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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 10/10/2025 has been entered.
Application Status
This action is written in response to applicant’s correspondence received on 10/10/2025. Claims 1-10 are pending. Claims 1-2 have been amended. All pending claims are currently under examination.
Claim Rejections - 35 USC § 112 – Maintained/Updated in Response to Amendment
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-10 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
MPEP 2163.II.A.3.(a).i) states, “Whether the specification shows that applicant was in possession of the claimed invention is not a single, simple determination, but rather is a factual determination reached by considering a number of factors. Factors to be considered in determining whether there is sufficient evidence of possession include the level of skill and knowledge in the art, partial structure, physical and/or chemical properties, functional characteristics alone or coupled with a known or disclosed correlation between structure and function, and the method of making the claimed invention”.
For claims drawn to a genus, MPEP § 2163 states 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. See Regents of the University of California v. Eli Lilly & Co, 119 F.3d at 1568, 43 USPQ2d at 1406.
Regarding the nature of the invention, claim 1 recites synthetic yeast cells comprising at least one chromosome from each of at least 4 different yeast species.
Claim 1 is therefore claiming a yeast cell, where the required limitations encompass a yeast cell with at least one chromosome from 4 different yeast species. The number of chromosomes from each of the 4 different species in the cell is not limited by the claim language; the phrase “at least one chromosome” reasonably includes, for instance, a complete set of chromosomes from each of the 4 yeast species. This interpretation indeed appears to align with the language of both the claims and the specification. For instance, dependent claim 2 recites “the synthetic yeast cell comprises 4 to 16 sets of yeast chromosomes.” According to the specification, the phrase “set of chromosome” refers to a “complete” or “substantially complete” set of chromosomes (page 4, first paragraph). Given that claim 2 depends from claim 1, claim 1 in its broadest sense encompasses synthetic yeast cells of at least 4 yeast whole-genomes, where some chromosomal loss is permitted, per the Applicant’s definition of “sets of chromosomes” (i.e., a “substantially complete” set of chromosomes, in its broadest sense, allows for the set to be incomplete or complete). The breadth of this claim language encompasses a yeast cell comprising at least 4 whole or nearly whole, distinct genomes, and furthermore the language “at least” broadens the claim language to include yeast cells comprising more than 4 sets of chromosomes from three different species (e.g., sets of chromosomes, either complete or nearly complete, from four or more different species). This claim language is not commensurate with the scope of the specification for the reasons detailed below.
Regarding the guidance provided in the specification, the Applicant recites a method to generate allotetraploid yeast cells (Example 1, pages 20 to top of page 39). The Applicant also recites Example 2, where generation of higher order polyploid yeast cells were generated (page 39, beginning line 5 to page 40). While the Applicant recites that triple hybrid strains were created in Example 2 and Table 1, these hybrids appear to have been confirmed using only a PCR-RFLP strategy; such a tool does not confirm that the hybrids comprise “whole genomes” from the three different strains (see Table 1 and page 39, second paragraph). The single specific digestion pattern of a PCR amplification product from a single gene does not sufficiently describe whether the genomes of the hybrids were “whole” or “substantially complete” as embodiments of the phrase “sets of chromosomes” as encompassed by claims 1 and 2 (See Figure 8). Note that the strains in Table 1 are described as “putative hexaploid” cells because confirmation that they in fact comprise whole genomes for each of these strains is not provided (final column of Table 1, page 25). The Applicants further recite that even higher order ploidy cells were made, including both four and six species hybrids (page 39, third paragraph). For instance, the Applicants recite that a four-species hybrid was created and here refers to Figure 9 for Illumina sequencing data. However, Figure 9 in fact shows that not all chromosomes from the four species are represented in the strain (Figure 9). For instance, the second line of Figure 9, to the left of the first bar, shows that the first chromosome from the contributing strain is lost (Figure 9, line 2). There also appears to be partial chromosomal loss from the third chromosome of the contributing strain in line 1 of Figure 9 (see Figure 9, line 1, between the second and third vertical bar). Thus, the Applicant was certainly not in possession of a yeast hybrid strain with four whole chromosome sets from different species, as is reasonably encompassed by the language of claims 1 and 2, and arguably was not in possession of a yeast hybrid strain with three whole chromosomes either according to Figure 9. This is problematic because, although the Applicant has amended claim 1 to recite “at least one chromosome from each of at least 4 different yeast species,” this claim language still encompasses embodiments comprising 4 complete genomes because “at least one chromosome” reasonably includes all of the chromosomes of a given species. Furthermore, with regards to claim 2, “sets of chromosomes” still includes “complete” chromosomes, per the Applicant’s definition of “set of chromosome” at page 4, first paragraph.
