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 .
Status of the Claims
Claims 1-4 are pending and examined herein.
No claims are canceled.
Priority
As detailed on the 11 January 2024 filing receipt, the application claims priority as early as 16 November 2016 to provisional application 62/423,196. At this point in examination, all claims have been interpreted as being accorded this priority date as the effective filing date.
Information Disclosure Statement
Information disclosure statements (IDS) were filed on 17 August 2023 and 06 March 2024. The submissions are in compliance with the provisions of 37 CFR 1.97. Accordingly, the references are being considered by the examiner.
Specification
The disclosure is objected to because of the following informality: “mitochondrial” is misspelled as “mitochodrial” (pg. 14, paragraph [73]).
Appropriate correction is required.
35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-4 are rejected under 35 USC § 101 because the claimed inventions are directed to an abstract idea without significantly more. "Claims directed to nothing more than abstract ideas (such as a mathematical formula or equation), natural phenomena, and laws of nature are not eligible for patent protection" (MPEP 2106.04 § I). Abstract ideas include mathematical concepts, and procedures for evaluating, analyzing or organizing information, which are a type of mental process (MPEP 2106.04(a)(2)). The claims as a whole, considering all claim elements individually and in combination, are directed to a judicial exception at Step 2A, Prong 2, and the additional elements of the claims, considered individually and in combination, do not provide significantly more at Step 2B than the abstract idea of identifying gene.
MPEP 2106 organizes JE analysis into Steps 1, 2A (Prong One & Prong Two), and 2B as analyzed below.
Step 1: Are the claims directed to a process, machine, manufacture, or composition of matter (MPEP 2106.03)?
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of
nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Step 1: Are the claims directed to a 101 process, machine, manufacture, or composition of matter (MPEP 2106.03)?
The claims are directed to a method (claims 1-4), which falls within one of the categories of statutory subject matter. [Step 1: Yes]
Step 2A, Prong One: Do the claims recite a judicially recognized exception, i.e., a law of nature, a natural phenomenon, or an abstract idea (MPEP 2106.04(a-c))?
With respect to Step 2A, Prong One, the claims recite judicial exceptions in the form of abstract ideas. MPEP § 2106.04(a)(2) further explains that abstract ideas are defined as:
• mathematical concepts (mathematical formulas or equations, mathematical relationships
and mathematical calculations) (MPEP 2106.04(a)(2)(I));
• certain methods of organizing human activity (fundamental economic principles or practices, managing personal behavior or relationships or interactions between people) (MPEP 2106.04(a)(2)(II)); and/or
• mental processes (concepts practically performed in the human mind, including observations, evaluations, judgments, and opinions) (MPEP 2106.04(a)(2)(III)).
Claim 1 recites querying a set of sequencing, interpreted as searching for those sequences in a larger sequence, which is a step of data evaluation which is practically performed by the human mind.
Claim 1 recites identifying a gene satisfying certain conditions, also interpreted as a step of data evaluation practically performed by the human mind.
Claims 2 and 3 recite additional information about the sequence being searched for.
Claim 4 recites additional information about the number of strains being compared.
Thus, the claims recite abstract ideas and thus must be examined further to determine whether elements in addition to the abstract ideas integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). [Step 2A Prong One: Yes]
Step 2A, Prong Two: If the claims recite a judicial exception under Prong One, then is the judicial exception integrated into a practical application by an additional element (MPEP 2106.04(d))?
Because the claims recite judicial exceptions, direction under Step 2A Prong Two provides that the claims must be examined further to determine whether they recite elements in addition to the abstract ideas which integrate the judicial exceptions into a practical application (MPEP 2106.04(d)). A claim can be said to integrate a judicial exception into a practical application when it applies, relies on, or uses the judicial exception in a manner that imposes a meaningful limit on the judicial exception. This is performed by analyzing the additional elements of the claim to determine if the judicial exceptions are integrated into a practical application (MPEP 2106.04(d)(I); MPEP 2106.05(a-h)). If the claim contains no additional elements beyond the judicial exceptions, the claim is said to fail to integrate the judicial exceptions into a practical application (MPEP 2106.04(d)(III)).
The claims recite no elements in addition to the abstract ideas and thus the abstract ideas are not integrated into a practical application. [Step 2A Prong One: Yes]
Step 2B: Do the claims recite a non-conventional arrangement of elements in addition to any identified judicial exception(s) (MPEP 2106.05)?
Claims found to be directed to a judicial exception are then further evaluated to determine if the claims recite an inventive concept that provides significantly more than the judicial exception itself. Step 2B of 101 analysis determines whether the claims contain additional elements that amount to an inventive concept, and an inventive concept cannot be furnished by an abstract idea itself (MPEP 2106.05). The claims recite no elements in addition to the abstract ideas and thus no inventive concept. [Step 2B: No]
Conclusion: Claims are Directed to Non-statutory Subject Matter
For these reasons, the claims, when the limitations are considered individually and as a whole,
are directed to an abstract idea and lack an inventive concept. Hence, the claimed invention does not
constitute significantly more than the abstract idea, so the claims are rejected under 35 USC § 101 as being directed to non-statutory subject matter.
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.
Claims 1-4 are rejected under 35 U.S.C. 103 as being unpatentable over Weber (Nucleic Acids Research 43: 237-243, 2015; previously cited on the 17 August 2023 IDS form) in view of Keller (Nat Chem Biol 11(9): 18 pgs., 2015; previously cited on the 17 August 2023 IDS form).
