DETAILED ACTION
1. This office action is in response to application 19/040,032 filed on 1/29/2025. The preliminary amendment filed on 10/1/2025 has been entered. Claims 1, 4, 10, 11 and 15 have been amended. Claims 2, 3, 5, 9, 13, 14 and 16-44 have been cancelled and claims 45-57 have been added. Accordingly, claims 1, 4, 10-12, 15 and 45-57 are pending in this office action.
Notice of Pre-AIA or AIA Status
2. The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Double Patenting
3. 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.
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Claims 1, 4, 12, 48-50, 52 and 53 rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 5-8 of U.S. Patent No. 12,243,623 in view of US 2007/0117749 (hereinafter Dawson). Although the claims at issue are not identical, they are not patentably distinct from each other because the limitations in bold are the same and the differences would have been obvious to an artisan of ordinary skill in the art. For instance U.S. Patent No. 12,243,623 does not disclose wherein the proximity zone is no more than 100 kb upstream or downstream of the at least one biosynthetic gene in the biosynthetic gene cluster. Dawson however discloses: wherein the proximity zone is no more than 100 kb upstream or downstream of the at least one biosynthetic gene in the biosynthetic gene cluster (See paragraphs 0289, 0322 and 0325 note the system will express upstream or downstream positions based on where the activity occurs, however there are still limited zones with an expected band of below 20 kb). It would have been obvious to an artisan of ordinary skill in the pertinent at the time the instantly claimed invention was filed to have incorporated the teaching of Dawson into the system of U.S. Patent No. 12,243,623. The modification would have been obvious because the two references are concerned with the solution to problem of determining biosynthetic information within genes based on clusters (See Dawson abstract and U.S. Patent No. 12,243,623 claims), therefore there is an implicit motivation to combine these references (i.e. motivation from the references themselves). In other words, the ordinary skilled artisan, during his/her quest for a solution to the cited problem, would look to the cited references at the time the invention was made. Consequently, the ordinary skilled artisan would have been motivated to combine the cited references since Dawson’s teaching would enable users of the U.S. Patent No. 12,243,623 system to have more efficient processing.
As for claim 4 the rejection of claim 1 is incorporated and further Dawson renders obvious wherein a proximity zone is no more than 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 20, 30, 40, 50, 60, 70, 80, 90, or 100 kb upstream or downstream of a biosynthetic gene in the cluster. (See paragraphs 0289, 0322 and 0325 note the system will express upstream or downstream positions based on where the activity occurs, however there are still limited zones with an expected band of below 20 kb). It would have been obvious to an artisan of ordinary skill in the pertinent at the time the instantly claimed invention was filed to have incorporated the teaching of Dawson into the system of U.S. Patent No. 12,243,623. The modification would have been obvious because the two references are concerned with the solution to problem of determining biosynthetic information within genes based on clusters (See Dawson abstract and U.S. Patent No. 12,243,623 claims), therefore there is an implicit motivation to combine these references (i.e. motivation from the references themselves). In other words, the ordinary skilled artisan, during his/her quest for a solution to the cited problem, would look to the cited references at the time the invention was made. Consequently, the ordinary skilled artisan would have been motivated to combine the cited references since Dawson’s teaching would enable users of the U.S. Patent No. 12,243,623 system to have more efficient processing.
19/040,032 12,243,623
1. A method for identifying a modulator of a human target comprising steps of: a) querying a set of nucleic acid sequences, each of which is found in a fungal strain and comprises a biosynthetic gene cluster; and b) identifying within at least one of the fungal nucleic acid sequences an embedded target gene (ETaG) sequence characterized in that the ETaG is not required for or is not involved in the biosynthesis of the product of the biosynthetic gene cluster; the ETaG is within a proximity zone relative to at least one biosynthetic gene in the cluster, wherein the proximity zone is no more than 100 kb upstream or downstream of the at least one biosynthetic gene in the biosynthetic gene cluster; the ETaG is optionally co-regulated with at least one biosynthetic gene in the cluster; and the ETaG or a portion thereof, is a homolog of a nucleic acid sequence that encodes the human target; c) assaying an effect of the product of the biosynthetic gene cluster, or an analog of the product, on the human target.
1. A method comprising steps of: a) querying a set of nucleic acid sequences, each of which is found in a fungal strain and comprises a biosynthetic gene cluster; and b) identifying within at least one of the fungal nucleic acid sequences an embedded target gene (ETaG) sequence characterized in that it: is not required for or is not involved in the biosynthesis of the product of the biosynthetic gene cluster; is within a proximity zone relative to at least one gene in the cluster; is homologous to a mammalian nucleic acid sequence; and is optionally co-regulated with at least one biosynthetic gene in the cluster; and c) assaying an effect of the product of the biosynthetic gene cluster, or an analog of the product, on a human target.
12. (Original) The method of claim 10, wherein the small molecule is a biosynthetic product of the biosynthetic gene cluster.
8. The method of claim 7, wherein the ETaG sequences encode a protein that provides resistance to a small molecule product of the biosynthetic gene cluster while proteins encoded by the second nucleic acid sequence do not.
48. The method of claim 1, wherein the ETaG sequence is or comprises a sequence
that is homologous to a second nucleic acid sequence or a portion thereof in the same genome.
5. The method of claim 1, wherein the ETaG sequence is or comprises a sequence that encodes a product that is homologous to a product or a portion thereof encoded by a second nucleic acid sequence in the same genome.
49. The method of claim 1, wherein the ETaG sequence is or comprises a sequence that encodes a product that is homologous to a product or a portion thereof encoded by a second nucleic acid sequence in the same genome.
5. The method of claim 1, wherein the ETaG sequence is or comprises a sequence that encodes a product that is homologous to a product or a portion thereof encoded by a second nucleic acid sequence in the same genome.
50. The method of claim 49, wherein the homology is at least 50%, 60%, 70%, 75%,
80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 99.5%.
6. The method of claim 5, wherein the homology is at least 50%, 60%, 70%, 75%, 80%, 85%, 90%, 91%, 92%, 93%, 94%, 95%, 96%, 97%, 98%, 99% or 99.5%.
52. The method of claim 49, wherein the ETaG sequences encode a product that provides resistance to a product of the biosynthetic gene cluster while the second nucleic acid sequence does not.
7. The method of claim 5, wherein the ETaG sequences encode a product that provides resistance to a product of the biosynthetic gene cluster while the second nucleic acid sequence does not.
53. The method of claim 52, wherein the ETaG sequences encode a protein that provides resistance to a small molecule product of the biosynthetic gene cluster while proteins encoded by the second nucleic acid sequence do not.
8. The method of claim 7, wherein the ETaG sequences encode a protein that provides resistance to a small molecule product of the biosynthetic gene cluster while proteins encoded by the second nucleic acid sequence do not.
Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ELIYAH STONE HARPER whose telephone number is (571)272-0759. The examiner can normally be reached on Monday-Friday 10:00 am - 6:00 pm.
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/Eliyah S. Harper/Primary Examiner, Art Unit 2166 January 7, 2026