Thus, the Applicant has not shown possession of the breadth of the claims, which reasonably include complete sets of chromosomes from 4 different yeast species, per the language of the specification and dependent claim 2.
Furthermore, even if claim 1 were interpreted to mean a synthetic yeast cell where complete chromosome structures from 4 different species is not required, where pieces of the chromosomes and/or entire chromosomes can be lost from the 4 contributing species, the Applicant was still not in possession of this broad genus of yeast cells because they have not provided a common structure or yeast cell which would encompass such a genus which would accurately predict or model what chromosomal loss may occur. As discussed further below, it is unpredictable as to how polypoidal yeast cells lose chromosomal components over time; the Applicant has not characterized the genus as a whole by providing only Figure 9 as an example of one single yeast cell with “at least one chromosome from each of at least 4 different yeast species” because there is no way to know how or what chromosomal segments will be lost to render such synthetic genomes (see below).
Furthermore, the specification appears to corroborate the idea that higher order ploidy cells are unstable. For instance, the specification itself states that the RFLP analysis of the six-species hybrid only indicates “the presence of at least 5 of the parental lines” (page 6, lines 25-29). The specification further teaches that the diverse morphology of the 6 species hybrid as illustrated in Figure 11A “suggests chromosome instability” (page 40, line 1). The specification further states that extensive prior work has shown that yeast polyploid strains are relatively unstable, and rapidly lose chromosomes to form aneuploid strains (page 17, lines 16-18). Thus, the teachings and data of the specification itself speak to the instability of higher order polyploid yeast cells (Figure 9, Table 1, page 6 lines 25-29, page 40 line 1, and page 17 lines 16-18).
Importantly, as seen in Figure 9, the first chromosome of the second yeast species (line 2 of Figure 9, to the left of the first bar of this line) has completely dropped out of the yeast cell. The Applicant does not offer mechanistic insight into how or why such chromosomal drop-out occurred, and there is no evidence in the specification that such chromosomal loss can be forecasted or predicted in a reliable way using structural or functional predictions from the yeast cell’s chromosomal composition. For instance, the specification offers no guidance concerning what potential chromosomes may be lost upon the generation of a synthetic cell using four different yeast species from those of Figure 9. Indeed, it is known in the art that chromosomal loss and instability, as also recited in the specification (above), is uncharacterized and unpredictable (see below). The Applicant has thus not shown representative species of the genus of yeast cells comprising at least one chromosome from at least 4 different yeast species to show possession of the claimed invention because such polypoidal/aneuploid cells are known to be unpredictable regarding chromosomal loss and instability (see discussion below).
It is known in the art that higher order yeast ploidy cells are genetically unstable. For instance, the post-filing research article Hirota (Hirota S et al. J Biosci Bioeng. 2024 Feb;137(2):77-84), teaches that polyploid genomes are known to be unstable in Saccharomyces cerevisiae (Abstract). Furthermore, Hirota teaches that high levels of chromosome instability occur in polyploid strains of S. cerevisiae when diploid (2N), triploid (3N), and tetraploid (4N) are compared with haploid (1N) cells, where the frequency of chromosome non-disjunction in triploid (3N) and tetraploid (4N) increased 30- and 1000-fold compared with diploid cells, respectively (Introduction, third paragraph). Hirota further teaches that higher order ploidy yeast cells of 8N, 16N, and 32N have drastically increased chromosome loss or nondisjunction events: it is therefore known in the art that higher order polyploid yeast cells are genetically unstable, and it is unpredictable as to how or what chromosomal loss may occur in higher order yeast ploidy cells (Introduction, fifth paragraph).
Additionally, Zhu (Zhu J et al. PLoS Genet. 2012;8(5):e1002719) teaches that aneuploid yeast cells, i.e., cells with abnormal chromosome numbers, correlate with an increase in genetic instability and elevated chromosomal instability, or the propensity to gain or lose a chromosome (Abstract). Zhu teaches that:
“[s]everal studies have shown that aneuploid yeast cells not only are characterized by phenotypic variation but also exhibit genome instability. For example, two independent studies with congenic aneuploid strains obtained by sporulation of triploid or pentaploid yeast found that, while some of the aneuploid strains were relatively stable, the majority of the strains were chromosomally unstable,” (page 1, right column, second paragraph)
Thus, Zhu teaches that yeast cells comprising aberrant numbers of chromosomes are characterized by phenotypic variation and genomic instability. Given that such phenotypic and chromosomal variations exist, the Applicant has not shown possession of the diverse genus of yeast cells presently recited simply by the one example offered in Figure 9. Furthermore, Zhu teaches that the underlying mechanism governing chromosomal instability and the products (cells) generated by such instability are still uncharacterized (page 2, left column, second paragraph). Thus, both the given phenotype or chromosomal composition of a given synthetic cell presently recited is unpredictable as taught in the art.
