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 .
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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 09/02/2025 has been entered.
Claim Objections
Claims 31 and 54 are objected to because of the following informalities:
The abbreviation DFDSM should be defined upon its first use in the claims.
Appropriate correction is required.
Claim Interpretation
Claim 31 a liquid composition having a polypeptide having arabinofuranosidase configured to be dosed in a range of 0.01-200 mg arabinofuranosidase protein per kg substrate and a GH10 or GH11 xylanase polypeptide configured to be dosed in a range of 0.01-200 mg xylanase protein per kg substrate.
Claim 31 is interpreted as requiring an arabinofuranosidase polypeptide, a xylanase polypeptide and one or more generic formulating agents. Claim 31 is not interpreted as requiring a “substrate” as part of the structure of the liquid composition nor that any positive act of a method be performed for infringement. Rather, “per kg substrate” is recited only as part of a definition for a quantity of arabinofuranosidase or xylanase polypeptide present.
The isolated claim language “wherein the polypeptide has arabinofuranosidase activity and is configured to be dosed in a range of 0.01-200 mg per kg substrate arabinofuranosidase protein of the polypeptide having arabinofuranosidase activity per kg substrate” does not establish any required concentration. That is, arabinofuranosidase protein having any arbitrary concentration can be dosed in a range of 0.01-200 mg arabinofuranosidase per kg substrate. For example if concentration of arabinofuranosidase is 1 mg/ml, 0.01 ml can be added to dose at 0.01 mg/kg substrate or 200 ml can be added to dose at 200 mg/kg substrate. If the solution was 10X as concentrated (10 mg/ml), then 0.001 ml can be added to dose at 0.1 mg/kg substrate or 20 ml can be added to dose at 200 mg/kg. However, “wherein the polypeptide has arabinofuranosidase activity and is configured to be dosed in a range of 0.01-200 mg arabinofuranosidase protein of the polypeptide having arabinofuranosidase activity per kg substrate” may exclude very dilute concentrations wherein a volume of the liquid composition that would need to be added very large, but high concentrations of enzyme in the liquid composition are not excluded.
While recitation of configured to be dosed in a range of 0.01-200 ppm does not establish a minimum or maximum concentration, the requirement of the same applicable for both the recited arabinofuranosidase and xylanase does limit a ratio between the arabinofuranosidase and xylanase present. That is, a ratio between arabinofuranosidase:xylanase polypeptides can range from 20000:1 to 1:20000 by weight. For example, a liquid composition with the following concentrations meets the limitations of both the arabinofuranosidase and xylanase be configured to be dosable in range of 0.01-200 ppm:
-1 mg/mL arabinofuranosidase and 0.05 µg/mL xylanase; and
-1 mg/mL xylanase and 0.05 µg/mL arabinofuranosidase.
Further dependent claims recite narrower ranges such as claim 34 reciting 0.1-50 ppm dosing for the arabinofuranosidase enzyme. Such dependent claims are interpreted consistent with above, and, for example, a liquid composition with 1 mg/mL arabinofuranosidase and 0.05 µg/mL xylanase is consistent with claim 34.
Claim 31 further recites:
the GH10 or GH11 polypeptide having xylanase activity and the polypeptide having arabinofuranosidase activity together solubilise at least 2 times more xylose from DFDSM than the GH10 or GH11 polypeptide having xylanase activity in the absence of the polypeptide having arabinofuranosidase.
The claim does not specify precise conditions for such solubilization (e.g. pH, temperature, reaction time). The above claim feature is interpreted as requiring that when an embodiment of the liquid composition having a specific concentration of arabinofuranosidase and xylanase is employed, that the functional at least 2 times more xylose from DFDSM than the GH10 or GH11 polypeptide having xylanase activity in the absence of the polypeptide having arabinofuranosidase is achievable under some condition. As such, “solubilise at least 2 times more xylose from DFDSM than the GH10 or GH11 polypeptide having xylanase activity in the absence of the polypeptide having arabinofuranosidase” is a property of the recited liquid composition rather than a property of the arabinofuranosidase and xylanase as applied in a certain ratio or dosing, for example at a dosing of 10 mg/kg DFDSM as recited in the claims prior to the amendment of 09/02/2025. This interpretation of claim 31 is required by removal of the following limitation by amendment: wherein (c) and (d) are performed under the reaction conditions: (i) 10 mg of the GH10 or GH11 polypeptide having xylanase activity per kg DFDSM, (ii) 10 mg of the polypeptide having arabinofuranosidase activity per kg DFDSM, and (iii) incubation at 40°C, pH 5 for 4 hours.
Independent claim 54 is interpreted consistent with claim 31 discussed above except claim 54 is constrained to a ratio of xylanase to arabinofuranosidase in the range 50:1 to 1:50. As such, a liquid composition with 1 mg/mL xylanase and 20 µg/mL arabinofuranosidase, or 1 mg/mL arabinofuranosidase and 20 µg/mL xylanase meets the ratio limitation of claim 54 with, for example, dependent claim 62 further narrowing the ratio range to 5:1 to 1:5.
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 50-53 and 75-78 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 50 recites “The composition of claim 41 31.” It is unclear if claim 50 depends from both claims 41 and 31 or in the alternative. Further, claim 41 is cancelled wherein a claim depending from a cancelled claim is necessarily indefinite since it is unclear which claim features are incorporated. For these reasons, an ordinarily skilled artisan cannot determine how to avoid infringement.
