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 election of Group I, encompassing claims 1-10 in part, SEQ ID NOs: 1, 3, 6 and 22 (claim 7) and as species GTP3’-8 cyclase (claim 6), GPD1 (claim 9), glycerol dehydrogenase (claim 10) and ethanol (claim 17) without traverse following claim amendments and addition of a new claim 23 in the reply filed on 09/16/2025 is acknowledged. Thus, amended claims 1-19 and 23 are pending in this application; elected Group I, encompassing claims 1-10 and 23 in part, SEQ ID NOs: 1, 3, 6 and 22 (claim 7) and as species GTP3’-8 cyclase (claim 6), GPD1 (claim 9), glycerol dehydrogenase (claim 10) and ethanol (claim 17) is now under consideration for examination; and claims 11-19 are withdrawn from further consideration pursuant to 37 CFR 1.142(b), as being drawn to a nonelected inventions, there being no allowable generic or linking claim.
Priority
Applicants’ claim for the benefit of priority under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, or 365(c) is acknowledged. This application is a 371 of PCT/EP2021/077334 filed on 10/05/2021, which claims the benefit of priority under 35 U.S.C. 119(e) to the US Provisional application: 63/087,642 filed on 10/05/2020.
Information disclosure statement
The information disclosure statements (IDS) submitted on 04/03/2023 are in compliance with the provisions of 37 CFR 1.97. Accordingly, the IDS statements are considered and initialed by the examiner.
Miscellaneous
A cursory review of the sequence search shows many applications filed by the current assignee of the instant application (Danisco US) which disclose the polypeptides of SEQ ID NOs: 1, 3 and 6. Furthermore, said SEQ ID NOs: 1, 3 and 6 correspond to different SEQ ID NOs designation in different applications. The examiner has made an earnest attempt at identifying double patenting issues in some of these applications as shown above. However, in view of the large number of applications already filed/matured into patents and the fact that new applications are being filed, the examiner hereby requests applicants’ collaboration in pointing out to the examiner those applications which could raise double patenting issues that the examiner has not been able to identify; specifically sequences with different SEQ ID NOs and having 100% sequence identity to SEQ ID NOs: 1, 3 and 6 of the instant application. Examiner would like to reiterate to applicants’, that it is their duty to disclose to the examiner any or all applications and allowed patents that either claims the same subject matter or related subject matter and those that are material to the prosecution of this instant application, such that double patenting can be avoided. Examiner urges the applicants’ to provide a list of their conflicting/related applications, identical to that claimed herein and a list of claims filed in other applications and take steps at their end to avoid double patenting.
Objections-Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. The specification contains hyperlinks to various site domains, for example, paragraphs [047], [054], [093-094], [114], Table 5, and [146] of the instant application. Applicants’ are required to thoroughly scrutinize the specification and delete all embedded hyperlink and/or other form of browser-executable code. See MPEP § 608.01. Appropriate correction is required.
Claims Objections
I. Claim 1 and claims 2-10 and 23 depending therefrom are objected: Recitation of “and/or” in claims 1, 3, 5, 6-7 and 10 makes the claim indefinite, as it is not clear what limitations must be present. Correction and clarification is required. Examiner suggests amending the claim to recite “…or …”.
II. Claim 7 is objected: claim 7 recites non-elected SEQ ID NOs:.. .
III. Claim 9 is objected and indefinite in the recitation of “GPD1, GPD2, GPP1 and GPP2”, for the following reasons. As taught in the specification and the prior art, the terms of “GPD1, GPD2, GPP1 and GPP2” are Saccharomyces cerevisiae gene(s) name which appear to encode glycerol phosphate dehydrogenase and glycerol phosphate phosphatase associated with glycerol metabolism. However, as written, the terms appear to be generically used and not limited to a specific organism Saccharomyces cerevisiae. While the gene nomenclature used may be appropriate for Saccharomyces cerevisiae gene, the use of this nomenclature for genes encoding proteins of identical function in other organisms or yeast may not be accurate. As known in the art, genes encoding proteins of identical function in two different organisms may use different designations. Furthermore, examiner suggests expanding the abbreviations to recite the full form of what the abbreviation stands for at least in the first recitation. Appropriate correction is required. For examination purposes “GPD1, GPD2, GPP1 and GPP2” is interpreted as glycerol phosphate dehydrogenase and glycerol phosphate phosphatase associated with glycerol metabolism.