The art and specification therefore speak to the unpredictability synthetic yeast strains with higher order ploidy (see discussion of Hirota and the specification, above). The Applicant was therefore not in possession of the claimed invention at the time of filing.
Claims 2-10, which depend from claim 1, do not resolve this 112(a) issue and are therefore also rejected.
Furthermore, the Applicant has not offered species commensurate in scope with the claims. For instance, Figure 9 shows chromosomal loss in both lines 1 and 2, but the Applicant has not demonstrated or taught a mechanism to predict chromosomal loss and instability in higher order polyploid yeast cells, or which parts of the chromosome/genes will be lost in different growth conditions. Given that the art and specification teach unpredictability concerning chromosomal stability in higher order yeast ploidy cells, the Applicant was not in possession of the genus of synthetic yeast cells as recited in claims 1-3, which are not required to be complete sets of chromosomes (specification, page 4, first paragraph, and see discussion of the rejection of claim 1, above). In other words, the embodiment in Figure 9, comprising “sets of chromosomes” from at least four yeast cells, where “sets of chromosomes” is interpreted to mean “substantially complete” genomes, does not predictably describe the genus as a whole because chromosomal decay is unpredictable in higher order aneuploids. The Applicant is not in possession of the broadly claimed genus because it is unknown what chromosomal information will be lost to render “substantially complete” genomes, as chromosomal instability is unpredictable as taught by Hirota and Zhu (above).
The specification further recites that unstable polyploid strains in different conditions will result in the creation of different strains depending on that condition (page 17, third paragraph). Claims 1-3 appear to be claiming any strain that could result from placing, for instance, a 6N yeast strain in different conditions, where chromosomal loss is encompassed by the claim language by use of the phrase “at least one chromosome.” The Applicant was not in possession of this genus because chromosomal loss is not predictable as discussed above.
With regards to the unpredictability of chromosomal stability/loss in different environmental conditions such as fermentation (e.g., claims 9-10), it is known in the art that yeast cells undergo unpredictable chromosomal changes dependent growth conditions in fermentation reactions such as those recited in claims 9-10. For instance, Lucena (Lucena BT et al. Genet Mol Res. 2007 Oct 5;6(4):1072-84) teaches that:
“[t]he bioethanol fermentation process can be considered a very stressing industrial environment, in which yeast cells are constantly submitted to oscillations in sucrose and ethanol concentrations, as well as temperature fluctuations and variations of the pH in the medium. In such an environment, cells are continuously recycled in the course of the harvesting period, which can last over six months. This imposes a continuous periodic selection that favors the establishment of dominant strains that are more adapted than their counterparts. Industrial yeast strains have a complex genome constitution with variable chromosome number and a ploidy state that may contribute to that adaptation. While laboratory strains of S. cerevisiae tend to present 16 chromosomes, this number may vary in industrial strains. Whether chromosome polymorphism is a cause or a consequence of such an adaptation is still a matter of divergence among scientific reports,” (Discussion, first paragraph)
Thus, Lucena teaches that industrial fermentation conditions involve constant changes of cellular stressors to yeast cells, where such cells adapt and change in such environments, where furthermore industrial yeast strains comprise complex genomes with variable adaptations (above). The Applicant has not offered species of such synthetic yeast cells to show possession of complex aneuploidal/polypoidal cells encompassed by for instance claim 9, which involves culturing high order polyploid yeast cells in fermentation environments with constantly oscillating conditions. The Applicant has not shown possession of how such unique environmental changes would affect synthetic cells recited in claim 1 (i.e., it is unknown what synthetic yeast cells would result after such fermentation culturing methods). Furthermore, Lucena teaches that chromosomal changes in industrial fermentation yeasts are specific to the genetic background (Abstract) and therefore teaches that each genetic background would need to be specifically evaluated empirically.
Lucena further teaches that:
“a high degree of chromosome polymorphism has been detected among yeast isolates collected from sugar cane fermentation tanks. These different chromosome patterns could be a result of GCR in the yeast genome induced by the environmental conditions,” (Introduction, second paragraph).
Thus, Lucena teaches that environmental conditions, and chromosome polymorphism which result from culturing in such conditions, produce high degrees of variability within a yeast strain/population. The Applicant has not shown possession of a representative number of species of such diverse yeast strains which are involved in fermentation processes but is claiming the genus of these unknown polymorphic cells as a whole.
Similarly, claims 4-8 recite “chromosomal segments,” however, the specification does not recite a common structure of what chromosomal segments are encompassed by the synthetic yeast strains recited. As discussed above, chromosomal stability is unpredictable, and further the specification recites that different environments and growth conditions can yield different components of the genome after chromosomal loss occurs (i.e., the loss of “chromosomal segments”); the Applicants have not identified a core mechanism or structure that would predict the creation of new strains as chromosomal loss occurs, and were therefore not in possession of the genus of “chromosomal segments” as recited (page 17, third paragraph).
