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 .
Claim Status
Claims 1, 3-5, 7-9, 11-12, 15-16 and 19-37 are pending and being examined.
All previous objections and rejections not set forth below have been withdrawn in view of applicant’s amendments to the claims.
Claim Objections
Claim 9 is objected to because of the following informalities:
Claim 9 recites “IAA9 (IAA9)”. The Applicant is requested to delete “(IAA9)”, as it is a duplication.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
Regarding claims 20-23, claims 20-23 depends from the cancelled claim 13. Thus, the claims are deemed indefinite and not examined any further.
Claims 3, 11-12, 15-16, 29 and 32 are 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.
Claims 3, 11-12, 15-16, 29 and 32 directly or indirectly depend from claim 1. Claim 1 requires at least one specific amino acid substitution(s) at positions K721, D771, E773, D775 or D781 of SEQ ID NO: 1. All these amino acids are in the PB1 domain, as discussed later.
Claims 3, 11-12, 15-16, 29 and 32 require the deletion of the entire PB1 domain (as recited in claim 32) or a portion of the PB1 domain which could encompass at least one of the amino acid(s) at positions K721, D771, E773, D775 or D781 of SEQ ID NO: 1; e.g., claim 3 recites “deletion of a portion of the PB1 domain” , claim 11 recites “a deletion of an amino acid from amino acids 716-804 of SEQ ID NO: 1”, claim 12 recites “deletion of a portion of amino acids 716-804 of SEQ ID NO: 1” etc.
It is not clear to the Examiner if the claims 3, 11-12, 15-16, 29 and 32 require “one or more amino acid substitutions at positions K721, D771, E773, D775 or D781 of SEQ ID NO: 1”, as recited in claim 1. It is also not clear to the Examiner if the “… a mutation in Phox and Bam1 (PB1) domain…” would include any deletion mutation in the PB1 domain, considering the invention as a whole and the instant description.
It is noted here that deleting one or more amino acid(s) in the PB1 domain and/or anywhere before the PB1 domain can change amino acid positions in the polypeptide significantly, in regards to identifying amino acid(s) in equivalent positions of K721, D771, E773, D775 or D781 SEQ ID NO: 1.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 3, 11-12, 15-16, 29 and 32 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claims 3, 11-12, 15-16, 29 and 32 directly or indirectly depend from claim 1. Claim 1 requires at least one specific amino acid substitution(s) at positions K721, D771, E773, D775 or D781 of SEQ ID NO: 1. All these amino acids are in the PB1 domain, as discussed later.
Claims 3, 11-12, 15-16, 29 and 32 require the deletion of the entire PB1 domain (as recited in claim 32) or a portion of the PB1 domain which could encompass at least one of the amino acid(s) at positions K721, D771, E773, D775 or D781 of SEQ ID NO: 1; e.g., claim 3 recites “deletion of a portion of the PB1 domain” , claim 11 recites “a deletion of an amino acid from amino acids 716-804 of SEQ ID NO: 1”, claim 12 recites “deletion of a portion of amino acids 716-804 of SEQ ID NO: 1” etc.
If the dependent claims 3, 11-12, 15-16, 29 and 32 include a deletion mutation comprising one of more of the recited amino acid(s) at the specific positions s recited in the base claim 1, then the dependent claims 3, 11-12, 15-16, 29 and 32 do not further limit the claim form which it depends.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 112(a)
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Written Description
Claims 1, 3-5, 7-9, 11-12, 15-16 and 19-37 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claim 1 and thus, all the claims directly or indirectly depending from claim 1 require at least one specific amino acid substitution(s) at positions K721, D771, E773, D775 or D781 of SEQ ID NO: 1. All these amino acids are in the PB1 domain, as discussed later.
The Applicant describes several deletion mutations (p. 61, Table 6) of tomato ARF8A polypeptide (SEQ ID NO: 1) (p. 17, Table 1) and transformed a tomato plant via agrobacterium (p. 42, para 0104, line 1-4). The Applicant describes that expression of a truncated SIARF8A that lacks the C-terminal PB1 domain under its own promoter (PARF8A:SIARF8A-NT) in transgenic tomato plants led to the production of large seedless fruits (p. 54, para 0135, line 3-5).
