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 .
Priority
This application is a CON of PCT/JP2022/002034 filed 01/20/2022. Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d) based on application RUSSIAN FEDERATION 2021101096 filed 01/20/2021. Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Information Disclosure Statement
The information disclosure statement (IDS) submitted on 04/06/2026 complies with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Status of the Claims
Claims 1-4 and 7-22 are pending. Claims 1, 3, 4, 7, 10 and 20 are amended. Claims 5 and 6 are cancelled. Claims 7-9 and 12 are withdrawn.
Claims 1-4, 10, 11 and 13-22 (claim set filed 04/06/2026) are examined on the merits herein.
Withdrawal of Rejections
The response and amendment filed on 04/06/2026 are acknowledged. All of the amendment and arguments have been thoroughly reviewed and considered.
For the purposes of clarity of the record, the reasons for the Examiner's withdrawal and/or maintaining if applicable, of the substantive or essential claim rejections are detailed directly below and/or in the Examiner's response to arguments section.
The previous claim 20 rejection under 35 U.S.C. 112(a) (scope of enablement) has been withdrawn necessitated by amendment of claims 1 and 20. Claim 20 was amended to remove limitation: “in the amount larger than that obtainable with a non-modified yeast” and hence no longer require increase in production of PHS and/or PHC by yeast modifications described in claim 1.
Amendment of Claims (1.121)
“Amendments to a claim must be made by rewriting the entire claim with all changes (e.g., additions and deletions) as indicated in this subsection, except when the claim is being canceled. Each amendment document that includes a change to an existing claim, cancellation of an existing claim or addition of a new claim, must include a complete listing of all claims ever presented, including the text of all pending and withdrawn claims, in the application. The claim listing, including the text of the claims, in the amendment document will serve to replace all prior versions of the claims, in the application. 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).” (MPEP 1.121).
The Applicant has amended claim 1 to incorporate claims 5 and 6, however incorporated claims 5 and 6 were amended by removing limitations and those changes are not indicated in amended claim 1.
The claim 1 is not-compliant, however, in the interest of compact prosecution the Examiner will proceed with the examination of the application.
New Rejections
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-3, 10, 11 and 13-22 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 1 recites: “expression and/or activity of a Nem1/Spo7 complex comprising proteins encoded by a NEM1 and SPO7 gene is reduced 50% or less”. It is not clear whether the reduction itself is of 50% or less or expression and/or activity is reduced to residual expression and/or activity of 50% or less. The scope and boundaries of claim 1 are not certain making claim 1 indefinite.
Claims 2, 3, 10, 11 and 13-22, dependent on claim 1, do not resolve the issue mentioned above and are rejected.
Claim 4 recites “reduction by deletion of the gene” and that results in 0% of expression and activity, resolving the uncertainty of claim 1 and therefore claim 4 is not rejected.
Claim 1 is interpreted as directed to reduction of expression and/or activity of Nem1/Spo7 protein complex to 50% or less since the specification describes the degree of reduction of activity and expression of a protein to 50% or less (paragraphs 0097 and 0098).
Maintained/Modified Rejections
The following rejections are maintained and/or modified taking into consideration amendment to claims filed on 04/06/2026.
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 1-4, 10, 11 and 13-22 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.
Claim 1 recites the limitation for the protein encoded by the NEM1 gene to have 95% or higher sequence identity to the amino acid sequence of SEQ ID NO: 26 and the limitation for the protein encoded by the SPO7 gene to have 95%or higher sequence identity to the amino acid sequence of SEQ ID NO: 28 (elected species). Claim 1 mentions activity of a Nem1/Spo7 complex comprising proteins encoded by NEM1 and SPO7. Claim 1 is interpreted as directed to the protein complex comprising protein encoded by NEM1 wherein 5% or less of the sequence vary from SEQ ID NO: 26 and protein encoded by SPO7 wherein 5% or less of the sequence vary from SEQ ID NO: 28 and wherein Nem1/Spo7 protein complex has activity.
