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 14 April 2026 is acknowledged. Claims 13-26 are currently pending. Of those, claims 13-14 and 16-17 are amended. Claims 18-26 are new, and no claims are withdrawn. Claims 1-12 are cancelled. Claims 13-26 will be examined on the merits herein.
Response to Amendment
Applicants’ arguments filed 14 April 2026 are acknowledged. For clarity, in this Action, said arguments will be referred to as “Remarks” and the Non-Final Office Action mailed 14 January 2026 will be referred to as “NFOA”.
Objection(s) and Rejection(s) Withdrawn
The rejection of claims 13 and 17 under 35 U.S.C. 112(b) is withdrawn in view of the amendments to the claims.
The rejection of claim 14 under 35 U.S.C. 112(d) is withdrawn in view of the claim amendments.
The rejection of claims 13-17 under 35 U.S.C. 102 is withdrawn in view of the amendments to the claims.
Objection(s)
Nucleotide and/or Amino Acid Sequence Disclosures
REQUIREMENTS FOR PATENT APPLICATIONS CONTAINING NUCLEOTIDE AND/OR AMINO ACID SEQUENCE DISCLOSURES
Items 1) and 2) provide general guidance related to requirements for sequence disclosures.
37 CFR 1.821(c) requires that patent applications which contain disclosures of nucleotide and/or amino acid sequences that fall within the definitions of 37 CFR 1.821(a) must contain a "Sequence Listing," as a separate part of the disclosure, which presents the nucleotide and/or amino acid sequences and associated information using the symbols and format in accordance with the requirements of 37 CFR 1.821 - 1.825. This "Sequence Listing" part of the disclosure may be submitted:
In accordance with 37 CFR 1.821(c)(1) via the USPTO patent electronic filing system (see Section I.1 of the Legal Framework for Patent Electronic System (https://www.uspto.gov/PatentLegalFramework), hereinafter "Legal Framework") as an ASCII text file, together with an incorporation-by-reference of the material in the ASCII text file in a separate paragraph of the specification as required by 37 CFR 1.823(b)(1) identifying:
the name of the ASCII text file;
ii) the date of creation; and
iii) the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(1) on read-only optical disc(s) as permitted by 37 CFR 1.52(e)(1)(ii), labeled according to 37 CFR 1.52(e)(5), with an incorporation-by-reference of the material in the ASCII text file according to 37 CFR 1.52(e)(8) and 37 CFR 1.823(b)(1) in a separate paragraph of the specification identifying:
the name of the ASCII text file;
the date of creation; and
the size of the ASCII text file in bytes;
In accordance with 37 CFR 1.821(c)(2) via the USPTO patent electronic filing system as a PDF file (not recommended); or
In accordance with 37 CFR 1.821(c)(3) on physical sheets of paper (not recommended).
When a “Sequence Listing” has been submitted as a PDF file as in 1(c) above (37 CFR 1.821(c)(2)) or on physical sheets of paper as in 1(d) above (37 CFR 1.821(c)(3)), 37 CFR 1.821(e)(1) requires a computer readable form (CRF) of the “Sequence Listing” in accordance with the requirements of 37 CFR 1.824.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed via the USPTO patent electronic filing system as a PDF, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the PDF copy and the CRF copy (the ASCII text file copy) are identical.
If the "Sequence Listing" required by 37 CFR 1.821(c) is filed on paper or read-only optical disc, then 37 CFR 1.821(e)(1)(ii) or 1.821(e)(2)(ii) requires submission of a statement that the "Sequence Listing" content of the paper or read-only optical disc copy and the CRF are identical.
Specific deficiencies and the required response to this Office Action are as follows:
Specific deficiency - This application fails to comply with the requirements of 37 CFR 1.821 - 1.825 because it does not contain a "Sequence Listing" as a separate part of the disclosure and the CRF of the “Sequence Listing” filed 14 April 2026 is defective.
