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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on December 08, 2025 has been entered.
Status of Claims / Response to Amendment
This office action is in response to an amendment filed on December 08, 2025.
Claims 1-4, 6-9, 11, 13-15, 20, 23, 25, 27-32 were previously pending. Applicant amended claims 1-3 and 8-9; cancelled claims 6 and 32.
Claims 1-4, 7-9, 11, 13-15, 20, 23, 25, 27-31 are currently pending, with claims 13-15, 20, 25 and 27-31 withdrawn.
Claims 1-4, 7-9, 11 and 23 are under consideration.
All of the previously presented rejections have been withdrawn as being addressed or obviated by the amendment of the claims 1.
Applicant' s amendments and arguments have been thoroughly reviewed, but are not persuasive to place the claims in condition for allowance for the reasons that follow.
This office action contains new grounds for rejection necessitated by amendment.
Priority
The priority date of the instant claims 1-4, 7-9, 11 and 23 is May 31, 2019, filling date of the FINLAND Patent Application Number 20195454, to which the present application claims priority.
Claim Interpretation -- Updated
In evaluating the patentability of the claims presented in this application, claim terms have been given their broadest reasonable interpretation (BRI) consistent with the specification, as understood by one of ordinary skill in the art, as outlined in MPEP§ 2111.
For the purpose of applying prior art, claim 1 has been amended to recite "detecting a presence or an absence of a natural deletion in the promoter of STA1 gene of the sample."
The application's disclosure does not define the term "natural deletion," the specification provides the following relevant description regarding "natural deletion":
"FIGS. 3A-E show phenotypic results of the reverse engineered strain, WY3711_D1. Three STA1+ strains were compared: WY3711 (no deletion in STA1 promoter), WY3711_D1 (CRISPR-mediated deletion in STA1 promoter), and WLP570 (natural deletion in STA1 promoter). " (page 5)
Therefore, under BRI and in light of the specification, "a natural deletion in the promoter of STA1 gene" is understood as a deletion located within the promoter region of STA1 gene and is not generated through genetic modification methods, such as CRISPR. Thus, this term encompasses "domesticated" yeast strains cultivated in a lab (see in instant specification, Table 1, WLP570 having natural deletion in STA1 promoter is sourced from a lab), which may or may not have undergone artificial strain optimization, such as selective crossing. Such approaches do not rely on recombinant DNA technology for genetic modification.
For the purpose of applying prior art, claim 1 recites "a primer or a probe capable of hybridizing with at least a portion of the promoter of STA1 gene."
MPEP§ 2111.04 states:
"Claim scope is not limited by claim language that suggests or makes optional but does not require steps to be performed, or by claim language that does not limit a claim to a particular structure."
The term "capable of" suggests intended use, without claiming specific structures in the claimed primer or probe that directly support or relate to these functional language. Hybridization is a common molecular biology technique that relies heavily on specific environmental conditions to occur (See Simple Cloning Lab: Hybridisation ; www.bioinformatics.nl). Environmental factors such as temperature, ionic strength, and the presence of other solutes significantly influence the binding specificity in hybridization between nucleotide sequences. Two nucleotide sequences can be capable of binding to each other, or unable to bind depending on these environmental factors. Therefore, there is insufficient connection between the functional language and any specific structural characteristics in the recited primer.
Thus, such intended use limitation does not distinguish a claimed primer or probe from a prior art primer or probe that satisfies all the structural limitations in the claim. Since the application's disclosure does not define the recited primer or probe with any specific structural features such as specific sequences, lengths, or modifications, the primers and probes are understood under BRI to share the common structure of oligonucleotides as recognized in the field and are therefore encompassed by any primers or probes known in the prior art.
Therefore, "a primer or a probe capable of hybridizing with at least a portion of the promoter of STA1 gene," without any clear and specific structural limitation, is interpreted under BRI to encompass any primer or probe.
