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 .
Election/Restrictions
In the response received on Aug. 7, 2026, the Applicant elected without traverse to prosecute Group II, including claims 1, 2, 5, and 6, and directed to a rice grain comprising an aleurone, a starchy endosperm, a means for causing the aleurone of the rice grain to be thickened relative to aleurone from a corresponding wild-type rice grain, including wherein the ROS1a polypeptide in the grain is reduced in DNA glycosylase activity. Applicant has canceled claims 2, 6, and 9-20. This leaves claim 5 as the only remaining claim requiring a ROS1a polypeptide with reduced DNA glycosylase activity. The linking claim, claim 1, has been amended such that the rice grain is no longer required to have a thickened aleurone relative to the aleurone of a corresponding wild-type rice grain. The amended claim 1 now requires a ROS1a gene with reduced activity instead. Claims 3 and 4 belong in the non-elected group of group I which required a reduced amount of ROS1a polypeptide, claims 7 and 8 belong in the non-elected group of group III which required an aleurone with about 3-6 layers of cells or an increase in thickness. Claims 1, 3-5, 7, and 8 are pending. Claims 3, 4, 7, and 8 are withdrawn for being directed to non-elected inventions there being no linking claim allowed to cause rejoinder. Claims 1 and 5 are examined in this Office Action.
Information Disclosure Statement
The listing of references in the specification on pages 95-98 is not a proper information disclosure statement. 37 CFR 1.98(b) requires a list of all patents, publications, or other information submitted for consideration by the Office, and MPEP § 609.04(a) states, "the list may not be incorporated into the specification but must be submitted in a separate paper." Therefore, unless the references have been cited by the examiner on form PTO-892, they have not been considered.
Specification
The title of the invention is not descriptive. A new title is required that is clearly indicative of the invention to which the claims are directed.
The following title is suggested: - - RICE GRAIN WITH REDUCED ROS1A GENE ACTIVITY - - .
Claim Interpretation
The following is a quotation of 35 U.S.C. 112(f):
(f) Element in Claim for a Combination. – An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The following is a quotation of pre-AIA 35 U.S.C. 112, sixth paragraph:
An element in a claim for a combination may be expressed as a means or step for performing a specified function without the recital of structure, material, or acts in support thereof, and such claim shall be construed to cover the corresponding structure, material, or acts described in the specification and equivalents thereof.
The claims in this application are given their broadest reasonable interpretation using the plain meaning of the claim language in light of the specification as it would be understood by one of ordinary skill in the art. The broadest reasonable interpretation of a claim element (also commonly referred to as a claim limitation) is limited by the description in the specification when 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is invoked.
As explained in MPEP § 2181, subsection I, claim limitations that meet the following three-prong test will be interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph:
(A) the claim limitation uses the term “means” or “step” or a term used as a substitute for “means” that is a generic placeholder (also called a nonce term or a non-structural term having no specific structural meaning) for performing the claimed function;
(B) the term “means” or “step” or the generic placeholder is modified by functional language, typically, but not always linked by the transition word “for” (e.g., “means for”) or another linking word or phrase, such as “configured to” or “so that”; and
(C) the term “means” or “step” or the generic placeholder is not modified by sufficient structure, material, or acts for performing the claimed function.
Use of the word “means” (or “step”) in a claim with functional language creates a rebuttable presumption that the claim limitation is to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites sufficient structure, material, or acts to entirely perform the recited function.
Absence of the word “means” (or “step”) in a claim creates a rebuttable presumption that the claim limitation is not to be treated in accordance with 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph. The presumption that the claim limitation is not interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, is rebutted when the claim limitation recites function without reciting sufficient structure, material or acts to entirely perform the recited function.
Claim limitations in this application that use the word “means” (or “step”) are being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action. Conversely, claim limitations in this application that do not use the word “means” (or “step”) are not being interpreted under 35 U.S.C. 112(f) or pre-AIA 35 U.S.C. 112, sixth paragraph, except as otherwise indicated in an Office action.
