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 .
DETAILED ACTION
This application is a US national phase of PCT/US2020/065293, filed December 16, 2024, with provisional application 62/948415, filed December 16, 2019. Applicant’s amendment filed October 14, 2025 is acknowledged. Claims 1-31 are canceled and claims 32, 38, and 44 are amended. Currently claims 32-49 are pending and under examination.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on October 14, 2025 has been entered.
Claim Objections
Claims 38 and 44 are objected to because of the following informalities: both recite “…wherein the xylanase is a GH10 xylanase…” needs to be changed to “…wherein the thermostable xylanase is a GH10 xylanase…” to maintain claim language consistency. Appropriate correction is required.
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 32-49 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.
Claims 32-49 are drawn to a process for producing ethanol from a starch-containing material that is corn or wheat, comprising the steps of liquefying the starch material at a temperature between 70-95⁰C in the presence of a thermostable GH10 xylanase from Thermotoga containing the motif YITEMD that is resistant to inhibition by copper, iron, and zinc metal ions, saccharifying using a glucoamylase, and fermenting using a fermenting organism to produce the ethanol. The claims are also drawn to a process of increasing amounts of short-chain oligosaccharides. The specification defines ‘a thermostable metal ion inhibition resistant xylanase’ as having a Melting Point (DSC) above 80°C, and as a part of a GH10 xylanase family, as a species from the genus Thermotoga, such as Thermotoga maritima, as a Thermotoga containing the motif YITEMD, and as having at least 60% identity to SEQ ID NO’s: 2-4. The Specification also defines ‘thermostable’ as the enzyme retains significant amount of activity from 75⁰C-100⁰C for a particular period of time, ranging from 10 minutes to 2 hours. To satisfy the written description requirement, a patent specification must describe the claimed invention in sufficient detail that one skilled in the art can reasonably conclude that the inventor had possession of the claimed invention. See, e.g., Moba, B.V. v. Diamond Automation, Inc., 325 F.3d 1306, 1319, 66 USPQ2d 1429, 1438 (Fed. Cir. 2003); Vas-Cath, Inc. v. Mahurkar, 935 F.2d at 1563, 19 USPQ2d at 1116. Guidelines for the Examination of Patent Applications Under the 35 U.S.C. 112(a) or Pre-AIA 35 U.S.C. 112, first paragraph, "Written Description" Requirement (MPEP2163).
In analyzing whether the written description requirement is met for genus claims, it is first determined whether a representative number of species have been described by their complete structure. In the instant case, the specification merely gives working examples of xylanase derived from Dictyloglomus thermophilum (SEQ ID NO: 1) and Thermotoga maritage (SEQ ID NO: 2). The working examples describe testing thermostability of the xylanases, wherein the thermostable xylanase according to SEQ ID NO: 2 exhibited resistance to metal ions, specifically higher activity in the presence of copper, iron, and zinc, compared to SEQ ID NO: 1. While the genus of a GH10 thermostable xylanase from Thermotoga resistant to copper, iron, and zinc encompasses a large number of variants that have the same activity in kind and the genus encompasses a large number of variants that have a different structure, the specification does not describe the complete structure of a representative number of species of the large genus of GH10 thermostable xylanase derived from Thermotoga containing the YITEMD motif variants that is resistant to copper, iron, and zinc or functional equivalents thereof.
Next, then, it is determined whether a representative number of species have been sufficiently described by other relevant identifying characteristics, specific features, and functional attributes that would distinguish different members of the claimed genus. In the instant case, the only identifying characteristic of GH10 thermostable xylanase resistant to copper, iron, and zinc can have at least 60% identity according to SEQ ID NO’s: 2-4, while maintaining relative activity in the presence of various metal ions, may contain the motif YITEMD, and is able to maintain at least 70% of activity at temperatures ranging from 75-100⁰C. Such broad limitations cannot be an identifying characteristic for the claimed diverse genus of GH10 thermostable xylanase variants from Thermotoga that are resistant to copper, iron, and zinc, since by Applicant’s definition of variant or functional equivalent thereof all members of the claimed genus will have that characteristic.
The inventions of claims 33-37, 39-43, and 45-49 require the use of the invention of claims 32, 38, and 44, and therefore are likewise rejected under 35 U.S.C. 112, first paragraph, as failing to comply with the written description requirement. Applicant’s disclosure of the species of GH10 thermostable xylanase variants from Thermotoga containing the YITEMD motif that are resistant to copper, iron, and zinc of the claimed broad genus is not deemed sufficient to reasonably convey to one skilled in the art that Applicant was in possession of the claimed broad genus at the time the application was filed. Thus, it is concluded that the written description requirement is not satisfied for the claimed genus.
