol. 36 (3): 307-340) also highlight the difficulties associated with “Prediction of protein function from protein sequence and structure”; “To reason from sequence and structure to function is to step onto much shakier ground”, closely related proteins can change function, either through divergence to a related function or by recruitment for a very different function, in such cases, assignment of function on the basis of homology, in the absence of direct experimental evidence, will give the wrong answer (page 309, paragraph 4), it is difficult to state criteria for successful prediction of function, since function is in principle a fuzzy concept. Given three sequences, it is possible to decide which of the three possible pairs is most closely related. Given three structures, methods are also available to measure and compare similarity of the pairs. However, in many cases, given three protein functions, it would be more difficult to choose the pair with most similar function, although it is possible to define metrics for quantitative comparisons of different protein sequences and structures, this is more difficult for proteins of different functions (page 312, paragraph 5), in families of closely related proteins, mutations usually conserve function but modulate specificity i.e., mutations tend to leave the backbone conformation of the pocket unchanged but to affect the shape and charge of its lining, altering specificity (page 313, paragraph 4), although the hope is that highly similar proteins will share similar functions, substitutions of a single, critically placed amino acid in an active-site residue may be sufficient to alter a protein’s role fundamentally (page 323, paragraph 1).
(c) This finding is reinforced in the following scientific teachings for specific proteins in the art that suggest, even highly structurally homologous polynucleotides and encoded polypeptides do not necessarily share the same function. For example, Witkowski et al., (Biochemistry 38:11643-11650, 1999), teaches that one conservative amino acid substitution transforms a b-ketoacyl synthase into a malonyl decarboxylase and completely eliminates b-ketoacyl synthase activity. Seffernick et al., (J. Bacteriol. 183(8): 2405-2410, 2001), teaches that two naturally occurring Pseudomonas enzymes having 98% amino acid sequence identity catalyze two different reactions: deamination and dehalogenation, therefore having different function. Broun et al., (Science 282:1315-1317, 1998), teaches that as few as four amino acid substitutions can convert an oleate 12-desaturase into a hydrolase and as few as six amino acid substitutions can transform a hydrolase to a desaturase.
As stated above, no information beyond the characterization of specific cellular context/engineered Saccharomyces cerevisiae ATCC 96581 strain comprising specific structures, a Oleate hydratase encoded by the polynucleotide sequence of SEQ ID NO: 1, and a Linalool dehydratase encoded by the polynucleotide sequence of SEQ ID NO: 2, method of making and method of use of said Saccharomyces cerevisiae ATCC 96581 strain for the production of ethanol (see Examples 1-2, ¶ [0068-0076], pages 18-21 of specification), has been provided by the applicants’, which would indicate that they had possession of the claimed genera of host cells/genera of cellular context selected from Saccharomyces cerevisiae, Nitrospiraceae family and Nitrobacteraceae family (fermenting organisms producing C2-4 alkene from C2-4 alkanol; as in claims 1-3, 6-8, 10-12 and 33-40); comprising a cellular machinery able to produce any C2-4 alkene from any C2-4 alkanol (genera of products and substrates; as in claims 1-3, 6-8, 10-12 and 33-37) and comprising any undefined genetic modification i.e., wherein the engineered host cell comprises S-Adenosyl-L-methionine (SAM) pathway enzymes, selected from the group consisting of any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase including variants, mutants and homologs of undefined and unlimited structures and any non-native enzyme of undefined and unlimited structures catalysing the conversion of C2-4 alkanol (as in claims 1-3, 6-8, 10-12 and 33-40; also see claims objections for claims interpretation). As the claimed genera of polypeptides and encoding polynucleotides having widely variable structures and associated function in the claimed genera of engineered host cells, since minor changes in structure may result in changes affecting function and no additional information (species/variant/mutant) correlating structure with function has been provided. Furthermore, “Possession may not be shown by merely describing how to obtain possession of members of the claimed genus or how to identify their common structural features” (See University of Rochester, 358 F.3d at 927, 69 USPQ2d at 1895).
