DETAILED ACTION
Examiner’s note
Please note that the examiner of record has changed. Please address all subsequent correspondences to Georgiana Reglas, Examiner AU1651.
Status of claim rejections
The objections of record are withdrawn in view of Applicant’s amendments to the claims in the response filed 06/29/2026.
The rejection of record under 35 USC 112(a) is withdrawn in view of Applicant’s amendments to the claims in the response filed 06/29/2026.
The rejection of record under 35 USC 112(b) is withdrawn in view of Applicant’s amendments to the claims in the response filed 06/29/2026.
The rejection of record under 35 USC 103 are maintained/modified in view of Applicant’s amendments to the claims in the response filed 06/29/2026.
New Claim Rejections - 35 USC § 112(b)
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 20 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.
Claim 20 recites the limitation "the activity" in line 1. There is insufficient antecedent basis for this limitation in the claim because there is no previous recitation of any “activity” in the claim or in claim 14 from which this claim depends. Thus, the claim is indefinite.
Maintained/Modified 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) 1-14, 16-20 are rejected under 35 U.S.C. 103 as being unpatentable over Sibbesen et al. (US2009/0155413; prior art of record) in view of Alponti et al. (Intern. J. Biol. Macromol., 2016, Vol. 87, pp.522-528; of record in IDS filed 6/25/2024).
Sibbesen teaches variant xylanase polypeptides having one or more modifications at any one or more amino acid residue positions: 3-7, 19-28, 38-45, 55-60, 64-94, 108-110, 126-131, 158-172, and 179-183 of the Bacillus subtilis amino acid sequence of SEQ ID NO: 1 (see paragraph [0038]-[0040], [0042]-[0043], [0050], and [0064]-[0065]). SEQ ID NO: 1 as disclosed by Sibbesen corresponds to wild-type B. subtilis xylanase A and has 100% sequence identity to SEQ ID NO: 1 of the instant invention (see paragraph [0015] and Appendix A for sequence alignment). Sibbesen teaches the xylanase mutant D11F/R122D is uninhibited by wheat endogenous xylanase inhibitor and has a slight reduction in function measured by viscosity of a flour slurry (see paragraphs [0203]-[0207] and Tables 10-11). Sibbesen further teaches its variant xylanase polypeptides have improved properties that make them suitable for a variety of applications such as bakery since the xylanase substrates are found in wheat (see paragraphs [0012], [0047], [0049], [0058], and [0153]). Thus, Sibbesen teaches a xylanase polypeptide having 98.9% sequence identity to SEQ ID NO: 1 (183/185 = 0.989) of the instant invention and the substitutions D11F/R122D relative to SEQ ID NO: 1, reading on the limitations of Claim 1 elements (i) and (ii), Claim 2, and Claims 4-5.
Sibbesen does not teach an amino acid exchange at the position corresponding to amino acid S22 in SEQ ID NO: 1.
Alponti teaches that the single substitution of S22E in Bacillus subtilis XynA resulted in significant improvement in thermostability of the XynA enzyme (see p.525, left column, last paragraph, right column, 1st paragraph,-p.526, left column, 1st passage, and Fig. 3). The mutation S22E reads on Claim 1 element (iii) and Claim 3.
Therefore, it would have been obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have further included the substitution S22E in Bacillus subtilis XynA, as taught by Alponti, in the double mutant xylanase of SEQ ID NO: 1 having the substitutions D11F/R122D, as taught by Sibbesen, to arrive at the claimed invention. One of ordinary skill in the art would have been motivated to improve the thermostability of the B. subtilis XynA double mutant D11F/R122D uninhibited by endogenous wheat xylanase inhibitor by further including the mutation S22E since these xylanases are useful for bakery applications which often require elevated temperatures, yielding predictable results. One of ordinary skill in the art would have had a reasonable expectation of success since each of Sibbesen and Alponti teach their beneficial mutations in B. subtilis XynA and Sibbesen suggests mutations at position 22. Thus, Sibbesen in view of Alponti render obvious a xylanase polypeptide having 98.38% sequence identity to SEQ ID NO: 1 and the substitutions D11F/S22E/R122D, which corresponds to SEQ ID NO: 6 of the instant invention, reading on claim 6 and 17.
Regarding claim 7, Sibbesen teaches polynucleotides of their invention comprise nucleic acid sequences encoding the variant polypeptide sequences of the invention (see paragraphs [0087]-[0088]).
Regarding claim 8, Sibbesen teaches the polynucleotides comprising nucleic acid sequences encoding the variant polypeptides can be incorporated into a recombinant replicable vector, reading on said polynucleotide is comprised in an expression construct (see paragraphs [0089]-[0096]).
Regarding claim 9, Sibbesen teaches the recombinant vector can be expressed in a suitable host cell (see paragraphs [0045]-[0046], [0074], [0087], [0089]-[0110], and [0116]-[0126]).
Regarding claim 10, Sibbesen teaches the host cell is preferably a Bacillus species like Bacillus subtilis (see paragraphs [0103], [0106], [0112], [0116], and [0118]).
Regarding claim 11, Sibbesen teaches a method of making a polypeptide by transforming a host cell with a nucleic acid encoding said polypeptide and culturing the transformed cell and expressing said polypeptide (see paragraphs [0046] and [0089]).