The Applicant discusses amino acid substitution mutation(s) at positions K721, D771, E773, D775 or D781 of SEQ ID NO: 1 (e.g., spec, p.22, para 0058, last 3 lines; p. 25, para 0069, last 4 lines). However, the Applicant does not provide any working example of one or more amino acid substitution(s) at positions K721, D771, E773, D775 or D781 of SEQ ID NO: 1, especially in relation to obtaining ovary-derived seedless fruits. The Applicant also does not describe any structure function relationship between one or more amino acid substitution mutation(s) at positions K721, D771, E773, D775 and D781 of SEQ ID NO: 1 with production of ovary-derived seedless fruits.
The status of the art at the time of filing also does not describe any structure function relationship between one or more amino acid substitution mutation(s) at positions K721, D771, E773, D775 and D781 of SEQ ID NO: 1 with production of ovary-derived seedless fruits. Current status of the art also does not describe if the one or more specific substitution(s) at positions K721, D771, E773, D775 and D781 of SEQ ID NO: 1 in terms of inactivating the function of PB1 domain which is known to be involved in production of seedless fruits.
A skilled artisan would acknowledge that a single specific substitution with one or more specific amino acid(s) (out of 21 probable options) at a specific amino acid position can drastically change the biological activity of a protein and/or a specific domain in a protein. That change in the function of the protein does not assure achieving any specific loss-of-function or gain-of-function trait(s) including obtaining the specific gain-of-function of ovary-derived seedless fruits. It is also known in the art that compensatory mutation(s) neutralize(s) or balance(s) effects of the mutation(s) at a different position(s) in a protein (Bhattacherjee et al., Compensatory Mutations Occur Within the Electrostatic Interaction Range of Deleterious Mutations in Protein Structure, 2015, J. Mol. Evol., 80:10–12; abstract). Thus, the effect of a substitution mutation with a specific amino acid at one or more specific amino acid(s) at positions K721, D771, E773, D775 and D781 of SEQ ID NO: 1 can be compensated by substitutions and/or mutations including deletion(s) in other amino acid positions without achieving the specific gain-of-function trait of ovary-derived seedless fruits.
Considering the breadth of the claims, lack of representative species of the broad genus claimed, lack of structure function relationship of the broad genus claimed, and unpredictability of the art, the Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
Claim Rejections - 35 USC § 102(a)(1)
Claims 3, 11-12, 15-16, 29 and 32 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Goetz et al. (Expression of Aberrant Forms of AUXIN RESPONSE FACTOR8 Stimulates Parthenocarpy in Arabidopsis and Tomato, 2007, Plant Physiology, 145:351–366), in evidence of Pandolfini, T (Seedless Fruit Production by Hormonal Regulation of Fruit Set, 2009, Nutrients, 1:168-177).
Claim 3 depends from claim 1 and is drawn to a deletion of a portion of the PB1 domain. As discussed in the rejection above under 35 U.S.C. 112(b) and 112(d), it is unclear whether the modified ARF8 of the plants of claims 3, 11-12, 15-16, 29, and 32 still comprise amino acid substitution(s) at the position(s) corresponding to K721, D771, E773, D775 and/or D781 of SEQ ID NO: 1.
Goetz et al. teaches that mutations in the AUXIN RESPONSE FACTOR8 (ARF8) uncouple fruit initiation from fertilization resulting in the formation of seedless, parthenocarpic fruit (abstract). Goetz et al. also describes genetically modified flowering plants that express an allele of Arabidopsis ARF8 (atarf8-4) gene and a tomato SlARF8 gene (abstract). The Arabidopsis and tomato ARF8 proteins are orthologs (page 356, right column, para 1). Tomato ARF8 protein (GenBank Accession No. EF667342) is also an ortholog of tomato ARF8A polypeptide consisting of SEQ ID NO: 1 and share high sequence identity to instant SEQ ID NO: 1, as shown below.
