DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
The response filed 6-30-2025 has been entered into the record.
Status of Claims
The preliminary amendment filed 11-21-2023 has been entered into the record. Claims 1-57 have been canceled and claims 58-77 are pending.
Sequence Requirements
This application contains sequence disclosures that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 C.F.R. § 1.821(a)(1) and (a)(2). However, this application fails to comply with the requirements of 37 C.F.R. § § 1.821-1.825 for the reason(s) set forth below.
The sequences in the drawings are not followed by a specific sequence identifier. Sequences presented in drawings/figures are required to comply with the sequence rules (see MPEP 2412.06. Substitute drawings are required.
Full compliance with the sequence rules is required in response to this office action.
Priority
Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Election/Restrictions
Applicant’s election without traverse of Group I in the reply filed on 6-30-2025 is acknowledged. Claims 58-71 are under examination. Claims 72-77 are withdrawn from consideration.
Information Disclosure Statement
The information disclosure statements have been considered. Initialed copies are enclosed.
Specification
The disclosure is objected to because of the following informalities: The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01. Applicant’s attention is drawn to at least pages 11, 55, 56, 71 and 80. Applicant should review the specification for any other browser-executable code and amend or delete as appropriate.
Appropriate correction is required.
Claim Objections
Claims 58-71 are objected to because of the following informalities: the claims use the acronym ILV2, ILV3, ILV5 and ILV6 without first defining the specific item to which the acronym/abbreviation represents. Appropriate correction is required.
Claim Rejections - 35 USC § 112
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 58-71 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
The claims are drawn to yeast strains having a specifically claimed number of functional genes encoding various enzymes wherein the genes (ILV2, ILV3, ILV5, ILV6, BAT1 and BAT2) are encoded by various SEQ ID NOS or functional homologues sharing at least 80% sequence identity with any of a variety of sequences. Wherein the yeast strains have particular genotypic (claims 58-67) and phenotypic characteristics (claims 68-71). The claims are not limited to any specific yeast genus/species or variant and there are thousands of different yeast species.
The specification teaches four Saccharomyces pastorianus variant strains at pages 67-68 Table 11 which have specific genotypic characteristics:
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The specification teaches alterations of Saccharomyces pastorianus W-34/78 gene copy number to mirror the relevant genotype of low diacetyl strains, however the strain carries a plasmid and is therefore not “within” the yeast genome as recited in the claims. None of the “FGMO” strains meet this limitation as they also comprise plasmids which are not within the yeast genome.
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All the manipulations of the W-34/78 strain use genetic recombination techniques and had heterologous DNA present in the form of antibiotic resistance genes for selection of the recombinant strains. The genetically engineered strains did not meet the phenotypic characteristics of claims 68-71 (see table 19 and 20 pages 83-84) even though they had a functional gene copy number that fell within the scope of the claims. Thus, using genetic engineering techniques, it appears that the phenotypic characteristics of the ZAD1-3 were unable to be replicated. The specification provides for no additional recombinant strains that represent additional gene copy numbers to demonstrate that recombinant techniques could arrive at the invention in any yeast as claimed, or in S. pastorianus strains. The full scope of the claims e.g. no more than 15 function genes encoding iLV3 and/or ILV15, specific copy number of BAT1 and BAT2 has not been demonstrated to have been altered from the starting strain.
The specification teaches that the invention is a yeast strain with lower total diacetyl production for the use in lager/beer fermentation. At no point did the specification teach how the strains ZAD1-3 were obtained or recombinantly made. The specification is silent on how to make or obtain these strains that meet the phenotypic characteristics set forth in claims 68-71. The courts have held that "... whenever there is no disclosure of any specific starting material or of any of the conditions under which a process can be carried out undue experimentation is required; there is a failure to meet the enablement requirement that cannot be rectified by asserting that all the disclosure related to the process is within the skill of the art. It is the specification, not the knowledge of one skilled in the art, that must supply the novel aspects of the invention in order to constitute adequate enablement." Genetech Inc. v. Novo Nordisk A/S 42USPQ2d 1001. “A patent is not a hunting license. It is not a reward for search, but compensation for its successful conclusion.” (Genentech, Inc. v. Novo Nordisk, A/S, 108 F.3d 1361, 1365, 42 USPQ2d 1001, 1004 (Fed. Cir. 1997)).
