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 .
This office action is in response to the amendment filed on November 7, 2025. New claims 21 and 22 have been added. Claim 1 has been withdrawn previously. Newly submitted claims 21 and 22 are directed to an invention that is independent or distinct from the invention originally claimed for the following reasons: the examined claims are drawn to a method of processing a substance.
Since applicant has received an action on the merits for the originally presented invention, this invention has been constructively elected by original presentation for prosecution on the merits. Accordingly, claims 21 and 22 are withdrawn from consideration as being directed to a non-elected invention. See 37 CFR 1.142(b) and MPEP § 821.03.
To preserve a right to petition, the reply to this action must distinctly and specifically point out supposed errors in the restriction requirement. Otherwise, the election shall be treated as a final election without traverse. Traversal must be timely. Failure to timely traverse the requirement will result in the loss of right to petition under 37 CFR 1.144. If claims are subsequently added, applicant must indicate which of the subsequently added claims are readable upon the elected invention.
Should applicant traverse on the ground that the inventions are not patentably distinct, applicant should submit evidence or identify such evidence now of record showing the inventions to be obvious variants or clearly admit on the record that this is the case. In either instance, if the examiner finds one of the inventions unpatentable over the prior art, the evidence or admission may be used in a rejection under 35 U.S.C. 103 or pre-AIA 35 U.S.C. 103(a) of the other invention.
Claims 2-20 are currently pending and are under examination.
Withdrawal of Rejections
Any objection or rejection not reiterated below has been withdrawn based on the amendment to the claims.
Pending Rejections
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claim 22 is 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.
This rejection is presented to a withdrawn claim to reduce prosecution time if the claim was intended to be a method claim as the currently examined claims.
Claim 22 is dependent on method claim 2, but refers to a synthetic variant polypeptide as a composition claim. It is improperly dependent on a method claim. Clarification is requested about claim 22.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 2, 10, and 11 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kitamoto (Journal of Bacteriology Vol. 17, No. 12, p. 5848-5854 (Dec. 1988); 12/21/2022 IDS, NPL Doc. AB; previously cited) and Callen et al. (U.S. Patent 8,334,118 B2; previously cited).
Kitamoto et al. disclose a beta-amylase from Clostridium thermosulfurogenes that has 99% identity with SEQ ID NO: 3 of the instant application. The alignment is shown below. There are S280A, S319T, and S322C amino acid substitions in relation to SEQ ID NO: 3 as shown in the alignment below. The disclosed beta-amylase from Kitamoto et al. also has a modification at position 273 of currently claimed SEQ ID NO: 6 and has 99.6% identity. The disclosed beta-amylase from Kitamoto et al. also has a modification at position 286 of currently claimed SEQ ID NO: 4 and has 99.6% identity. Kitamoto et al. disclose that beta amylase hydrolyzes starch (see first sentence of Introduction, p. 5848).
Where the claimed and prior art products are identical or substantially identical in structure or composition, or are produced by identical or substantially identical processes, a prima facie case of either anticipation or obviousness has been established. In re Best, 562 F.2d 1252, 1255, 195 USPQ 430, 433 (CCPA 1977). “When the PTO shows a sound basis for believing that the products of the applicant and the prior art are the same, the applicant has the burden of showing that they are not.” In re Spada, 911 F.2d 705, 709, 15 USPQ2d 1655, 1658 (Fed. Cir.1990). Therefore, the prima facie case can be rebutted by evidence showing that the prior art products do not necessarily possess the characteristics of the claimed product. In re Best, 562 F.2d at 1255, 195 USPQ at 433. It is art recognized that the structure of the polypeptide will determine the function of the polypeptide.