Claim Rejections: 35 USC § 112(b)
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.
I. Claim 1 and claims 2-10 and 23 depending therefrom 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 pre-AIA the applicant regards as the invention; recitation of “and/or” in claims 1, 3, 5, 6-7 and 10 makes the claims indefinite, as it is not clear what limitations must be present. The metes and bounds of claims 1-10 and 23 are not clear and thus, it would not be possible to one of ordinary skill in the art to define the metes and bounds of the desired patent protection. The rejection may be overcome by amending the claims to recite “… or …”. Correction and clarification is required. Examiner suggests amending the claim to recite “…or …”.
II. Claim 9 is rejected under of 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 applicant regards as the invention.
Claim 9 is 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 applicant regards as the invention. Claim 9 recites the phrase ““GPD1, GPD2, GPP1 and GPP2” and is indefinite for the following reasons. As written, the term appears to be generic to yeast and not limited to a particular species or specific strain of yeast. While the gene nomenclature used may be appropriate for Saccharomyces cerevisiae, the use of this nomenclature for genes encoding proteins of identical function in other yeasts may not be accurate. As known in the art, genes encoding proteins of identical function in two different organisms may use different designations. For example, the ARO4 gene of Candida albicans encodes a DAHP synthase whereas the E. coli counterpart is the AroF gene. See Sousa et al. (Microbiology, 2002, Vol. 148: 1291-1303; reference not enclosed). As such, the use of gene terminology which is applicable to some microorganism and not to others is confusing since the claims use this gene nomenclature with respect to any yeast. For examination purposes, the terms is interpreted as “GPD1, GPD2, GPP1 and GPP2” is interpreted as glycerol phosphate dehydrogenase and glycerol phosphate phosphatase associated with glycerol metabolism. If applicant wishes to retain the gene nomenclature used, it is suggested that the protein encoded by said gene or the structure be placed in parentheses next to the recited gene. Correction is required.
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 1-10 and 23 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 1-10 and 23 recite a genera of polynucleotides and encoded polypeptides of undefined and unlimited structures including variants, mutants and homologs in the claimed recombinant Saccharomyces yeast cell i.e., any nucleic acid sequence encoding an enzyme having NADH-dependent nitrate reductase activity and/or any acid sequence encoding an enzyme having NADH-dependent nitrite reductase activity; said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding a flavin adenine dinucleotide (FAD), any heme prosthetic groups, and/or any molybdenum cofactor (MoCo); further comprising: any nucleic acid sequence encoding any GTP 3',8-cyclase …(no structure is recited, as in claims 1-6 and 23); said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding any modified/variants polypeptides having no defined activity (no corresponding activity is recited); and said modified/variant encoded polypeptide having a sequence identity of at least 70% with SEQ ID NOs: 1, 3, 6 and 22 (as in claim 7); said recombinant Saccharomyces yeast cell is free of glycerol phosphate phosphatase activity or have reduced glycerol phosphate phosphatase activity compared to corresponding wild-type cells, wherein the Saccharomyces yeast cells comprise any undefined genomic mutation in at least one gene selected from the group consisting of GPD1… (no structure is recited; as in claims 8-10); and said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding further comprising any nucleic acid sequence encoding any glycerol dehydrogenase of undefined and unlimited structures (as in claim 10).