Thus, claim 1 broadly encompasses a genus of Nem1/Spo7 protein complex with 95% or more sequence identity of Nem1 to SEQ ID NO: 26 and 95% or more sequence identity of Spo7 to SEQ ID NO: 28. This would represent large pool of variant amino acid sequences encoding the respective proteins which are functional since they provide activity to Nem1/Spo7 complex. At the same time proteins can have 5% or less of sequences that can differ from SEQ ID NO: 26 and 28. The Specification describes Nem1 and Spo7 as a catalytic and regulatory subunits of Nem1/Spo7 protein phosphatase (paragraph 0056). However, the Specification does not provide structure function correlation for catalytic and regulatory subunits of Nem1-Spo7 protein complex and does not describe domains and/or amino acid residues essential for Nem1 and Spo7 proteins and domain and/or amino acid residues which can be modified without loss or increase of Nem1-Spo7 protein activity. Further, applicants have not shown possession of a representative number of species for the functional catalytic and regulatory subunits of Nem1-Spo7 protein complex as Specification provides only examples of deletion of NEM1 gene leading to nonfunctional Nem1-Spo7 protein complex (paragraph 0156). The specification describes that functional variants of protein can have conservative substitutions (paragraph 0068). However, even conservative mutations can lead to significant functional change. For instance, Mirheydari (Mirheydari et al. J. Biol. Chem, 2020, 295, 11473-11485) teaches domains of Nem1 and Spo7 and indicates serines as phosphorylation sites in both subunits phosphorylation of which by protein kinases A and C affect the New1-Spo7 function (p. 11475, Figure 2, p. 11473, right column, 2nd paragraph). Thus, conservative substitution of Ser of phosphorylation sites with Ala or Cys as described in the paragraph 0156 of the Specification will change the functioning of catalytic and regulatory subunits of Nem1-Spo7 protein.
Therefore, one of ordinary skill in the art would not be able to identify which polypeptide sequences that have 95% or higher sequence identity to SEQ ID NO:26 and SEQ ID NO:28 encode for functional Nem1/Spo7 protein complex. One of ordinary skill in the art would conclude based on the lack of representative number of species and the lack of describing the domains or amino acid residues of SEQ ID NO: 26 and 28 critical for the activity of Nem1/Spo7 protein complex, that the Applicant was not in possession of the claimed genus and that the specification fails to satisfy the requirements of written description under 35 U.S.C. 112 (a). Therefore, claim 1 is rejected.
Claims 2-4, 10, 11 and 13-22, dependent on claim 1, do not resolve the issue mentioned above and are rejected.
Response to Arguments
Applicant's arguments filed 04/06/2026 have been fully considered but they are not persuasive.
Please note that claims 5 and 6 were rejected in the previous Office Action for failing to comply with 112(a) written description and not with 112(a) enablement as recited by the Applicant in the Remarks, p. 6. Arguments related to written description will be addressed.
Applicant argues (addressing p. 7-8 of the Remarks) that limitations from cancelled claims 5 and 6 recited in claim 1 were amended to change sequence identity from 90% to 95% and by removing functional language. Applicant argues that Nem1/Spo7 complex is well characterized and its structure-function relationships were intensively studied and are part of the established knowledge in the art. These arguments are not persuasive because:
MPEP 2163 states: “The disclosure of only one species encompassed within a genus adequately describes a claim directed to that genus only if the disclosure "indicates that the patentee has invented species sufficient to constitute the gen[us]." See Enzo Biochem, 323 F.3d at 966, 63 USPQ2d at 1615; Noelle v. Lederman, 355 F.3d 1343, 1350, 69 USPQ2d 1508, 1514 (Fed. Cir. 2004) (Fed. Cir. 2004) ("[A] patentee of a biotechnological invention cannot necessarily claim a genus after only describing a limited number of species because there may be unpredictability in the results obtained from species other than those specifically enumerated."). In instant case, 5% variability represents about 22 variant amino acid residues for Nem1 (from total of 446 amino acid residues) and about 13 amino acid residues for Spo7 (from total of 259 amino acid residues), i.e. about 35 variable amino acids for the complex. Although the functional language for SEQ ID NO:26 to represent catalytic subunit and for SEQ ID NO:28 to function as a regulatory subunit of Nem1/Spo7 protein phosphatase was removed, claim 1 has limitation of reduction in expression and/or activity of Nem1/Spo7 complex and hence function of Nem1/Spo7 needs to be considered. However, the specification does not provide description of the structure function relationship for Nem1 and Spo7 proteins. The specification does not have representative species to variant polypeptides with at least 95% sequence identity to SEQ ID NO: 26 or 28 and describes only complete deletion of Nem1 encoded gene. Thus, Applicant have not demonstrated a representative number of species within the claimed genus for the skilled artisan to envisage that Applicant possessed the claimed genus. Additionally, the prior art presented in IDS does not provide structure function relationship. The prior art of Su, Applicant refers to, is directed to the mechanism of Nem1/Spo7 catalyzed reaction rather than its structure. Mirheydari concentrates on residues 54-56 (LLI) of Spo7, mentions domains of Nem1 and Spo7 and serines as phosphorylation sites essential for New1-Spo7 function but not the other conserved and/or critical residues (p. 11475, Figure 2, p. 11473, right column, 2nd paragraph). Thus, since the specification does not describe the domains and/or amino acid residues of SEQ ID NO: 26 and 28 essential for Nem1/Spo7 activity and does not provide the representative species one would conclude that the Applicant does not have possession of the full scope of the claimed invention and therefore the 35 U.S.C. 112(a) rejection (written description) is maintained.