Claim Rejections - 35 USC § 103
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 32-49 are rejected under 35 U.S.C. 103 as being unpatentable over Kang et al. (WO 2017 /112540 A1, cited in PTO-892 mailed 1/10/2025, hereinafter “Kang”) in view of Zhengqiang et al. (Jrnl of Biosci and Bioeng, 2001, vol. 92, no. 5, pgs. 423-428, hereinafter “Zheng”), as evidenced by Wang et al. (Bioresource Technology 222 (2016) 277–284, cited in PTO-892 mailed 8/14/2025, hereinafter “Wang”), Song et al. (Environmental Earth Sciences (2021) 80:452, pgs. 1-10, cited in PTO-892 mailed 8/14/2025, hereinafter “Song”), and Fears (<www.bunting-redditch.com/getting-metal-out-of-grain-and-cereals/>, October, 2021, cited in PTO-892 mailed 8/14/2025).
Kang teaches processes for producing fermentation products from starch-containing material using an alpha-amylase and a thermostable hemicellulase (abstract). Kang teaches liquefying the starch-containing material such as corn or wheat at a temperature from 70-95⁰C using a hemicellulase enzyme that is preferably a xylanase having a melting point above 82⁰C, saccharifying using a glucoamylase, and fermenting using a fermenting organism to produce ethanol, which meets the limitations in claims 32, 33, 38, 39, and 44-45 (claims 1-3, 12, 15, 19-21, 23). In Example 21, Kang teaches adding thermostable xylanase in the liquefaction of ground corn flour from an industrial corn ethanol plant, and its effect on ethanol yield (pg. 129). The thermostable xylanase is from Talaromyces leycettanus (TI Xyl) and combined with thermostable glucoamylase had a 1.5% increase in ethanol production and up to 18.3% increase of solubilized feruloylated arabinoxylan (SFA) which is a short-chain oligosaccharide over the method not utilizing the xylanase, thus meeting the limitations in claims 36-38, 42-44, and 48-49 (pg. 130, Tables 26 & 27). The TI Xyl is a GH10 xylanase, and as evidenced by Wang, is inherently resistant to numerous metal ions, such as zinc, copper, and iron which displayed 104%, 95%, and 96% relative activity in the presence of 5mM of each metal ion respectively (pg. 281, Table 2).
Although Kang is silent on the metal ion concentration in the corn flour from industrial ethanol plants used in the experiments, the various liquified corn mashes from industrial ethanol plants disclosed in the instant specification inherently possess various metal ions, including copper, iron, and zinc (Example 4). Furthermore, Song also discloses heavy metal concentrations like Copper and Zinc in commercial corn grains can be as high as 1 mg/kg and 17 mg/kg respectively (pg. 5, Fig. 1). Thus, the corn flour from industrial ethanol plants used in the experiments taught by Kang would inherently possess the specified metal ions, and the substrate would have behaved the same way as in the claimed method, especially when utilizing thermostable glucoamylase and thermostable xylanase taught by Kang. Similarly, it would have been obvious to adjust the average metal ion concentration in the corn by any well-understood and routine laboratory method, such as dilution or magnetic separators, as disclosed by Fears (pg. 3), to arrive at the claimed metal ion concentrations in the method.
Kang does not teach a thermostable xylanase from Thermotoga containing the motif YITEMD.
However, Zheng teaches characterization of a thermostable family 10 endo-xylanase (XynB) from Thermotoga maritima (title). Zheng teaches at 50°C, XynB
displayed an optimum pH of 6.14 and at this pH the temperature for optimal enzyme activity was 90°C (abstract). Zheng teaches the xylanase gene (xynB, TM0070, AEO01693) has 100% local similarity to instant SEQ ID NO: 2 and contains the YITEMD motif (See sequence comparison below) (pg. 424, col. 1, para 2).
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Zheng teaches the influence of metal ions was tested on XynB activity and found that inhibition by metal ions was only minimal, with iron and zinc ions actually stimulating enzymatic activity (pg. 426, col. 1 ,para 1). Zheng also teaches XynB exhibited a broad substrate specificity, and was highly active towards p-nitropheny-β-D-xylobioside and p-nitropheny-β-D-xyloside (abstract).
Therefore, it would have been prima facie obvious to one of ordinary skill in the art before the effective filing date to modify the method of producing ethanol from ground corn flour with a combination of an alpha-amylase and a thermostable xylanase as taught by Kang, and substitute the XynB thermostable xylanase from T. maritima, as taught by Zheng, for Kang’s thermostable xylanase, that is inherently resistant to metal ions, to increase enzymatic activity enhanced by iron or zinc as taught by Zheng with a reasonable expectation of success. One of ordinary skill in the art would have been motivated to use the metal ion-resistant XynB from T. maritima in breaking down industrial corn mashes that are known to possess varying levels of heavy metal contamination as disclosed by Song, since it is generally known that enzymes can be inhibited by metal ions as taught by Zheng.