For the purpose of applying prior art, claim 1 recites:
"allowing a primer or a probe capable of hybridizing with at least a portion of the promoter of STA1 gene to hybridize with a polynucleotide of the sample, wherein said promoter comprises nucleotides 1127-2288 as numbered in SEQ ID NO: 1."
The "wherein" clause above is interpreted as not limiting the scope of the claim, because none of the claimed steps require the recited specific nucleotides sequence: "1127-2288 as numbered in SEQ ID NO: 1," and the claim does not necessarily require the promoter of STA1 gene.
The "allowing" step in claim 1 recites hybridization of a primer or probe with a polynucleotide with undefined structure. The claim does not require the polynucleotide to include the promoter of STA1 gene or even associated with a "yeast carrying STA1 gene," as recited in the claim's preamble. Therefore, the promoter of STA1 gene as described by the nucleotide range in the "wherein" clause is not required by this step.
The following step in the claim recites "detecting a presence or an absence of a natural deletion in the promoter of STA1 gene of a sample," but this step also does not require the recited specific nucleotides sequence in the "wherein" clause, identified as "nucleotides 1127-2288 as numbered in SEQ ID NO: 1." First, the step covers scenarios where the deletion lies outside of the specified region comprised by the promoter. Second, it also covers scenarios in which the promoter of STA1 gene is entirely absent from the sample .
In such cases, the absence of deletion is still detected ꟷ i.e., the assay detects the absence of a deletion because the promoter itself is not present.
Per MPEP 2111.04, a wherein clause can limit a method claim if it contributes meaning and purpose to the manipulative steps. In the instant claim, however, the "wherein" clauses do not integrate any additional action or decision-making process into the method, and merely provides additional description of the promoter of STA1 gene; which is not required by the claimed method. Therefore, these claim languages are interpreted as descriptive statements without any associated active steps and do not further limit the scope.
For the purpose of applying prior art, claim 1 recites:
"c) determining that the sample does not include a spoilage yeast strain if the presence of a natural deletion in the promoter of the STA1 gene is detected, or that the sample does include a spoilage yeast strain if the absence of a natural deletion in the promoter of the STA1 gene is detected."
The application's disclosure does not define the term "spoilage yeast strain."
The specification provides the following relevant descriptions:
"Some diastatic strains of yeast are considered spoilage microorganisms in industrial lager fermentations. These strains, including but not limited to Saccharomyces cerevisiae formerly known as Saccharomyces diastaticus, are capable of producing an extracellular glucoamylase that enables fermentation of starch and oligosaccharides. This in turn, causes super-attenuation in the beer, which leads to increased carbon dioxide and ethanol levels, possible off-flavours, and a drier mouthfeel. In the case of contamination in packaged beer, diastatic S. cerevisiae may even cause exploding bottles and cans, endangering the consumer.
The extracellular glucoamylase in diastatic S. cerevisiae is coded for by the STA genes (Tamaki, 1978, MGG Mol. Gen. Genet. Volume 164, issue 2, 205-209; Yamashita et al., 1985, J. Bacteriol. 161, 574-582; Yamashita, et al., 1985, J. Bacteriol. 161, 567-573). Three highly homologous STA genes (STA1-3) have been described (Tamaki, 1978, MGG Mol. Gen. Genet. Volume 164, issue 2, 205-209; Lambrechts et al. 1991, Gene, vol. 100, 95-103). STA1p is the main cause of spoilage features in said S. cerevisiae. Genetic differentiation of spoilage and non-spoilage yeast strains is important e.g. for the food industry in order to minimize the production costs and optimize the quality of end products." (page 1-2, "BACKGROUND OF THE INVENTION") [emphasis added]
Thus, the term "spoilage yeast strain" is interpreted under BRI and in light of the specification as encompassing yeast strains that express functional extracellular glucoamylase.
Claim Rejections - 35 USC § 112(a) – New
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.