The art teaches that the expression mechanism and recombinant process can produce vastly different results in the reduction of diacetyl in yeasts and final fermentation results. For example, Kusunoki et al (Yeast 29:435-442, 2012) teach that homo-integration of ILV5 provided for a reduced diacetyl level and shortening of the brewing time (see abstract). In contrast, hetero-insertion did not result in the reduction of diacetyl levels (see page 440, column 2, description and Figure 4). While the skill in the art of molecular genetics is high, it is clear that the method of genetic modification in yeast has an unpredictable effect on downstream diacetyl levels. The specific mechanism of integration/recombinant expression in the yeast has unpredictable effects on diacetyl levels during fermentation. Furthermore, the art indicates that there is significant variation in S. pastorianus strain behavior under the same practical incubation conditions see Muller-Auffermann et al (Brewing Science, 68:46-57, 2015), page 57, column 1, summary. Thus, the skilled artisan would have to randomly select (1) the starting strain any yeast or of S. pastorianus in particular (2) the starting genotype and phenotype of the selected strain (3) the probes/primers and vectors for expression or deletion of specific genes or functional homologues thereof (4) the genomic site for modification and (5) the methods to recombinantly produce or isolate by unknown, undescribed means to produce any yeast with the claimed characteristics. The specification does not teach how, where and what needs to be modified in the starting yeast genome to achieve the low diacetyl producing strains of the invention having the desired phenotypic characteristics and the art teaches that recombinant procedures have an unpredictable downstream effect on diacetyl levels. Consequently, in the absence of further specific and detailed guidance from Applicant, it would require undue experimentation to make and use the claimed strains having the characteristics claimed with low diacetyl production.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 58-71 are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claim(s) does/do not fall within at least one of the four categories of patent eligible subject matter because a judicial exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly more.
Instant claim 58 and dependent claims 59-71 are drawn to new strains of yeast having a particular genetic and phenotypic profile. The specification describes three new apparently naturally occurring Saccharomyces pastorianus yeast strains: ZDA1, ZDA2 and ZDA3 (see specification at page 56, lines 15-25). The strains are apparently naturally occurring variant strains of an existing Saccharomyces pastorianus and have no disclosed or described genetic manipulation to introduce heterologous DNA or any genetic engineering applied to obtain such. They are described as new hybrid yeast strains and Saccharomyces pastorianus is a naturally occurring hybrid yeast strain used in lager production. Saccharomyces pastorianus is generally accepted as a natural, insterspecific hybrid of S. cerevisiae and S. eubayanus (see van den Broek et al (Applied Environmental Microbiology 81(18):page 2, second paragraph). However, the identification of new hybrid yeast strains and the characterization of the strains by genotyping (specification Example 7, e.g. Table 11, at page 67-68) and phenotyping (specification page 60, Table 6) does not make naturally occurring variant hybrid strains not a judicial exception. A single recombinant strain derived from the Saccharomyces pastorianus ssp carlsbergensis strain W-34/78 was derived to match copy numbers of relevant genes in the genotype of ZDA1 and ZDA2 (see page 72, Example 10). The claims however are not limited to the recombinant hybrid strain(s).