Claim Rejections - 35 USC § 103
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Claims 1-4 and 15-22 are rejected under 35 U.S.C. 103 as being unpatentable over Schwab (WO 2017033463 A1 on record in IDS) in view of Santos-Rosa (Santos-Rosa et al. The EMBO, 2005, 24, 1931- 1941) as evidenced by Siniossoglou (Siniossoglou et al. The EMBO Journal, 1998, 17, 6449-6464), GenBank AAB6843.1 (GenBank, 2008, Yhr004cp [Saccharomyces cerevisiae] [retrieved on 12/26/2025]. Retrieved from the Internet: <Yhr004cp [Saccharomyces cerevisiae] - Protein - NCBI>) and GenBank AAC04949.1 (GenBank, 2004, Spo7p [Saccharomyces cerevisiae] [retrieved on 12/26/2025]. Retrieved from the Internet: <Spo7p [Saccharomyces cerevisiae] - Protein - NCBI>).
Regarding claim 1, Schwab teaches a method for producing an objective substance such as spingoid bases and sphingolipids by cultivating yeast in the presence of additive and collecting objective substance (Abstract). The spingoid bases include phytosphingosine (PHS) (paragraph 0013) and sphingolipids include phytoceramide (PHC) (paragraph 0014). Schwab describes modification of the yeast to reduce expression and/or activity of several proteins encoded by the corresponding genes, such as LCB4 (paragraph 0006).
Schwab does not teach modification of the yeast to reduce expression and/or activity of a Nem1/Spo7 complex to 50% or less (see interpretation of claim 1 for 112(b) rejection), the protein encoded by NEM1 gene to comprise an amino acid sequence having 95% or higher sequence identity to SEQ ID NO: 26 (elected species) and the protein encoded by SPO7 gene to comprise an amino acid sequence having 95% or higher sequence identity to SEQ ID NO: 28 (elected species).
Santos-Rosa teaches that Smp2, the yeast homologue of mammalian lipin, is a key regulator of nuclear membrane growth during cell cycle (Abstract). Santos-Rosa describes that Smp2 is phosphorylated by Cdc28/Cdka and dephosphorylated by phosphatase complex consisting of Nem1 and Spo7. The dephosphorylation of Smp2 inhibits cell division (Abstract). Santos-Rosa mentions that deletion of Nem1-Spo7 (that reads on reduction in expression and/or activity to 50% or less) induces nuclear expansion (p. 1934, right column, last paragraph), however, cells grow normally (p. 1932, left column, 3rd paragraph). Santos -Rosa discloses that accumulation of dephosphorylated Smp2 is toxic, results in significant increase of cells with short metaphase spindle and inhibits mitotic division (p. 1935, left column, 1st paragraph; p. 1939, left column, 1st paragraph).
Santos-Rosa teaches that Nem1 is the catalytic subunit and Spo7 is the regulatory subunit of Nem1-Spo7 holoenzyme (p. 1934, left column, 1st paragraph). Santos-Rosa refers to identification of Nem1 and Spo7 proteins in prior art of Siniossoglou (p. 1932, left column, 2nd paragraph). The identified Nem1 and Spo7 proteins have the GenBank accession No. 500822 for NEM1 and GenBank accession No 349744 for SPO7 as evidenced by Siniossoglou (p. 6450, right column, 1st paragraph). The GenBank accession No. 500822 provides amino acid sequence for the protein encoded by NEM1 gene which is 100% identical to instant SEQ ID NO: 26 according to BLAST analysis as evidenced by GenBank AAB6831.1. The GenBank accession No. 349744 provides amino acid sequence for the protein encoded by SPO7 gene which is 100% identical to instant SEQ ID NO: 28 according to BLAST analysis as evidenced by GenBank AAC04949.1.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to combine teachings of Schwab and Santos-Rosa and modify yeast used in the method of production of PHS and/or PHC taught by Schwab by reducing expression and/or activity of Nem1-Spo7 phosphatase described by Santos-Rosa. One would have been motivated to make this modification since Santos-Rosa teaches that Nem1-Spo7 dephosphorylate Smp2 that leads to inhibition of cell division and hence reduction of Nem1-Spo7 activity will provide proliferation of yeast necessary for production of the objective substance of Schwab teaching.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to follow Santos-Rosa teaching and use genes NEM1 and SPO7 encoding amino acid sequences for Nem1 and Spo7 proteins which are 100% identical to instant SEQ ID NO: 26 and SEQ ID NO: 28, respectively, as evidenced by Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1, for modification of the yeast producing PHS and/or PHC based on Schwab and Santos -Rosa teachings. One would have been motivated to do that since GenBank AAB6831.1 and GenBank AAC04949.1 provide amino acid sequences identified by Siniossoglou and used by Santos-Rosa for Nem1 and Spo7 and Santos-Rosa teaches that Nem1 is the catalytic subunit and Spo7 is the regulatory subunit of Nem1-Spo7 phosphatase that dephosphorylates Smp2 leading to inhibition of cell division. A skilled artisan would have reasonably expected success in that because Schwab provides method of production of PHS and/or PHC in yeast, Santos-Rosa teaching suggests modification to support yeast growth and proliferation and Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 provide sequences of Nem1 and Spo7 for modification. Thus, teachings of Schwab and Santos-Rosa as evidenced by Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 render claim 1 obvious.