Claims 1-4, 7-9, 11 and 23 are rejected under 35 U.S.C. 112(a) as failing to comply with the written description requirement. The claims contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Regarding claim 1, it recites a step of "detecting a presence or an absence of a natural deletion in the promoter of STA1 gene of the sample," but the applicant's disclosure lacks sufficient detail to demonstrate possession of the invention, as required under 35 U.S.C. 112(a).
Specifically, the disclosure describes detection of a STA1 gene promoter deletion generally, but does not support detecting a natural deletion as distinct from a non-natural or engineered deletion, as required by the claim.
The specification discloses two strains having deletions in the promoter of STA1 gene: one genetically engineered strain (WY3711_D1) and one strain having a natural deletion (WLP570) (page 5, lines 25-26). However, the disclosure detects both types of deletions using the same PCR assay (page 5, lines 19-21) and reports indistinguishable results (Fig. 2D).
There is no description of a method that specifically identifies a natural deletion from an engineered deletion.
Further, the specification does not disclose any structural or sequence characteristic that is unique to a natural deletion and that can be used in a detecting step to differentiate it from an engineered deletion.
Claim 1 broadly recites "a yeast carrying STA1 gene in a sample," which encompasses both naturally occurring and genetically modified yeasts. The disclosure does not explain how the claimed method detects only natural deletions when both natural and engineered deletions may be present in the sample. Instead, the disclosure describes a general detection method that identifies promoter deletions regardless of their origin.
Therefore, the application's disclosure does not reasonably convey to a person of ordinary skill in the art that the inventors had possession of a method for detecting a natural deletion in the promoter of STA1 gene, as required by claim 1.
Claims 2-4, 7-9, 11 and 23 are rejected because they depend from claim 13 and inherit the deficiencies of the base claim.
Claim Rejections - 35 USC § 103 -- New
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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 following are new grounds of rejections necessitated by Applicant's amendments. Although the claims were previously rejected as being unpatentable over some of the same reference(s), Applicant's amendments have necessitated the inclusion of new grounds of rejections in this Office action. It is noted that, to the extent that they apply to the present rejection; Applicant's arguments are addressed following the rejection.
Claims 1-4, 7-9, 11 and 23 are rejected under 35 U.S.C. 103 as being unpatentable over Mitro (Mitro, A. (2018, October 16). Demystifying diastaticus (part 1). Escarpment Labs.; escarpmentlabs.com/en-us/blogs/resources/demystifying-diastaticus-part-1) , in view of
Meier-Dörnberg (Meier-Dörnberg et al. Saccharomyces cerevisiae variety diastaticus friend or foe? -spoilage potential and brewing ability of different Saccharomyces cerevisiae variety diastaticus yeast isolates by genetic, phenotypic and physiological characterization. FEMS Yeast Res. 2018 Jun 1;18(4). doi: 10.1093/femsyr/foy023. PMID: 29518233; cited as NPL#20 in IDS filed on 11/30/2021) and
Shima (Shima et al. (1989). Upstream Regions of the Yeast Glucoamylase Gene Which Are Required for Efficient Transcription. Agricultural and Biological Chemistry, 53(3), 749–755. doi.org/10.1080/00021369.1989.10869353; cited as NPL#25 in IDS filed on 11/30/2021); as evidenced by
Salinas (Salinas et al. Natural variation in non-coding regions underlying phenotypic diversity in budding yeast. Sci Rep 6, 21849 (2016). doi.org/10.1038/srep21849);
Steensels (Steensels et al.; Improving industrial yeast strains: exploiting natural and artificial diversity. FEMS Microbiol Rev. 2014 Sep;38(5):947-95. doi: 10.1111/1574-6976.12073. Epub 2014 May 8. PMID: 24724938; PMCID: PMC4293462.)