The structural elements recited in claims 1-10 and 23 are not sufficient structure to form an “NADH-dependent nitrate reductase activity; NADH-dependent nitrite reductase activity; flavin adenine dinucleotide (FAD), any heme prosthetic groups, molybdenum cofactor (MoCo) activity; … glycerol dehydrogenase activity” 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 i.e., “NADH-dependent nitrate reductase activity; NADH-dependent nitrite reductase activity; flavin adenine dinucleotide (FAD), any heme prosthetic groups, molybdenum cofactor (MoCo) activity; … glycerol dehydrogenase activity” and possibly fall within the claims and those amino acid sequences that do not have “NADH-dependent nitrate reductase activity; NADH-dependent nitrite reductase activity; flavin adenine dinucleotide (FAD), any heme prosthetic groups, molybdenum cofactor (MoCo) activity; … glycerol dehydrogenase activity”. As such, claims 1-10 and 23 recite a genera of biomolecules described only by a functional characteristics (i.e., being “NADH-dependent nitrate reductase activity; NADH-dependent nitrite reductase activity; flavin adenine dinucleotide (FAD), any heme prosthetic groups, molybdenum cofactor (MoCo) activity; … glycerol dehydrogenase 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 “NADH-dependent nitrate reductase activity; NADH-dependent nitrite reductase activity; flavin adenine dinucleotide (FAD), any heme prosthetic groups, molybdenum cofactor (MoCo) activity; … glycerol dehydrogenase activity” activity, claims 1-10 and 23 have no defined outer bounds for the scope of “NADH-dependent nitrate reductase activity; NADH-dependent nitrite reductase activity; flavin adenine dinucleotide (FAD), any heme prosthetic groups, molybdenum cofactor (MoCo) activity; … glycerol dehydrogenase 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 structures having the amino acid sequences of SEQ ID NOs: 1, 3, 6, 22, encoding polynucleotides and comprised in a specific cellular context Saccharomyces cerevisiae yeast cell as disclosed in the prior art WO2011010923, method of making and method of use said Saccharomyces cerevisiae yeast cell for the production of ethanol (see ¶ [119], page 51 of specification) has been provided by the applicants’, which would indicate that they had possession of the claimed genera of polynucleotides and encoded polypeptides of undefined and unlimited structures including variants, mutants and homologs in the claimed recombinant Saccharomyces yeast cell i.e., any nucleic acid sequence encoding an enzyme having NADH-dependent nitrate reductase activity and/or any acid sequence encoding an enzyme having NADH-dependent nitrite reductase activity; said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding a flavin adenine dinucleotide (FAD), any heme prosthetic groups, and/or any molybdenum cofactor (MoCo); further comprising: any nucleic acid sequence encoding any GTP 3',8-cyclase …(no structure is recited, as in claims 1-6 and 23); said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding any modified/variants polypeptides having no defined activity (no corresponding activity is recited); and said modified/variant encoded polypeptide having a sequence identity of at least 70% with SEQ ID NOs: 1, 3, 6 and 22 (as in claim 7); said recombinant Saccharomyces yeast cell is free of glycerol phosphate phosphatase activity or have reduced glycerol phosphate phosphatase activity compared to corresponding wild-type cells, wherein the Saccharomyces yeast cells comprise any undefined genomic mutation in at least one gene selected from the group consisting of GPD1… (no structure is recited; as in claims 8-10); and said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding further comprising any nucleic acid sequence encoding any glycerol dehydrogenase of undefined and unlimited structures (as in claim 10).
The genus of polynucleotides and encoded polypeptides required in the claimed invention is an extremely large structurally and functionally variable genus. 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 of SEQ ID NOs: 1, 3, 6 and 22 and the encoding polynucleotides, 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 structures having the amino acid sequences of SEQ ID NOs: 1, 3, 6, 22, encoding polynucleotides and comprised in a specific cellular context Saccharomyces cerevisiae yeast cell as disclosed in the prior art WO2011010923, method of making and method of use said Saccharomyces cerevisiae yeast cell for the production of ethanol (see ¶ [119], page 51 of specification), has been provided by the applicants’, which would indicate that they had possession of the claimed genera of polynucleotides and encoded polypeptides of undefined and unlimited structures including variants, mutants and homologs in the claimed recombinant Saccharomyces yeast cell i.e., any nucleic acid sequence encoding an enzyme having NADH-dependent nitrate reductase activity and/or any acid sequence encoding an enzyme having NADH-dependent nitrite reductase activity; said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding a flavin adenine dinucleotide (FAD), any heme prosthetic groups, and/or any molybdenum cofactor (MoCo); further comprising: any nucleic acid sequence encoding any GTP 3',8-cyclase …(no structure is recited, as in claims 1-6 and 23); said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding any modified/variants polypeptides having no defined activity (no corresponding activity is recited); and said modified/variant encoded polypeptide having a sequence identity of at least 70% with SEQ ID NOs: 1, 3, 6 and 22 (as in claim 7); said recombinant Saccharomyces yeast cell is free of glycerol phosphate phosphatase activity or have reduced glycerol phosphate phosphatase activity compared to corresponding wild-type cells, wherein the Saccharomyces yeast cells comprise any undefined genomic mutation in at least one gene selected from the group consisting of GPD1… (no structure is recited; as in claims 8-10); and said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding further comprising any nucleic acid sequence encoding any glycerol dehydrogenase of undefined and unlimited structures (as in claim 10). As the claimed genera of polypeptides and encoding polynucleotides having widely variable structures and associated function, 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.