Claim 1 part (iii) recites “means for reducing the activity of at least one ROS1a gene in the rice grain relative to a corresponding wild-type rice grain.”
Applicant defines the term as follows: “As used herein, the term “reduce the activity of at least one ROS1a gene” as it relates to the “one or more genetic variations” or “one or more introduced genetic variations” refers to the genetic variation resulting in a reduction in the amount or activity of a ROS1a polypeptide expressed by the gene when compared to a corresponding wild-type rice plant.” (Spec 35). The Examiner will be using this definition during examination to define the broadest reasonable interpretation of the claims.
The specification provides the following means for reducing the activity of at least one ROS1a gene:
(a) a ROS1a gene encoding a mutant ROS1a polypeptide with reduced DNA glycosylase activity relative to the wild-type ROS1a polypeptide (SEQ ID NO:2);
(b) a ROS1a gene which when expressed produces a reduced level of a wild- type ROS1a polypeptide, for example which comprises a splice-site mutation that results in a reduced level of expression of the ROSla gene, relative to the wild-type ROSla gene whose cDNA sequence is provided as SEQ ID NO:8, or which ROSla gene comprises a mutation in its promoter which results in reduced expression of the ROSla gene relative to the wild-type ROSla gene;
(c) an exogenous nucleic acid construct which encodes a polynucleotide which reduces expression of a ROS1a gene in the rice plant, preferably wherein the nucleic acid construct comprises a DNA region encoding the polynucleotide operably linked to a promoter which is expressed in developing grain of the rice plant at least at a time point between the time of anthesis and 7 days post-anthesis, and
(d) a ROS1a gene comprising a premature translational stop codon in its protein coding region such that the gene encodes, but may or may not produce, a truncated polypeptide relative to a wild-type ROS1a polypeptide (Spec 6).
To clarify the type of “structure” the Examiner considers to be encompassed in this list ((a), (b), (c), and (d)) and “equivalents thereof”, the Examiner provides examples of what they consider to fall within the scope of the claim. The Examiner interprets claim 1 in include: mutations that alter the codons in the ROS1a gene which results in a change in amino acids in the encoded ROS1a protein; transgenes that recombinantly express ROS1a protein with amino acid substitutions, mutations in the regulatory elements or intron splice sites of the native ROS1a gene that result in reduced expression; antisense, RNAi, hpRNA, or miRNA targeting the native ROS1a gene; or a mutation in the native ROS1a gene that results in a premature stop codon. This is not intended to be an exhaustive list of every possibility, but is intended to be examples of the types of things that would be considered equivalents.
Claim 5 recites “means for causing ROS1a polypeptide in the grain to be reduced in DNA glycosylase activity”. This is interpreted to comprise mutations that alter the amino acid sequence of ROS1a protein or truncate the ROS1a protein.
Claim Rejections - 35 USC § 112
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.
Inadequate Written Description
Claims 1 and 5 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The claims are broadly drawn to a rice grain comprising an aleurone, a starchy endosperm, and a means for reducing the activity of at least one ROS1a gene in the rice grain relative to a corresponding wild-type rice grain (claim 1) including wherein the means for reducing the activity comprises a means for causing ROS1a polypeptide in the grain to be reduced in DNA glycosylase activity (claim 5).
Applicant describes 7 mutant versions of SEQ ID NO: 2 that confer the thick aleurone phenotype: S156F, S214F, S1412N, A441V, S1357F, K501S, and R482K (Spec 84-85 Table 3). They also demonstrate possession of three more mutants with the thick aleurone phenotype, however, they did not describe them because the mutations are “to be determined” (Id.).
Applicant does not describe any reduction in the activity of the ROS1a gene, instead they describe alterations in the protein that generate either less protein accumulation or less enzymatic activity for these mutant proteins. Applicant does not describe any measurement of DNA glycosylase activity for any of their mutants. Applicant does not describe any grains comprising an exogenous nucleic acid construct for reducing expression of a ROS1a gene. Applicant does not describe any mutant ROS1a genes having a premature stop codon resulting in a truncated program, other than the ta2 mutant that was taught in the prior art (Ono et al) and was shown to result in aborted embryos lacking aleurone and starchy endosperm due to stalling at the early endosperm development stage when homozygous for the mutant allele.