A) Mitro teaches a PCR method for determining a yeast having extracellular glucoamylase STA1p activity in a sample (entire document). Specifically, Mitro teaches detecting STA1 gene in Saccharomyces cerevisiae var. diastaticus – a beer yeast that can break down longer-chained carbohydrates (dextrins and starches) that regular yeast can’t. It doesn’t actually consume them directly, but it secretes an enzyme (glucoamylase) that breaks down dextrins outside the cell into smaller sugars that the yeast can then metabolize. The gene encoding this glucoamylase is STA1. Diastatic yeast is often problematic for brewers, causing unintended hyper attenuation and secondary fermentation post-packaging, which can lead to over-carbonated product and the dreaded exploding cans. ( page 1, para 1). Therefore, Diastatic yeast is a naturally occurring microorganism contaminant in the brewing process.
Regarding claim 1, Mitro teaches allowing a primer to hybridize with a polynucleotide of the sample in a PCR reaction (page 4, colony PCR Setup).
While Mitro teaches detecting STA1 gene, encoding glucoamylase, it does not specifically teach detecting a presence or an absence of a deletion in the promoter of STA1 gene, to determine whether the sample includes a spoilage yeast strain.
Mitro further notes that although its PCR method is useful in detecting STA1 gene for extracellular glucoamylase activity, it could result in false positives for detecting samples containing yeast that contains non-functional versions of the STA1 gene. Slight genetic variations in STA1 could radically alter its function:
“Although PCR is a powerful tool, it does have its limitations as it is only able to amplify specific DNA regions and does not test for protein functionality. This means that a sample containing dead, non-viable diastatic yeast or yeast that contains non-functional versions of the STA1 gene will test positive in a PCR test, while exerting no net effect on the integrity of the sample. The reason for this is still unclear. Early research identified important components of the genetic code for STA1, such as the domain required for its export from the cell. Slight genetic variations in STA1 could radically alter its function. The public availability of many beer yeast whole genomes may help understand diastatic yeasts in greater detail moving forward.” (page 3, para2)
Therefore, not all diastatic yeast that carry the STA1 gene are capable of causing spoilage.
B) Meier-Dörnberg supports this known limitation in PCR detection assay for STA1 gene as taught in Mitro. It compares natural diastaticus yeast strains (Table 1, spoilage yeast strains isolated from brewery and lemonade) via genetic, phenotypic and physiological characterization (entire document). Meier-Dörnberg concludes: “It could be shown that the spoilage potential of S. cerevisiae var. diastaticus and therefore the super-attenuating2 power is strain dependent.” (page 23)
Meier-Dörnberg teaches recalling samples including a spoilage yeast strain or a product from which the sample is taken (page 2, left-hand col, para 2). However, Meier-Dörnberg also explains that although PCR detection of the STA1 gene is reliable for species identification, it does not correlate with spoilage potential (i.e., potential for super-attenuation caused by extracellular glucoamylase activity) (page 24, right-hand col, lines 1-6).
In other words, some yeast strains carry STA1 gene but do not exhibit spoilage potential, and these benign strains may be erroneously identified as diastatic using existing molecular methods. As a result, recalling products based solely on detection of STA1 gene could lead to unnecessary disposal of products that contain yeast strain carrying STA1 gene but lacking spoilage potential.
Accordingly, there was a recognized need in the art for improved molecular assays capable of differentiating spoilage and non-spoilage yeast strains.
C) While Mitro suggests that yeast strains carrying non-functional STA1 gene may arise due to genetic variation, it does not identify any specific variation responsible for the loss of function. Shima addresses this gap in knowledge.
Shima teaches a detailed analysis of the promoter region of STA1 gene in diastaticus yeast (entire document, for examples see Figure 3; page 754, right-hand col, lines 6-15; Abstract, Deletion analysis), and identifies multiple upstream activation sequences (UAS) that are located in the promoter region of STA1, and deletion of these specific UASs, such as UAS 1, UAS 2-1 and UAS 2-2 result in lack of glucoamylase protein expression and functional activity due to failed transcription/translation (abstract; page 755, left-hand col, para 1; page 753, left-hand col; Figure 3).