Required response - Applicant must provide:
A "Sequence Listing" part of the disclosure, as described above in item 1); together with
An amendment specifically directing its entry into the application in accordance with 37 CFR 1.825(a)(2);
A statement that the "Sequence Listing" includes no new matter as required by 37 CFR 1.825(a)(4); and
A statement that indicates support for the amendment in the application, as filed, as required by 37 CFR 1.825(a)(3)
If the "Sequence Listing" part of the disclosure is submitted according to item 1) a) or b) above, Applicant must also provide:
A substitute specification in compliance with 37 CFR 1.52, 1.121(b)(3) and 1.125 inserting the required incorporation-by-reference paragraph, consisting of:
A copy of the previously-submitted specification, with deletions shown with strikethrough or brackets and insertions shown with underlining (marked-up version);
A copy of the amended specification without markings (clean version); and
A statement that the substitute specification contains no new matter.
If the "Sequence Listing" part of the disclosure is submitted according to item 1) c) or d) above, Applicant must also provide:
A CRF in accordance with 37 CFR 1.821(e)(1) or 1.821(e)(2) as required by 37 CFR 1.825(a)(5); and
A statement according to item 2) a) or b) above.
Claim Objections
Claim 14 is newly objected to because of the following informalities: in line 2, “yeast cells of a nucleic acid” should read “yeast cells a nucleic acid”. 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 13-17 remain rejected and claims 18-19 and 24-25 are newly rejected under 35 U.S.C. 102(a)(1) as being anticipated by Bursać and Lithgow (2009, FEBS Letters; cited in IDS; herein “Bursać”).
The previous rejection has been amended to reflect the amendments to the claims.
Regarding claims 13-14 and 24, Bursać teaches a method comprising fermenting a carbohydrate substrate (i.e., glucose or glycerol) with modified yeast cells, which are derived from parental Saccharomyces cerevisiae cells and comprise a plasmid for the over expression of Jid1 under the control of the GAL1 promoter (i.e., a genetic alteration that causes the modified yeast cells to produce an increased amount of JID1 polypeptides compared to the parental yeast cells and a nucleic acid capable of directing the expression of a JID1 polypeptide to a level above that of the parental cell) (sections 2.1 and 2.2).
Regarding the limitations “for increased production of alcohol from a carbohydrate substrate” and “wherein the modified yeast cells produce during fermentation an increased amount of alcohol compared to the amount of alcohol produced by the otherwise identical parent yeast cells” in claim 13 and the limitations of claims 15-17 and 25, Bursać teaches a composition that is substantially identical to that recited in claims 13-14, i.e., modified yeast cells comprising a genetic alteration that causes the modified yeast cells to produce an increased amount of JID1 polypeptides compared to parental yeast cells; therefore, the function of increased production of alcohol from a carbohydrate substrate and producing during fermentation an increased amount of alcohol compared to the amount of alcohol produced by the otherwise identical parent yeast cells (as in claim 13), the properties of increased alcohol production of at least 0.5% (as in claim 15), at least a 20% increase in the amount of JID1 polypeptides compared to parental yeast cells grown under equivalent conditions (as in claim 16), at least a 2-fold increase in the amount of JID1 mRNA compared to parental yeast cells grown under equivalent conditions (as in claim 17), and the function of increased production of ethanol (as in claim 25) are presumed to be inherent to the S. cerevisiae cells taught by Bursać. From MPEP 2112.02(II): “[W]hen the claim recites using an old composition or structure and the ‘use’ is directed to a result or property of that composition or structure, then the claim is anticipated. In re May, 574 F.2d 1082, 1090, 197 USPQ 601, 607 (CCPA 1978).” See also MPEP 2111.02 and 2112 for a discussion of inherency (“Where the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977).”). Thus, claims 13-17 and 25 are anticipated by Bursać.
Regarding claims 18-19, Bursać teaches that the over-expression of Jid1 is attained by introduction of the pYX233 expression cassette containing the JID1 open reading frame (i.e., an exogenous JID1 gene; section 2.2).