Regarding claim 2, Santos-Rosa teaches that Nem1 and Spo7 form a complex and that both subunits are required for the catalytic activity against its substrate, Smp2 (p. 1938, right column, 1st paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention that reduction of the expression and/or activity of the catalytic subunit of Nem1/ Spo7 protein complex, i.e. Nem1, is sufficient to reduce activity of Nem1-Spo7 phosphatase against Smp2 and provide cell proliferation. One would have been motivated to make assumption with the reasonably expected success because Santos-Rosa teaches that both subunits of Nem1-Spo7 are required for the catalytic activity of Nem1-Spo7. Thus, Schwab and Santos-Rosa teachings as evidenced by Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 render claim 2 obvious.
Regarding claims 3 and 4, Schwab teaches that modification of the yeast to reduce activity of the protein modified can be attained by reducing expression of the gene encoding the protein (paragraph 0079) or disrupting the gene (paragraph 0081). Schwab mentions that disruption of the gene can be done by deleting part or the whole coding region of the gene (paragraph 0082).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to reduce activity of Nem1/Spo7 complex by reducing expression or disrupting the genes encoding these proteins. One would have been motivated to do that with the reasonably expected success because Schwab teaches different techniques for reduction of expression and disruption of several genes and the same techniques can be applied to NEM1 and SPO7 genes . Thus, teachings of Schwab and Santos-Rosa as evidenced by Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 render claims 3 and 4 obvious.
Regarding claim 15, Schwab teaches phytosphingosine C18 PHS which has a saturated C18 alkyl chain (paragraph 0013) that corresponds to claimed C18:0 PHS (elected species) since the Specification describes that C18:0 PHS has saturated C18 alkyl chain (paragraph 0033). Thus, teachings of Schwab and Santos-Rosa as evidenced by Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 render claim 15 obvious.
Regarding claims 16 and 17, Schwab teaches that the culture medium contains an additive that is able to associate with, bind to, solubilize and/or capture the objective substance (paragraph 0006). The additive includes cyclodextrin (elected species) (paragraph 0006). Thus, teachings of Schwab and Santos-Rosa as evidenced by Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 render claims 16 and 17 obvious.
Regarding claims 18 and 19 Schwab teaches the yeast to belong to Saccharomyces and being Saccharomyces cerevisiae (paragraph 0006). Thus, teachings of Schwab and Santos-Rosa as evidenced by Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 render claims 18 and 19 obvious.
Regarding claim 20, Schwab teaches production of PHS by different modified yeast strains. Schwab refers to producing ability as ability to produce and accumulate an objective substance in culture medium or cells (paragraph 0011). In Example 3 (paragraph 0121) Schwab shows that production of PHS in the basic strain reaches 1 mg/L and in the modified strain – more than 16 mg/L (Figure 2) in the presence of cyclodextrin. Santos-Rosa teaches that Nem1/Spo-7 dephosphorylate Smp2 and that can inhibit cell division and is expected to support production of PHS as described above for claim 1.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to expect that the yeast modification of reduction of the expression and/or activity of Nem1/Spo7 protein phosphatase as taught by Santos-Rosa will provide the level of produced and accumulated objective substance of 5 mg/L or more when applied to method of production of PHS and PHC taught by Schwab for other modifications. One would have been motivated to come to that conclusion with the reasonably expected success because Schwab showed significant increase of produced PHS in modified yeast strains and Santos-Rosa teaches that dephosphorylation of Smp2 by Nem1/Spo7 can result in inhibition of cell division and hence reduction of Nem1/Spo7 expression and/or activity can support yeast cells growth and proliferation and increase production of objective substance by method taught by Schwab. Additionally, one of ordinary skill in the art would expect the amount of produced objective substance to increase with the increase of the reaction incubation time and, since claim does not contain time parameters, the amount of 5 mg/L can be eventually reached even for unmodified yeast of Schwab teaching producing 1 mg/L of PHS. Thus, Schwab and Santos-Rosa teachings as evidenced by Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 render claim 20 obvious.