Claims 75-78 recites the limitation "the plant based material" in line 1. There is insufficient antecedent basis for this limitation in the claim. There is no literal antecedent basis for “the plant based material” in either claim 31 or 54 nor is there any prior recited claim term that provides a reasonable inherent antecedent basis for “the plant based material.” As such, it is unclear as to what claim feature "the plant based material" references and how infringement of claims 75-78 can be avoided.
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 31-40, 46-69 and 75-78 (all pending claims) 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.
The purpose of the written description requirement is to ensure that the inventor had possession, at the time the invention was made, of the specific subject matter claimed. For a broad generic claim, the specification must provide adequate written description to identify the genus of the claim.
“A written description of an invention involving a chemical genus, like a description of a chemical species, 'requires a precise definition, such as by structure, formula, [or] chemical name,' of the claimed subject matter sufficient to distinguish it from other materials." Fiers, 984 F.2d at 1171, 25 USPQ2d 1601; In re Smythe, 480 F.2d 1376, 1383, 178 USPQ 279, 284985 (CCPA 1973) (“In other cases, particularly but not necessarily, chemical cases, where there is unpredictability in performance of certain species or subcombinations other than those specifically enumerated, one skilled in the art may be found not to have been placed in possession of a genus.”). Regents of the University of California v. Eli Lilly & Co., 119, F.3d 1559, 1568, 43 USPQ2d 1398, 1405 (Fed. Cir. 1997).
MPEP § 2163 further states that if a biomolecule is described only by a functional characteristic, without any disclosed correlation between function and structure of the biomolecule, it is "not sufficient characteristic for written description purposes, even when accompanied by a method of obtaining the claimed biomolecule.”
“The written description requirement for a claimed genus may be satisfied through sufficient description of a representative number of species by actual reduction to practice . . ., reduction to drawings . . ., or by disclosure of relevant, identifying characteristics, i.e., structure or other physical and/or chemical properties, by functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the claimed genus.” MPEP 2163(II)(3)(a).
Furthermore, a “‘representative number of species’ means that the species which are adequately described are representative of the entire genus. Thus, when there is substantial variation within the genus, one must describe a sufficient variety of species to reflect the variation within the genus. 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.’). ‘A patentee will not be deemed to have invented species sufficient to constitute the genus by virtue of having disclosed a single species when … the evidence indicates ordinary artisans could not predict the operability in the invention of any species other than the one disclosed.’ In re Curtis, 354 F.3d 1347, 1358, 69 USPQ2d 1274, 1282 (Fed. Cir. 2004).” MPEP 2163(II)(3)(a).
The Claim Interpretation section above is incorporated herein by reference. As indicated above, the claims require the a genus of liquid compositions with a ratio of arabinofuranosidase:xylanase in a range from 1:20000 to 20000:1 in the broadest claim (claim 31), 5:1 to 1:5 (as in claim 62) and 2:1 to 1:2 (claim 66). Claims 34 and 37 requires a ratio of arabinofuranosidase:xylanase ranging from 5000:1 to 1:2000. Claims 33 and 36 requires a ratio of arabinofuranosidase:xylanase ranging from 10000:1 to 1:4000. Claims 54 and 58 directly state rations in the range of 50:1 to 1:50 and 25:1 to 1:25.
In claim 54 (and claims depending therefrom) a genus of liquid composition having a range of ratios of arabinofuranosidase:xylanase defined therein and claim 31 (and claims depending therefrom) require a range of ratios of arabinofuranosidase:xylanase as a result of requiring a configuration to be dosed in a range of mass of enzyme per kg substrate which constrains the concentration of arabinofuranosidase and xylanase to be in a ratio such that the recited dosing can be achieved. By reciting a specific maximum ratio value of 50:1 to 1:50 in claim 54 and disability of as low as 0.01 mg/kg and as high as 200 mg/kg for each enzyme, the claims assert, for example, possession of a genus of liquid compositions with a ratio of 50:1 or 1:50 arabinofuranosidase:xylanase having the following functional property:
the GH10 or GH11 polypeptide having xylanase activity and the polypeptide having arabinofuranosidase activity together solubilise at least 2 times more xylose from DFDSM than the GH10 or GH11 polypeptide having xylanase activity in the absence of the polypeptide having arabinofuranosidase.
“In other cases, particularly but not necessarily, chemical cases, where there is unpredictability in performance of certain species or subcombinations other than those specifically enumerated, one skilled in the art may be found not to have been placed in possession of a genus.”
The specification asserts that the dual action of arabinofuranosidase and xylanase (having the structure recited) can solubilize a greater amount of xylose from DFDSM than xylanase acting alone at the same dosing level.
The following Tables from the specification are representative of disclosure of the specification.