Title: US-18-629-315-1
Perfect score: 4457
Sequence: 1 MKLSTSGMGQQAHEGENKCL..........NSADGRDFMSGLPSIGSLDY 844
Searched: 1 seqs, 843 residues
Database : AASEQ2_07312025_163623.pep:*
RESULT 1
AASEQ2_07312025_163623
Query Match 87.3%; Score 3891; DB 1; Length 843; Best Local Similarity 88.2%;
Matches 747; Conservative 39; Mismatches 53; Indels 8; Gaps 6;
Qy 1 MKLSTSGMGQQAHEGENKCLNSELWHACAGPLVCLPTVGSRVVYFPQGHSEQVAATTNKE 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MKLSTSGMGQQAHEGENKCLNSELWHACAGPLVCLPTVGSRVVYFPQGHSEQVAATTNKE 60
Qy 61 VDIHIPNYPNLPPQLICQLHNVTMHADVETDEVYAQMTLQPLTLQEQKDTYLPVELGIPS 120
:|||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||
Db 61 LDIHIPNYPNLPPQLICPLHNVTMHADVETDEVYAQMTLQPLTLQEQKDTYLPVELGIPS 120
Qy 121 RQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFPPLDFSQTPPCQELIARDLHDIEWKFR 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 RQPTNYFCKTLTASDTSTHGGFSVPRRAAEKVFPPLDFSQTPPCQELIARDLHDIEWKFR 180
Qy 181 HIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLFLGIRRATRPQTVMPSSVL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 HIFRGQPKRHLLTTGWSVFVSAKRLVAGDSVLFIWNEKNQLFLGIRRATRPQTVMPSSVL 240
Qy 241 SSDSMHIGLLAAAAHAASTNSCFIVFFNPRASPSEFVIPLSKYIKAVYHTRVSVGMRFRM 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 SSDSMHIGLLAAAAHAASTNSCFIVFFNPRASPSEFVIPLSKYIKAVYHTRVSVGMRFRM 300
Qy 301 LFETEESSVRRYMGTITGIGDLDPVRWANSHWRSVKVGWDESTAGERQPRVSLWEIEPLT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 LFETEESSVRRYMGTITGIGDLDPVRWANSHWRSVKVGWDESTAGERQPRVSLWEIEPLT 360
Qy 361 TFPMYPSLFPLRLKRPWYPGTSSFQENNSEAINGMTWLRGESSEQGPHLLNLQSFGGMFP 420
||||||||||||||||:| ||||:|::|:|||| |:|||| : | | | :||||| || |
Db 361 TFPMYPSLFPLRLKRPFYQGTSSYQDSNNEAINRMSWLRGNAGELGHHSMNLQSF-GMLP 419
Qy 421 WMQQRVDPTMLRNDLNQQYQAMLASGLQNFGSGDLMKQQLMQFPQPVQYVQHAGSVNPQL 480
||||||| |:| ||:|| ||||||:|||:||||||:||||||| |||||:||| : | |
Db 420 WMQQRVDSTILPNDINQHYQAMLATGLQSFGSGDLLKQQLMQFQQPVQYLQHASTENSIL 479
Qy 481 -QQQQQQQETMQQTIHHHMLPAQTQ---DNLQRQQQQHVSNQTEEQSHQHSYQDAYQIPN 536
|||||||: ||| :| |||||||| :||||| | :||:|||:|||:||:|:|:|:
Db 480 HQQQQQQQQIMQQAVHQHMLPAQTQMLSENLQRQSQHQSNNQSEEQAHQHTYQEAFQLPH 539
Qy 537 SQLQQKQPSNVPSPSFSKPDIADPSSKFSASIAPSGMPTALGSLCSEGTTNFLNFNIIGQ 596
||||:||||| || | | | || :||||||:||||: ||||||||: | || | ||
Db 540 DQLQQRQPSNVTSP-FLKADFADLTSKFSASVAPSGVQNMLGSLCSEGSNNSLNINRTGQ 598
Qy 597 QPVIMEQQQQQKSWMAKFANSQLNMGSSSPSLSGYGKETSNSQETCSLDAQNQSLFGANV 656
||:|| || |||:|| |||| |:| || |||:| | : ||||:||||||||||
Db 599 S-VIIEQSPQQ-SWMSKFTESQLNTCSNSSSLPTYGKDTFNPRGNCSLDSQNQSLFGANV 656
Qy 657 DSSGLLLPTTVSNVATTSIDADISSMPLGTSGFPNPLYSYVQDSTDLLHNVGQADAQTVP 716
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 657 DSSGLLLPTTVSNVATTSIDADISSMPLGTSGFPNPLYSYVQDSTDLLHNVGQADAQTVP 716
[AltContent: rect][AltContent: rect][AltContent: rect][AltContent: rect]
Qy 717 RTFVKVYKSASLGRSLDITRFNSYHELRQELGQMFGIEGFLENPQRSGWQLVFVDRENDV 776
||||||||||||||||||||||||||||||||||||||| ||:|||||||||||||||||
Db 717 RTFVKVYKSASLGRSLDITRFNSYHELRQELGQMFGIEGLLEDPQRSGWQLVFVDRENDV 776
[AltContent: rect]
Qy 777 LLLGDDPWEEFVNNVWYIKILSPEDVQKLGKEEVGSLNRGPPERMSSNNSADGRDFMSGL 836