Regarding claim 21, Schwab teaches collecting the objective substance from cells of the yeast and/or culture medium (paragraph 0006). Thus, teachings of Schwab and Santos-Rosa as evidenced by Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 render claim 21 obvious.
Regarding claim 22, Schwab teaches producing sphingoid base (which is PHS as described in the Specification (paragraph 0033)) and converting it to PHC by chemical reaction of sphingoid base and fatty acid (paragraph 0109). Thus teachings of Schwab and Santos-Rosa as evidenced by Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 render claim 22 obvious.
Claims 10, 11, 13 and 14 are rejected under 35 U.S.C. 103 as being unpatentable over Schwab (WO 2017033463 A1 on record in IDS) in view of Santos-Rosa (Santos-Rosa et al. The EMBO, 2005, 24, 1931-1941) as evidenced by Siniossoglou (Siniossoglou et al. The EMBO Journal, 1998, 17, 6449-6464), GenBank AAB6843.1 (GenBank, 2008, Yhr004cp [Saccharomyces cerevisiae] [retrieved on 12/26/2025]. Retrieved from the Internet: <Yhr004cp [Saccharomyces cerevisiae] - Protein - NCBI>) and GenBank AAC04949.1 (GenBank, 2004, Spo7p [Saccharomyces cerevisiae] [retrieved on 12/26/2025]. Retrieved from the Internet: <Spo7p [Saccharomyces cerevisiae] - Protein - NCBI>) as applied to claim 1 above, and further in view of Obeid (Obeid et al. Biochim. Biophys. Acta, 2002, 1585, 163-171).
The teachings of Schwab and Santos-Rosa have been set forth above.
Regarding claim 10, Schwab teaches that expression of the gene coding for protein can be increased 1.5 times (paragraph 0056) and describes different approaches to achieve that (paragraphs 0057-0067). However, Schwab and Santos-Rosa do not teach modification of the yeast to increase expression and/or activity of the protein encoded by YPC1 for production of PHS (elected species).
Regarding claims 10 and 11, Obeid teaches metabolism and biology of yeast sphingolipids (Abstract). Obeid describes that ceramides, sphingoid bases and their phosphates can be generated from breakdown of sphingolipids (p. 167, right column, 3rd paragraph). Obeid discloses that yeast YPC1p is a phytoceramidase that preferentially hydrolyzes phytoceramide (PHC) (p. 165, right column, 4th paragraph). Obeid mentions that PHS can be generated from de novo or breakdown pathway, i.e. from hydrolysis of phytoceramide by phytoceramidase encoded by YPC1 (p. 167, right column, last paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to follow guidance of Obeid and further modify the yeast producing PHS based on Schwab and Santos-Rosa teachings by increasing expression of phytoceramidase encoded by YPC1. One would have been motivated to do that since Obeid teaches that PHS can be generated by hydrolysis of phytoceramide which is the preferential reaction catalyzed by phytoceramidase encoded by YPC1 gene and increased expression of YPC1 gene will lead to increased production of PHS and Schwab teaches different methods to increase expression of protein and indicates that expression of protein can increase 1.5 times. A skilled artisan would have reasonably expected success in this combination because Schwab provides method of production of PHS in yeast and methods of modification of protein expression, Santos-Rosa teaching suggests modification to support yeast growth and proliferation and Obeid teaching points to further yeast modification to add PHS produced by phytoceramide hydrolysis to de novo production of PHS. Thus, Schwab, Santos-Rosa and Obeid teachings as evidenced by Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 render claims 10 and 11 obvious.
Regarding claims 13 and 14, Schwab teaches that modification of the yeast to increase activity of the protein modified can be attained by increasing expression of the gene encoding the protein (paragraph 0056). Schwab mentions that expression of the gene can be increased by improving the transcription efficiency of the gene and transcription efficiency can be improved by modifying an expression control sequence of the gene (paragraph 0066). Schwab provides description of several strong promoters that can be used to increase transcriptional efficiency (paragraph 0067).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to increase activity of phytoceramidase by increasing expression of YPC1 gene encoding phytoceramidase and increase expression by modifying an expression control sequence of the gene as described by Schwab. One would have been motivated to do that with the reasonably expected success because Schwab provides instructions to increase expression of gene of interest including modification of the expression control sequence of the gene and the same techniques can be applied to YPC1 gene. Thus, teachings of Schwab, Santos-Rosa and Obeid as evidenced by Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 render claims 13 and 14 obvious.
