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 .
Claim Status
The amended claim set filed on 1 October 2025 is acknowledged. Claims 1-2, 4, 6, 9-16, and 19-22 are currently pending. Of those, claims 1-2, 4, 6, and 9-14 are amended. There are no new claims and claims 14-16 and 19-22 are withdrawn. Claims 3, 5, 7-8, 17-18, and 23 are cancelled. Claims 1-2, 4, 6, and 9-13 will be examined on the merits herein.
Please note: In the claim set filed on 1 October 2025, claims 14-16 and 19-22, which were previously withdrawn as being drawn to a nonelected invention, are not identified as “withdrawn” 37 CFR 1.121(c) states (emphasis added), “In the claim listing, the status of every claim must be indicated after its claim number by using one of the following identifiers in a parenthetical expression: (Original), (Currently amended), (Canceled), (Withdrawn), (Previously presented), (New), and (Not entered)…. If a withdrawn claim is currently amended, its status in the claim listing may be identified as ‘withdrawn— currently amended.’” Appropriate correction is required.
Response to Amendment
The Applicants’ arguments filed 1 October 2026 are acknowledged. For clarity, in this action, said arguments will be referred to as “Remarks” and the Non-Final Office Action mailed 1 July 2026 will be referred to “NFOA”.
Objection(s) and Rejection(s) Withdrawn
The objections to and rejections of claims 3, 5, and 7-8 are moot because the claims are cancelled.
The objections to claims 1-2, 6, and 9-13 are withdrawn in view of the claim amendments.
The rejection under 35 U.S.C. 112(b) of claims 6 and 9-13 is withdrawn in view of the amendments to the claims.
Claim Interpretation
Claim 6 is amended to recite, “the strain of the genus Yarrowia is Yarrowia lipolytica.” The broadest reasonable interpretation of this limitation is that “the strain” may be any strain of the species Yarrowia lipolytica.
Claim 9 is amended to recite, “the fat is triacylglycerol (TAG).” The broadest reasonable interpretation of the limitation is that “the fat” may be any species of fat within the genus triacylglycerol.
Objection(s) Maintained
Claim 4 remains objected to because of the following informalities: “Yarrowia” should be italicized. Appropriate correction is required.
New Objection(s)
Claim 1 is newly objected to because of the following informalities: “cho2 gene or opi3 gene” should read “a cho2 gene or an opi3 gene”. Appropriate correction is required.
Rejection(s) Maintained
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claim Rejections - 35 USC § 102
Claims 1-2, 4, 6, and 9-13 remain rejected under 35 U.S.C. 102(a)(1) as being anticipated by Yang et al. (US 2014/0322771 A1; herein “Yang”) as evidenced by Fakas (2017, Eng. Life Sci.), NCBI Reference Sequence XM_503613.1 (2017; cited in IDS; herein “XM_503613.1”), NCBI Reference Sequence XM_503863.2 (2017; cited in IDS; herein “XM_503863.2”), and Boumann et al. (2006, Mol. Biol. Cell; cited in IDS; herein “Boumann”) for the reasons of record and the reasons herein.
The following rejection has been amended to reflect the amendments to the claims.
Regarding claims 1 and 9, Yang teaches a method for producing a genetically modified organism, which may be a Yarrowia cell (para. 123), where the genetic modification inhibits the phospatidylethanolamine N-methyltransferase (PEMT) pathway in the cell, including the PEMT or phospholipid methyltransferase proteins (para. 27-30, 136 and 143). Yang teaches that the PEMT pathway may be inhibited by introducing one or more genetic modifications that reduces expression of the gene encoding phosphatidylethanolamine methyltransferase or phospholipid methyltransferase (para. 237-239), which in Y. lypolytica correspond to the genes YALI0E06061g and YALI0E12441g, respectively, also referred to as cho2 and opi3, respectively (as evidenced by Fakas, Table 1). Yang teaches that inhibition of the target genes encoding the target proteins may be achieved by inactivating the target gene (para. 177) and that target genes may be inactivated by replacing them (i.e., deleting the target gene of the host cell) through homologous recombination (para. 178).
Regarding the limitation, “the variant strain of the genus Yarrowia has an increased fat content, as compared with a wild type Yarrowia strain,” Yang teaches that the method of producing the genetically modified organism (i.e., Yarrowia strain) comprises making a modification to the organism that results in increases triacylglycerol production (which increases triacylglycerol content) in the cell when compared to a corresponding wild-type cell (para. 26).
Regarding the limitation, “the variant strain of the genus Yarrowia is a choline auxotrophic strain,” Yang teaches that the genetic modification(s) to the cell may include reducing the expression of one or more genes encoding PEMT and phospholipid methyltransferase (i.e., cho2 and opi3, respectively) (para. 237-239). PEMT and phospholipid methyltransferase are two of the enzymes in the pathway that converts phosphatidylethanolamine (PE) into phosphatidylcholine (PC); the inability to utilize PE in such cells is remedied by utilizing choline to produce PC through a different pathway (as evidenced by Boumann, Figure 1 and pg. 1008, right col., para. 1 and Fakas, Figure 1). PC is a major structural component of organelle membranes in eukaryotes (as evidenced by Boumann, pg. 1006, left col., para. 1); thus, eukaryotes lacking one or both of PEMT and phospholipid methyltransferase are inherently choline auxotrophs. See MPEP 2112 for a discussion on inherency.