Response to Arguments
The Applicant’s arguments filed 10/10/2025 have been considered but are not persuasive. The Applicant has amended claim 1 to now recite “a synthetic yeast cell comprising at least one chromosome from each of at least 4 different yeast species.” The Applicant argues that Figure 9 shows evidence that they were in possession of this genus of synthetic yeast cells as a whole because Figure 9 depicts a synthetic yeast cell with at least one chromosome from at least 4 different species. This argument is not persuasive because the genus claimed is unpredictable, and the embodiment in Figure 9 is not a representative species of the entire genus for reasons outlined in the 112(a) rejection, above.
As an initial matter, the Applicant’s amendments have broadened their original claim language with respect to the number of chromosomes allowed by the claims. The Applicant is now claiming a genus of synthetic yeast cells where the cells comprise as few as one chromosome from four different species, where no upper limit of chromosome is recited in the claim. Thus, the present claim set still encompasses embodiments of yeast cells comprising full or nearly full sets of chromosomes (“sets of chromosomes,” as defined by the specification at page 4, second paragraph). This claim interpretation of claim 1, where claim 1 encompasses “sets of chromosomes,” which by Applicant’s definition includes full genomes or substantially full genomes, appears to be reasonable, as claim 2 – which depends from and therefore limits claim 1 – includes the language “sets of yeast chromosomes.” The Applicant argues that claim 1 “no longer requires substantially complete or whole-genome presence in a hybrid yeast cell.” This argument is not persuasive because claim 1 encompasses such an embodiment because the claim recites “at least one chromosome” with no upper boundary, which reasonably includes “all” or “substantially all” of the chromosomes. This interpretation seems appropriate particularly in light of the fact that dependent claim 2 uses claim language (“sets of chromosomes”) which encompasses entire genome or substantially complete genomes (page 4, second paragraph of specification).
However, even if claim 1 were read with a different interpretation, where “complete” or “substantially complete” genomes did not read on the claim language, the Applicants were still not in possession of the recited genus of synthetic yeast strains recited because of the unpredictability of said genus (see 112(a) rejection, above). To summarize, chromosomal instability leads to unpredictable outcomes with regards to downstream, resultant yeast strains, where factors such as unique genetic background and environmental changes can trigger different chromosomal make-ups of polyploid yeast cells (Lucena, Zhu, and Hirota). The Applicant has not characterized this widely variable and unpredictable genus of cells to a degree commensurate in scope with what is being claimed. For instance, the Applicant offers Figure 9 in an attempt to argue possession of the presently claimed subject matter. The data in Figure 9 show that the first chromosome of the synthetic strain is missing from species 2 (line 2 of Figure 9, note that there is chromosomal drop-out to the left of the first bar of this line). However, the Applicants do not teach any mechanistic underpinnings of chromosomal instability which could be used to reliably predict what genetic material/chromosomes may be lost in such synthetic strains as those claimed (i.e., they can not reliably predict what chromosomal loss will occur over time, with different growth conditions used to generate the strain, or what chromosomal instability may be observed with a different set of four yeast species from those used in Figure 9, see 112(a) rejection). Given that chromosomal instability is not fully characterized in the art, where factors such as unique genetic background and environmental influence affect chromosomal makeup in unpredictable ways (e.g., Lucena discussion, 112(a) rejection), the Applicant can not be said to have been in possession of the recited genus by the limited examples which they have provided.
The Applicant argues that chromosomal instability can offer beneficial features. This argument is not persuasive because the mere fact that evolutionary adaptation and changes which result from chromosomal instability could be beneficial is irrelevant to the question of whether or not the Applicant was in possession of the claimed invention. For instance, the Applicant argues that higher order ploidy yeast cells demonstrate the ability to select for traits, where such selection may be the result of rapid adaptation to a condition, and further that claim 1 as amended focuses on the “retained chromosomal material,” (remarks filed 10/10/2025, page 5, final paragraph). These arguments are not persuasive because, importantly, the Applicant has not identified nor offered a way in which to reasonably predict what such “retained chromosomal material” might be in such cells as those recited, which the art teaches is inherently unstable and unpredictable. The Applicant was not in possession of what such chromosomal losses, which chromosomes from which species, and in what copy number such chromosomes might be retained, and were therefor not in possession of the genus of yeast cells comprising “at least one chromosome from each of at least 4 different yeast species.”
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to DOUGLAS CHARLES RYAN whose telephone number is (571)272-8406. The examiner can normally be reached M-F 8AM - 5PM.
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/D.C.R./Examiner, Art Unit 1635
/KIMBERLY CHONG/Primary Examiner, Art Unit 1636