Therefore, one skilled in the art cannot reasonably conclude that applicant had possession of the claimed invention at the time the instant application was filed. Applicants are referred to the revised guidelines concerning compliance with the written description requirement of 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, published in the Official Gazette and also available at www.uspto.gov.
Applicants’ have traversed the above written-description with the following arguments: (see pages 9-10 of Applicants’ REMARKS dated 05/29/2026).
Applicants’ argue: “…As amended, Claim 1 clearly limits the claimed genus to "one or more enzymes from the S-Adenosyl-L-methionine (SAM) pathway, selected from the group consisting of methylthio- alkane reductase, MarBHDK, and Cys, Met /SAM synthase." Thus, there are now defined bounds for the claimed enzymes of the SAM pathway. The written description contains sufficient evidence of these three enzymes, see Example 1. Furthermore, the amendments to Claim 1 limit the claimed genus of microorganism to Saccharomyces cerevisiae and microorganisms from the Nitrospiraceae family and the Nitrobacteraceae family. Thus, as amended, Claim 1 contains defined bounds for the claimed microorganisms. The written description contains sufficient evidence of these microorganisms. Example 1 provides evidence for the claimed enzymes expressed in Saccharomyces cerevisiae (see paragraph 0069) and Example 3 provides evidence for microorganisms from the Nitrospiraceae family and the Nitrobacteraceae family (see paragraph 0077).”
Reply: Applicants' arguments have been considered but are found to be non-persuasive for the following reasons. Examiner continues to maintain the rejection for reasons stated on record (dated 12/31/2025) and additionally for the following reasons.
Examiner continues to maintain the following: The claims encompass a large genus of proteins which are substantially unrelated or completely unrelated and includes random mutants of “any S-Adenosyl-L-methionine (SAM) pathway enzymes… any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase of undefined and unlimited structures catalysing the conversion of C2-4 alkanol” activity in a genus of cellular context i.e., Nitrospiraceae family and Nitrobacteraceae family fermenting organisms producing C2-4 alkene from C2-4 alkanol. Therefore, the scope of the instant claims are broad despite the guidance of the art and specification, the claims remain not commensurate with evidence of possession or in scope with the enabled invention. An important consideration is that structure is not necessarily a reliable indicator of function. Given this scenario, a skilled artisan needs to be provided with the specific structure associated with the function. The specification does not provide support for the full scope and breadth of the claims, thus examiner continues to hold the position the experimentation left to those skilled in the art is unnecessarily, and improperly extensive and undue. Therefore, taking into consideration the extremely broad scope of the claims, the lack of guidance, the amount of information provided, the lack of knowledge about a correlation between structure and the desired function, and the high degree of unpredictability of the prior art in regard to structural changes and their effect on function, one of ordinary skill in the art would have to go through the burden of undue experimentation in order to practice the claimed invention. Thus, Applicant has not provided sufficient guidance to enable one of ordinary skill in the art to make and use the invention in a manner reasonably correlated with the scope of the claims in the claimed method.
MPEP 2163.II.A.2. (a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the 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”;
“The basic quid pro quo contemplated by the Constitution and the Congress for granting a patent monopoly is the benefit derived by the public from an invention with substantial utility”, [u]nless and until a process is refined and developed to this point-where specific benefit exists in currently available form-there is insufficient justification for permitting an applicant to engross what may prove to be a broad field”, and “a patent is not a hunting license”,[i]t is not a reward for the search, but compensation for its successful conclusion.”