Response to Arguments
Applicant argues (Remarks, pg. 7-9) that Bursać does not disclose a fermentation process, a method of producing alcohol, or cultivating a modified yeast cell under alcohol-producing conditions and that the instant claims are directed to the use of a modified yeast cell in a fermentation method that results in increased alcohol production.
Applicant also argues (Remarks, pg. 9) that the modified S. cerevisiae of Bursać does not inherently lead to increased alcohol production and that “the claimed increase in alcohol production does not necessarily result from practicing the reference as taught.”
This argument has been carefully considered but is not persuasive. Regarding the argument that Bursać does not disclose a fermentation process, a method of producing alcohol, or cultivating a modified yeast cell under alcohol-producing conditions, fermentation is known in the art to be a process of breaking down a substance by microorganisms, which necessarily occurs in the modified yeast of Bursać, which is grown on a carbohydrate source. As stated in the amended 102 rejection above, the S. cerevisiae of Bursać is substantially identical to the claimed modified yeast (i.e., modified yeast comprising a genetic alteration that causes the modified yeast cells to produce an increased amount of JID1 polypeptides); because that is the only structural requirement of the claimed modified yeast cell having a function of producing during fermentation an increased amount of alcohol compared to otherwise identical parental cells, one of ordinary skill in the art would presume that said function is inherent to any modified yeast having that structure, unless the art teaches otherwise. MPEP 2112.02(II) states, “[W] hen the claim recites using an old composition or structure and the ‘use’ is directed to a result or property of that composition or structure, then the claim is anticipated. In re May, 574 F.2d 1082, 1090, 197 USPQ 601, 607 (CCPA 1978)”
Regarding the argument that the method of Bursać does not inherently lead to increased alcohol production, MPEP 2112.01(I) states, “‘When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not.’ In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir. 1990). Therefore, the prima facie case can be rebutted by evidence showing that the prior art products do not necessarily possess the characteristics of the claimed product. In re Best, 562 F.2d at 1255, 195 USPQ at 433.” In the instant case, the amended rejection above sets forth the basis for believing that the prior art product is the same as that which is claimed, and applicant has not provided evidence showing that Bursać’s modified S. cerevisiae cells do not possess the same characteristics as that of the claimed modified yeast cells. Applicant is advised that MPEP 716.01(c) makes clear that “[t]he arguments of counsel cannot take the place of evidence in the record” (In re Schulze, 346 F.2d 600, 602, 145 USPQ 716, 718 (CCPA 1965)). Thus, Applicant should not merely rely upon counsel’s arguments in place of evidence in the record. Because no evidence has been presented, the argument is not persuasive and the claimed method is anticipated by Bursać.
New Rejection(s)
Claim Rejections - 35 USC § 103
Claims 13-20 and 24-25 are newly rejected under 35 U.S.C. 103 as being unpatentable over Bursać (2009, FEBS Letters; cited in IDS) in view of Zeevi et al. (2014, Genome Res.; herein “Zeevi”).
The teachings of Bursać with respect to claims 13-19 and 24-25 are set forth in para. 11-13 above.
However, Bursać does not teach that a sequence encoding the JID1 polypeptide is operably linked to an HTA1 promoter or an RPL37B promoter, as in claim 20.
Regarding claim 20, Zeevi teaches the use of the orthologous promoter RPL37B in S. cerevisiae (pg. 12 and Figure 5).