Response to Arguments
Applicant's arguments filed 04/06/2026 have been fully considered but they are not persuasive.
Applicant argues (addressing p. 9-12 of the Remarks) that reducing Nem1/Spo7 activity “results in accumulation of phosphorylated Smp2 which represents a fundamentally different cellular state with distinct regulatory consequences. Santos-Rosa does not teach or suggest that this alternative state promotes proliferation, nor that it is beneficial for production of sphingolipid-related compounds.” Applicant further argues that Santos-Rosa does not disclose that deletion of NEM1 or SPO7 results in improved yeast growth and reports that nem1∆ and spo7∆ grow normally. Additionally, deletion of Nem1-Spo7 results in nuclear membrane expansion that indicates cell cycle dysregulation not enhanced proliferation and teaches away. Applicant also argues that: “Schwab teaches production of PHS and PHC via yeast cultivation and suggests modifying certain genes to influence production. However, Schwab does not mention NEM1 or SPO7, nor does it suggest targeting regulators of nuclear membrane growth or cell cycle progression”. Applicant argues that there is no motivation to combine prior art and combination does not have reasonable expectation of success, is based on impermissible hindsight and does not provide any guidance linking Nem1/Spo7 to improved production of PHS and PHC.
These arguments are not persuasive because:
In response to applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971). In instant case, the rejection is based on combination of references wherein Schwab teaches method for producing the claimed objective substances, PHS and PHC, in modified yeast (Abstract) and Santos-Rosa suggests that dephosphorylation of Smp2 catalyzed by Nem1/Spo7 inhibits cell division (Abstract) providing motivation to reduce Nem1/Spo7 activity in yeast during objective substance production. Although Santos-Rosa does not show the increase in proliferation of cell with reduction of Nem1/Spo7 activity, Santos-Rosa discloses that accumulation of dephosphorylated Smp2 is toxic, results in significant increase of cells with short metaphase spindle and inhibits mitotic division (p. 1935, left column, 1st paragraph; p. 1939, left column, 1st paragraph) and hence prevention of Smp2 dephosphorylation is expected to prevent toxicity and provide cell division and proliferation which is necessary for production of objective substances. Regarding nuclear membrane expansion, Santos-Rosa teaches nucleus expansion during cell cycle of yeast as part of normal cell division (p 1931, right column, 2nd paragraph) and mentions that Nem1∆ and Spo7∆ mutant cells grow normally (p. 1932, left column, 3rd paragraph) and hence are expected to produce objective substances. It is noted that the amended claims do not require increase in the production of objective substance.
Therefore, the 35 U.S.C. 103 rejection is maintained and modified necessitated by amendment of claims.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 1-4, 15-19, 21 and 22 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4-6, 11-15, 18 and 20 of copending Application No. 18/351,225 (reference application) in view of Siniossoglou (Siniossoglou et al. The EMBO Journal, 1998, 17, 6449-6464) as evidenced by GenBank AAB6843.1 (GenBank, 2008, Yhr004cp [Saccharomyces cerevisiae] [retrieved on 12/26/2025]. Retrieved from the Internet: <Yhr004cp [Saccharomyces cerevisiae] - Protein - NCBI>) and GenBank AAC04949.1 (GenBank, 2004, Spo7p [Saccharomyces cerevisiae] [retrieved on 12/26/2025]. Retrieved from the Internet: <Spo7p [Saccharomyces cerevisiae] - Protein - NCBI>) .
Claim 1 of instant application is directed to a method for producing an objective substance comprising cultivating yeast to produce the objective substance which is selected from PHS and PHC wherein the yeast is modified to reduced expression and/or activity of a Nem1/Spo7 complex to 50% or less wherein a protein encoded by NEM1 gene comprises an amino acid sequence having 95% or higher sequence identity to SEQ ID NO: 26 and a protein encoded by SMO7 gene comprises an amino acid sequence having 95% or higher sequence identity to SEQ ID NO: 26.