Table 8:
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216
670
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Greyscale
Table 10:
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213
668
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Greyscale
Table 19:
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213
648
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Greyscale
Table 30:
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229
672
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Greyscale
As can be seen, the recited technical effect of 2 times greater xylose solubility is demonstrated for compositions wherein the ratio of arabinofuranosidase:xylanase is 1:1 or wherein xylanase is in excess in an amount of up to 5-fold or 2-fold (i.e. arabinofuranosidase:xylanase is 1:5 or 2:1). It is speculative and unpredictable if the recited technical effect of 2 times greater xylose solubility is achievable wherein the amount of arabinofuranosidase is significantly less than demonstrated in the working embodiments of the specification; or example, wherein a ratio of xylanase:arabinofuranosidase can be 20000:1, 10000:1, 100:1, 50:1 or 25:1 as recited in the claims, nor wherein the amount of arabinofuranosidase is greater than xylanase such as a ratio of xylanase:arabinofuranosidase or 1:5 or 1:2 as recited in claim 62 or 66 and even higher as allowed by other claims.
That is, the specification demonstrates that the recited functional limitation “together solubilize 2 times more xylose from DFDSM” is achievable where xylanase and arabinofuranosidase are present at equal weight amounts or concentrations within a liquid composition applied to solubilize xylose from DFDSM and wherein xylanase in in excess by a factor of up to about two, i.e. 2:1 ratio of xylanase to arabinofuranosidase. There is unpredictability in performance and operability of the ratios within the recited genus of ratios to have the recited function “together solubilize 2 times more xylose from DFDSM,” including values wherein xylanase is in large excess by weight over arabinofuranosidase, such as 10 times, 50 times, 100 times or even 20000 times greater weight of xylanase relative to arabinofuranosidase and/or wherein arabinofuranosidase is in significant weight excess over xylanase (e.g. 2 or 5 times more arabinofuranosidase by weight than xylanase) such that there is not sufficient written description report for the recited ratios, both those ratios recited in the claims and/or required as a consequence of “configured to be dosed” limitations as discussed in the Claim Interpretation section, to achieve the recited function “together solubilize 2 times more xylose from DFDSM.”
The narrow ratios demonstrated to be functional in the specification are not representative of the much broader range of ratios recited in the claims. “A patentee will not be deemed to have invented species sufficient to constitute the genus by virtue of having disclosed a single species when … the evidence indicates ordinary artisans could not predict the operability in the invention of any species other than the one disclosed.” Here, the disclosure of ratios of xylanase to arabinofuranosidase of 1:1, 2:1, 5:1 and similar values do not allow for ordinarily skilled artisans to predict operability of other species/ratios wherein xylanase is in a very large excess (or wherein arabinofuranosidase is in large excess over weight of xylanase) such that sufficient species/ratios to constitute the genus of range of ratios claimed are not disclosed such that written description for the genus being ranges of xylanase and arabinofuranosidase present with specific operability to “together solubilize 2 times more xylose from DFDSM” is lacking.
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 31-40 and 46-53 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-15 of U.S. Patent No. 11,053,490 B2 further in view of Powers et al. (U.S. 2011/0086408 A1) (see IDS). Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons.
Patented claim 1 states:
1. A composition comprising
a GH10 or GH11 polypeptide having xylanase activity and at least 80% sequence identity to the polypeptide of SEQ ID NO: 78, and
a GH62 polypeptide having arabinofuranosidase activity and at least 80% sequence identity to the polypeptide of SEQ ID NO: 27,
wherein:
(a) the GH10 or GH11 polypeptide and the GH62 polypeptide together solubilise at least 2.0% xylose from defatted destarched maize (DFDSM); and
(b) the GH10 or GH11 polypeptide and the GH62 polypeptide together solubilise at least 2 times more xylose from DFDSM than the GH10 or GH11 polypeptide in the absence of the GH62 polypeptide;
wherein (a) and (b) are performed under the reaction conditions: (i) 25 mg GH10 or GH11 polypeptide per kg DFDSM, (ii) 12.5 mg GH62 polypeptide per kg DFDSM, and (iii) incubation at 40° C., pH 5 for 4 hours.
Patented claim 1 is considered to directly imply and suggest a composition having a ratio of GH10/11 xylanase to arabinofuranosidase of 2:1 as to facilitate addition of 25 mg xylanase and 12.5 mg arabinofuranosidase per kg of DFDSM substrate as to anticipate or suggest the features of all of the rejected claims.
Claim 31 is understood as requiring the arabinofuranosidase and xylanase enzymes both to be dosable in an amount of 0.01-200 mg protein per kg of substrate (or subranges thereof as recited in certain dependent claims); however, the xylanase to arabinofuranosidase to ratio of 2:1 indicated in the patented claims is considered to meet this feature.
A formulating agent includes water and/or a buffer. For example, Powers, abstract, teaches “compositions and methods relating to cellulase/hemicellulase enzyme blends for improving the enzymatic hydrolysis of cellulosic and hemicellulosic materials, as commonly found in biomass.” Powers, para. [0077], teaches that it is common and known in the prior art to include an appropriate buffer (sodium acetate in Powers) in enzyme compositions for degrading biomass including those having arabinofuranosidase and/or xylanase as taught by Powers. As such, at the time of filing an ordinarily skilled artisan would have been motivated to include water and an appropriate buffer as formulating agents within compositions of the patented claims since the same is understood in the prior art to be beneficial (e.g. pH stability protects enzymes from possibly denaturing conditions).
Claims 31-40 and 46-53 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 11,926,852 B2 further in view of Powers et al. (U.S. 2011/0086408 A1). Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons.