Therefore, it would have been prima facie obvious, before the effective filing date of the claimed invention, to a person of ordinary skill in the art, to substitute the GAL1 promoter taught by Bursać with the RPL37B promoter taught by Zeevi, thereby arriving at the invention of claims 13-20 and 24-25. The person of ordinary skill in the art would have been motivated to make the modification because the RPL37B promoter is not an inducible promoter and can therefore function in the absence of galactose. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of success because Bursać teaches the use of a promoter linked to the JID1 gene in S. cerevisiae and Zeevi teaches that RPL37B may be successfully used as a promoter in S. cerevisiae. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that the simple substitution of one known element for another to obtain predictable results is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that "the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results". In the instant case, the prior art (Bursać) teaches a product that only differs from that of the claimed invention by the substitution of a single component (i.e., substitution of the promoter used); the substituted element (i.e., RPL37B) was already known and already shown to function as a promoter, therefore no change in the function of the substituted element occurred; and one of ordinary skill in the art would be capable of substituting one promoter for another with a reasonable expectation of success (i.e., the substitution of the element would lead to predictable results). Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Claims 13-19, 21-22, and 24-25 are newly rejected under 35 U.S.C. 103 as being unpatentable over Bursać (2009, FEBS Letters; cited in IDS) in view of Sonderegger et al. (2004, Appl. Environ. Microbiol.; herein “Sonderegger”).
The teachings of Bursać with respect to claims 13-19 and 24-25 are set forth in para. 11-13 above.
However, Bursać does not teach a modified yeast further comprising a PKL pathway, as in claim 22.
Regarding claims 21-22 and 24-25, Sonderegger teaches a modified S. cerevisiae comprising a functional phosphoketolase (PKL) pathway comprising a heterologous phosphostransacetylase and acetaldehyde dehydrogenase with the native phosphoketolase (which catalyzes the cleavage of sugar phosphate, i.e., a carbohydrate processing enzyme) (Abstract). Sonderegger teaches that the expression of this pathway increased the production of ethanol by 25% (Abstract).
Therefore, it would have been prima facie obvious, before the effective filing date of the claimed invention, to a person of ordinary skill in the art, to modify the S. cerevisiae over expressing JID1 taught by Bursać by expressing the PKL pathway taught by Sonderegger, thereby arriving at the invention of claims 13-19, 21-22, and 24-25. The person of ordinary skill in the art would have been motivated to make the modification because Sonderegger teaches that the expression of the PKL pathway in S. cerevisiae results in increased production of ethanol. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of success because Sonderegger teaches that the pathway may be successfully expressed in S. cerevisiae and teaches the methodological details to do it (pg. 2893, paragraph bridging columns). Therefore, the combination leads to expected results because each element performs the same function as is does individually.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that combining prior art elements according to known methods to yield predictable results, is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. In the instant case, all elements (i.e., modified yeast cell comprising an increased amount of JID1 polypeptides, S. cerevisiae, PKL pathway, ethanol production by yeast, etc.) were known in the art. In addition, combining these elements yields a method/composition wherein each element merely performs the same function as it does separately; thus, the results of the combination would be recognized as predictable to one of ordinary skill in the art. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Claim(s) 13-19, 21-22, and 24-26 are newly rejected under 35 U.S.C. 103 as being unpatentable over Bursać (2009, FEBS Letters; cited in IDS) in view of Sonderegger (2004, Appl. Environ. Microbiol.) as applied to claims 13-19, 21-22, and 24-25 above, and further in view of De Bruijn (WO 2019/063544 A1).
The combination of Bursać and Sonderegger is set forth in para. 25-41 above and teaches all limitations of claims 13-19, 21-22, and 24-25.
However, neither Bursać nor Sonderegger teach that the modified yeast is fermented with corn starch as a carbohydrate substrate, as in claim 26.
Regarding claims 24-26, De Bruijn teaches a method comprising producing bioethanol by S. cerevisiae from corn starch as a carbohydrate substrate (pg. 1, lines 12-16). De Bruijn teaches that the yeast may further comprise one or more genes encoding a PKL pathway enzyme (i.e., phosphoketolase or phosphotransacetylase (pg. 2, lines 27-29).