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.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 32-49 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3 and 6-29 of U.S. Patent No. 10689630B2 (‘630) in view of Zheng, as evidenced by Song and Fears.
Patent claims 1-3 and 6-29 of ‘630 recite a process for producing a fermentation product from starch containing material comprising liquefying using an alpha amylase and GH10 xylanase having a melting point above 80 ⁰C, saccharifying using a glucoamylase enzyme, and fermenting using a fermenting organism, wherein the starch containing material is corn. Claims 1-3 and 6-29 are silent of the inherent characteristics of the GH10 xylanase related to metal ion resistance, decreasing the amount of residual starch, and increasing the amount of short-chain oligosaccharides, and is silent regarding the specific metal ions (Cu, Fe, and Zn) as well as the concentrations in the corn.
However, Zheng teaches characterization of a thermostable family 10 endo-xylanase (XynB) from Thermotoga maritima (title). Zheng teaches at 50°C, XynB
displayed an optimum pH of 6.14 and at this pH the temperature for optimal enzyme activity was 90°C (abstract). Zheng teaches the xylanase gene (xynB, TM0070, AEO01693) has 100% local similarity to instant SEQ ID NO: 2 and contains the YITEMD motif (See sequence comparison below) (pg. 424, col. 1, para 2). Zheng teaches the influence of metal ions was tested on XynB activity and found that inhibition by metal ions was only minimal, with iron and zinc ions actually stimulating enzymatic activity (pg. 426, col. 1 ,para 1). Zheng also teaches XynB exhibited a broad substrate specificity, and was highly active towards p-nitropheny-β-D-xylobioside and p-nitropheny-β-D-xyloside (abstract).
Although ‘630 and Zheng are silent on the metal ion concentration in the corn flour from industrial ethanol plants used in the experiments, the various liquified corn mashes from industrial ethanol plants disclosed in the instant specification inherently possess various metal ions, including copper, iron, and zinc (Example 4). Furthermore, Song also discloses heavy metal concentrations like Copper and Zinc in commercial corn grains can be as high as 1 mg/kg and 17 mg/kg respectively (pg. 5, Fig. 1). Thus, the corn recited in the method of ‘630, would inherently possess the specified metal ions, and the substrate would have behaved the same way as in the claimed instant method and ‘630 method, especially when utilizing thermostable glucoamylase and thermostable xylanase as taught by Zheng.
Therefore, it would have been prima facie obvious to one of ordinary skill in the art to modify the method recited in ‘630 by including the thermostable GH10 xylanase from T. maritima as taught by Zheng with a reasonable expectation of success. One of ordinary skill in the art would have selected the GH10 xylanase disclosed by Zheng, since it is inherently resistant to Zn and Fe, which would enable the efficient liquification of the corn substrate used in the method of ‘630, that inherently possesses metal ion concentrations as evidenced by Song.
Furthermore, corn grains/flour from industrial ethanol plants inherently possess varying levels of metal ions as disclosed in Song, and it would have been prima facie obvious to one of ordinary skill in the art to adjust the average metal ion concentration in the corn by any well-understood and routine laboratory method, such as dilution or magnetic separators, as disclosed by Fears (pg. 3), to arrive at the claimed metal ion concentrations in the method.
Response to Arguments
Applicant's arguments filed October 14, 2025 have been fully considered but they are not persuasive.
Regarding Remarks directed to the 112(a) rejection, Applicant argues the disclosure of the 3 species of GH10 xylanases from the genus Thermotoga that all contain motif YITEMD (SEQ ID No’s 2-4) and are representative of the claimed xylanase genus. Applicant points to pg. 4 of the Specification stating that xylanases from Thermotoga were observed to contain the motif, wherein the glutamic acid residue is a catalytic residue.
Although the Examiner agrees there is generally an established structure-function relationship between thermostable xylanases from Thermotoga containing this motif, the claims also require the xylanase to be resistant to inhibition by Cu, Fe, and Zn metal ions, of which the specification fails to establish this structure-function relationship. Therefore, the written description requirement is still not satisfied.
Applicant’s arguments with respect to claims 32-49 in the previous rejection under 35 U.S.C. §102(a)(1), under 35 U.S.C. §103, and nonstatutory double patenting rejection, have been considered but are moot because the new ground of rejection does not rely on any reference applied in the prior rejection of record for any teaching or matter specifically challenged in the argument.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JESSICA EDWARDS whose telephone number is (571)270-0938. The examiner can normally be reached M-F 8am-5pm EST.
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/LOUISE W HUMPHREY/Supervisory Patent Examiner, Art Unit 1657
/JESSICA EDWARDS/
Examiner, Art Unit 1657