Thus, Shima discloses that deletion of promoter elements of STA1 gene results in loss of gene expression and its spoilage function by glucoamylase activity. Therefore, the teachings of Shima provides a reasonable genetic explanation for the phenomenon observed in Mitro and Meier-Dörnberg ꟷ namely, that naturally occurring yeast strains may carry STA1 gene but lack spoilage potential due to deletions in the promoter region of STA1, similar to those described in Shima. The detection of such deletions in the promoter region indicates the yeast strain lacks spoilage potential, even if the STA1 gene is present, because such strain lacks glucoamylase activity. This capability to distinguish spoilage-capable from non-spoilage yeast strains carrying STA1 gene offers clear value to the brewing industry, where contamination-triggered product recalls can result in substantial financial loss and reputational harm (see Meier-Dörnberg, page 2, left-hand col, para 2).
In view of the above, it would have been prima facie obvious to a person of ordinary skill in the art before the effective filing date of the claimed invention to combine the PCR-based detection method for the STA1 gene to identify the diastaticus yeast species, taught in Mitro and Meier-Dörnberg, with the teachings of detecting promoter deletions of STA1 in yeast as described by Shima, in order to further distinguish spoilage-capable from non-spoilage yeast comprising STA1 gene in a brewery sample comprising natural yeast strains.
Mitro teaches using PCR with primers to detect the presence of STA1 gene as an indicator of diastaticus yeast having glucoamylase activity, but Mitro acknowledges its limitation in distinguishing functional from non-functional gene variants.
Meier-Dörnberg further demonstrates that detecting the STA1 gene alone does not reliably indicate spoilage potential, as the mere presence of detectable STA1 gene does not correlate with glucoamylase activity.
Shima helps to elucidate genetic determinants behind the variable diastatic ability that has been observed in Mitro and Meier-Dörnberg. It provides a reasonable explanation by teaching that specific deletions in the promoter region of the STA1 gene abolish gene expression and protein function, even when the gene is present. Given the prevalence of natural variation in yeast non-coding regions, such as promoter regions, and the resulting phenotypic diversity as evidenced by Salinas (entire document), a skilled artisan would reasonably expect that deletions in the promoter regions taught in Shima, although artificially generated in that study, could also occur naturally. This is further supported by Steensels, which teaches that genetic variations, specifically deletions, are naturally occurring (see Figure 2). It would have been obvious for a skilled artisan to take the logical next step of analyzing whether similar promoter deletions are present in natural, non-genetically modified yeast strains that comprise the STA1 gene but lack enzyme activity, as described in Mitro and Meier-Dörnberg. This follows directly from common understanding in the art that when a gene is present and intact but not expressed, defects in upstream regulatory regions controlling transcription (e.g., promoter) are a likely cause 3.
Therefore, a skilled artisan would recognize that further incorporation of detection for the promoter deletions, as taught by Shima, into the PCR methods of Mitro and Meier-Dörnberg would improve assay specificity and can potentially reduce waste and unnecessary costs related to product recalls caused by false positives.
By identifying the specific promoter deletions taught in Shima, it would be possible to differentiate diastaticus yeast strains with functional glucoamylase activity (spoilage strains) from those without such activity (non-spoilage strains). For example, if a sample tests positive for the presence of STA1 gene but the promoter of the gene contains the specific deletion taught in Shima, it can be determined that the sample does not contain a spoilage yeast strains, as the yeast would lack glucoamylase activity.
