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 .
Status of Application, Amendments, And/Or Claims
The Applicants amendments/remarks received 6/10/2026 are acknowledged. Claims 1, 11-13, 15 and 20-21 are amended; claims 5 and 14 are canceled; no claims are withdrawn; claims 1-4, 6-13 and 15-21 are pending and have been examined on the merits.
Information Disclosure Statement
The information disclosure statement submitted on 4/25/2024 has been considered by the examiner. NPL cite 12 is lined through because the author name and journal name are incorrect.
The PTO-892 Notice of References Cited sent by the previous examiner on 3/10/2026 has been amended to add proper bibliographic information to cite V.
Claim Objections
The objections to claims 13, 15 and 20-21, as set forth at pp. 2-3 of the previous Office Action, are withdrawn in view of the amendment of the claims.
Claim Rejections - 35 USC § 112
The rejection of claim 5 under 35 U.S.C. § 112(b), as set forth at pp. 3-4 of the previous Office Action, is moot due to cancelation of the claim.
Claim Rejections - 35 USC § 101/112(b)
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
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.
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.
Claims 15-21 are rejected under 35 U.S.C. 101 and 35 U.S.C. 112(b) because claims 15, 20 and 21 constitute “use” claims.
Attempts to claim a process without the claim setting forth any method steps fails to comply with 35 U.S.C. 101 because a claim which merely recites a use without any active, positive steps delimiting how this use is actually practiced does not constitute a process complying with 35 U.S.C. 101. Additionally, a claim which merely recites a use without any active, positive steps delimiting how this use is actually practiced is indefinite; hence, the claims are also rejected under 35 U.S.C. 112(b).
Claims 16-19 depend from claim 15 and do not resolve the indefiniteness of claim 15 nor constitute effective process claims; hence, claims 15-21 are rejected under 35 U.S.C. 101 and 35 U.S.C. 112(b).
Claim Rejections - 35 USC § 101
The rejection of claim 12 under 35 U.S.C. § 101, as set forth at p. 4 of the previous Office Action, is withdrawn in view of the amendment of the claims.
Claim 11 is rejected under 35 U.S.C. 101 because the claimed invention is directed to a natural product without significantly more.
Claim 11 recites a composition comprising i) a protein comprising an amino acid sequence of SEQ ID NO: 01 or an amino acid sequence which has at least 98% sequence identity with the amino acid sequence of SEQ ID NO: 01, wherein the protein has glucoamylase activity; and ii) at least one protein selected from the group consisting of: (a) a protein having alpha 1,4-glucosidase activity; (b) a protein having alpha 1,6-glucosidase activity; (c) a protein having beta-glucosidase activity; and (d) a protein having alpha 1,1 -glucosidase activity.
The glucoamylase of SEQ ID NO: 01 has alpha 1,4-glucosidase activity and alpha 1,6-glucosidase activity; hence, a composition of at least two molecules of functional glucoamylase with ≥98% identity to SEQ ID NO: 01 would meet i) and ii) of claim 11 as there is nothing in the claim reciting that the protein in limitation ii) cannot also have ≥98% identity with SEQ ID NO: 01.
Couturier et al., 2015 (cite V, PTO-892, 3/10/2026) discloses the amino acid sequence of the naturally occurring glucoamylase of Pyncnoporus coccineus (Accession Number OSD07483.1) which is 98% identical to instant SEQ ID NO: 01 (see “OSD07483” (cite W, attached PTO-892) and “Comparison of instant SEQ 1 (Query) to OSD07483 (Sbjct)” (cite U, attached PTO-892)).
Hence, claim 11 is drawn to the natural product, a judicial exception, of a composition of Pyncnoporus coccineus comprising the glucoamylase whose amino acid sequence is disclosed in Accession Number OSD07483.1.
This judicial exception is not integrated into a practical application because the claim is for the composition per se. The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because no further elements are recited in the claim. Thus, claim 11 is rejected under 35 U.S.C. 101.
Response to Arguments
Applicant's arguments filed 6/10/2026 have been fully considered but they are not persuasive. Arguments of the Applicant’s Response on pp. 6-13 regarding the objections and rejections under 35 U.S.C. § 112(b), 102(a)(1) and 103 are moot as the rejections have been withdrawn.