(Query 1: SEQ ID NO: 3 with Kitamoto ref Sbjct: GenBank: AAA23204.1)
Score Expect Method Identities Positives Gaps
1055 bits(2729) 0.0 Compositional matrix adjust. 515/519(99%) 517/519(99%) 0/519(0%)
Query 1 SIAPNFKVFVMGPLEKVTDFNAFKDQLITLKNNGVYGITTDIWWGYVENAGENQFDWSYY 60
SIAPNFKVFVMGPLEKVTDFNAFKDQLITLKNNGVYGITTDIWWGYVENAGENQFDWSYY
Sbjct 33 SIAPNFKVFVMGPLEKVTDFNAFKDQLITLKNNGVYGITTDIWWGYVENAGENQFDWSYY 92
Query 61 KTYADTVRAAGLKWVPIMSTHASGGNVGDTVNIPIPSWVWTKDTQDNMQYKDEAGNWDNE 120
KTYADTVRAAGLKWVPIMSTHA GGNVGDTVNIPIPSWVWTKDTQDNMQYKDEAGNWDNE
Sbjct 93 KTYADTVRAAGLKWVPIMSTHACGGNVGDTVNIPIPSWVWTKDTQDNMQYKDEAGNWDNE 152
Query 121 AVSPWYSGLTQLYNEFYSSFASNFSSYKDIITKIYISGGPSGELRYPSYNPSHGWTYPGR 180
AVSPWYSGLTQLYNEFYSSFASNFSSYKDIITKIYISGGPSGELRYPSYNPSHGWTYPGR
Sbjct 153 AVSPWYSGLTQLYNEFYSSFASNFSSYKDIITKIYISGGPSGELRYPSYNPSHGWTYPGR 212
Query 181 GSLQCYSKAAITSFQNAMKSKYGTIAAVNSAWGTSLTDFSQISPPTDGDNFFTNGYKTTY 240
GSLQCYSKAAITSFQNAMKSKYGTIAAVNSAWGTSLTDFSQISPPTDGDNFFTNGYKTTY
Sbjct 213 GSLQCYSKAAITSFQNAMKSKYGTIAAVNSAWGTSLTDFSQISPPTDGDNFFTNGYKTTY 272
Query 241 GNDFLTWYQSVLTNELANIASVAHSCFDPVFNVPIGAKISGVHWLYNSPTMPHAAEYCAG 300
GNDFLTWYQSVLTNELANIASVAHSCFDPVFNVPIGAKI+GVHWLYNSPTMPHAAEYCAG
Sbjct 273 GNDFLTWYQSVLTNELANIASVAHSCFDPVFNVPIGAKIAGVHWLYNSPTMPHAAEYCAG 332
Query 301 YYNYSTLLDQFKASNLAMSFTSLEMDDSNAYVSPYYSAPMTLVHYVANLANNKGIVHNGE 360
YYNYSTLLDQFKASNLAM+FT LEMDDSNAYVSPYYSAPMTLVHYVANLANNKGIVHNGE
Sbjct 333 YYNYSTLLDQFKASNLAMTFTCLEMDDSNAYVSPYYSAPMTLVHYVANLANNKGIVHNGE 392
Query 361 NALAISNNNQAYVNCANELTGYNFSGFTLLRLSNIVNSDGSVTSEMAPFVINIVTLTPNG 420
NALAISNNNQAYVNCANELTGYNFSGFTLLRLSNIVNSDGSVTSEMAPFVINIVTLTPNG
Sbjct 393 NALAISNNNQAYVNCANELTGYNFSGFTLLRLSNIVNSDGSVTSEMAPFVINIVTLTPNG 452
Query 421 TIPVTFTINNATTYYGQNVYIVGSTSDLGNWNTTYARGPASCPNYPTWTITLNLLPGEQI 480
TIPVTFTINNATTYYGQNVYIVGSTSDLGNWNTTYARGPASCPNYPTWTITLNLLPGEQI
Sbjct 453 TIPVTFTINNATTYYGQNVYIVGSTSDLGNWNTTYARGPASCPNYPTWTITLNLLPGEQI 512
Query 481 QFKAVKIDSSGNVTWEGGSNHTYTVPTSGTGSVTITWQN 519
QFKAVKIDSSGNVTWEGGSNHTYTVPTSGTGSVTITWQN
Sbjct 513 QFKAVKIDSSGNVTWEGGSNHTYTVPTSGTGSVTITWQN 551
Claim Rejections - 35 USC § 103
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.