Therefore, it would have been prima facie obvious, before the effective filing date of the claimed invention, to a person of ordinary skill in the art, to modify the combination of Bursać and Sonderegger by substituting the carbohydrate substrate for corn starch as is taught by De Bruijn, thereby arriving at the invention of claims 13-19, 21-22, and 24-26. The person of ordinary skill in the art would have been motivated to make the modification because Sonderegger teaches that plant materials are cheap substrates for bioethanol production (pg. 2892, left col., para. 1). Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of success because De Bruijn teaches the successful fermentation of S. cerevisiae comprising PKL enzymes on corn starch. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that the simple substitution of one known element for another to obtain predictable results is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that "the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results". In the instant case, the prior art Bursać and Sonderegger teaches a method that only differs from the claimed invention by the substitution of a single component (i.e., substitution of the carbohydrate substrate used); the substituted element (i.e., corn starch) was already known and already shown to function as a carbohydrate substrate, therefore no change in the function of the substituted element occurred; and one of ordinary skill in the art would be capable of substituting one carbohydrate substrate for another with a reasonable expectation of success (i.e., the substitution of the element would lead to predictable results). Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Claims 13-19 and 23-24 are newly rejected under 35 U.S.C. 103 as being unpatentable over Bursać (2009, FEBS Letters; cited in IDS) in view of Nevoight et al. (US 9,175,270 B2; cited in IDS; herein “Nevoight”).
The teachings of Bursać with respect to claims 13-19 and 24-25 are set forth in para. 11-13 above.
However, Bursać does not teach a method comprising fermenting modified yeast cells which further comprise an alteration in the glycerol pathway and/or the acetyl-CoA pathway, as in claim 23.
Regarding claims 23-25, Nevoight teaches a S. cerevisiae that is able to produce increased ethanol fermented from sugars achieved by reducing the activity of Gpd1 protein and/or the Gpd2 protein (col. 3, lines 9-17 and col. 8, lines 10-42). Nevoight teaches that Gpd1 and Gpd2 are isogenes for glycerol 3-phosphate dehydrogenase (GPDH), which is involved in glycerol biosynthesis (i.e., glycerol pathway) (col. 1, lines 39-45).
Therefore, it would have been prima facie obvious, before the effective filing date of the claimed invention, to a person of ordinary skill in the art, to modify the S. cerevisiae taught by Bursać to reduce the activity of Gpd1 and/or Gpd2, as is taught by Nevoight, thereby arriving at the invention of claims 13-19 and 23-25. The person of ordinary skill in the art would have been motivated to make the modification because Nevoight teaches that the reduction in Gpd1 and/or Gpd2 activity results in an increase in ethanol production. Therefore, the combination is also desirable (see MPEP 2144(II)). The person of ordinary skill in the art would have had a reasonable expectation of success because Nevoight teaches the successful reduction of Gpd1 and/or Gpd2 in S. cerevisiae as well as the methodological details to perform the modification. Therefore, the combination leads to expected results because each element performs the same function as is does individually.
Additionally, KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007), discloses that combining prior art elements according to known methods to yield predictable results, is obvious unless its application is beyond that person's skill. KSR International Co. v. Teleflex Inc., 127 S. Ct. 1727, 1741 (2007) also discloses that the combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results. In the instant case, all elements (i.e., S. cerevisiae with a genetic alteration resulting in an increased amount of JID1 polypeptides, glycerol pathway alteration in S. cerevisiae, increased ethanol production, etc.) were known in the art. In addition, combining these elements yields a method/composition wherein each element merely performs the same function as it does separately; thus, the results of the combination would be recognized as predictable to one of ordinary skill in the art. Therefore, the claimed invention is prima facie obvious in view of the teachings of the prior art, absent any convincing evidence to the contrary.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). 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.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BAILEY M MORGAN whose telephone number is (703)756-5388. The examiner can normally be reached M-F 9-5 ET.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, SAMIRA JEAN-LOUIS can be reached at (571) 270-3503. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/BAILEY M MORGAN/Examiner, Art Unit 1645
/SAMIRA J JEAN-LOUIS/Supervisory Patent Examiner, Art Unit 1642
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