The broadest reasonable interpretation is that the claimed strains of yeast and at least one embodiment encompassed within the broadest reasonable interpretation (BRI) of instant claims is directed to a statutory category, i.e., a product (Step 1: YES). The as-filed specification at teaches that VSA strains are variant yeast strains (see page 12, lines 20-24) but does not teach the method of isolation, screening or new hybridization of different species. Given the limitations of claim 62, it is readily apparent that the claims encompass naturally occurring variants and hybrid variant strains and therefore the invention encompasses strains isolated from a naturally occurring source, i.e., from naturally occurring hybrid strain Saccharomyces pastorianus. The characterization of the new strain variants by genotyping and phenotyping does not provide for something more. There is no evidence that the claimed yeast strain(s) are modified in any way and the strain(s) are markedly different from what exist in nature. Additionally, derivation procedures are described encompass naturally occurring mutagenesis that would provide for anything but screening naturally occurring Saccharomyces pastorianus strains for the requisite and claimed properties. Mere screening naturally occurring yeast strains for desirable properties as recited in the claims does not provide for something that is not naturally occurring. The Supreme Court has made it clear in Myriad that eligibility requires the creation of something not naturally occurring, which is markedly different from what exists in nature. Unlike the Chakrabarty bacterium, which was new “with markedly different characteristics from any found in nature” Diamond v. Chakrabarty, 447 U.S. 303 (1980) at 310, 100 S. Ct. 2204, 65 L. Ed. 2d 144, due to the multiple additional plasmids and resultant “capacity for degrading oil”, there is no indication that the instantly claimed strain(s) or derivatives are genetically manipulated or structurally modified in any marked or significant way such that the structural difference results in change of properties of the strain(s). The properties of the “derivatives” are inseparable from said naturally occurring strain(s) and therefore are a handiwork of nature. In Chakrabarty and Myriad, the marked difference inquiry was focused on the modified structural characteristics of the product, not how it was used or how it was made. Note that “….. patents cannot issue for the discovery of phenomena of nature”. Le Roy v. Tatham, 14 How. 156, 175 (1853). The qualities of the bacteria, like the heat of the sun, electricity, or the qualities of metals, are part of the storehouse of knowledge of all men. They are manifestations of laws of nature, free to all men and reserved exclusively to none.” See Funk Brothers Seed Co. v. Kalo Inoculant Co., 333 U.S. at 130, 1948. In Funk Brothers, the Court held that the composition was not patent eligible because the patent holder did not alter the bacteria in any way. In the instant case, yeasts having specific genotype and phenotypes claimed does not add significantly more to the natural products such that the judicial exception if is practically applied. Thus, each component of the instantly claimed product is a ‘product of nature’ exception, and the claims are directed to a judicial exception (Step 2A Prong One: YES). Judicial exceptions include all natural products including those derived from natural sources or patients such as naturally occurring microorganisms, proteins, peptides, glycoproteins, glycopeptides, carbohydrates, and other substances found in or derived therefrom, or from nature. Next, the claims as a whole are analyzed to determine whether any additional element, or combination of elements, is sufficient to ensure that the claims amount to significantly more than the exceptions. There is nothing that provides significantly more or that integrates the claimed naturally occurring yeast strains i.e., the judicial exceptions, into a practical application (Step 2A Prong Two: NO). No elements or claim limitations apply or use the exception(s) in any meaningful way and integrate the law of nature into a practical application. The claims when considered as a whole do not amount to significantly more than ‘products of nature’ (Step 2B: NO). Therefore, the claims are not directed to a patent eligible subject matter. The rationale for this determination is formed in view of the 2019 PEG, the 2015 Update of the 2014 Interim Guidance on Patent Subject Matter Eligibility (79 FR 4618) (hereafter Interim Eligibility Guidance) dated 16 December 2014, the Life Sciences Examples issued in May 2016, and in view of Myriad v Ambry, CAFC 2014-1361, -1366, 17 December 2014. The unpatentability of laws of nature was confirmed by the U.S. Supreme Court in Mayo Collaborative Services v. Prometheus Laboratories, Inc., No. 10-1150 (March 20, 2012). The unpatentability of natural products was confirmed by the U.S. Supreme Court in Association for Molecular Pathology v. Myriad Genetics, Inc., 569 U. S. (June13, 2013).
Claim Rejections - 35 USC § 103
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries 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 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.
Claim(s) 58-62 and 67-71 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al (CN 110846238A, Feb 28, 2020, see English translation of record. All references are to the English translation) in view of Wang et al (International Journal of Food Science and Technology 43:989-994, 2008).