Given the breadth of the claims and the limited number of embodiments having been reduced to practice, the instant claims are not adequately described.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
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 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.
Rejection Under 35 USC §§ 102/103
Claim(s) 1 is/are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as anticipated by Fischer et al (US Pre-Grant Publication US 2003/0135890) or, in the alternative, under 35 U.S.C. 103 as obvious over Fischer et al (US Pre-Grant Publication US 2003/0135890) in view of Pennell et al (US Pre-Grant Publication US 2005/0081261).
The claim is directed to a rice grain comprising an aleurone, a starchy endosperm, and a means for reducing the activity of at least one ROS1a gene in the rice grain relative to a corresponding wild-type rice grain.
Fischer claims an expression cassette having a polynucleotide operably linked to a promoter in antisense orientation (see claim 14) wherein the polynucleotide encodes a polypeptide comprising amino acid sequences with at least 40% identity to Domain A, Domain B, or Domain C of DMT (see claims 13 and 1). DMT is a demethylation polypeptide, such as a glycosylase, and they teach a rice homolog which they refer to as SEQ ID NO: 17 that has 99.3% identity to the instant SEQ ID NO: 2 (Fischer 52 and alignment, below):
ALIGNMENT BETWEEN SEQ ID NO: 2 AND FISCHER’S SEQ ID NO: 17
RESULT 23
ADM39548
ID ADM39548 standard; protein; 1954 AA.
XX
AC ADM39548;
XX
DT 03-JUN-2004 (first entry)
XX
DE DMT polypeptide #8.
XX
KW DMT; glycosylase; demethylation; DNA repair;
KW plant organ modulation identity; plant organ number modulation;
KW endosperm development enhancement; seed development; endosperm; embryo;
KW seed coat; flowering time; DNA methylation; pre-harvest sprouting;
KW cereal; rice.
XX
OS Oryza sativa.
XX
CC PN US2003135890-A1.
XX
CC PD 17-JUL-2003.
XX
CC PF 23-APR-2001; 2001US-00840743.
XX
PR 21-APR-2000; 2000US-00553690.
XX
CC PA (FISC/) FISCHER R.
CC PA (CHOI/) CHOI Y.
CC PA (HANN/) HANNON M.
CC PA (OKAM/) OKAMURO J.
CC PA (TATA/) TATARINOVA T.
XX
CC PI Fischer R, Choi Y, Hannon M, Okamuro J, Tatarinova T;
XX
DR WPI; 2003-829656/77.
XX
CC PT New DMT gene, useful for controlling plant development (e.g. seed
CC PT development, flowering time, chromosomal DNA methylation or transcription
CC PT in plants), or for developing plant lines with a variety of desired
CC PT phenotypes.
XX
CC PS Example 6; SEQ ID NO 17; 75pp; English.
XX
CC The invention relates to DMT domain polypeptides and the polynucleotides
CC encoding them. The invention also relates to an expression cassette
CC comprising a promoter operably linked to a heterologous polynucleotide
CC sequence or its complement which encodes a DMT polypeptide cited above, a
CC method of modulating transcription comprising introducing into a host
CC cell the expression cassette and selecting a host cell with modulated
CC transcription and a method of detecting a nucleic acid in a sample
CC comprising providing the new isolated nucleic acid, contacting the
CC isolated nucleic acid molecule with a sample to permit a comparison of
CC the sequence of the isolated nucleic acid with the sequence of the DNA in
CC the sample and analysing the result of the comparison. The polypeptides
CC are capable of exhibiting at least one activity chosen from glycosylase
CC activity, demethylation of polynucleotides, DNA repair, plant organ
CC modulation identity, plant organ number modulation, plant flowering time
CC delay and endosperm development enhancement. The polynucleotides are
CC useful in plant genetic engineering, particularly for controlling plant
CC development and for modulating seed (specifically endosperm, embryo and
CC seed coat) development, flowering time, chromosomal DNA methylation and
CC transcription in plants. The polynucleotides are also useful for
CC developing plant lines with a variety of desired phenotypes. The plants
CC obtained may be used to prevent pre-harvest sprouting in seeds,
CC especially those derived from cereals. This sequence represents a DMT
CC polypeptide used in the scope of the invention.