Claim 1 of reference application teaches a method for producing an objective substance comprising cultivating yeast to produce the objective substance in a medium containing a fatty acid wherein the objective substance is selected from PHS and PHC. Claim 4 of reference application teaches modification of the expression and/or activity of selected genes, including NEM1 and SPO7 genes. Claim 6 of reference application teaches that activity of recited proteins is reduced by deletion of the gene encoding the protein. That corresponds to reduction in expression and/or activity of Nem1/Spo7 complex to less than 50%.
Regarding claim 1, reference claim 1, 4 and 6 do not teach the protein encoded by NEM1 gene to comprise an amino acid sequence having 95% or higher sequence identity to SEQ ID NO: 26 (elected species) and the protein encoded by SPO7 gene to comprise an amino acid sequence having 95% or higher sequence identity to SEQ ID NO: 28 (elected species). Regarding fatty acid in the medium of the reference claim, instant claim 1 had “comprising” language for the method that does not exclude presence of additional components in the medium.
Siniossoglou teaches identification of Nem1 and Spo7 proteins (Abstract). The identified Nem1 and Spo7 proteins have the GenBank accession No. 500822 for NEM1 and GenBank accession No 349744 for SPO7 as described by Siniossoglou (p. 6450, right column, 1st paragraph). The GenBank accession No. 500822 provides amino acid sequence for the protein encoded by NEM1 gene which is 100% identical to instant SEQ ID NO: 26 according to BLAST analysis as evidenced by GenBank AAB6831.1. The GenBank accession No. 349744 provides amino acid sequence for the protein encoded by SPO7 gene which is 100% identical to instant SEQ ID NO: 28 according to BLAST analysis as evidenced by GenBank AAC04949.1.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to follow Siniossoglou teaching and use genes NEM1 and SPO7 encoding amino acid sequences for Nem1 and Spo7 proteins which are 100% identical to instant SEQ ID NO: 26 and SEQ ID NO: 28, respectively, as evidenced by GenBank AAB6831.1 and GenBank AAC04949.1 for modification of the yeast producing PHS and/or PHC based on reference claims 1, 4 and 6. One would have been motivated to do that since reference claims teach reduction in expression and/or activity of Nem1 and Spo7 proteins for production of PHS and PHC and GenBank AAB6831.1 and GenBank AAC04949.1 provide amino acid sequences identified by Siniossoglou. A skilled artisan would have reasonably expected success in that because reference claims provides method of production of PHS and/or PHC in yeast by modification of NEM1 and SPO7 genes and Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 provide sequences of Nem1 and Spo7 for modification. Thus, claims 1, 4 and 6 of reference application and Siniossoglou teaching as evidenced by GenBank AAB6831.1 and GenBank AAC04949.1 render claim 1 obvious.
Claim 2 of instant application is directed to reduction of the expression and/or activity of at least protein encoded by NEM1 gene. That corresponds to reference claim 4 teaching reduction of expression and/or activity of group of genes, including NEM1 gene.
Claim 3 of instant application is directed to reduction of activity of one or more genes in Nem1/Spo7 complex by disrupting one or more genes encoding these proteins. That correspond to reference claim 5.
Claim 4 of instant application is drawn to reduction of the expression and/or activity of the protein complex by deletion of the gene encoding the protein. That corresponds to reference claim 6.
Claim 15 of instant application is drawn to selection of PHS including C18:0 PHS (elected species). That correspond to claim 11 of reference application.
Claim 16 of instant application is drawn to an additive that is able to associate with, bind to, solubilize, and/or capture the objective substance. That correspond to claim 12 of reference application.
Claim 17 of instant application is drawn to selected additive which is cyclodextrin (elected species). That correspond to claim 13 of reference application.
Claim 18 of instant application is drawn to the yeast belonging to Saccharomyces. That correspond to claim 14 of reference application.
Claim 19 of instant application is drawn to the yeast being Saccharomyces cerevisiae. That correspond to claim 15 of reference application.
Claim 21 of instant application is drawn to collecting the objective substance from cells of the yeast and/or from the culture medium. That correspond to claim 18 of reference application.
Claim 22 of instant application is drawn to producing PHC comprising producing PHS and converting it to the PHC. That correspond to claim 20 of reference application.
Claims 10, 11, 13, 14 and 20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1, 4 and 6-9 of copending Application No. 18/351,225 (reference application) in view of Siniossoglou (Siniossoglou et al. The EMBO Journal, 1998, 17, 6449-6464) as evidenced by GenBank AAB6843.1 (GenBank, 2008, Yhr004cp [Saccharomyces cerevisiae] [retrieved on 12/26/2025]. Retrieved from the Internet: <Yhr004cp [Saccharomyces cerevisiae] - Protein - NCBI>) and GenBank AAC04949.1 (GenBank, 2004, Spo7p [Saccharomyces cerevisiae] [retrieved on 12/26/2025]. Retrieved from the Internet: <Spo7p [Saccharomyces cerevisiae] - Protein - NCBI>) as applied to claim 1 above and further in view of Schwab (WO 2017033463 A1 on record in IDS).