Regarding the rejection of claims 11-12 under 35 U.S.C. 101, Applicant asserts that claims 11 and 12 are directed to a non-naturally occurring combination of proteins and are not directed to a natural product. This is persuasive regarding claim 12, for which the 101 rejection has been withdrawn. Claim 11 still encompasses a natural product as discussed in the rejection above; hence, the rejection is maintained with modification to address amended claim 11.
Claim Rejections - 35 USC § 102
The rejection of claims 1, 3-5, 11-12, 15, 18 & 20 under 35 U.S.C. § 102(a)(1) over Yazdi et al., WO 2018/098381 (Foreign Patent Document cite 21, IDS, 4/25/2024) as set forth at pp. 5-6 of the previous Office Action, is moot regarding claim 5 due to cancelation of the claim and is withdrawn regarding the remaining claims in view of the amendment of the claims.
Claim 11 is rejected under 35 U.S.C. 102(a)(1) as being anticipated by Couturier et al., 2015 (cite V, PTO-892, 3/10/2026; herein “Couturier”) in light of “OSD07483” (cite W, attached PTO-892) and “Comparison of instant SEQ 1 (Query) to OSD07483 (Sbjct)” (cite U, attached PTO-892).
Couturier is in possession of compositions of Pycnoporus coccineus CIRM-BRFM310 (Trametes coccinea) (p. 12, “Fungal strain and enzymes”, “Pycnoporus coccineus culture conditions and secretome preparation”) which would necessarily comprise at least two molecules of the Pycnoporus coccineus glucoamylase of amino acid sequence disclosed at Accession # OSD07483 by Couturier (see “OSD07483”) which is 98% identical to SEQ ID NO: 01 (see “Comparison of instant SEQ 1 (Query) to OSD07483 (Sbjct)” and necessarily comprises glucoamylase activity, alpha 1,4-glucosidase activity and alpha 1,6-glucosidase activity anticipating claim 11 because at least one molecule of the glucoamylase meets limitation i) that the protein has ≥98% identity with SEQ ID NO: 01 and at least one molecule of the glucoamylase meets limitation ii) by having alpha 1,4-glucosidase activity and/or alpha 1,6-glucosidase activity.
Claim Rejections - 35 USC § 103
The rejection of claim 2 under 35 U.S.C. § 103(a) over Yazdi as set forth at pp. 7-8 of the previous Office Action, is withdrawn in view of the amendment of the claims.
The rejection of claims 6-10 under 35 U.S.C. § 103(a) over Yazdi in view of De Waal et al., WO 2018/172328 (Foreign Patent Document cite 22, IDS, 4/25/2024) as set forth at pp. 8-10 of the previous Office Action, is withdrawn in view of the amendment of the claims.
The rejection of claims 13, 16-17, 19 & 21 under 35 U.S.C. § 103(a) over Yazdi in view of De Bruijn et al., WO 2019/063543 (Foreign Patent Document cite Q, PTO-892, 3/10/2026) as set forth at pp. 10-12 of the previous Office Action, is withdrawn in view of the amendment of the claims.
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-4, 11, 15, 18 and 20 are rejected under 35 U.S.C. 103 as being unpatentable over Yazdi et al., US 2019/0338319 (cite A, attached PTO-892; herein “Yazdi”) in view of “OSD07483” in light of “Comparison of Yazdi SEQ 18 (Query) to OSD07483 (Sbjct)” and “Comparison of instant SEQ 1 (Query) to OSD07483 (Sbjct)”.
Yazdi teaches compositions and methods for producing ethanol from starch-containing material using recombinant yeast expressing heterologous glucoamylase (Abst.) wherein the overexpressed glucoamylase can be from a Pycnoporus genus and have >94% sequence identity with SEQ ID NO: 18 ([0350-1], [0976], [1258]).
OSD07483 discloses a Pycnoporus glucoamylase which has 95% sequence identity with SEQ ID NO: 18 of Yazdi as demonstrated in “Comparison of Yazdi SEQ 18 (Query) to OSD07483 (Sbjct)”.
Hence, a person of ordinary skill in the art at the time of filing would have found it obvious to produce recombinant yeast overexpressing the glucoamylase of OSD07483 to use in Yazdi’s methods of producing ethanol from starch feedstocks with recombinant yeasts which overexpress glucoamylase; therefore, claims 1, 3-4, 11, 15 and 20 are prima facie obvious.
Note: OSD07483 is 98% identical to SEQ ID NO: 01 (see “Comparison of instant SEQ 1 (Query) to OSD07483 (Sbjct)”).