Enablement
Claims 1-10 and 23 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 structures having the amino acid sequences of SEQ ID NOs: 1, 3, 6, 22, encoding polynucleotides and comprised in a specific cellular context Saccharomyces cerevisiae yeast cell as disclosed in the prior art WO2011010923, method of making and method of use said Saccharomyces cerevisiae yeast cell for the production of ethanol (see ¶ [119], page 51 of specification). However, specification does not reasonably provide enablement for a genera of polynucleotides and encoded polypeptides of undefined and unlimited structures including variants, mutants and homologs in the claimed recombinant Saccharomyces yeast cell i.e., any nucleic acid sequence encoding an enzyme having NADH-dependent nitrate reductase activity and/or any acid sequence encoding an enzyme having NADH-dependent nitrite reductase activity; said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding a flavin adenine dinucleotide (FAD), any heme prosthetic groups, and/or any molybdenum cofactor (MoCo); further comprising: any nucleic acid sequence encoding any GTP 3',8-cyclase …(no structure is recited, as in claims 1-6 and 23); said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding any modified/variants polypeptides having no defined activity (no corresponding activity is recited); and said modified/variant encoded polypeptide having a sequence identity of at least 70% with SEQ ID NOs: 1, 3, 6 and 22 (as in claim 7); said recombinant Saccharomyces yeast cell is free of glycerol phosphate phosphatase activity or have reduced glycerol phosphate phosphatase activity compared to corresponding wild-type cells, wherein the Saccharomyces yeast cells comprise any undefined genomic mutation in at least one gene selected from the group consisting of GPD1… (no structure is recited; as in claims 8-10); and said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding further comprising any nucleic acid sequence encoding any glycerol dehydrogenase of undefined and unlimited structures (as in claim 10). 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 1-10 and 23 are so broad as to encompass: a genera of polynucleotides and encoded polypeptides of undefined and unlimited structures including variants, mutants and homologs in the claimed recombinant Saccharomyces yeast cell i.e., any nucleic acid sequence encoding an enzyme having NADH-dependent nitrate reductase activity and/or any acid sequence encoding an enzyme having NADH-dependent nitrite reductase activity; said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding a flavin adenine dinucleotide (FAD), any heme prosthetic groups, and/or any molybdenum cofactor (MoCo); further comprising: any nucleic acid sequence encoding any GTP 3',8-cyclase …(no structure is recited, as in claims 1-6 and 23); said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding any modified/variants polypeptides having no defined activity (no corresponding activity is recited); and said modified/variant encoded polypeptide having a sequence identity of at least 70% with SEQ ID NOs: 1, 3, 6 and 22 (as in claim 7); said recombinant Saccharomyces yeast cell is free of glycerol phosphate phosphatase activity or have reduced glycerol phosphate phosphatase activity compared to corresponding wild-type cells, wherein the Saccharomyces yeast cells comprise any undefined genomic mutation in at least one gene selected from the group consisting of GPD1… (no structure is recited; as in claims 8-10); and said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding further comprising any nucleic acid sequence encoding any glycerol dehydrogenase of undefined and unlimited structures (as in claim 10). 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. 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 characterization of specific structures having the amino acid sequences of SEQ ID NOs: 1, 3, 6, 22, encoding polynucleotides and comprised in a specific cellular context Saccharomyces cerevisiae yeast cell as disclosed in the prior art WO2011010923, method of making and method of use said Saccharomyces cerevisiae yeast cell for the production of ethanol (see ¶ [119], page 51 of specification). It would require undue experimentation of the skilled artisan to make and use the claimed polypeptides i.e., a genera of polynucleotides and encoded polypeptides of undefined and unlimited structures including variants, mutants and homologs in the claimed recombinant Saccharomyces yeast cell i.e., any nucleic acid sequence encoding an enzyme having NADH-dependent nitrate reductase activity and/or any acid sequence encoding an enzyme having NADH-dependent nitrite reductase activity; said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding a flavin adenine dinucleotide (FAD), any heme prosthetic groups, and/or any molybdenum cofactor (MoCo); further comprising: any nucleic acid sequence encoding any GTP 3',8-cyclase …(no structure is recited, as in claims 1-6 and 23); said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding any modified/variants polypeptides having no defined activity (no corresponding activity is recited); and said modified/variant encoded polypeptide having a sequence identity of at least 70% with SEQ ID NOs: 1, 3, 6 and 22 (as in claim 7); said recombinant Saccharomyces yeast cell is free of glycerol phosphate phosphatase activity or have reduced glycerol phosphate phosphatase activity compared to corresponding wild-type cells, wherein the Saccharomyces yeast cells comprise any undefined genomic mutation in at least one gene selected from the group consisting of GPD1… (no structure is recited; as in claims 8-10); and said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding further comprising any nucleic acid sequence encoding any glycerol dehydrogenase of undefined and unlimited structures (as in claim 10). 