Maintained-Enablement
Claims 1-3, 6-8, 10-12 and 33-40 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification is enabling for the characterization of specific cellular context/engineered Saccharomyces cerevisiae ATCC 96581 strain comprising specific structures, a Oleate hydratase encoded by the polynucleotide sequence of SEQ ID NO: 1, and a Linalool dehydratase encoded by the polynucleotide sequence of SEQ ID NO: 2, method of making and method of use of said Saccharomyces cerevisiae ATCC 96581 strain for the production of ethanol (see Examples 1-2, ¶ [0068-0076], pages 18-21 of specification). However, specification does not reasonably provide enablement for a genera of host cells/genera of cellular context selected from Saccharomyces cerevisiae, Nitrospiraceae family and Nitrobacteraceae family (fermenting organisms producing C2-4 alkene from C2-4 alkanol; as in claims 1-3, 6-8, 10-12 and 33-40); comprising a cellular machinery able to produce any C2-4 alkene from any C2-4 alkanol (genera of products and substrates; as in claims 1-3, 6-8, 10-12 and 33-37) and comprising any undefined genetic modification i.e., wherein the engineered host cell comprises S-Adenosyl-L-methionine (SAM) pathway enzymes, selected from the group consisting of any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase including variants, mutants and homologs of undefined and unlimited structures and any non-native enzyme of undefined and unlimited structures catalysing the conversion of C2-4 alkanol (as in claims 1-3, 6-8, 10-12 and 33-40; also see claims objections for claims interpretation). The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Factors to be considered in determining whether undue experimentation is required are summarized in In re Wands (858 F.2d 731, 8 USPQ 2nd 1400 (Fed. Cir. 1988)) as follows: (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claim(s).
Claims 1-3, 6-8, 10-12 and 33-40 are so broad as to encompass a genera of host cells/genera of cellular context selected from Saccharomyces cerevisiae, Nitrospiraceae family and Nitrobacteraceae family (fermenting organisms producing C2-4 alkene from C2-4 alkanol; as in claims 1-3, 6-8, 10-12 and 33-40); comprising a cellular machinery able to produce any C2-4 alkene from any C2-4 alkanol (genera of products and substrates; as in claims 1-3, 6-8, 10-12 and 33-37) and comprising any undefined genetic modification i.e., wherein the engineered host cell comprises S-Adenosyl-L-methionine (SAM) pathway enzymes, selected from the group consisting of any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase including variants, mutants and homologs of undefined and unlimited structures and any non-native enzyme of undefined and unlimited structures catalysing the conversion of C2-4 alkanol (as in claims 1-3, 6-8, 10-12 and 33-40; also see claims objections for claims interpretation). The scope of the claim is not commensurate with the enablement provided by the disclosure with regard to the extremely large number of polynucleotides and encoded polypeptides broadly encompassed by the claims in a genus of engineered host cells. Since the amino acid sequence of a protein encoded by a polynucleotide determines its structural and functional properties, predictability of which changes can be tolerated in a protein's amino acid sequence and obtain the desired activity requires a knowledge of and guidance with regard to which amino acids in the protein's sequence and the respective codons in its polynucleotide, if any, are tolerant of modification and which are conserved (i.e., expectedly intolerant to modification), and detailed knowledge of the ways in which the encoded proteins' structure relates to its function. However, in this case the disclosure is limited to the characterization of specific cellular context/engineered Saccharomyces cerevisiae ATCC 96581 strain comprising specific structures, a Oleate hydratase encoded by the polynucleotide sequence of SEQ ID NO: 1, and a Linalool dehydratase encoded by the polynucleotide sequence of SEQ ID NO: 2, method of making and method of use said Saccharomyces cerevisiae ATCC 96581 strain for the production of ethanol (see Examples 1-2, ¶ [0068-0076], pages 18-21 of specification). It would require undue experimentation of the skilled artisan to make and use the claimed polypeptides and engineered host cells i.e., a genera of host cells/genera of cellular context selected from Saccharomyces cerevisiae, Nitrospiraceae family and Nitrobacteraceae family (fermenting organisms producing C2-4 alkene from C2-4 alkanol; as in claims 1-3, 6-8, 10-12 and 33-40); comprising a cellular machinery able to produce any C2-4 alkene from any C2-4 alkanol (genera of products and substrates; as in claims 1-3, 6-8, 10-12 and 33-37) and comprising any undefined genetic modification i.e., wherein the engineered host cell comprises S-Adenosyl-L-methionine (SAM) pathway enzymes, selected from the group consisting of any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase including variants, mutants and homologs of undefined and unlimited structures and any non-native enzyme of undefined and unlimited structures catalysing the conversion of C2-4 alkanol (as in claims 1-3, 6-8, 10-12 and 33-40; also see claims objections for claims interpretation). The specification but provides no guidance with regard to the making of variants and mutants or with regard to other uses. In view of the great breadth of the claims, amount of experimentation required to make and use the claimed polypeptides, the lack of guidance, working examples, and unpredictability of the art in predicting function from a polypeptide primary structure (for example, see Whisstock et al., Prediction of protein function from protein sequence and structure. Q Rev Biophys. 2003, Aug. 36 (3): 307-340. Review), the claimed invention would require undue experimentation. As such, the specification fails to teach one of ordinary skill how to make and use the full scope of the polypeptides and the encoding polynucleotides encompassed by the claims. However, claims reading on significant numbers of inoperative embodiments would render claims non-enabled when the specification does not clearly identify the operative embodiments and undue experimentation is involved in determining those that are operative.” Atlas Powder Co. v. E.I. duPont de Nemours & Co., 750 F.2d 1569, 1577, 224 USPQ 409, 414 (Fed. Cir. 1984); In re Cook, 439 F.2d 730, 735, 169 USPQ 298, 302 (CCPA 1971); MPEP 2164.08(b). Here, the claims read on a significant number of inoperative embodiments.