XX
SQ Sequence 1954 AA;
Query Match 99.3%; Score 10132; DB 4; Length 1954;
Best Local Similarity 99.6%;
Matches 1949; Conservative 0; Mismatches 1; Indels 6; Gaps 5;
Qy 1 MQDFGQWLPQSQTTADLYFSSIPIPSQFDTSIETQTRTSAVVSSEKESANSFVPHNGTGL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MQDFGQWLPQSQTTADLYFSSIPIPSQFDTSIETQTRTSAVVSSEKESANSFVPHNGTGL 60
Qy 61 VERISNDAGLTEVVGSSAGPTECIDLNKTPARKPKKKKHRPKVLKDDKPSKTPKSATPIP 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 VERISNDAGLTEVVGSSAGPTECIDLNKTPARKPKKKKHRPKVLKDDKPSKTPKSATPIP 120
Qy 121 STEKVEKPSGKRKYVRK--KTSPGQPPAEQAASSHCRSELKSVKRSLDFGGEVLQESTQS 178
||||||||||||||||| |||||||||||||||||||||||||||||||||||||||||
Db 121 STEKVEKPSGKRKYVRKKTKTSPGQPPAEQAASSHCRSELKSVKRSLDFGGEVLQESTQS 180
Qy 179 GSQVPVAEICTGPKRQSIPSTIQRDSQSQLACHVVSSTSSIHTSASQMVNAHLFPPDNMP 238
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 GSQVPVAEICTGPKRQSIPSTIQRDSQSQLACHVVSSTSSIHTSASQMVNAHLFPPDNMP 240
Qy 239 NGVLLDLNNSTSQLQNEHAKFVDSPARLFGSRIRQTSGKNSLLEIYAGMSDRNVPDLNSS 298
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 NGVLLDLNNSTSQLQNEHAKFVDSPARLFGSRIRQTSGKNSLLEIYAGMSDRNVPDLNSS 300
Qy 299 ISQTHSMSTDFAQYLLSSSQASVRETQMANQMLNGHRMPENPITPSHCIERAALKEHLNH 358
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 ISQTHSMSTDFAQYLLSSSQASVRETQMANQMLNGHRMPENPITPSHCIERAALKEHLNH 360
Qy 359 VPHAKAAVMNGQMPHSYRLAQNPILPPNHIEGYQVMENLSELVTTNDYLTASPFSQTGAA 418
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 VPHAKAAVMNGQMPHSYRLAQNPILPPNHIEGYQVMENLSELVTTNDYLTASPFSQTGAA 420
Qy 419 NRQHNIGDSMHIHALDPRRESNASSGSWISLGVNFNQQNNGWASAGAADAASSHAPYFSE 478
||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||
Db 421 NRQHNIGDSMHIHALDPRR-SNASSGSWISLGVNFNQQNNGWASAGAADAASSHAPYFSE 479
Qy 479 PHKRMRTAYLNNYPNGVVGHFSTSSTDLSNNENENVASAINSNVFTLADAQRLIAREKSR 538
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 480 PHKRMRTAYLNNYPNGVVGHFSTSSTDLSNNENENVASAINSNVFTLADAQRLIAREKSR 539
Qy 539 ASQRMISFRSSKNDMVNRSEMVHQHGRPAPHGSACRESIEVPDKQFGLMTEELTQLPSMP 598
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 540 ASQRMISFRSSKNDMVNRSEMVHQHGRPAPHGSACRESIEVPDKQFGLMTEELTQLPSMP 599
Qy 599 NNPQREKYIPQTGSCQLQSLEHDMVKGHNLAGELHKQVTSPQVVIQSNFCVTPPDVLGRR 658
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 600 NNPQREKYIPQTGSCQLQSLEHDMVKGHNLAGELHKQVTSPQVVIQSNFCVTPPDVLGRR 659
Qy 659 TSGEHLRTLIAPTHASTCKDTLKALSCQLESSRDIIRPPVNPIGPSSADVPRTDNHQVKV 718
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 660 TSGEHLRTLIAPTHASTCKDTLKALSCQLESSRDIIRPPVNPIGPSSADVPRTDNHQVKV 719