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 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 polynucleotides and encoded polypeptides of undefined and unlimited structures including variants, mutants and homologs in the claimed recombinant Saccharomyces yeast cell i.e., any nucleic acid sequence encoding an enzyme having NADH-dependent nitrate reductase activity and/or any acid sequence encoding an enzyme having NADH-dependent nitrite reductase activity; said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding a flavin adenine dinucleotide (FAD), any heme prosthetic groups, and/or any molybdenum cofactor (MoCo); further comprising: any nucleic acid sequence encoding any GTP 3',8-cyclase …(no structure is recited, as in claims 1-6 and 23); said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding any modified/variants polypeptides having no defined activity (no corresponding activity is recited); and said modified/variant encoded polypeptide having a sequence identity of at least 70% with SEQ ID NOs: 1, 3, 6 and 22 (as in claim 7); said recombinant Saccharomyces yeast cell is free of glycerol phosphate phosphatase activity or have reduced glycerol phosphate phosphatase activity compared to corresponding wild-type cells, wherein the Saccharomyces yeast cells comprise any undefined genomic mutation in at least one gene selected from the group consisting of GPD1… (no structure is recited; as in claims 8-10); and said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding further comprising any nucleic acid sequence encoding any glycerol dehydrogenase of undefined and unlimited structures (as in claim 10), because the specification does not establish: (A) a rational and predictable scheme for modifying specific amino acid residues in any “NADH-dependent nitrate reductase; NADH-dependent nitrite reductase; flavin adenine dinucleotide (FAD), any heme prosthetic groups, molybdenum cofactor (MoCo); … glycerol dehydrogenase” having no specific structural elements and an expectation of obtaining the desired biological/biochemical function; (B) a rational and predictable scheme for modifying any amino acid residue with an expectation of obtaining the desired biological/biochemical function; (C) defined core regions/motifs involved in the desired catalytic activity of encoded polypeptide; (D) the tertiary structure of the molecule and folding patterns that are essential for the desired activity and tolerance to modifications; and (E) 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 structures having the amino acid sequences of SEQ ID NOs: 1, 3, 6, 22, encoding polynucleotides and comprised in a specific cellular context Saccharomyces cerevisiae yeast cell as disclosed in the prior art WO2011010923, method of making and method of use said Saccharomyces cerevisiae yeast cell for the production of ethanol (see ¶ [119], page 51 of specification), however, the scope of claims 1-10 and 23 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. While enablement is not precluded by the necessity for routine screening, if a large amount of screening is required, the specification must provide a reasonable amount of guidance with respect to the direction in which the experimentation should proceed (guided mutants). Such guidance has not been provided in the instant specification or in the prior art. The art also teaches the following regarding complexity of the structure/function relationship: The reference of Chica et al., (Curr. Opin. Biotechnol., 2005, Vol. 16: 378-384) teaches that the complexity of the structure/function relationship in enzymes has proven to be the factor limiting the general application of rational enzyme modification and design, where rational enzyme modification and design requires in-depth understanding of structure/function relationships. The reference of Sen et al., (Appl. Biochem. Biotechnol., 2007, Vol.143: 212-223), teaches in vitro recombination techniques such as DNA shuffling, staggered extension process (STEP), random chimera genesis on transient templates (RACHITT), iterative truncation for the creation of hybrid enzymes (ITCHY), recombined extension on truncated templates (RETT), and so on have been developed to mimic and accelerate nature's recombination strategy. However, such rational design and directed evolution techniques only provide guidance for searching and screening for the claimed polypeptide which is not guidance for making and/or using the claimed polypeptide. Additionally, knowledge is not extant in the art to assay all possible enzymatic activities, how to express all possible enzymes or how predictably assay for such activities. For example, the reference of Banerjee et al., (Bioenerg. Res. 2010, Vol. 3: 82-92), on page 84, right column, second paragraph, describe that “enzymes have critical properties besides specific activity and thermal tolerance that must be considered but which can be difficult to assay in vitro. For example, besides catalyzing a particular chemical reaction, enzymes must be efficiently translated and secreted, able to resist proteases, act cooperatively with other enzymes, and have low product and feedback inhibition. One can easily imagine that an “improved” enzyme, based on assay in isolation on a model substrate, might perform poorly in a real-world situation”.