Claim(s) 2-11 are rejected under 35 U.S.C. 103 as being unpatentable over Kitamoto (Journal of Bacteriology Vol. 17, No. 12, p. 5848-5854 (Dec. 1988); 12/21/2022 IDS, NPL Doc. AB; previously cited) and Callen et al. (U.S. Patent 8,334,118 B2; previously cited).
Kitamoto et al. disclose a beta-amylase from Clostridium thermosulfurogenes that has 99% identity with SEQ ID NO: 3 of the instant application. The alignment is shown below. There are S280A, S319T, and S322C amino acid substitions in relation to SEQ ID NO: 3 as shown in the alignment below (current claim 2b). The disclosed beta-amylase from Kitamoto et al. also has a modification at position 273 of currently claimed SEQ ID NO: 6 and has 99.6% identity. The disclosed beta-amylase from Kitamoto et al. also has a modification at position 286 of currently claimed SEQ ID NO: 4 and has 99.6% identity. Kitamoto et al. do not disclose the method of preparing a dough or a baked product, the method of cleaning, the method of making ethanol, the method of feeding an animal, or the method of making syrup using beta amylase.
Callen et al. disclose the use of a beta amylase for a method of hydrolyzing starch comprising contacting a substance containing starch with the polypeptide of an alpha amylase and a second enzyme including a beta amylase under conditions which facilitate the hydrolysis of the starch in the substance by the polypeptides (see claim 15).
Callen et al. disclose the use of a beta amylase for a method for washing an object comprising contacting said object with a beta amylase under conditions sufficient for said washing. A method for textile desizing, comprising contacting a textile with a beta amylase under conditions effective for desizing. A method for producing a high-maltose, a high-glucose syrup or a mixed syrup comprising liquefying starch using an effective amount of a beta amylase to obtain a soluble starch hydrolysate; and saccharifying the soluble starch hydrolysate, thereby producing the high-maltose, the high-glucose syrup or the mixed syrup. A method for making ethanol comprising contacting a starch-comprising composition with a beta amylase to produce a sugar, and fermenting the sugar to produce ethanol. A method for corn wet milling comprising (a) providing a beta amylase, and (b) contacting corn or a corn starch with a beta amylase under conditions sufficient for a beta amylase to hydrolyze the starch. A method for dry milling comprising: (a) providing a beta amylase, and (b) contacting a whole ground grain comprising starch with a beta amylase under conditions sufficient for a beta amylase to hydrolyze the starch. A method for liquefying or removing starch from a composition comprising contacting a composition comprising starch with a beta amylase, under conditions wherein a beta amylase liquefies the composition or removes the starch from the composition. Callen et al. disclose the use of amylases for detergents, baking processes, beverages, and in oilfields (see col.1, lines 53-59, and claims 7-15).
Therefore, it would have been obvious to use equivalents for the same purpose as currently claimed. It is obvious to the person having ordinary skill in the art to use the beta amylase claimed, because the art has shown the use of beta amylase for the methods claimed in the art as disclosed by Callen et al. in particular at claim 15.