The person of ordinary skill would have had a reasonable expectation of success in incorporating the detection of promoter deletions into the PCR method of Mitro and Meier-Dörnberg, because all three references are in the same or overlapping field of fermentation microbiology, specifically focus on yeast strain analysis and molecular detection of STA1 gene function, and their teachings are complementary. Mitro and Meier-Dörnberg already teaches PCR and RT-PCR using primers targeting STA1, and Shima provides detailed sequence information regarding the promoter and its functional elements (i.e. UASs). Primer design for targeting specific regions (e.g. UASs) with known sequences is well-known and conventional in the art, and Shima provides sufficient guidance on which promoter regions are functionally significant. Therefore, a skilled artisan would have recognized that adding primers to specifically detect deletions in the promoter of STA1 would enhance the utility of PCR based method in distinguishing between functional and non-functional gene variants. Doing so would have yielded the predictable result of an improved PCR assay that not only detects the presence of STA1, but also distinguishes between functional and non-functional gene variants in different yeast strains, thereby reducing false positives.
The skilled artisan would have been motivated to do so to address the known limitation of the PCR-based assays in the art, as indicated by Mitro and Meier-Dörnberg; and to improve assay reliability for applications such as fermentation monitoring, where detection accuracy has direct economic consequences, as indicated in Mitro (page 1, para 1-2).
Additionally, this combination would have been obvious as it represents the KSR principle of predictable use of prior art elements (i.e., promoter deletion detection for determining functional activity of the gene, taught by Shima) according to a known method (i.e., PCR detection of STA1 gene in diastaticus yeast, disclosed by both Mitro and Meier-Dörnberg) to yield predictable results. (See MPEP §2143).
D) Regarding claim 2, Shima teaches a deletion which is largely within nucleotides 1127-2288 as numbered in SEQ ID NO: 1 (See Fig 5b, X-526-5 deletion for example, which largely overlaps with nucleotides 1127-2288 in SEQ ID NO: 1).
PNG
media_image1.png
558
1222
media_image1.png
Greyscale
As indicated by Fig 5b, UAS 2 sequence in STA1 gene is largely encompassed by the nucleotides region 1127-2288 in SEQ ID NO: 1 (1116-1628, except for 11 nts at the beginning of UAS2), thus the claimed limitation "deletion within nucleotides 1127-2288 as numbered in SEQ ID NO: 1" would have been obvious because Shima teaches deletion of UAS2 region, which is almost entirely contained within the nucleotides region 1127-2288 in SEQ ID NO: 1. A skilled artisan would recognize that detecting deletions within nucleotides region 1127-2288 in SEQ ID NO: 1 would include deletion of UAS2 as taught by Shima. "[A] prior art reference that discloses a range encompassing a somewhat narrower claimed range is sufficient to establish a prima facie case of obviousness." In re Peterson, 315 F.3d 1325, 1330, 65 USPQ2d 1379, 1382-83 (Fed. Cir. 2003).
Regarding claims 3-4, Mitro teaches polymerase chain reaction (PCR) (entire document, PCR).
Regarding claim 7, Mitro teaches a primer used for detecting STA1 (page 4, colony PCR Setup).
Regarding claims 8 and 9, they are obvious over the combined teaching of Mitro and Shima, because they both recite wherein clauses that do not further limit the claimed method.
Claim 8 recites:
"wherein the absence of the deletion in the promoter of STA1 gene indicates presence of extracellular glucoamylase STA1p activity of the yeast. "
Claim 9 recites:
"wherein the presence of the deletion in the promoter of STA1 gene indicates decreased extracellular glucoamylase STA1p activity of the yeast, or wherein the presence of the deletion in the promoter of STA1 gene results in decreased ethanol formation, carbon dioxide formation, hydrolysis of maltotriose and/or diastatic capability of the yeast compared to another yeast lacking the deletion in the promoter of STA1 gene."
These wherein clauses are interpreted to assert only correlations between the presence or absence of deletion and levels of extracellular glucoamylase STA1p activity of the yeast. The claims recite "wherein the absence of the deletion in the promoter of STA1 gene indicates…" and "wherein the presence of the deletion in the promoter of STA1 gene indicates…,"
which do not involve any active method step or lead to a further step based on any indication.