Qy 719 SEETVTAKLPEKRKVGRPRKELKPGEKPKPRGRPRKGKVVGGELASKDSHTN-PLQNEST 777
|||||||||||||||||||||||||||||||||||||||||||||||||||| |||||||
Db 720 SEETVTAKLPEKRKVGRPRKELKPGEKPKPRGRPRKGKVVGGELASKDSHTNIPLQNEST 779
Qy 778 SCSYGPYAGEASVGRAVKANRVGENISGAMVSLLDSLDIVIQKIKVLDINKSEDPVTAEP 837
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 780 SCSYGPYAGEASVGRAVKANRVGENISGAMVSLLDSLDIVIQKIKVLDINKSEDPVTAEP 839
Qy 838 HGALVPYNGEFGPIVPFEGKVKRKRSRAKVDLDPVTALMWKLLMGPDMSDCAEGMDKDKE 897
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 840 HGALVPYNGEFGPIVPFEGKVKRKRSRAKVDLDPVTALMWKLLMGPDMSDCAEGMDKDKE 899
Qy 898 KWLNEERKIFQGRVDSFIARMHLVQGDRRFSPWKGSVVDSVVGVFLTQNVSDHLSSSAFM 957
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 900 KWLNEERKIFQGRVDSFIARMHLVQGDRRFSPWKGSVVDSVVGVFLTQNVSDHLSSSAFM 959
Qy 958 ALAAKFPVKPEASEKPANVMFHTISENGDCSGLFGNSVKLQGEILVQEASNTAASFITTE 1017
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 960 ALAAKFPVKPEASEKPANVMFHTISENGDCSGLFGNSVKLQGEILVQEASNTAASFITTE 1019
Qy 1018 DKEGSNSVELLGSSFGDGVDGAAGVYSNIYENLPARLHATRRPVVQTGNAVEAEDGSLEG 1077
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1020 DKEGSNSVELLGSSFGDGVDGAAGVYSNIYENLPARLHATRRPVVQTGNAVEAEDGSLEG 1079
Qy 1078 VVSSENSTISSQNSSDYLFHMSDHMFSSMLLNFTAEDIGSRNMPKATRTTYTELLRMQEL 1137
||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||
Db 1080 VVSSENSTISSQNSSDYLFHMSDHMFSSMLLNFTAEDIGSR-MPKATRTTYTELLRMQEL 1138
Qy 1138 KNKSNETIESSEYHGVPVSCSNNIQVLNGIQNIGSKHQPLHSSISYHQTGQVHLPDIVHA 1197
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1139 KNKSNETIESSEYHGVPVSCSNNIQVLNGIQNIGSKHQPLHSSISYHQTGQVHLPDIVHA 1198
Qy 1198 SDLEQSVYTGLNRVLDSNVTQTSYYPSPHPGIACNN-ETQKADSLSNMLYGIDRSDKTTS 1256
|||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
Db 1199 SDLEQSVYTGLNRVLDSNVTQTSYYPSPHPGIACNNKETQKADSLSNMLYGIDRSDKTTS 1258
Qy 1257 LSEPTPRIDNCFQPLSSEKMSFAREQSSSENYLSRNEAEAAFVKQHGTSNVQGDNTVRTE 1316
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1259 LSEPTPRIDNCFQPLSSEKMSFAREQSSSENYLSRNEAEAAFVKQHGTSNVQGDNTVRTE 1318
Qy 1317 QNGGENSQSGYSQQDDNVGFQTATTSNLYSSNLCQNQKANSEVLHGVSSNLIENSKDDKK 1376
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1319 QNGGENSQSGYSQQDDNVGFQTATTSNLYSSNLCQNQKANSEVLHGVSSNLIENSKDDKK 1378
Qy 1377 TSPKVPVDGSKAKRPRVGAGKKKTYDWDMLRKEVLYSHGNKERSQNAKDSIDWETIRQAE 1436
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1379 TSPKVPVDGSKAKRPRVGAGKKKTYDWDMLRKEVLYSHGNKERSQNAKDSIDWETIRQAE 1438
Qy 1437 VKEISDTIRERGMNNMLAERIKDFLNRLVRDHGSIDLEWLRYVDSDKAKDYLLSIRGLGL 1496