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 777 LLLGDDPWEEFVNNVWYIKILSPEDVQKLGKEEVGSLNRGPPERMSSNNSADGRDFMSGL 836
Qy 837 PSIGSLD 843
|||||||
Db 837 PSIGSLD 843
Goetz et al. describes identifying a SlARF8 cDNA sequence comprising a 5-bp deletion in the DNA binding domain of the encoded polypeptide. The deletion introduced an early stop codon immediately after the deletion and the truncated AFR8 protein containing N-terminal 185 amino acids (page 358, left column, para 2, line 1-9; Fig. 6A), wherein the entirety of its PB1 domain consisting of amino acid residues 712-811 (Spec, page 4, para 0014; Fig. 1a) including the amino acids in similar or orthologous positions of K721, D771, E773, D775 or D781 of SEQ ID NO: 1 (as marked by the black boxes in the sequence alignment above and as recited in claim 1), are deleted.
The Phox and Bem1 (PB1) domain of SlARF8 (GenBank Accession No. EF667342) is from amino acid residues 717-801 (highlighted in darker grey in the sequence alignment above, as predicted by Uniprot), which correlates with the PB1 domain comprising of amino acid at position 712 to 811 (page 3, para 0014; Fig. 1a) of SlARF8A (SEQ ID NO: 1). There are several mutations in the PB1 domain of SlARF8 (GenBank Accession No. EF667342) aligning with the PB1 domain spanning from amino acid at 712 to amino acid at 811 (highlighted in lighter grey, above) in SEQ ID NO: 1 (Instant Fig. 1A).
It is well acknowledged in the art that the onset of fruit development starts in ovary after fertilization of the ovules (evidence from Pandolfini, T; abstract). All fruits, irrespective of fertilization of the ovule, are derived from ovaries and fruit growth can be uncoupled from fertilization and seed development (Pandolfini, T, page 168, para 1, line 5-6) to develop seedless fruits.
Regarding claims 15-16, claims 15-16 are drawn to a genetically modified flowering plant of claim 6, wherein the modified S1ARF8A ortholog comprises Solanum lycopersicum S1ARF8B comprising a deletion of full length or a portion of amino acids 715-803 of SEQ ID NO: 83. As SlARF8A and SlARF8B are orthologs, the Examiner interprets claims 15-16 would include a S1ARF8A ortholog comprising a deletion that includes deletion of all of amino acids 715-803 of SEQ ID NO: 83. Thus, the genetically modified flowering plant containing an ortholog of SlAFR8, as described by Goetz et al. and as discussed above, fulfils all the claim limitations of the claims 15-16.
Conclusion
No claim is 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.
Communication
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JAY CHATTERJEE whose telephone number is (703)756-1329. The examiner can normally be reached (Mon - Fri) 8.30 am to 5.30 pm..
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bratislav Stankovic can be reached at (571) 270-0305. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/Jay Chatterjee/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/Supervisory Patent Examiner, Art Units 1616 & 1662
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