While enzyme isolation techniques, recombinant and mutagenesis techniques are known, and it is not routine in the art to screen for multiple substitutions or multiple modifications as encompassed by the instant claims, the specific amino acid positions within a protein's sequence where amino acid modifications can be made with a reasonable expectation of success in obtaining the desired activity/utility are limited in any protein and the result of such modifications is unpredictable. In addition, one skilled in the art would expect any tolerance to modification for a given protein to diminish with each further and additional modification, e.g. multiple substitutions.
The specification does not support the broad scope of the claims which encompass: a genera of host cells/genera of cellular context selected from Saccharomyces cerevisiae, Nitrospiraceae family and Nitrobacteraceae family (fermenting organisms producing C2-4 alkene from C2-4 alkanol; as in claims 1-3, 6-8, 10-12 and 33-40); comprising a cellular machinery able to produce any C2-4 alkene from any C2-4 alkanol (genera of products and substrates; as in claims 1-3, 6-8, 10-12 and 33-37) and comprising any undefined genetic modification i.e., wherein the engineered host cell comprises S-Adenosyl-L-methionine (SAM) pathway enzymes, selected from the group consisting of any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase including variants, mutants and homologs of undefined and unlimited structures and any non-native enzyme of undefined and unlimited structures catalysing the conversion of C2-4 alkanol (as in claims 1-3, 6-8, 10-12 and 33-40; also see claims objections for claims interpretation), because the specification does not establish: (A) a rational and predictable scheme for modifying specific amino acid residues in any “any S-Adenosyl-L-methionine (SAM) pathway enzymes… any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase of undefined and unlimited structures catalysing the conversion of C2-4 alkanol” activity having no specific structural elements and an expectation of obtaining the desired biological/biochemical function; (B) defined core regions/motifs involved in the desired catalytic activity of encoded polypeptide; (C) the tertiary structure of the molecule and folding patterns that are essential for the desired activity and tolerance to modifications; and (D) the specification provides insufficient guidance as to which of the essentially infinite possible choices is likely to be successful.
While as discussed above, the specification provides guidance with regard to the characterization of specific cellular context/engineered Saccharomyces cerevisiae ATCC 96581 strain comprising specific structures, a Oleate hydratase encoded by the polynucleotide sequence of SEQ ID NO: 1, and a Linalool dehydratase encoded by the polynucleotide sequence of SEQ ID NO: 2, method of making and method of use said Saccharomyces cerevisiae ATCC 96581 strain for the production of ethanol (see Examples 1-2, ¶ [0068-0076], pages 18-21 of specification), however, the scope of claims 1-3, 6-8, 10-12 and 33-40 is so broad and the lack of guidance either in the specification or in the prior art, the claims remains not commensurate in scope with the enabled invention and therefore for the rejected claims, this would clearly constitute undue experimentation.