Regarding claims 3-4, OSD07483 is the wild type glucoamylase of Pycnoporus coccineus (also known as Trametes coccinea) which would necessarily have glucoamylase activity and alpha 1,6-glycosidic activity; therefore, claims 3-4 are prima facie obvious.
Regarding claim 11, the recombinant yeast overexpressing OSD07483 made obvious by Yazdi in view of OSD07483 would comprise a composition comprising at least two molecules of the Pycnoporus coccineus glucoamylase of amino acid disclosed in OSD07483 (98% identical to SEQ ID NO: 01) necessarily comprising glucoamylase activity, alpha 1,4-glucosidase activity and alpha 1,6-glucosidase activity wherein at least one molecule of the glucoamylase meets limitation i) that the protein has ≥98% identity with SEQ ID NO: 01 and at least one molecule of the glucoamylase meets limitation ii) by having alpha 1,4-glucosidase activity and/or alpha 1,6-glucosidase activity; therefore, claim 11 is prima facie obvious.
Regarding claims 15 and 20, starch constitutes a carbon source; hence, a person of ordinary skill in the art at the time of filing would have found it obvious to practice a method of producing ethanol made obvious by Yazdi in view of OSD07483 comprising converting a carbon source using the recombinant yeast overexpressing the glucoamylase of OSD07483; therefore, claims 15 and 20 are prima facie obvious.
Regarding claim 18, Yazdi teaches liquifying the starch with an alpha-amylase and saccharifying with a glucoamylase before fermentation with the recombinant yeast comprising the heterologous glucoamylase [0012-17]; hence, a person of ordinary skill in the art at the time of filing would have found it obvious that the carbon source comprises one or more disaccharides and/or oligosaccharides; therefore, claim 18 is prima facie obvious.
Regarding claim 2, Yazdi teaches codon-optimizing the nucleic acid sequence of the glucoamylase in the expression construct for expression in S. cerevisiae [1445]. Instant SEQ ID NO: 2 is a nucleic acid sequence for the glucoamylase of SEQ ID NO: 1 which has been codon-optimized for expression in S. cerevisiae.
Hence, a person of ordinary skill in the art at the time of filing would have found it obvious to produce recombinant yeast wherein the nucleic acid sequence encoding a glucoamylase of OSD07483 has been codon-optimized for expression in S. cerevisiae; therefore, claim 2 is prima facie obvious.
Response to Arguments
Regarding the rejection of claims 1-5, 11-12, 15, 18 and 20 under 35 U.S.C. § 103 over Yazdi, as set forth on pp. 7-8 of the previous Office action, Applicant argues (pp. 8-11) that Yazdi fails to teach a protein "compris[ing] an amino acid sequence of SEQ ID NO: 01 or an amino acid sequence which has at least 98% sequence identity with the amino acid sequence of SEQ ID NO: 01." Yazdi in view of OSD07483 makes obvious a recombinant yeast comprising a nucleotide sequence encoding a protein comprising an amino acid sequence of SEQ ID NO: 01 or an amino acid sequence which has at least 98% sequence identity with the amino acid sequence of SEQ ID NO: 01 as set forth in the rejection above.
Claims 1-4, 6, 9-13 and 15-21 are rejected under 35 U.S.C. 103 as being unpatentable over Yazdi in view of OSD07483 and De Bruijn et al., US 2020/0407733 (cite B, attached PTO-892; herein “De Bruijn”)).
The discussion of Yazdi and OSD07483 regarding claims 1-4, 11, 15, 18 and 20 set forth in the rejection above is incorporated herein.
The method made obvious by Yazdi in view of OSD07483 comprises liquifying starch with an alpha-amylase and saccharifying with a glucoamylase before fermentation with the recombinant yeast comprising the heterologous glucoamylase [0012-17], but Yazdi does not specifically teach that the total weight percentage of disaccharides and/or oligosaccharides, based on the weight of saccharides present in the carbon source, is equal to or more than 1% w/w.
However, a person of ordinary skill in the art at the time of filing would have found it obvious to use a carbon source with a >1% w/w disaccharides and/or oligosaccharides in view of the disclosure of De Bruijn.