Zhang et al teach Saccharomyces uvarum strains by partially knocking out the ILV2 gene that encodes alpha-acetolactate synthase, in combination with over expression of dihydroxyisovalerate dehydratase (ILV3) and/or hydroxyacid reductoisomerse (ILV5) (see page 7, paragraphs 48-53) and page 2. Paragraph 116 at page 16 discloses the low production of diacetyl and/or higher alcohols by the generated strains. The sequences of ILV2, ILV3 and ILV5 are identical to the corresponding genes of S. cerevisiae. The partial knockout of the ILV2 gene is characterized by deletion of 1, 2, or 3 alleles of ILV2 (paragraphs 128-134). Zhang et al teach that the invention is not limited to the particularly disclosed embodiments and technical means are well known methods to those skilled in the art. The phenotypically claimed characteristics such as incubation products/ratios under particularly defined culturing conditions are necessarily present in the S. uvarum strains of Zhang et al absent convincing factual evidence to the contrary. The embodiments are illustrative and not limiting scope of the invention as shown at page 2. Zhang et al differ by not teaching the specific number of functional genes or ratios thereof within its genome of the isoleucine-valent (ILV) pathway including ILV6 and BAT1/2 in its genome.
Wang et al teach construction of self-cloning brewing yeasts with low-diacetyl production. Wang et al teach that there are two kins of cloning techniques about gen manipulations in industrial yeasts on the basis of the gene origin: self-cloning and non-self cloning. When using non-self cloning technique heterologous DNA such as bacteria gene is introduced into the recombined yeast. When the yeast strain is genetically modified by the self cloning technique, the increased DAN fragments in the self transforming yeast come from the yeast itself. As no heterologous DAN is carried into the yeast after self-cloning modification, the improved strains will be more acceptable for the commercial application (see page 989, column 1, second paragraph).Wang et al teach self-cloning technique was applied in constructing a low diacetyl brewer’s yeast by disrupting the ILV2 gene and inserting a GSH1 gene.
It would have been prima facie obvious to one having ordinary skill in the art at the time the invention was filed to optimize the copy number and/or ratios of the ILV2, ILV3 and ILV5 genes in the genome of the yeast strains of Zhang et al by means of self-cloning genetic means as taught by Wang et al in order to provide for a reduced diacetyl production and maintain the desired fermentation characteristics for alcohol production for a strain that would be more acceptable for the commercial fermentation applications.
Claim(s) 58-62 and 67-71 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al (CN 110951633A, April 3, 2020, see English translation of record. All references are to the English translation) in view of Wang et al (International Journal of Food Science and Technology 43:989-994, 2008).
Zhang et al teach Saccharomyces uvarum strains by partially knocking out the ILV2 gene that encodes alpha-acetolactate synthase, in combination with over expression of dihydroxyisovalerate dehydratase (ILV3) and/or hydroxyacid reductoisomerse (ILV5) (see page 4, paragraphs 7-13; pages 7-8, paragraphs 48-61) and claims at page 2. Paragraph 159-133 at page 16 discloses the low production of diacetyl and/or higher alcohols by the generated strains. The sequences of ILV2, ILV3 and ILV5 are identical to the corresponding genes of S. cerevisiae. The partial knockout of the ILV2 gene is characterized by deletion of 1, 2, or 3 alleles of ILV2 (Table 4; paragraph 133 of specification) in combination with overexpression of ILV3 has a synergistic effect on decreased diacetyl production. Zhang et al teach that the invention is not limited to the particularly disclosed embodiments and technical means are well known methods to those skilled in the art. The embodiments are illustrative and not limiting scope. he phenotypically claimed characteristics such as incubation products/ratios under particularly defined culturing conditions are necessarily present in the S. uvarum strains of Zhang et al absent convincing factual evidence to the contrary. The embodiments are illustrative and not limiting scope of the invention as shown at page 2. Zhang et al differ by not teaching the specific number of functional genes or ratios thereof within its genome of the isoleucine-valent (ILV) pathway including ILV6 and BAT1/2 in its genome.
Wang et al teach construction of self-cloning brewing yeasts with low-diacetyl production. Wang et al teach that there are two kins of cloning techniques about gen manipulations in industrial yeasts on the basis of the gene origin: self-cloning and non-self cloning. When using non-self cloning technique heterologous DNA such as bacteria gene is introduced into the recombined yeast. When the yeast strain is genetically modified by the self cloning technique, the increased DAN fragments in the self transforming yeast come from the yeast itself. As no heterologous DAN is carried into the yeast after self-cloning modification, the improved strains will be more acceptable for the commercial application (see page 989, column 1, second paragraph).Wang et al teach self-cloning technique was applied in constructing a low diacetyl brewer’s yeast by disrupting the ILV2 gene and inserting a GSH1 gene.