Teaching of the reference claims 1, 4 and 6, Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 rendering claim 1 obvious have been set forth above.
Claims 10 and 11 of instant application are drawn to further modification of the yeast producing PHS to increase expression and/or activity of the protein encoded by YPC1 gene (elected species) 1.5 times. Reference claim 7 is directed to modification of the gene selected from the group including YPC1 gene to increase its expression and/or activity for production of PHS. However, the reference claim 7, Siniossoglou, GenBank AAB6831.1 and GenBank AAC04949.1 do not teach increase in expression and/or activity 1.5 times.
Regarding claim 10, Schwab teaches a method for producing an objective substance such as PHS and PHC (Abstract, paragraph 0014). Schwab describes modification of the yeast to increase expression and/or activity of several proteins encoded by the corresponding genes (paragraph 0006). Schwab teaches that expression of the gene coding for protein can be increased 1.5 times (paragraph 0056) and describes different approaches to achieve that (paragraphs 0057-0067).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to follow Schwab teaching and apply provided instructions to increase expression of a gene 1.5 times to YPC1 gene taught in reference claim 7 for producing PHS based on reference claims 1, 4 and 6. One would have been motivated to do that with reasonably expected success since reference claims teaches increase of expression and/or activity of YPC1 gene in yeast and Schwab provides instructions for manipulation of genes expression in yeast and both reference claims and Schwab teach production of PHS in modified yeast. Thus, reference claims 1, 4, 6 and 7, Siniossoglou and Schwab teachings as evidenced by GenBank AAB6831.1 and GenBank AAC04949.1 render claims 10 and 11 obvious.
Claim 13 of instant application is drawn to increase in activity of the protein by increasing the expression of the gene encoding the protein. That correspond to claim 8 of reference application.
Claim 14 of instant application is drawn to increase in expression and/or activity of the protein by modifying an expression control sequence of the gene encoding the protein (elected species). That correspond to claim 9 of reference application.
Claim 20 of instant application is directed to production and accumulation of 5 mg/L or more of the objective substance. Reference claim 1 teaches production of objective substance, PHS and PHC, however, does not teach production and accumulation of 5 mg/L or more of objective substance.
Schwab teaches production of PHS by different modified yeast strains. Schwab refers to producing ability as ability to produce and accumulate an objective substance in culture medium or cells (paragraph 0011). In Example 3 (paragraph 0121) Schwab shows that production of PHS in the basic strain reaches 1 mg/L and in the modified strain – more than 16 mg/L (Figure 2) in the presence of cyclodextrin.
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to expect that the yeast modification of reduction of the expression and/or activity of NEM1 and/or SPO7 genes as taught by reference claims 1, 4 and 6 will increase the level of produced and accumulated objective substance to 5 mg/L or more as described by Schwab for other modifications. One would have been motivated to make that conclusion with the reasonably expected success because Schwab showed significant increase of produced PHS in modified yeast strains from 1 mg/L to 16 mg/L and besides, one of ordinary skill in the art would expect the amount of produced objective substance to increase with the increase of the incubation time and since instant claim 20 does not contain time parameters the amount of 5 mg/L can be eventually reached even for unmodified yeast of Schwab teaching producing 1 mg/L of PHS. Thus, reference claims 1, 4 and 6, Siniossoglou and Schwab teachings as evidenced by GenBank AAB6831.1 and GenBank AAC04949.1 render claim 20 obvious.
Therefore, since instant claims 1-4, 10, 11 and 13-22 encompass the subject matter of the reference claims 1, 4-9, 11-15, 18 and 20, they are rejected under obviousness double patenting.
This is a provisional nonstatutory double patenting rejection.
Response to Arguments
Applicant's arguments filed 04/06/2026 have been fully considered but they are not persuasive.
Applicant’s argues (addressing p. 12 of the Remarks) that since claims 5-6 were not rejected under double patenting and claims 5 and 6 are combined with amended claim 1 from which all claims depend, the claims are prima facie free of the double patenting rejection.
Current rejection is made non-final to correct errors of the double patenting rejection of the first non-final rejection and modified double patenting rejection is applied as described above.
Conclusion
No claims are allowed.
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/L.G.K./Examiner, Art Unit 1653
/SHARMILA G LANDAU/Supervisory Patent Examiner, Art Unit 1653
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