As discussed, claims do not require any specific concentration of xylanase or arabinofuranosidase polypeptides wherein regardless of the concentration of xylanase or arabinofuranosidase polypeptides present in an embodiment (for example, 0.1 mg/mL for each polypeptide) a volume of the liquid composition can be added to a substrate as to “dose” as substrate (DFDSM) at 0.05, 0.1 or 1 mg of xylanase and/or arabinofuranosidase polypeptides per kg of substrate. As such, a liquid composition having any concentration of xylanase and/or arabinofuranosidase polypeptides is considered to be an embodiment of the claims.
Patented claim 1 states:
1. A composition comprising:
a glycoside hydrolase family 10 (GH10) polypeptides having xylanase activity and at least 80% sequence identity to the polypeptide of SEQ ID NO: 95; and
a glycoside hydrolase family 62 (GH62) polypeptides having arabinofuranosidase activity and at least 80% sequence identity to the polypeptide of SEQ ID NO: 27, wherein:
(a) the GH10 polypeptide and the GH62 polypeptide together solubilise at least 2.0% xylose from defatted destarched maize (DFDSM); and
(b) the GH10 polypeptide and the GH62 polypeptide together solubilise at least 2 times more xylose from DFDSM than the GH10 polypeptide can when the GH62 polypeptide is not present;
wherein (a) and (b) are performed under the reaction conditions:
i) 25 mg GH10 polypeptide per kg DFDSM,
ii) 12.5 mg GH62 polypeptide per kg DFDSM, and
iii) incubation at 40° C., pH 5 for 4 hours.
Patented claim 1 is considered to directly imply and suggest a composition having a ratio of GH10/11 xylanase to arabinofuranosidase of 2:1 as to facilitate addition of 25 mg xylanase and 12.5 mg arabinofuranosidase per kg of DFDSM substrate as to anticipate or suggest the features of all of rejected claims.
Claim 31 is understood as requiring the arabinofuranosidase and xylanase enzymes both to be dosable in an amount of 0.01-200 mg protein per kg of substrate (or subranges thereof as recited in certain dependent claims); however, the xylanase to arabinofuranosidase to ratio of 2:1 indicated in the patented claims is considered to meet this feature.
Further, a formulating agent includes water and/or a buffer. For example, Powers, abstract, teaches “compositions and methods relating to cellulase/hemicellulase enzyme blends for improving the enzymatic hydrolysis of cellulosic and hemicellulosic materials, as commonly found in biomass.” Powers, para. [0077], teaches that it is common and known in the prior art to include an appropriate buffer (sodium acetate in Powers) in enzyme compositions for degrading biomass including those having arabinofuranosidase and/or xylanase as taught by Powers. As such, at the time of filing an ordinarily skilled artisan would have been motivated to include water and an appropriate buffer as formulating agents within compositions of the patented claims since the same is understood in the prior art to be beneficial (e.g. pH stability protects enzymes from possibly denaturing conditions).
Claims 31-40 and 46-69 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-18 of U.S. Patent No. 11,649,298 B2 further in view of Powers et al. (U.S. 2011/0086408 A1) and Isaksen et al. (WO 2014/020141 A1). Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons.
As discussed, the claims do not require any specific concentration of xylanase or arabinofuranosidase polypeptides wherein regardless of the concentration of xylanase or arabinofuranosidase polypeptides present in an embodiment (for example, 0.1 mg/mL for each polypeptide) a volume of the liquid composition can be added to a substrate as to “dose” as substrate (DFDSM) at 0.05, 0.1 or 1 mg of xylanase and/or arabinofuranosidase polypeptides per kg of substrate. As such, a liquid composition having any concentration of xylanase and/or arabinofuranosidase polypeptides is considered to be an embodiment of the claims.
Patented claims include:
1. A process for treating crop kernels, comprising:
a) soaking kernels in water to produce soaked kernels;
b) grinding the soaked kernels to form ground kernels;
c) separating the germ from the ground kernels to produce a slurry comprising fiber, starch and protein; and
d) treating the slurry in a fiber washing step to separate fiber from the starch and protein in the presence of an effective amount of a polypeptide having arabinofuranosidase activity, wherein the polypeptide having arabinofuranosidase activity comprises an amino acid sequence having at least 60% sequence identity to SEQ ID NO: 27.
12. The process of claim 1, wherein step d) further comprises treating the slurry in the presence of a GH10 xylanase or a GH11 xylanase.
A “slurry” as recited in the patented claims is understood to mean a slurry with water such that any arabinofuranosidase or GH10/11 xylanase for treatment therein is within the broadest reasonable interpretation of an aqueous slurry or a liquid composition. As such, at least patented claim 12 anticipates or suggests the features of the rejected claims except for specific claims reciting a ratio of xylanase:arabinofuranosidase.
Powers, abstract, teaches “compositions and methods relating to cellulase/hemicellulase enzyme blends for improving the enzymatic hydrolysis of cellulosic and hemicellulosic materials, as commonly found in biomass.” More specifically, Powers, Table 1 and para. [0076], teaches enzyme compositions having a GH62 arabinofuranosidase (ABF2) and a GH10 xylanase (XYN3) or GH11 xylanase (XYN2). Table 2 teaches the specific use of such enzyme compositions to hydrolyze hemicellulose materials with 5 mg of XYN2 and 5 mg of ABF2 or a 1:1 ratio of a GH11 xylanase:GH62 arabinofuranosidase. As such, the prior art directly teaches and suggest that in treating hemicellulose or cellulose substrates (such as the crop kernels of the patented claims), that it is appropriate to apply GH11 xylanase:GH62 arabinofuranosidase at a 1:1 ratio such that at the time of filing an ordinarily skilled would have been motivated to form embodiments of at least patented claim 12 to have a 1:1 ratio (with the polypeptide of SEQ ID NO: 27 as a GH62 arabinofuranosidase) as to meet all of the features of the claims except for indication of specific xylanase species.