Regarding claim 2, the phosphatidylethanolamine methyltransferase gene in Y. lypolytica is the gene YALI0E06061g, also referred to as cho2 (as evidenced by Fakas, Table 1), which has a nucleotide sequence identical to that of instant SEQ ID NO: 1 (as evidenced by XM_503613.1; see alignment in Figure 1 of the FAOM).
Regarding claim 4, the phospholipid methyltransferase gene in Y. lypolytica is the gene YALI0E12441g, also referred to as opi3 (as evidenced by Fakas, Table 1), which has a nucleotide sequence identical to that of instant SEQ ID NO: 11 (as evidenced by XM_503863.2, see alignment in Figure 2 of the FAOM).
Regarding claim 6, Yang teaches that the strain of the genus Yarrowia may be Yarrowia lypolytica (para. 123).
Regarding claims 10-13, Yang teaches a method of producing biofuel comprising cultivating (i.e., culturing) the genetically modified organism of the invention (para. 266); thus, Yang teaches a composition comprising a culture of the variant strain of Yarrowia. Yang also teaches extracting the lipids produced by the cells (i.e., an extract of the strain; para. 269-270), and biofuels, such as biodiesel, comprising the extracted lipids (para. 272-274); thus, Yang also teaches a composition comprising a fat recovered from the genetically modified cells and/or culture.
With respect to the limitation in the preambles of claims 10-13, “cosmetic composition”, “food composition”, “feed composition”, and “medical composition”, respectively, please note that MPEP 2111.02(II) states "a preamble generally is not limiting when the claim body describes a structurally complete invention such that deletion of the preamble phrase does not affect the structure or steps of the claimed invention." In the instant case, the claims are drawn to compositions comprising “one or more of the variant strain of the genus Yarrowia of claim 1, a culture of the strain, an extract of the strain, a dry product of the strain, a lysate of the strain, and a fat…”, and the preamble does not affect the structure of the composition, as is evidenced by each of the claims reciting identical limitations. Therefore, the preambles in this case recite a statement of purpose or use, and therefore does not further limit the claims.
Response to Arguments
Applicant argues (Remarks, pg. 7-9) “Yang does not disclose that cho2Δ and opi3Δ necessarily increase the fat production in a S. cerevisiae cell” and “Yang’s disclosure for cho2Δ and opi3Δ in S. cerevisiae is in direct contrast to the presently claimed variant strain of the genus Yarrowia.”
These arguments have been fully considered but are not persuasive. Regarding the argument that cho3 and/or opi3 deletion does not necessarily increase the fat production in S. cerevisiae, Applicant admits that “Yang discloses that the cho2Δ and opi3Δ in S. cerevisiae could increase the production of SLDs in specific choline-free conditions….” Furthermore, Yang teaches that the Δcho2 and Δopi3 mutant S. cerevisiae did result in increased production of SLDs in SC media (Table 1) and increased levels of TAG (para. 298). The instant claims only require that the variant Yarrowia strain have an increase fat content when compared to a wild type Yarrowia strain, but does not specify that this must occur in any specific conditions, including choline free conditions. As set forth in para. 19-22 and 25 of the FAOM, Yang teaches that the method of producing the genetically modified Yarrowia comprises making a modification to the organism (i.e., inhibiting PEMT pathway; para. 143 and 146-148) that results in increased TAG production in the cell when compared to the corresponding wild type cell (para. 26). In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993). Thus, one of ordinary skill in the art would believe that Δcho2 and Δopi3 mutant S. cerevisiae demonstrate increased fat production relative to the WT strain, and because Yang teaches that their methods may be performed using Yarrowia, including Yarrowia lipolytica (para. 123), one would “at once envisage” a variant Yarrowia strain comprising a deletion of either the cho2 or opi3 gene (see MPEP 2131.02(III)).
Applicant argues (Remarks, pg. 9) that Fakas “discloses the differences between S. cerevisiae and Yarrowia lipolytica… thereby providing evidence that these two different organisms are indeed not interchangeable in several lipid biosynthesis pathways.”
These arguments have been fully considered but are not persuasive. The teachings of Fakas cited in the FAOM were only used to demonstrate that the Yarrowia genes YALI0E06061g and YALI0E12441g correspond to the gene names cho2 and opi3 (see FAOM para. 20 and 22), not to assert any similarities between S. cerevisiae and Y. lipolytica. Regarding the differences between S. cerevisiae and Y. lipolytica, Yang teaches that Yarrowia can be used in their invention (para. 123).
Conclusion
No claim is allowed.
THIS ACTION IS MADE FINAL. Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
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/BAILEY M MORGAN/Examiner, Art Unit 1645
/VANESSA L. FORD/Supervisory Patent Examiner, Art Unit 1674
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