Per MPEP 2111.04, a wherein clause can limit a method claim if it contributes meaning and purpose to the manipulative steps. In the instant claim, however, the wherein clauses do not integrate any additional action or decision-making process into the method, and merely presents a scenario for correlating the presence or absence of deletion with indications for enzyme activity.
Therefore, these claim languages are interpreted as descriptive statements without any associated active steps and do not further limit the scope.
Regarding claim 11, Mitro teaches detecting the presence or absence of STA1 gene (entire document, page 4, colony PCR Setup).
Regarding claim 23, Mitro teaches food sample (page 1, para 2; page 5, beer sample).
Response to Applicant Arguments
The previously set forth 103 rejections of claims 1-4, 6-9, 11, 23 and 32 have been withdrawn in view of the recent claim amendment filed on December 08, 2025, which added new limitations to the claims, that are not addressed in the previous rejections.
Applicant's arguments filed on November 25, 2025 have been fully considered but are not found persuasive.
First, the amended method is obvious in view of the cited references, as explained in the new grounds of rejection above.
Applicant further argues the following:
"Applicant emphasizes that the knowledge of Shima has been around for 35 years, and yet the connection between deletions in the STAI promoter and spoilage potential has not been made until the filing of the instant application (nor has the presence of natural deletions in the STAI promoter been recognized at all)" (Remarks, page 9)
This argument is not persuasive.
Applicant argues that because the prior art allegedly did not recognize a connection between natural STA1 promoter deletions and yeast-caused food or beverage spoilage, the claimed method is not obvious.
This argument is not persuasive.
First, the asserted connection is not required by the claim. Claim 1 broadly recites "a yeast carrying STA1 gene in a sample," which encompasses both naturally occurring and genetically modified yeasts. The claim does not require that the yeast carry a natural deletion in the STA1 promoter, nor does it exclude yeasts having engineered deletions or require an absence of spoilage potential. The disclosure does not explain how the claimed method detects only natural deletions when both natural and engineered deletions may be present in the sample. Rather, the disclosure describes a general detection method that identifies promoter deletions regardless of their origin.
Second, as discussed in the 112 (a) section above, the disclosure lacks written description support for detecting a natural deletion as distinct from a non-natural or engineered deletion. The specification does not describe any distinguishing feature, criterion, or detection step that would allow one of ordinary skill in the art to identify only natural deletions.
Third, in view of the prior art, it would have been obvious to test for such promoter deletions in natural yeast strains. As detailed in the rejection above, the STA1 gene was known to be associated with yeast strains with spoilage function. Shima already teaches that deletion of promoter elements of STA1 gene results in loss of gene expression and its spoilage function by glucoamylase activity. The rejection further provides motivation and rationale for a skilled artisan to test natural yeast strains for such deletions in order to distinguish spoilage from non-spoilage yeast in brewery samples and reduce waste and unnecessary costs related to product recalls caused by false positives.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to TIAN NMN YU whose telephone number is (703)756-4694. The examiner can normally be reached Monday - Friday 8:30 am - 5:30 pm.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Gary Benzion can be reached at (571) 272-0782. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/TIAN NMN YU/Examiner , Art Unit 1681 /AARON A PRIEST/Primary Examiner, Art Unit 1681
1 The previously set forth 101 rejection has been withdrawn in view of the incorporation of a practical application in independent claim 1 ꟷ assessing the quality of product based on the presence of a spoilage yeast strain, and taking action to recall or utilize the product based on that assessment.
2 Super-attenuation is defined as a result of extracellular glucoamylase activity (Meier-Dörnberg, page 3, left-hand col, lines 1-4)
3 For example, see Metzger et al. Contrasting Frequencies and Effects of cis- and trans-Regulatory Mutations Affecting Gene Expression, Molecular Biology and Evolution, Volume 33, Issue 5, May 2016, Pages 1131–1146, in abstract "we find that cis-regulatory mutations are skewed toward decreased expression"