Claim 31 is understood as requiring the arabinofuranosidase and xylanase enzymes both to be dosable in an amount of 0.01-200 mg protein per kg of substrate (or subranges thereof as recited in certain dependent claims); however, the xylanase to arabinofuranosidase to ratio of 1:1 indicated in the patented claims is considered to meet this feature as well as the ratio recited in claim 54 and claims depending therefrom.
Further, a formulating agent includes water and/or a buffer. Powers, para. [0077], teaches that it is common and known in the prior art to include an appropriate buffer (sodium acetate in Powers) in enzyme compositions for degrading biomass including those having arabinofuranosidase and/or xylanase as taught by Powers. As such, at the time of filing an ordinarily skilled artisan would have been motivated to include water and an appropriate buffer as formulating agents within compositions or fiber washing step of the patented claims since the same is understood in the prior art to be beneficial (e.g. pH stability protects enzymes from possibly denaturing conditions).
Regarding claim 54 reciting specific xylanase species, in practicing any embodiment of patented claims, a specific embodiment a GH10/11 xylanase must be used. Isaksen teaches feed additives that include a xylanase having SEQ ID NO: 12 of Isaksen that is identical to recited SEQ ID NO: 88, wherein the function of the xylanase is to degrade/hydrolyze plant material and particularly fiber in plant material. Isaksen, abstract, claim 1, para. [0008] and para. [0237]. The xylanase of the patented (or co-pending) claims is for treating plant material including fiber, and as discussed the xylanase of Isaksen having recited SEQ ID NO: 88 (SEQ ID NO: 12 of Isaksen) is expressly taught as being useful for degradation and hydrolysis of plant material. As such, at the time of filing an ordinarily skilled artisan would have been motivated to apply the xylanase of Isaksen having recited SEQ ID NO: 88 (SEQ ID NO: 12 of Isaksen) as an embodiment of the patented (or co-pending) claims since the same xylanase is expressly taught as appropriate and beneficial for treating plant material.
Regarding recitation in claim 31 and 54 of “the GH10 or GH11 polypeptide having xylanase activity and the polypeptide having arabinofuranosidase activity together solubilise at least 2 times more xylose from DFDSM than the GH10 or GH11 polypeptide having xylanase activity in the absence of the polypeptide having arabinofuranosidase” the preceding is not interpreted as requiring the performance of any active step of a method (the claims recite a composition of matter) but rather requiring the xylanase and arabinofuranosidase polypeptides to latently possess such properties as recited. The claims and the specification evidence that a combination of a polypeptide having arabinofuranosidase with recited SEQ ID NO: 27 and a xylanase polypeptide with SEQ ID NO: 88 inherently have these recited properties. "’The fact that appellant has recognized another advantage which would flow naturally from following the suggestion of the prior art cannot be the basis for patentability when the differences would otherwise be obvious.’ Ex parte Obiaya, 227 USPQ 58, 60 (Bd. Pat. App. & Inter. 1985).” MPEP 2145(II).
Claims 31-40 and 46-69 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 11,987,649 B2 further in view of Powers et al. (U.S. 2011/0086408 A1) and Isaksen et al. (WO 2014/020141 A1). Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons.
Patented claims include:
1. A process for treating crop kernels, comprising:
a) soaking kernels in water to produce soaked kernels;
b) grinding the soaked kernels to form ground kernels;
c) separating the germ from the ground kernels to produce a slurry comprising fiber, starch and protein; and
d) treating the slurry in a fiber washing step to separate fiber from the starch and protein in the presence of an effective amount of a polypeptide having arabinofuranosidase activity, wherein the polypeptide having arabinofuranosidase activity comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 27.
10. The process of claim 1, wherein step d) further comprises treating the slurry in the presence of a GH10 xylanase or a GH11 xylanase.
A “slurry” as recited in the patented claims is understood to mean a slurry with water such that any arabinofuranosidase or GH10/11 xylanase for treatment therein is within the broadest reasonable interpretation of an aqueous slurry or a liquid composition. As such, at least patented claim 10 anticipates or suggests the features of the claims except for specific claims reciting a ratio or amounts of xylanase:arabinofuranosidase and specific xylanase species.
Powers, abstract, teaches “compositions and methods relating to cellulase/hemicellulase enzyme blends for improving the enzymatic hydrolysis of cellulosic and hemicellulosic materials, as commonly found in biomass.” More specifically, Powers, Table 1 and para. [0076], teaches enzyme compositions having a GH62 arabinofuranosidase (ABF2) and a GH10 xylanase (XYN3) or GH11 xylanase (XYN2). Table 2 teaches the specific use of such enzyme compositions to hydrolyze hemicellulose materials with 5 mg of XYN2 and 5 mg of ABF2 or a 1:1 ratio of a GH11 xylanase:GH62 arabinofuranosidase. As such, the prior art directly teaches and suggest that in treating hemicellulose or cellulose substrates (such as the crop kernels of the patented claims), that it is appropriate to apply GH11 xylanase:GH62 arabinofuranosidase at a 1:1 ratio such that at the time of filing an ordinarily skilled would have been motivated to form embodiments of at least patented claim 10 to have a 1:1 ratio (with the polypeptide of SEQ ID NO: 27 as a GH62 arabinofuranosidase) as to meet all of the features of the claims except for the identity of specific xylanase species.