Thus, applicants’ have not provided sufficient guidance to enable one of ordinary skill in the art to make and use the claimed invention in a manner reasonably correlated with the scope of the claims broadly including polynucleotides and encoded polypeptides with an enormous number of modifications in a genera of cellular context. The scope of the claim must bear a reasonable correlation with the scope of enablement (In re Fisher, 166 USPQ 19 24 (CCPA 1975)). Without sufficient guidance, determination of polynucleotides and encoded polypeptides/enzymes having the desired biological characteristics is unpredictable and the experimentation left to those skilled in the art is unnecessarily, and improperly, extensive and undue. See In re Wands 858 F.2d 731, 8 USPQ2nd 1400 (Fed. Cir, 1988).
Although the claims are examined in the light of the specification, specification cannot be read into the claims, i.e., the limitations of the specification cannot be read into the claims (see MPEP 2111 R-5).
Applicants’ have traversed the above enablement rejection with the following arguments: (see pages 10-11 of Applicants’ REMARKS dated 05/29/2026).
Applicants’ argue: “…As amended, Claim 1 recites, "A microorganism engineered to express one or more enzymes which enhances the microorganism's ability to produce C2-4 alkene from C2-4 alkanol, wherein the microorganism is selected from Saccharomyces cerevisiae, the Nitrospiraceae family, and the Nitrobacteraceae family, and wherein the one or more enzymes are from the S- Adenosyl-L-methionine (SAM) pathway, selected from the group consisting of methylthio- alkane reductase, MarBHDK, and Cys, Met /SAM synthase." Claim 1 is amended to clearly define the claimed genus of both SAM pathway enzyme and microorganism. Claim 1 is limited to Saccharomyces cerevisiae and microorganisms from the Nitrospiraceae family and the Nitrobacteraceae family. The specification is enabling for these microorganisms as evidenced by Examples 1 and 2 for Saccharomyces cerevisiae (see paragraphs 0069 and 0070) and by Example 3 for the Nitrospiraceae family and the Nitrobacteraceae family (see paragraph 0077). Furthermore, the specification is enabling for the claimed SAM pathway enzymes as evidenced in Example 1 (see paragraph 0069). As applicant has provided evidence that the claimed methods work, for the rejection to be valid, the Office Action must provide some evidence to refute Applicant's claims.”
Reply: Applicants' arguments have been considered but are found to be non-persuasive for the following reasons. Applicants’ arguments filed on 05/29/2026 for the traversal of enablement rejection is on similar lines to the arguments presented for traversing the written-description, said arguments have been fully considered but they are not persuasive. Examiner continues to maintain the rejection for reasons stated on record, supporting evidence and arguments presented above in maintaining the written-description rejection also applies to enablement rejection.
For the above cited reasons, examiner is maintaining the written-description and enablement rejection for claims 1-3, 6-8, 10-12 and 33-40.
New-Claim Rejections: 35 USC § 103
Necessitated by claim amendments
The following is a quotation of 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102 of this title, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter pertains. Patentability shall not be negatived by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims under 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of 35 U.S.C. 103(c) and potential 35 U.S.C. 102(e), (f) or (g) prior art under 35 U.S.C. 103(a).
The factual inquiries set forth in Graham v. John Deere Co., 383 U.S. 1, 148 USPQ 459 (1966), that are applied for establishing a background for determining obviousness under 35 U.S.C. 103(a) 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.
Claims 1-3, 6-8, 10-12 and 33-40 are rejected under 35 U.S.C. 103(a) as being unpatentable over North et al., (US 2024/0060037 A1; priority 03/25/2021) and further in view of Larsson et al., (IET Proc.: Syst. Biol. 2011, Vol. 5: 245-251), Berry et al., (WO 2009/111513 A1), Voight et al., (US 9,040,266 B2) and Wood et al., (US 2020/0337314 A1).
Claims 1-3, 5-9, 12, 33-34, 36-37 and 39-40 as interpreted are directed to a genera of host cells/genera of cellular context selected from Saccharomyces cerevisiae, Nitrospiraceae family and Nitrobacteraceae family (fermenting organisms producing C2-4 alkene from C2-4 alkanol; as in claims 1-3, 6-8, 10-12 and 33-40); comprising a cellular machinery able to produce any C2-4 alkene from any C2-4 alkanol (genera of products and substrates; as in claims 1-3, 6-8, 10-12 and 33-37) and comprising any undefined genetic modification i.e., wherein the engineered host cell comprises S-Adenosyl-L-methionine (SAM) pathway enzymes, selected from the group consisting of any methylthio-alkane reductase, any MarBHDK, and any Cys, Met/SAM synthase including variants, mutants and homologs of undefined and unlimited structures and any non-native enzyme of undefined and unlimited structures catalysing the conversion of C2-4 alkanol (as in claims 1-3, 6-8, 10-12 and 33-40; also see claims objections for claims interpretation).