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. 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 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).
Claim Rejections: 35 USC § 102 (AIA )
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
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 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.
Claims 1-7 and 23 are rejected under 35 U.S.C. 102(a)(1) and 35 U.S.C. 102(a)(2) as being anticipated by Daran et al., (WO 2020/209718 A1, filing date 04/09/2020 and foreign priority 04/09/2019, in IDS) when given the broadest reasonable interpretation.
Claims 1-7 and 23 as interpreted are directed to a genera of polynucleotides and encoded polypeptides of undefined and unlimited structures including variants, mutants and homologs in the claimed recombinant Saccharomyces yeast cell i.e., any nucleic acid sequence encoding an enzyme having NADH-dependent nitrate reductase activity and/or any acid sequence encoding an enzyme having NADH-dependent nitrite reductase activity; said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding a flavin adenine dinucleotide (FAD), any heme prosthetic groups, and/or any molybdenum cofactor (MoCo); further comprising: any nucleic acid sequence encoding any GTP 3',8-cyclase …(no structure is recited, as in claims 1-6 and 23); said recombinant Saccharomyces yeast cell further comprising any nucleic acid sequence encoding any modified/variants polypeptides having no defined activity (no corresponding activity is recited); and said modified/variant encoded polypeptide having a sequence identity of at least 70% with SEQ ID NOs: 1, 3, 6 and 22 (as in claim 7).
Daran et al., (WO 2020/209718 A1, filing date 04/09/2020 and foreign priority 04/09/2019, in IDS) disclose recombinant Saccharomyces yeast cell and a method of production of ethanol; wherein said Saccharomyces yeast cell is a Saccharomyces cerevisiae and comprising nitrate reductase, i.e., in a preferred embodiment, the Moco dependent nitrate assimilation pathway gene set comprises one or more of a gene encoding nitrate transporter, a gene encoding nitrate reductase (Abstract; page 14, lines 12-16; and entire document) and recombinant Saccharomyces yeast cell comprising a pathway, encoding polynucleotides and polypeptides leading to synthesis of GTP 3',8-cyclase, Cyclic pyranopterin monophosphate synthase, Molybdopterin synthase catalytic subunit, Molybdopterin synthase sulfur carrier subunit, Molybdopterin adenylyltransferase, Molybdopterin-synthase adenylyltransferase and/or a Molybdopterin molybdenumtransferase and comprising molybdenum co-factor (Moco), mono-oxo Moco co-factor (Moco-S), MPTcytosine dinucleotide co-factor (MCD) and/or MPT guanine dinucleotide co-factor (bis-MGD) and paves the way to the expression of Moco dependent enzymes, including for example a nitrogen transporter (page 9, lines 1-15); said reference nitrogen transporter protein having 96.2% sequence identity to SEQ ID NO: 6 of the instant invention (see provided sequence alignments); said reference recombinant Saccharomyces yeast cell is able to produce ethanol (Fig. 11 & 13). Applicants are also directed to the following sections in Daran et al., (WO 2020/209718 A1, filing date 04/09/2020 and foreign priority 04/09/2019, in IDS): Table 3; page 51, lines 25-36 to page 57, lines 1-20; page 60, lines 10-20; claims, pages 67-68.
Therefore, the reference of Daran et al., (WO 2020/209718 A1, filing date 04/09/2020 and foreign priority 04/09/2019, in IDS) is deemed to anticipate claims 1-7 and 23 as written and when given the broadest reasonable interpretation.
Claim Rejections: 35 USC § 103
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