Claim 31 is understood as requiring the arabinofuranosidase and xylanase enzymes both to be dosable in an amount of 0.01-200 mg protein per kg of substrate (or subranges thereof as recited in certain dependent claims); however, the xylanase to arabinofuranosidase to ratio of 1:1 indicated in the patented claims is considered to meet this feature as well as the ratio recited in claim 54 and claims depending therefrom.
Further, a formulating agent includes water and/or a buffer. Powers, para. [0077], teaches that it is common and known in the prior art to include an appropriate buffer (sodium acetate in Powers) in enzyme compositions for degrading biomass including those having arabinofuranosidase and/or xylanase as taught by Powers. As such, at the time of filing an ordinarily skilled artisan would have been motivated to include water and an appropriate buffer as formulating agents within compositions or washing step of the patented claims since the same is understood in the prior art to be beneficial (e.g. pH stability protects enzymes from possibly denaturing conditions).
Regarding claim 54 reciting specific xylanase species, in practicing any embodiment of patented claims, a specific embodiment a GH10/11 xylanase must be used. Isaksen teaches feed additives that include a xylanase having SEQ ID NO: 12 of Isaksen that is identical to recited SEQ ID NO: 88, wherein the function of the xylanase is to degrade/hydrolyze plant material and particularly fiber in plant material. Isaksen, abstract, claim 1, para. [0008] and para. [0237]. The xylanase of the patented (or co-pending) claims is for treating plant material including fiber, and as discussed the xylanase of Isaksen having recited SEQ ID NO: 88 (SEQ ID NO: 12 of Isaksen) is expressly taught as being useful for degradation and hydrolysis of plant material. As such, at the time of filing an ordinarily skilled artisan would have been motivated to apply the xylanase of Isaksen having recited SEQ ID NO: 88 (SEQ ID NO: 12 of Isaksen) as an embodiment of the patented (or co-pending) claims since the same xylanase is expressly taught as appropriate and beneficial for treating plant material.
Regarding recitation in claim 31 of “the GH10 or GH11 polypeptide having xylanase activity and the polypeptide having arabinofuranosidase activity together solubilise at least 2 times more xylose from DFDSM than the GH10 or GH11 polypeptide having xylanase activity in the absence of the polypeptide having arabinofuranosidase” the preceding is not interpreted as requiring the performance of any active step of a method (the claims recite a composition of matter) but rather requiring the xylanase and arabinofuranosidase polypeptides to latently possess such properties as recited. The claims and the specification evidence that a combination of a polypeptide having arabinofuranosidase with recited SEQ ID NO: 27 and a xylanase polypeptide with SEQ ID NO: 88 inherently have these recited properties. "’The fact that appellant has recognized another advantage which would flow naturally from following the suggestion of the prior art cannot be the basis for patentability when the differences would otherwise be obvious.’ Ex parte Obiaya, 227 USPQ 58, 60 (Bd. Pat. App. & Inter. 1985).” MPEP 2145(II).
Claims 31-40 and 46-69 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 13-22 of U.S. Patent No. 12,005,456 B2 further in view of Powers et al. (U.S. 2011/0086408 A1) and Festersen et al. (U.S. 2007/0148741 A1). Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons.
SEQ ID NO: 7 of the patented claims is identical to recited SEQ ID NO: 27.
The patented claims include:
13. A method to improve starch yield and/or gluten yield from corn kernels in a wet milling process, comprising the steps of:
a) soaking the kernels in water to produce soaked kernels;
b) grinding the soaked kernels;
c) separating germs from the ground and soaked kernels to produce a corn kernel mass comprising fiber, starch and gluten; and
d) subjecting the resultant corn kernel mass, to a fiber washing procedure;
wherein during step d) one or more fractions of the corn kernel mass is contacted with an effective amount of one or more hydrolytic enzymes, and wherein the fiber washing procedure is performed with a fiber washing system in a corn kernel wet milling system comprising a plurality of screen units being fluidly connected in a counter current washing configuration from a most upstream screen unit to a most downstream screen unit; each screen unit is configured for separating a stream of corn kernel mass and liquid into two fractions:
a first fraction (s) and a second fraction (f), said second fraction (f) containing a higher amount measured in wt % fiber than the first fraction (s);
a space (V) is a separate container being fluidly connected with one or more screen units to receive one of said first fraction (s), one of said second fraction (f), or a mixed first and second fraction (s,f), and wherein the space (V) is configured to provide an incubation time in which the first fraction (s), the second fraction (f), or the mixed first and second fraction (s,f) received in the space (V) are contacted with the one or more hydrolytic enzymes to produce incubated fractions; and outletting the incubated fractions to a downstream screen unit,
16. The method according to claim 13, wherein the one or more of said hydrolytic enzymes comprise a xylanase, which is a GH10 xylanase.