It would have been prima facie obvious to one having ordinary skill in the art at the time the invention was filed to optimize the copy number and/or ratios of the ILV2, ILV3 and ILV5 genes in the genome of the yeast strains of Zhang et al by means of self-cloning genetic means as taught by Wang et al in order to provide for a reduced diacetyl production and maintain the desired fermentation characteristics for alcohol production for a strain that would be more acceptable for the commercial fermentation applications.
Claims 63-66 are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al (CN 110846238A, Feb 28, 2020, see English translation of record. All references are to the English translation) and Wang et al (International Journal of Food Science and Technology 43:989-994,008) and applied to claims 58-62 and 67-71 supra and further in view of Duong et al (Metabolic Engineering 13:638-647, 2011) and Duong, Cam-Thuy (Dissertation 2009).
The combination of Zhang et al and Wang et al is set forth surpa. The combination differs by not teaching the specific number of functional genes or ratios thereof within its genome of the isoleucine-valent (ILV) pathway including ILV6 and BAT1/2 in its genome.
Duong et al 2011 teaches Sc-type ILV6 as a target to reduce diacetyl formation in lager brewer’s yeast which includes S. pastorianus. Duong et al 2011 teach a double deletion mutant of the lager brewer’s yeast with two Sc-type genes deleted. The deletion resulted in the reduction of total diacetyl concentration in green beer (see abstract and Introduction page 638). Duong et al 2011 teach that the Sc-ILV6 double deletion mutant (or corresponding self-cloned strain without any heterologous DNA sequences) resulting in a 65% reduction of final diacetyl concentration should be a very desirable strain for breweries.
Duong 2009 teaches that in addition to Sc-ILV6, non-Sc-BAT1 can be linked to the diacetyl production pathway. Non-ScBAT2 showed the same gene copy number among all strains (pages 108-116). Duong 2009 teach that potential novel target genes for reduction of diacetyl production or Sc-ILV6, Sc-BAT1, non-SC-BAT1 and non-Sc-BAT2. When transcriptomes of the three studied lager brewers’ yeast strains were compared, several significant differences were identified for genes whose products are involved in the valine biosynthesis pathway (Sc-ILV6, Sc-BAT1, non-Sc-BAT1 and non-Sc-BAT2) and differences in their expression could thus be directly relevant for diacetyl formation (page 108). In brewers’ yeast, so far there has not been any study of ILV6, BAT1 and BAT2 expression level in relation to diacetyl formation. Regarding these above analyses, these Sc-ILV6, Sc-BAT1, and non-Sc-BAT2 ORFs can be considered as the novel potential target genes for reducing diacetyl production in yeast. The roles of these genes in diacetyl formation can be verified via the deletion of Sc-BAT1 and Sc-ILV6 in strains A or C or via overexpression of non-Sc-BAT2 genes in strain A. In addition, the role of non-Sc-BAT1 in diacetyl formation can also be verified via the overexpression of this gene in any selected lager yeast strain (pages 110-112).
As to claims 64-66, it would have been prima facie obvious to one having ordinary skill at the time of invention in the art to modify the strain of Zhang et al and Wang et al combined by a Sc-ILV6 double deletion mutation (or a corresponding self-cloned method) of Duong 2011 to optimize the production of the total diacetyl concentration in alcoholic beverages. It further would have been obvious to have performed the all the modifications in a lager yeast such as S. pastorianus as Duong 2011 and Duong 2009 teach that such is desirable and the optimization of the number of each of the functional genes alone and in tandem and ratios thereof is prima facie obvious as each gene plays a different role in the production of diacetyl during fermentation. As to claim 63, it would have been prima facie obvious to optimize BAT1 and BAT2 functional gene numbers according to Duong 2009 as Duong 2009 teach that these genes are also involved in the isoleucine-valine production pathways and are potential targets for optimizing diacetyl production in yeast strains for production of beer/lager.
Conclusion
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/Patricia Duffy/ Primary Examiner, Art Unit 1645