(Query 1: SEQ ID NO: 3 with Kitamoto ref Sbjct: GenBank: AAA23204.1)
Score Expect Method Identities Positives Gaps
1055 bits(2729) 0.0 Compositional matrix adjust. 515/519(99%) 517/519(99%) 0/519(0%)
Query 1 SIAPNFKVFVMGPLEKVTDFNAFKDQLITLKNNGVYGITTDIWWGYVENAGENQFDWSYY 60
SIAPNFKVFVMGPLEKVTDFNAFKDQLITLKNNGVYGITTDIWWGYVENAGENQFDWSYY
Sbjct 33 SIAPNFKVFVMGPLEKVTDFNAFKDQLITLKNNGVYGITTDIWWGYVENAGENQFDWSYY 92
Query 61 KTYADTVRAAGLKWVPIMSTHASGGNVGDTVNIPIPSWVWTKDTQDNMQYKDEAGNWDNE 120
KTYADTVRAAGLKWVPIMSTHA GGNVGDTVNIPIPSWVWTKDTQDNMQYKDEAGNWDNE
Sbjct 93 KTYADTVRAAGLKWVPIMSTHACGGNVGDTVNIPIPSWVWTKDTQDNMQYKDEAGNWDNE 152
Query 121 AVSPWYSGLTQLYNEFYSSFASNFSSYKDIITKIYISGGPSGELRYPSYNPSHGWTYPGR 180
AVSPWYSGLTQLYNEFYSSFASNFSSYKDIITKIYISGGPSGELRYPSYNPSHGWTYPGR
Sbjct 153 AVSPWYSGLTQLYNEFYSSFASNFSSYKDIITKIYISGGPSGELRYPSYNPSHGWTYPGR 212
Query 181 GSLQCYSKAAITSFQNAMKSKYGTIAAVNSAWGTSLTDFSQISPPTDGDNFFTNGYKTTY 240
GSLQCYSKAAITSFQNAMKSKYGTIAAVNSAWGTSLTDFSQISPPTDGDNFFTNGYKTTY
Sbjct 213 GSLQCYSKAAITSFQNAMKSKYGTIAAVNSAWGTSLTDFSQISPPTDGDNFFTNGYKTTY 272
Query 241 GNDFLTWYQSVLTNELANIASVAHSCFDPVFNVPIGAKISGVHWLYNSPTMPHAAEYCAG 300
GNDFLTWYQSVLTNELANIASVAHSCFDPVFNVPIGAKI+GVHWLYNSPTMPHAAEYCAG
Sbjct 273 GNDFLTWYQSVLTNELANIASVAHSCFDPVFNVPIGAKIAGVHWLYNSPTMPHAAEYCAG 332
Query 301 YYNYSTLLDQFKASNLAMSFTSLEMDDSNAYVSPYYSAPMTLVHYVANLANNKGIVHNGE 360
YYNYSTLLDQFKASNLAM+FT LEMDDSNAYVSPYYSAPMTLVHYVANLANNKGIVHNGE
Sbjct 333 YYNYSTLLDQFKASNLAMTFTCLEMDDSNAYVSPYYSAPMTLVHYVANLANNKGIVHNGE 392
Query 361 NALAISNNNQAYVNCANELTGYNFSGFTLLRLSNIVNSDGSVTSEMAPFVINIVTLTPNG 420
NALAISNNNQAYVNCANELTGYNFSGFTLLRLSNIVNSDGSVTSEMAPFVINIVTLTPNG
Sbjct 393 NALAISNNNQAYVNCANELTGYNFSGFTLLRLSNIVNSDGSVTSEMAPFVINIVTLTPNG 452
Query 421 TIPVTFTINNATTYYGQNVYIVGSTSDLGNWNTTYARGPASCPNYPTWTITLNLLPGEQI 480
TIPVTFTINNATTYYGQNVYIVGSTSDLGNWNTTYARGPASCPNYPTWTITLNLLPGEQI
Sbjct 453 TIPVTFTINNATTYYGQNVYIVGSTSDLGNWNTTYARGPASCPNYPTWTITLNLLPGEQI 512
Query 481 QFKAVKIDSSGNVTWEGGSNHTYTVPTSGTGSVTITWQN 519
QFKAVKIDSSGNVTWEGGSNHTYTVPTSGTGSVTITWQN
Sbjct 513 QFKAVKIDSSGNVTWEGGSNHTYTVPTSGTGSVTITWQN 551
Claim(s) 2-11 are rejected under 35 U.S.C. 103 as being unpatentable over Kitamoto (Journal of Bacteriology Vol. 17, No. 12, p. 5848-5854 (Dec. 1988); 12/21/2022 IDS, NPL Doc. AB; previously cited), Callen et al. (U.S. Patent 8,334,118 B2; previously cited), and Tang and Fenton (Hum Mutat 38(9):1132-1143 (Sept 2017) HHS Public Access document version). Separate rejection to reject claims drawn to variant beta amylase enzymes with single alanine amino acid substitutions.