20. The method according to claim 13, wherein the one or more of said hydrolytic enzymes comprise a GH62 polypeptide with arabinofuranosidase activity, which is selected from the group consisting of:
i) an amino acid sequence as set forth in any one of SEQ ID NOs: 1-21;
A “slurry” as recited in the patented claims is understood to mean a slurry with water such that any arabinofuranosidase or GH10/11 xylanase for treatment therein is within the broadest reasonable interpretation of an aqueous slurry or a liquid composition. As such, at least patented claim 20 anticipates or suggests the features of claims 31-70 with respect to a liquid composition having a polypeptide of SEQ ID NO: 27 (SEQ ID NO: 7 of the patented claims) except for specific claims reciting a ratio xylanase:arabinofuranosidase. The patented claims indicate that more than one hydrolytic enzyme can be present and mentions xylanase combined with a GH62 arabinofuranosidase in claim 21.
Powers, abstract, teaches “compositions and methods relating to cellulase/hemicellulase enzyme blends for improving the enzymatic hydrolysis of cellulosic and hemicellulosic materials, as commonly found in biomass.” More specifically, Powers, Table 1 and para. [0076], teaches enzyme compositions having a GH62 arabinofuranosidase (ABF2) and a GH10 xylanase (XYN3) or GH11 xylanase (XYN2). Table 2 teaches the specific use of such enzyme compositions to hydrolyze hemicellulose materials with 5 mg of XYN2 and 5 mg of ABF2 or a 1:1 ratio of a GH11 xylanase:GH62 arabinofuranosidase. As such, the prior art directly teaches and suggest that in treating hemicellulose or cellulose substrates (such as the crop kernels of the patented claims), that it is appropriate to apply GH11 xylanase:GH62 arabinofuranosidase at a 1:1 ratio such that at the time of filing an ordinarily skilled would have been motivated to form embodiments of at least patented claim 20 to have a 1:1 ratio (with the polypeptide of SEQ ID NO: 27 as a GH62 arabinofuranosidase) as to meet all of the features of claims except for specific xylanase species.
Claim 31 is understood as requiring the arabinofuranosidase and xylanase enzymes both to be dosable in an amount of 0.01-200 mg protein per kg of substrate (or subranges thereof as recited in certain dependent claims); however, the xylanase to arabinofuranosidase to ratio of 1:1 indicated in the patented claims is considered to meet this feature as well as the ratio recited in claim 54 and claims depending therefrom.
Further, a formulating agent includes water and/or a buffer. Powers, para. [0077], teaches that it is common and known in the prior art to include an appropriate buffer (sodium acetate in Powers) in enzyme compositions for degrading biomass including those having arabinofuranosidase and/or xylanase as taught by Powers. As such, at the time of filing an ordinarily skilled artisan would have been motivated to include water and an appropriate buffer as formulating agents within compositions or fiber washing step of the patented claims since the same is understood in the prior art to be beneficial (e.g. pH stability protects enzymes from possibly denaturing conditions).
Regarding claim 54 (and claims depending therefrom), in practicing any embodiment of patented claims, a specific embodiment a GH10/11 xylanase must be used. Festersen teaches a mashing process that include a xylanase having SEQ ID NO: 8 of Festersen that is identical to recited SEQ ID NO: 72 (a GH10 xylanase), wherein the function of the xylanase is to degrade/hydrolyze plant material and particularly fiber in plant material. Festersen, abstract, claim 28, para. [0092] and Table 2. The xylanase of the patented (or co-pending) claims is for treating plant material including fiber, and as discussed the xylanase of Isaksen having recited SEQ ID NO: 72 (SEQ ID NO: 8 of Festersen) is expressly taught as being useful for degradation and hydrolysis of plant material. As such, at the time of filing an ordinarily skilled artisan would have been motivated to apply the xylanase of Isaksen having recited SEQ ID NO: 72 (SEQ ID NO: 8 of Festersen) as an embodiment of the patented (or co-pending) claims since the same xylanase is expressly taught as appropriate and beneficial for treating plant material.
Regarding recitation in claim 31 of “the GH10 or GH11 polypeptide having xylanase activity and the polypeptide having arabinofuranosidase activity together solubilise at least 2 times more xylose from DFDSM than the GH10 or GH11 polypeptide having xylanase activity in the absence of the polypeptide having arabinofuranosidase,” the preceding is not interpreted as requiring the performance of any active step of a method (the claims recite a composition of matter) but rather requiring the xylanase and arabinofuranosidase polypeptides to latently possess such properties as recited. The claims and the specification evidence that a combination of a polypeptide having arabinofuranosidase with recited SEQ ID NO: 27 and a xylanase polypeptide with SEQ ID NO: 27 inherently have these recited properties. "’The fact that appellant has recognized another advantage which would flow naturally from following the suggestion of the prior art cannot be the basis for patentability when the differences would otherwise be obvious.’ Ex parte Obiaya, 227 USPQ 58, 60 (Bd. Pat. App. & Inter. 1985).” MPEP 2145(II).
Claims 31-40 and 46-69 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 11,987,649 B2 further in view of Powers et al. (U.S. 2011/0086408 A1) and Isaksen et al. (WO 2014/020141 A1) (previously cited). Although the claims at issue are not identical, they are not patentably distinct from each other for the following reasons.
The rejections of claims under 35 U.S.C. 112(b) stated above are incorporated by reference.