Regarding claims 1-3, 7-9, 12, 33-34, 36 and 39-40, North et al., (US 2024/0060037 A1; priority 03/25/2021) disclose non-naturally occurring microbial organisms capable of producing ethylene, ethane, and/or methane, as well was methods for producing ethylene, ethane, and/or methane using the same; said non-naturally occurring microbial organism is genetically engineered to express Methylthio-alkane reductase/MarBHDK (Abstract; Fig. 1A, reproduced below; ¶ [0075]; Claims; and entire document); said non-naturally occurring microbial organism is Rhodobacter capsulatus, Rp, Rhodopseudomonas palustris; Ru, Rhodospirillum rubrum, R. rubrum (¶ [0018], [0030-0033], [0038], [0227-0232]); and carbon sources including ethanol the one or more carbon sources may be selected from one or more in combination of: carbon dioxide and carbon monoxide, mono and disaccharide sugars, organic acids (for example, malate, succinate, pyruvate, and fumarate), volatile fatty acids (for example, formate, acetate, propionate, and butyrate), alcohols (for example, ethanol and glycerol), (¶ [0152]). Certain relevant sections from North et al., (US 2024/0060037 A1; priority 03/25/2021) is reproduced below:
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The disclosure of North et al., (US 2024/0060037 A1; priority 03/25/2021) as applied to claims 1-3, 7-9, 12, 33-34, 36 and 39-40 is described above. However, North et al., are silent regarding wherein the microorganism is selected from Saccharomyces cerevisiae, the Nitrospiraceae family, and the Nitrobacteraceae family (as in claim 1); wherein the microorganism comprises a dehydratase enzyme (as in claim 6); wherein the microorganism is an engineered version of a fungal strain (as in claims 10-11); wherein the composition comprises the engineered microorganism in an amount of at least about 1 x 105 CFU/g (as in claim 35); and wherein the composition comprises the engineered microorganism as part of a consortium (as in claim 38).
Regarding claims 1 and 10-11, the following reference, Larsson et al., (IET Proc.: Syst. Biol. 2011, Vol. 5: 245-251), provide teaching, suggestion and motivation for engineering Saccharomyces cerevisiae comprising SAM pathway enzymes for the production of ethylene (see Abstract; col. 2, page 245 second ¶; Fig. 1, page 246; Table 1, page 248; Table 2, page 249; and entire document).
Regarding claims 1, 6 and 10-11, the following reference, Berry et al., (WO 2009/111513 A1), provide teaching, suggestion and motivation for engineering Saccharomyces cerevisiae, the Nitrospiraceae family, and the Nitrobacteraceae family comprising ethylene production pathway enzymes including a dehydratase (see Abstract; and entire document); ethylene and alkenes (¶ [0006], [0011], [0044], [0050], [000188-00192]); carbon chains C2, C4 (¶ [0017]); use of dehydratase enzyme(s) (¶ [0048], [00188-00192]; host cells Nitrospiraceae family, and the Nitrobacteraceae family (¶ [00131]; and host cells Saccharomyces cerevisiae (¶ [00136]).
Regarding claims 1, 10-11, 35 and 38, the following reference, Voight et al., (US 9,040,266 B2) discloses a recombinant organism, such as a yeast/Saccharomyces cerevisiae, expressing a heterologous S-adenosylmethionine (SAM)-dependent pathway enzyme and a carbon source in a cultivation medium under conditions to increase flux through a S-adenosyl-methionine (SAM) biosynthetic pathway (Abstract; Summary of invention, col. 1, lines 55-67 to col. 7, lines 1-6; Claims; and entire document) and suggest said genetically engineered yeast/Saccharomyces cerevisiae for the production of ethylene (col. 18, lines 29-45); cultivation/fermentation medium/culturing conditions and co-culturing/consortium of microorganisms comprising yeast and other genetically modified microorganisms (col. 22, lines 10-67 to col. 28, lines 1-7).