De Bruijn also teaches the production of ethanol using recombinant yeast expressing a heterologous glucoamylase in Simultaneous Saccharification Fermentation (SSF) mode [0166], wherein the recombinant yeast are directly cultured on corn mash, which according to the preparation recipe [0163], would comprise ≥1% disaccharide and/or oligosaccharide; hence, a person of ordinary skill in the art at the time of filing would have found it obvious to practice the method made obvious by Yazdi in view of OSD07483 comprising converting a carbon source wherein the carbon source comprises ≥1% disaccharide and/or oligosaccharide into ethanol by the fermentation of the recombinant yeast expressing the glucoamylase with the sequence in OSD07483; therefore, claim 19 is prima facie obvious.
The method made obvious by Yazdi in view of OSD07483 comprises liquifying starch with an alpha-amylase and saccharifying with a glucoamylase before fermentation with the recombinant yeast comprising the heterologous glucoamylase [0012-17], but Yazdi does not specifically teach external dosing of a glucoamylase at a concentration of 0.05 g/L or less, expressed as the total amount of glucoamylase enzyme in grams per liter of carbon source comprising feed or wherein the process is carried out without external dosing of any glucoamylase. However, a person of ordinary skill in the art at the time of filing would have found it obvious to practice the method made obvious by Yazdi in view of OSD07483 wherein the process is carried out without external dosing of any glucoamylase or external dosing of a glucoamylase at a concentration of 0.05 g/L or less, expressed as the total amount of glucoamylase enzyme in grams per liter of carbon source comprising feed in view of the disclosure of de Bruijn.
De Bruijn teaches that the production of ethanol can comprise external dosing of glucoamylase at a concentration of 0.05 g/L or less, expressed as the total amount of glucoamylase enzyme in grams per liter of corn slurry [0134] or the production of ethanol can be carried out without adding any glucoamylase [0138]; hence, a person of ordinary skill in the art at the time of filing would have found it obvious to practice the method made obvious by Yazdi in view of OSD07483 wherein the process is carried out comprising external dosing of glucoamylase at a concentration of 0.05 g/L or less, expressed as the total amount of glucoamylase enzyme in grams per liter of corn slurry or wherein the process is carried out without external dosing of any glucoamylase; therefore, claims 16-17 are prima facie obvious.
De Bruijn teaches recombinant yeast overexpressing a heterologous glucoamylase, i.e., having alpha 1,4-glucosidase activity and alpha 1,6-glucosidase activity, from Punctularia strigosozonata, (SEQ ID NO: 19, [0036], [0042]; 99% sequence identity to instant SEQ ID NO: 03; see “Comparison of SEQ 3 (Query) to De Bruijn SEQ 19 (Sbjct)”) for use in producing ethanol [0140-166].
Hence, a person of ordinary skill in the art at the time of filing would have found it obvious to produce compositions or kits comprising A) recombinant yeast overexpressing the glucoamylase with the sequence in OSD07483 and B) recombinant yeast overexpressing SEQ ID NO: 19 of De Bruijn because both reagents A and B are used for the fermentation of starch into ethanol; therefore, claims 12-13 and 21 are prima facie obvious.
MPEP § 2144.06 (I) states: "It is prima facie obvious to combine two compositions each of which is taught by the prior art to be useful for the same purpose, in order to form a third composition to be used for the very same purpose .... [T]he idea of combining them flows logically from their having been individually taught in the prior art." In re Kerkhoven, 626 F.2d 846, 850, 205 USPQ 1069, 1072 (CCPA 1980).
De Bruijn teaches that the recombinant yeast can further be improved for the production of ethanol by comprising a nucleotide sequence coding for a ribulose-1,5- biphosphate carboxylase oxygenase (EC 4.1.1.39), a nucleotide sequence coding for a phosphoribulokinase (EC 2.7.1.19) and a nucleotide sequence coding for a glycerol transporter [0093-98]; hence, a person of ordinary skill in the art at the time of filing would have found it obvious for the recombinant yeast made obvious by Yazdi in view of OSD07483 to further comprise a nucleotide sequence coding for Rubisco, a nucleotide sequence coding for a phosphoribulokinase and a nucleotide sequence coding for a glycerol transporter; therefore, claims 6 and 10 are prima facie obvious.
De Bruijn teaches that the recombinant yeast can further be improved for the production of ethanol by deleting or disrupting endogenous nucleotide sequences encoding a glycerol-3-phosphate dehydrogenase [0053]; hence, a person of ordinary skill in the art at the time of filing would have found it obvious for the recombinant yeast made obvious by Yazdi in view of OSD07483 to further comprise a deletion or disruption of endogenous nucleotide sequences encoding a glycerol-3-phosphate dehydrogenase; therefore, claim 9 is prima facie obvious.