The patented claims include:
1. A process for treating crop kernels, comprising:
a) soaking kernels in water to produce soaked kernels;
b) grinding the soaked kernels to form ground kernels;
c) separating the germ from the ground kernels to produce a slurry comprising fiber, starch and protein; and
d) treating the slurry in a fiber washing step to separate fiber from the starch and protein in the presence of an effective amount of a polypeptide having arabinofuranosidase activity, wherein the polypeptide having arabinofuranosidase activity comprises an amino acid sequence having at least 80% sequence identity to SEQ ID NO: 27.
10. The process of claim 1, wherein step d) further comprises treating the slurry in the presence of a GH10 xylanase or a GH11 xylanase.
A “slurry” as recited in the patented claims is understood to mean a slurry with water such that any arabinofuranosidase or GH10/11 xylanase for treatment therein is within the broadest reasonable interpretation of an aqueous slurry or a liquid composition.
Powers, abstract, teaches “compositions and methods relating to cellulase/hemicellulase enzyme blends for improving the enzymatic hydrolysis of cellulosic and hemicellulosic materials, as commonly found in biomass.” More specifically, Powers, Table 1 and para. [0076], teaches enzyme compositions having a GH62 arabinofuranosidase (ABF2) and a GH10 xylanase (XYN3) or GH11 xylanase (XYN2). Table 2 teaches the specific use of such enzyme compositions to hydrolyze hemicellulose materials with 5 mg of XYN2 and 5 mg of ABF2 or a 1:1 ratio of a GH11 xylanase:GH62 arabinofuranosidase. As such, the prior art directly teaches and suggest that in treating hemicellulose or cellulose substrates (such as the crop kernels of the patented claims), that it is appropriate to apply GH11 xylanase:GH62 arabinofuranosidase at a 1:1 ratio such that at the time of filing an ordinarily skilled would have been motivated to form embodiments of at least patented claim 10 to have a 1:1 ratio (with the polypeptide of SEQ ID NO: 27 as a GH62 arabinofuranosidase) as to meet all of the features of the claims except for identity of specific xylanase species.
Claim 31 is understood as requiring the arabinofuranosidase and xylanase enzymes both to be dosable in an amount of 0.01-200 mg protein per kg of substrate (or subranges thereof as recited in certain dependent claims); however, the xylanase to arabinofuranosidase to ratio of 1:1 indicated in the patented claims is considered to meet this feature as well as the ratio recited in claim 54 and claims depending therefrom.
Further, a formulating agent includes water and/or a buffer. Powers, para. [0077], teaches that it is common and known in the prior art to include an appropriate buffer (sodium acetate in Powers) in enzyme compositions for degrading biomass including those having arabinofuranosidase and/or xylanase as taught by Powers. As such, at the time of filing an ordinarily skilled artisan would have been motivated to include water and an appropriate buffer as formulating agents within compositions or fiber washing step of the patented claims since the same is understood in the prior art to be beneficial (e.g. pH stability protects enzymes from possibly denaturing conditions).
Regarding claim 54 reciting specific xylanase species, in practicing any embodiment of patented claims, a specific embodiment a GH10/11 xylanase must be used. Isaksen teaches feed additives that include a xylanase having SEQ ID NO: 12 of Isaksen that is identical to recited SEQ ID NO: 88, wherein the function of the xylanase is to degrade/hydrolyze plant material and particularly fiber in plant material. Isaksen, abstract, claim 1, para. [0008] and para. [0237]. The xylanase of the patented (or co-pending) claims is for treating plant material including fiber, and as discussed the xylanase of Isaksen having recited SEQ ID NO: 88 (SEQ ID NO: 12 of Isaksen) is expressly taught as being useful for degradation and hydrolysis of plant material. As such, at the time of filing an ordinarily skilled artisan would have been motivated to apply the xylanase of Isaksen having recited SEQ ID NO: 88 (SEQ ID NO: 12 of Isaksen) as an embodiment of the patented (or co-pending) claims since the same xylanase is expressly taught as appropriate and beneficial for treating plant material.
Regarding recitation in claim 31 of “the GH10 or GH11 polypeptide having xylanase activity and the polypeptide having arabinofuranosidase activity together solubilise at least 2 times more xylose from DFDSM than the GH10 or GH11 polypeptide having xylanase activity in the absence of the polypeptide having arabinofuranosidase,” the preceding is not interpreted as requiring the performance of any active step of a method (the claims recite a composition of matter) but rather requiring the xylanase and arabinofuranosidase polypeptides to latently possess such properties as recited. The claims and the specification evidence that a combination of a polypeptide having arabinofuranosidase with recited SEQ ID NO: 27 and a xylanase polypeptide with SEQ ID NO: 88 inherently have these recited properties. "’The fact that appellant has recognized another advantage which would flow naturally from following the suggestion of the prior art cannot be the basis for patentability when the differences would otherwise be obvious.’ Ex parte Obiaya, 227 USPQ 58, 60 (Bd. Pat. App. & Inter. 1985).” MPEP 2145(II).
Response to arguments
The prior rejections under 35 U.S.C. 112(b) and 112(a) are moot in view of applicant’s amendment. However, applicant’s amendment necessitate the new grounds of rejection made above. No particular transversal arguments are made with regards to double patenting rejections.
Conclusion
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/TODD M EPSTEIN/Primary Examiner, Art Unit 1652