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 .
Priority
Applicant’s claim for the benefit of a prior-filed application under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Drawings
The application contains at least one color drawing or color photograph. Color photographs and color drawings are not accepted in utility applications unless a petition filed under 37 CFR 1.84(a)(2) is granted. Any such petition must be accompanied by the appropriate fee set forth in 37 CFR 1.17(h), one set of color drawings or color photographs, as appropriate, if submitted via the USPTO patent electronic filing system or three sets of color drawings or color photographs, as appropriate, if not submitted via the via USPTO patent electronic filing system, and, unless already present, an amendment to include the following language as the first paragraph of the brief description of the drawings section of the specification:
The patent or application file contains at least one drawing executed in color. Copies of this patent or patent application publication with color drawing(s) will be provided by the Office upon request and payment of the necessary fee.
Color photographs will be accepted if the conditions for accepting color drawings and black and white photographs have been satisfied. See 37 CFR 1.84(b)(2).
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 1-8 are rejected under 35 U.S.C. 103 as being unpatentable over Purcell et al (ACS Synth Biol. 2014 Oct; hereinafter "Purcell;" See PTO-892) in view of Lutfiyya (US20090144849-A1; Published 2009-06-04; See PTO-892) and Tiwari et al (Plant J. 2012 Jun; hereinafter "Tiwari;" See PTO-892).
Regarding claim 1-3: Purcell described a method of designing synthetic transcription factors (sTFs) in eukaryotic cells. (See Purcell Abstract). Purcell indicated that “[o]ur grammar covers the design of sTFs that: 1) use any one of these systems, 2) use effector domains to activate or repress transcription, 3) use fluorescent reporter domains to enable quantification of sTF abundance, and 4) permit the design of sTFs that form dimeric complexes with other sTFs, which can be used to engineer cooperativity between sTF monomers.” (See Purcell p. 3, para 4). Purcell also indicated that their method uses a nuclear Localization Signal (NLS) at the 5′ of the protein. (See Prucell p. 5, bullet points). Further Purcell pointed out that “The CRISPR-TF system comprises a dCas9 domain (optionally fused to an Effector Domain) and a guide RNA (gRNA). dCas9 is a catalytically inactive form of the Cas9 nuclease. The gRNA itself is comprised of a sequence that binds through complementary base pairing to one strand of the DNA target sequence, and a ‘handle’ sequence: a hairpin forming sequence that dCas9 recognizes and binds to. The gRNA therefore ‘guides’ the dCas9 based TF to its target site and determines the DNA-binding specificity of the dCas9:gRNA complex, and therefore its effects on the expression of the target gene” (See Purcell p. 6 last para-p. 7 first para). As such Purcell taught a deactivated Cas9 as the DNA binding domain as required by claim 3. It is noted that Purcell did not teach or suggest an effector domain comprising an amino acid sequence of any one of SEQ ID NOs: 1-403.
Lutfiyya taught a transcription factor comprising SEQ ID NO: 1-1453, which encompasses a SEQ ID NO: 393. (Lutfiyya [0021]). It is noted that SEQ ID NO: 393 of Lutfiyya is 100% identical to instant SEQ ID NO: 1 (See alignment below). Tiwari demonstrated a method of identifying an activation domain in a transcription factor. Tiwari first performed sequence alignments (See Tiwari p.856,col. 2 1st para), followed by deletions especially of the C-terminal domain to demonstrate which part of the protein was involved in activation of transcription. Further, Tiwari used a reporter tagging assay to ensure the functionality of the transcriptional activator. (See Tiwari p.856,col. 2 1st para) . It is submitted that a person of ordinary skill in the art would have recognized that transcription factors have an effector domain. (See Purcell p. 2, para 4). Further the person would have been able to determine the exact sequence of the effector domain as enumerated in SEQ ID NO: 1 based on the teachings of Tiwari. The person would also know the sequence of instant SEQ ID NO:1 as a portion of a transcription factor given the teachings of Lutfiyya. As such one of ordinary skill in the art would have been motivated to find the effector domain of the transcription factor using the known methods in prior art to arrive at the claimed invention.