Regarding claim 12, Sibbesen teaches the variant xylanase polypeptides can be used in a process for preparing bakery products like dough productions and altering the viscosity of flour slurries (see paragraphs [0146] and [0153] and Examples 2 and 5). Sibbesen teaches flour slurry is made by mixing flour in water and teaches adding the variant xylanase polypeptides to the flour slurry and incubating for up to 20 minutes, reading on the limitations of Claim 12 (see Example 5, paragraphs [0204]-[0207], and Table 11).
Regarding claim 13, Sibbesen teaches the bakery produce is a dough, bread, pretzel, tortilla, cake, cookie, biscuit, cracker, etc., which reads on a dough or a baked good (see paragraph [0153] and Example 2).
Regarding claim 14, Sibbesen teaches dough compositions comprising a variant xylanase polypeptide, flour, and water (see Examples 2 and 5).
Regarding claim 16, Sibbesen teaches host cells for making the variant xylanase polypeptides is a Bacillus species like Bacillus subtilis (see paragraphs [0103], [0106], [0112], [0116], and [0118]).
Regarding claim 18, it is noted that claimed SEQ ID NO: 5 contains a D11Y mutation with S22E/R122D substitutions (see sequence listing XML 05/08/2024). Sibbensen explicitly teaches that the D11Y mutation, like the D11F mutation in xylanases cause the xylanase to be uninhibited by wheat endogenous xylanase inhibitor (see paragraph [203] and Table 10). Thus, D11Y is also recognized as a beneficial mutation to xynA in B. subtilis to advantageously confer inhibition protection to the enzyme.
Regarding claim 19-20, Sibbesen teaches xylanases all increased the volume of the baked bread and decreased stickiness (i.e., the composition is a “dough improver” and has activity of increasing volume of a baked good and decreasing stickiness; see Table 5; paragraphs [0178-79; 0181] and Table 7).
Accordingly, the claimed invention was prima facie obvious at the time of filing, especially in the absence of evidence to the contrary.
Response to Arguments
Applicant's arguments filed 06/29/2026 have been fully considered but they are not persuasive.
On pg. 7-9, Applicant argues that Sibbensen and Alponti do not provide any motivation to use thermostable xylanases in baking applications and teach away from the claimed invention. Applicant argues that there is no teaching that the xylanases would be useful in baking applications. Applicant argues “the D11F and R122D mutations make the xylanase resistant to endogenous inhibitors present in flour. These mutations are therefore relevant specifically for baking applications where the xylanase encounters wheat flour containing proteinaceous xylanase inhibitors” citing to Sibbesen and Sorensen. Applicant argues “Alponti teaches thermostable xylanases are of interest for high temperature industrial processes such as paper, textile, and biofuel. . . however there is no teaching in Alponti that thermostable xylanases could be of interest in baking appliccations”. Applicant then argues that a PHOSITA would have understood “thermostable xylanases are irrelevant and indeed detrimental in baking applications” because sough fermentation requires temperatures close to the optimum temperature for baker’s yeast and would not consider temperatures beyond 40 deg C in baking applications, citing to Example 3.1 showing temperatures during resting and fermentation was 26-27 deg and 32 deg C respsectively, well below the elevated temperatures at which Alponti’s S22E mutation provides thermostability. Applicant then argues that increasing thermostability of xylanase would increase risk of the xylanase remaining active after baking, detrimental to stability and storage properties and a PHOSITA would avoid using thermostable xylanases. Applicant then urges that the xylanase polypeptide was developed for its improved dough and baked good properties to significantly increase bread volume.
In response, the examiner disagrees. First, the examiner notes that while Applicant argues that none of the references cited teach or suggest using thermostable xylanase as of interest in baking applications and that the prior art teaches away from the combination of references, Applicant then cites to portions of Sibbesen and Sorensen that explicitly teach Applicant’s claimed mutations as relevant specifically for baking applications (see pg. 8 of the remarks). Sibbesen explicitly teaches that D11F, D11Y and R122D mutations (together and in combination) confer benefits to xylanases used in baking, including increased dough volume and decreased stickiness (i.e., the same advantages as instantly argued by Applicant; see para 0178-79 and Table 10). The combination of the teachings of Sibbesen and Alponti provide one of ordinary skill the teaching, suggestion, and motivation to use xylanases in a composition because both references in combination teach xylanases are useful for bakery applications which often require elevated temperatures, yielding predictable results (see above). Thus, while Alponti recognizes the S22 mutation as beneficial for thermostability, Sibbesen explicitly discloses the usefulness of such mutations specifically for the purpose of improving baked goods, as instantly claimed. Thus, the rejections are maintained as set forth above.
Conclusion
NO CLAIMS ALLOWED.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
The prior art made of record and not relied upon is considered pertinent to applicant's disclosure:
Hennick et al (EP3280264B1): teaches methods for preparing dough and baked products using, e.g., Talaromyces xylanase enzymes which result in an increased dough stability as compared to a reference dough after it has been stored frozen and thawed thereafter (see abstract; throughout; para 100-105).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to GEORGIANA C REGLAS whose telephone number is (571)270-0995. The examiner can normally be reached M-Th: 8:00am-2:00pm.
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/G.C.R./Examiner, Art Unit 1651
/THOMAS J. VISONE/Supervisory Patent Examiner, Art Unit 1672
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