Regarding claims 35 and 38, the following reference Wood et al., (US 2020/0337314 A1) teaches microbial based compositions including yeast/Saccharomyces cerevisiae in a consortium with other microorganisms; cocultured in consortium in culture medium and wherein microorganisms of interest are in an amount of at least about 1 x 105 CFU/g depending on the experimental need (see Abstract; ¶ [0003-0006], [0010], CFU/g [0020-0023]; and entire document).
As such, disclosure of strategy and methods for “recombinant organisms, such as Saccharomyces cerevisiae, the Nitrospiraceae family, and the Nitrobacteraceae family expressing a heterologous S-adenosylmethionine (SAM)-dependent pathway enzymes and ethylene biosynthetic production pathway genes including dehydratase and a carbon source in a cultivation medium under conditions to increase flux through a S-adenosyl-methionine (SAM) biosynthetic pathway and suggest said genetically engineered Saccharomyces cerevisiae, the Nitrospiraceae family, and the Nitrobacteraceae family for the production of ethylene”; and “compositions including yeast/Saccharomyces cerevisiae in a consortium with other microorganisms”; as in claims 1, 6, 10-11, 35 and 38, such as that of references of Larsson et al., Berry et al., Voight et al., and Wood et al., teaching the advantages of said modifications, clearly suggests to a skilled artisan to modify the teachings of North et al., and incorporate the structural and functional elements of Larsson et al., Berry et al., Voight et al., and Wood et al., in the claimed engineered host cell/choice of cellular context and method of use for the production of ethylene from ethanol as claimed in the instant invention. One of ordinary skill in the art would have a reasonable expectation of success, since engineered host cell/choice of cellular context, method of use for the production of ethylene are well known in the art.
Therefore, claims 1-3, 6-8, 10-12 and 33-40 are rejected under 35 U.S.C. 103(a) as being unpatentable over North et al., (US 2024/0060037 A1; priority 03/25/2021) and further in view of Larsson et al., (IET Proc.: Syst. Biol. 2011, Vol. 5: 245-251), Berry et al., (WO 2009/111513 A1), Voight et al., (US 9,040,266 B2) and Wood et al., (US 2020/0337314 A1).
Applicants’ have traversed the above 35 U.S.C. 103(a) rejection following claim amendments and said arguments are relevant to the new rejection (see pages 12-13 of Applicants’ REMARKS dated 05/29/2026).
Applicants’ argue: “…Neither Voight, Wood, nor Begmatov teach or even suggest the expression of methylthio- alkane reductase, MarBHDK, or Cys, Met /SAM synthase in Saccharomyces cerevisiae or microorganisms of the Nitrospiraceae family or the Nitrobacteraceae family for the production of a C2-4 alkene from a C2-4 alkanol. As neither, Wood not Begmatov rescue the deficiencies of North and Voight, none of the cited prior art alone or in combination teaches all the features of the presently amended claims. For this reason alone, the claims are not obvious. Applicant believes this rejection to be overcome and respectfully requests its withdrawal.”
Reply: Applicants’ arguments have been fully considered but are not deemed persuasive for the following reasons. Contrary to applicants’ arguments and assertions, examiner has provided new references Larsson et al., (IET Proc.: Syst. Biol. 2011, Vol. 5: 245-251) and Berry et al., (WO 2009/111513 A1), and the cited new references do indeed teach and suggest the structural and functional elements of the instant invention and motivation for the modification of primary reference North et al., (US 2024/0060037 A1; priority 03/25/2021) (for details see the rejection above).
Therefore, examiner continues to take the position that each and every element of the instant invention is taught in the combination of cited references and that the combined teachings in the cited prior art provides a reasonable expectation of success and predictability for the claimed method herein and the claimed benefits are very much expected and predictable.