Query Match 100.0%; Score 1423; Length 410;
Best Local Similarity 100.0%;
Matches 271; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 DEPNEGDQGFSFEHGAGYTYNLSQLPMLQSFDQRPSSSLGYGGGSWTDHRRQIYRSPWRG 60
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Db 140 DEPNEGDQGFSFEHGAGYTYNLSQLPMLQSFDQRPSSSLGYGGGSWTDHRRQIYRSPWRG 199
Qy 61 LTTRENTRTRQTMFSSQPGERYHGVSNSILNDKNKTISFRINSHEGVHDNNGVAGAVPRI 120
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Db 200 LTTRENTRTRQTMFSSQPGERYHGVSNSILNDKNKTISFRINSHEGVHDNNGVAGAVPRI 259
Qy 121 HRSFLEGMKTFNKSWGQSLSSNLKSSTATIPQDHIATTLNSYQWENAGVAEGSENVLKRK 180
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Db 260 HRSFLEGMKTFNKSWGQSLSSNLKSSTATIPQDHIATTLNSYQWENAGVAEGSENVLKRK 319
Qy 181 RLLFSDDCNKSDQDLDLSLSLKVPRTHDNLGECLLEDEVKEHDDHQDIKSLSLSLSSSGS 240
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Db 320 RLLFSDDCNKSDQDLDLSLSLKVPRTHDNLGECLLEDEVKEHDDHQDIKSLSLSLSSSGS 379
Qy 241 SKLDRTIRKEDQTDHKKRKISVLASPLDLTL 271
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Db 380 SKLDRTIRKEDQTDHKKRKISVLASPLDLTL 410
Regarding claim 4-5: As indicated above, a person of ordinary skill in the art would have been able to arrive at the effector domain of SEQ ID NO: 1 using the methods shown in the teachings of Tiwari in view of teachings of Lutfiyya and Purcell.
Regarding claim 6 and 8: Lutfiyya disclosed a vector comprising transcriptional factors. For example, Lutfiyya taught that “[a]ny of the nucleic acid molecules of the invention may be introduced into a plant cell in a permanent or transient manner in combination with other genetic elements such as vectors, promoters, enhancers, etc. Further, any of the nucleic acid molecules of the invention may be introduced into a plant cell in a manner that allows for overexpression of the protein or fragment thereof encoded by the nucleic acid molecule.” (Lutfiyya [0116]). It is noted that Lutfiyya did not teach the transcriptional factor as taught by Purcell or the effector domain as defined by SEQ ID NO: 1-403. However, as discussed above, one of ordinary skill in the art would have easily used the transcriptional factor construct as taught by Purcell and arrived at the sequence of SEQ ID NO: 1 using the teachings of Tiwari, in the vectors disclosed by Lutfiyya with a reasonable expectation of success.
Regarding claim 7: Purcell taught that their method of designing transcription factors will enable the more reliable, efficient, and automated design of synthetic cells with rich functionalities. As such Purcell taught the manufacture of cells as required by claim 7, with the claimed synthetic transcription factors. It is also noted that Lutfiyya taught that “[t]he use of Agrobacterium-mediated plant integrating vectors to introduce DNA into plant cells is well known in the art.” ([0102]). As such, Lutfiyya and Purcell taught a method to generate cells comprising vectors encoding the transcription factors. As indicated above, arrived at the sequence of SEQ ID NO: 1 using the teachings of Tiwari given the transcription factor disclosed by Lutfiyya.
Claim 9 is rejected under 35 U.S.C. 103 as being unpatentable over Purcell et al (ACS Synth Biol. 2014 Oct; hereinafter "Purcell;" See PTO-892) in view of Lutfiyya (US20090144849-A1; Published 2009-06-04; See PTO-892) and Tiwari et al (Plant J. 2012 Jun; hereinafter "Tiwari;" See PTO-892), and further in view of Dossani et al (Yeast. 2018 Mar; hereinafter "Dosani;" See PTO-892).
Regarding claim 9: The teachings of Purcell, in view of Lutiffya and Tiwari, are set forth above. It is noted that none of the references taught (a) one or more nucleic acids each encoding one or more transcription activators operatively linked to a first promoter and (b) one or more nucleic acids each encoding one or more independent genes of interest (GOI) each operatively linked to a promoter that is activated by the one or more transcription activators, wherein at least one transcription activator or transcription repressor is a synthetic transcription factor (TF) of claim 1, as required by claim 9.
However, Dossani taught a combinatorial approach to synthetic transcription factor‐promoter combinations for yeast strain engineering using a promoter driven synthetic transcription factor and a gene of interest linked to another hybrid promoter. (See Figure 1 of Dossani). One of ordinary skill in the art would have easily used the transcriptional factor construct as taught by Purcell and arrived at the sequence of SEQ ID NO: 1 using the teachings of Tiwari, in the vectors disclosed by Lutfiyya and used the synthetic transcription factor in the combinatorial approach taught by Dossani, with a reasonable expectation of success.
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 1-9 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-14 of copending Application No. 18/821,489 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other because of the reasons indicated below.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Regarding claim 1: Claim 6 and 13 of the reference application recites a nucleic acid encoding an activator domain of any one of SEQ ID NOs: 1-55 as part of a synthetic TF. SEQ ID NO: 1 of the reference application is 100% identical to the SEQ ID NO: 1 of the instant application.
Further the following claims in instant application correspond to the indicated claims in the reference application
Instant application
Reference application
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Conclusion
No claim is free of art.
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JAGAMYA VIJAYARAGHAVAN whose telephone number is (703)756-5934. The examiner can normally be reached 9:00a-5:00p.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Christopher M. Babic can be reached at 571-272-8507. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JAGAMYA NMN VIJAYARAGHAVAN/Examiner, Art Unit 1633
/EVELYN Y PYLA/Primary Examiner, Art Unit 1633