Kitamoto et al. disclose a beta-amylase from Clostridium thermosulfurogenes that has 99% identity with SEQ ID NO: 3 of the instant application. The alignment is shown below. There are S280A, S319T, and S322C amino acid substitions in relation to SEQ ID NO: 3 as shown in the alignment below (current claim 2b). The disclosed beta-amylase from Kitamoto et al. also has a modification at position 273 of currently claimed SEQ ID NO: 6 and has 99.6% identity. The disclosed beta-amylase from Kitamoto et al. also has a modification at position 286 of currently claimed SEQ ID NO: 4 and has 99.6% identity. Kitamoto et al. do not disclose the method of preparing a dough or a baked product, the method of cleaning, the method of making ethanol, the method of feeding an animal, or the method of making syrup using beta amylase.
Callen et al. disclose the use of a beta amylase for a method of hydrolyzing starch comprising contacting a substance containing starch with the polypeptide of an alpha amylase and a second enzyme including a beta amylase under conditions which facilitate the hydrolysis of the starch in the substance by the polypeptides (see claim 15).
Callen et al. disclose the use of a beta amylase for a method for washing an object comprising contacting said object with a beta amylase under conditions sufficient for said washing. A method for textile desizing, comprising contacting a textile with a beta amylase under conditions effective for desizing. A method for producing a high-maltose, a high-glucose syrup or a mixed syrup comprising liquefying starch using an effective amount of a beta amylase to obtain a soluble starch hydrolysate; and saccharifying the soluble starch hydrolysate, thereby producing the high-maltose, the high-glucose syrup or the mixed syrup. A method for making ethanol comprising contacting a starch-comprising composition with a beta amylase to produce a sugar, and fermenting the sugar to produce ethanol. A method for corn wet milling comprising (a) providing a beta amylase, and (b) contacting corn or a corn starch with a beta amylase under conditions sufficient for a beta amylase to hydrolyze the starch. A method for dry milling comprising: (a) providing a beta amylase, and (b) contacting a whole ground grain comprising starch with a beta amylase under conditions sufficient for a beta amylase to hydrolyze the starch. A method for liquefying or removing starch from a composition comprising contacting a composition comprising starch with a beta amylase, under conditions wherein a beta amylase liquefies the composition or removes the starch from the composition. Callen et al. disclose the use of amylases for detergents, baking processes, beverages, and in oilfields (see col.1, lines 53-59, and claims 7-15).
The additional reference Tang and Fenton is cited to disclose the state of the art of whole-protein alanine-scanning mutagenesis (see Abstract). Tang and Fenton disclose the use of whole-protein alanine-scanning mutagenesis to study functional effects of mutational analysis on whole-proteins (see entire document, particularly figures 2, 5, 6, and 9). The claims drawn to a single alanine substitution are separately rejected because it is obvious to one of ordinary skill in the art to make a variant enzyme with single alanine substitutions. It is not inventive to one of ordinary skill in the art to make a single amino acid modification with a substitution of an alanine in place of another amino acid to generate a variant enzyme.
Therefore, it would have been obvious to use equivalents for the same purpose as currently claimed. It is obvious to the person having ordinary skill in the art to use the beta amylase claimed, because the art has shown the use of beta amylase for the methods claimed in the art as disclosed by Callen et al. in particular at claim 15.
Conclusion
Claims 12-20 are allowable
Claims 2-11 are rejected. Claims 1, 21, and 22 are withdrawn.
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.
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/ANAND U DESAI/Supervisory Patent Examiner, Art Unit 1655