Response to Arguments
Regarding the rejection of claims 13, 16-17, 19, and 21 under 35 U.S.C. § 103 over Yazdi in view of De Bruijn, as set forth on pp. 11-12 of the previous Office action, Applicant argues (pp. 12-13) that Neither Yazdi nor De Bruijn, either alone or in combination, teach a protein "compris[ing] an amino acid sequence of SEQ ID NO: 01 or an amino acid sequence which has at least 98% sequence identity with the amino acid sequence of SEQ ID NO: 01".
Yazdi in view of OSD07483 makes obvious a recombinant yeast comprising a nucleotide sequence encoding a protein comprising an amino acid sequence of SEQ ID NO: 01 or an amino acid sequence which has at least 98% sequence identity with the amino acid sequence of SEQ ID NO: 01 as set forth in the rejection on pp. 7-10 above.
Claims 1-4, 6-13 and 15-21 are rejected under 35 U.S.C. 103 as being unpatentable over Yazdi in view of OSD07483, De Bruijn and De Waal et al., US 2020/0024619 (cite C, attached PTO-892; herein “DeWaal”).
The discussion of Yazdi, OSD07483 and De Bruijn regarding claims 1-4, 6, 9-13 and 15-21 set forth in the rejection above is incorporated herein.
None of Yazdi, OSD07483 nor De Bruijn teach that the recombinant yeast comprises a nucleotide sequence encoding a protein comprising phosphoketolase activity (EC4.1.2.9 or EC 4.1.2.22, PKL), a nucleotide sequence encoding a protein having phosphotransacetylase (PTA) activity (EC 2.3.1.8), a nucleotide sequence encoding a protein having acetate kinase (ACK) activity (EC 2.7.2.12) or a nucleotide sequence encoding a protein comprising NAD+ dependent acetylating acetaldehyde dehydrogenase activity (EC 1.2.1.10).
However, a person of ordinary skill in the art at the time of filing would have found it obvious for the recombinant yeast for the production of ethanol from starch to further comprise a nucleotide sequence encoding a protein comprising NAD+ dependent acetylating acetaldehyde dehydrogenase activity, a nucleotide sequence encoding a PKL activity, a nucleotide sequence encoding a PTA activity and a nucleotide sequence encoding an ACK activity in view of the disclosure of De Waal.
De Waal is drawn to recombinant yeast for use in the production of ethanol wherein the recombinant yeast can functionally express a nucleotide sequence encoding an enzyme having at least NAD+ dependent acetylating acetaldehyde dehydrogenase activity (EC 1.2 .1.10 or EC 1.1.1.2 ) (Abst.; [0009-13]), a nucleotide sequence encoding an enzyme having phosphoketolase (PKL) activity (EC 4.1.2.9 or EC4.1.2.22), a nucleotide sequence encoding an enzyme having phosphotransacetylase (PTA) activity and a nucleotide sequence encoding an enzyme having acetate kinase (ACK) activity [0074-77].
Hence, a person of ordinary skill in the art at the time of filing would have found it obvious for the recombinant yeast made obvious by Yazdi in view of OSD07483 to further express a nucleotide sequence coding for an NAD+ dependent acetylating acetaldehyde dehydrogenase activity, a nucleotide sequence coding for an enzyme having PKL activity, a nucleotide sequence coding for an enzyme having PTA activity and a nucleotide sequence coding for an enzyme having ACK activity; therefore, claims 7-8 are prima facie obvious.
Response to Arguments
Regarding the rejection of claims 6-10 under 35 U.S.C. § 103 over Yazdi in view of De Waal, as set forth on pp. 11-12 of the previous Office action, Applicant argues (pp. 11-12) that neither Yazdi nor De Waal teach the subject matter of claim 1.
Yazdi in view of OSD07483 makes obvious a recombinant yeast comprising a nucleotide sequence encoding a protein comprising an amino acid sequence of SEQ ID NO: 01 or an amino acid sequence which has at least 98% sequence identity with the amino acid sequence of SEQ ID NO: 01 as set forth in the rejection on pp. 7-10 above.
Conclusion
No claims are 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 Trent R Clarke whose telephone number is (571)272-2904. The examiner can normally be reached M-F 10-7 MST.
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/TRENT R CLARKE/ Examiner, Art Unit 1651
/DAVID W BERKE-SCHLESSEL/ Primary Examiner, Art Unit 1651
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