The Supreme Court has acknowledged: When a work is available in one field of endeavor, design incentives and other market forces can prompt variations of it, either in the same field or a different one. If a person of ordinary skill can implement a predictable variation...103 likely bars its patentability...if a technique has been used to improve one device, and a person of ordinary skill in the art would recognize that it would improve similar devices in the same way, using the technique is obvious unless its actual application is beyond that person's skill. A court must ask whether the improvement is more than the predictable use of prior-art elements according to their established functions ...... the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results (see KSR International Co. v. Teleflex Inc., 82 USPQ2d 1385 U.S. 2007) (emphasis added).
Examiner continues to hold the position that the cited references render claims 1-3, 6-8, 10-12 and 33-40 prima facie obvious to one of ordinary skill in the art when one applies the Teaching, Suggestion and Motivation (TSM) test under the rationale for arriving at a conclusion of obviousness as suggested by the KSR ruling. The rationale applied for this rejection is as follows:
(A) Combining prior art elements according to known methods to yield predictable results;
(B) Simple substitution of one known element for another to obtain predictable results;
(C) Use of known technique to improve similar devices (methods, or products) in the same way;
(D) Applying a known technique to a known device (method, or product) ready for improvement to yield predictable results;
(E) “Obvious to try”–choosing from a finite number of identified, predictable solutions, with a reasonable expectation of success;
(F) Known work in one field of endeavor may prompt variations of it for use in either the same field or a different one based on design incentives or other market forces if the variations are predictable to one of ordinary skill in the art;
(G) Some teaching, suggestion, or motivation in the prior art that would have led one of ordinary skill to modify the prior art reference or to combine prior art reference teachings to arrive at the claimed invention.
The combined teachings in the cited prior art provides a reasonable expectation of success and predictability for the claimed invention. In view of the foregoing, when all of the evidence is considered, the totality of the rebuttal evidence of nonobviousness fails to outweigh the evidence of obviousness.
Summary of Pending Issues
The following is a summary of issues pending in the instant application.
Claims 1-3, 6-8, 10-12 and 33-40 are rejected under 35 U.S.C. 112(a) for written-description and enablement.
Claims 1-3, 6-8, 10-12 and 33-40 are rejected under 35 U.S.C. 103(a) as being unpatentable over North et al., (US 2024/0060037 A1; priority 03/25/2021) and further in view of Larsson et al., (IET Proc.: Syst. Biol. 2011, Vol. 5: 245-251), Berry et al., (WO 2009/111513 A1), Voight et al., (US 9,040,266 B2) and Wood et al., (US 2020/0337314 A1).
Claims 13-32 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.
Conclusion
None of the claims are allowable. Claims 1-3, 6-8, 10-12 and 33-40 are objected/rejected for the reasons identified in the Rejections and Summary sections of this Office Action. Applicants’ must respond to the rejections in each of the sections in this Office Action to be fully responsive for prosecution.
THIS ACTION IS MADE FINAL. 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 extension fee 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.
Regarding filing an After Final amendment, Applicants are directed to MPEP 714.13, which states:
II. ENTRY NOT A MATTER OF RIGHT
It should be kept in mind that applicant cannot, as a matter of right, amend any finally rejected claims, add new claims after a final rejection (see 37 CFR 1.116) or reinstate previously canceled claims. Except where an amendment merely cancels claims, adopts examiner suggestions, removes issues for appeal, or in some other way requires ONLY A CURSORY REVIEW by the examiner (e.g., typographical errors), compliance with the requirement of a showing under 37 CFR 1.116(b)(3) is expected in all amendments after final rejection. An affidavit or other evidence filed after a final rejection, but before or on the same date of filing an appeal, may be entered upon a showing of good and sufficient reasons why the affidavit or other evidence is necessary and was not earlier presented in compliance with 37 CFR 1.116(e). See 37 CFR 41.33 and MPEP § 1206 for information on affidavit or other evidence filed after appeal. (Examiner's emphasis) If more than a cursory review is required, Applicants are referred to CFR §1.114.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GANAPATHIRAMA RAGHU whose telephone number is (571)272-4533. The examiner can normally be reached on M-F 8:30am-5pm EST.
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/GANAPATHIRAMA RAGHU/ Primary Examiner, Art Unit 1652
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