Claim 1 recites querying a set of nucleic acid sequences, each of which is found in a fungal strain and comprises a biosynthetic gene cluster.
Weber teaches searching for biosynthetic gene clusters (abstract) including from fungi (pg. 237, col. 2, first paragraph).
Claim 1 recites identifying as colocalizing with at least one of the fungal nucleic acid sequences a
gene encoding a protective homolog of a target protein characterized in that the gene encoding the protective homolog of the target protein is not required for or is not involved in the biosynthesis of the product of the biosynthetic gene cluster, is within or adjacent to the biosynthetic gene cluster, and
is homologous to a mammalian nucleic acid sequence.
Weber teaches homologous structures (Fig. 1) and function within (interpreted as colocalizing) a cluster (pg. 238, col. 2, first paragraph).
Keller teaches genes encoding for secondary metabolites which are clustered with – interpreted as colocalized with – other genes which are not part of the main gene (pg. 2, last paragraph) and thus not involved with the main gene, which have self-protection mechanisms which are duplications and resistant forms of the target (pg. 3, first paragraph). Keller teaches targeting the same molecule in humans and fungi (pg. 2, first paragraph), which suggests homology, where biosynthetic clusters have self-protective mechanisms (pg. 3, first paragraph).
Claim 2 recites the mammalian nucleic acid sequence is a human nucleic acid sequence.
Keller teaches targeting the same molecule in humans and fungi (pg. 2, first paragraph), which suggests homology.
Claim 3 recites the gene encoding the protective homolog of the target protein is homologous to the mammalian nucleic acid sequence in that the gene encoding the protective homolog of the target protein is homologous to that of the mammalian nucleic acid sequence.
Keller teaches biosynthetic gene clusters producing protection (abstract) and protection, such as by an antifungal, in a human and a fungus (pg. 2, second paragraph).
Claim 4 recites the set of nucleic acids comprises nucleic acid sequences from at least 500 distinct fungal strains.
Weber teaches comparison to 1172 biosynthetic gene clusters culled from GenBank (pg. 238, col. 2, first paragraph).
Combining Weber and Keller
An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have been motivated to combine the work of Weber, which is directed to searching for secondary metabolite producing biosynthetic gene clusters, with Keller because Keller teaches additional details about the biosynthetic gene clusters, not least of which is the importance of a relationship to humans, which is useful for, for example, immunosuppression or migraines (pg. 2, first paragraph). Both Weber and Keller are directed to the shared field of endeavor of detecting and screening biosynthetic gene clusters and thus the invention is prima facie obvious.
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 1-3 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 7 of U.S. Patent No. 12456540 B2.
Claim 4 is rejected in view of U.S. Patent No. 12456540 B2 as applied to claims 1-3 and further in view of Weber.
Claim 1 recites querying a set of nucleic acid sequences, each of which is found in a fungal strain and comprises a biosynthetic gene cluster, which is taught by reference claim 24 as identification of a target fungal protein cluster.
Claim 1 recites identifying as colocalizing with at least one of the fungal nucleic acid sequences a
gene encoding a protective homolog of a target protein characterized in that the gene encoding the protective homolog of the target protein is not required for or is not involved in the biosynthesis of the product of the biosynthetic gene cluster, is within or adjacent to the biosynthetic gene cluster, and
is homologous to a mammalian nucleic acid sequence.
Reference claim 1 teaches a distance threshold between regions, which is interpreted as colocalizing.
Reference claim 1 teaches a threshold of sequence identity, which is interpreted as having homology, and the target is mammalian.
Reference claim 1 teaches a protein similar to another protein, meaning they are distinct and thus not required in the biosynthesis of each other.
Reference claim 1 teaches inhibition function, which is interpreted as protective.
Claim 2 recites the mammalian nucleic acid sequence is a human nucleic acid sequence, which is taught by reference claim 7 as a human protein.
Claim 3 recites the gene encoding the protective homolog of the target protein is homologous to the mammalian nucleic acid sequence in that the gene encoding the protective homolog of the target protein is homologous to that of the mammalian nucleic acid sequence, which is taught by reference claim 1 as inhibition, interpreted as protection, based on a protein similar to – interpreted as homologous to – the target, where the target is mammalian.
Claim 4 recites the set of nucleic acids comprises nucleic acid sequences from at least 500 distinct fungal strains.
The reference claims do not teach a minimum numbers of sequences for comparison, but Weber teaches comparison to 1172 biosynthetic gene clusters culled from GenBank (pg. 238, col. 2, first paragraph).
An invention would have been obvious to one of ordinary skill in the art if some motivation in the prior art would have led that person to modify prior art reference teachings to arrive at the claimed invention prior to the effective filing date of the invention. One would have been motivated to combine the teachings of the reference claims with those of Weber because Weber is directed to searching for secondary metabolite producing biosynthetic gene clusters, and a high number of sequence comparators. This process is taught as advantageous and a very important feature as “(i) dereplication of existing compounds is crucial for effective discovery of novel natural products instead of finding the same molecules repeatedly, and (ii) comparative analysis of unknown and known gene clusters may provide
hints concerning the function of certain genes within the cluster, inferred from homology” (pg. 238, col. 2 first paragraph). The reference claims and Weber are both directed to searching for biosynthetic gene clusters and thus the invention is prima facie obvious.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Robert J Kallal whose telephone number is (571)272-6252. The examiner can normally be reached Monday through Friday 8 AM - 4 PM EST.
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/Robert J. Kallal/Examiner, Art Unit 1685
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