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1439 VKEISDTIRERGMNNMLAERIKDFLNRLVRDHGSIDLEWLRYVDSDKAKDYLLSIRGLGL 1498
Qy 1497 KSVECVRLLTLHHMAFPVDTNVGRICVRLGWVPLQPLPESLQLHLLEMYPMLENIQKYLW 1556
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1499 KSVECVRLLTLHHMAFPVDTNVGRICVRLGWVPLQPLPESLQLHLLEMYPMLENIQKYLW 1558
Qy 1557 PRLCKLDQRTLYELHYQMITFGKVFCTKSKPNCNACPMRAECKHFASAFASARLALPGPE 1616
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1559 PRLCKLDQRTLYELHYQMITFGKVFCTKSKPNCNACPMRAECKHFASAFASARLALPGPE 1618
Qy 1617 EKSLVTSGTPIAAETFHQTYISSRPVVSQLEWNSNTCHHGMNNRQPIIEEPASPEPEHET 1676
|||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Db 1619 EKSLVTSGTPIAAETFHQTYISSRPVVSQLEWNSNTCHHGMNKRQPIIEEPASPEPEHET 1678
Qy 1677 EEMKECAIEDSFVDDPEEIPTIKLNFEEFTQNLKSYMQANNIEIEDADMSKALVAITPEV 1736
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1679 EEMKECAIEDSFVDDPEEIPTIKLNFEEFTQNLKSYMQANNIEIEDADMSKALVAITPEV 1738
Qy 1737 ASIPTPKLKNVSRLRTEHQVYELPDSHPLLEGFNQREPDDPCPYLLSIWTPGETAQSTDA 1796
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1739 ASIPTPKLKNVSRLRTEHQVYELPDSHPLLEGFNQREPDDPCPYLLSIWTPGETAQSTDA 1798
Qy 1797 PKSVCNSQENGELCASNTCFSCNSIREAQAQKVRGTLLIPCRTAMRGSFPLNGTYFQVNE 1856
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1799 PKSVCNSQENGELCASNTCFSCNSIREAQAQKVRGTLLIPCRTAMRGSFPLNGTYFQVNE 1858
Qy 1857 VFADHDSSRNPIDVPRSWIWNLPRRTVYFGTSIPTIFKGLTTEEIQHCFWRGFVCVRGFD 1916
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1859 VFADHDSSRNPIDVPRSWIWNLPRRTVYFGTSIPTIFKGLTTEEIQHCFWRGFVCVRGFD 1918
Qy 1917 RTSRAPRPLYARLHFPASKITRNKKSAGSAPGRDDE 1952
||||||||||||||||||||||||||||||||||||
Db 1919 RTSRAPRPLYARLHFPASKITRNKKSAGSAPGRDDE 1954
Fischer suggests Oryza (rice) as a choice for a plant to be used in their invention (Fischer 14-15 ¶ 167). Fischer lists 56 possible plants for use in their invention (Id.). Fischer claims enhanced endosperm development when there is a reduction in expression in a plant (Fischer claim 26 part c). A plant transformed with an antisense construct comprises a “means for reducing the activity” of the targeted gene.
Fischer does not reduce to practice a rice plant transformed with an antisense construct to inhibit expression of the endogenous ROS1a gene. Given the express teaching of the rice gene encoding a protein with 99.3% identity to the instant SEQ ID NO: 2 and the list of possible plants for use in their invention, Fischer clearly envisions and contemplates rice plants comprising antisense constructs targeting the endogenous ROS1a gene.
In the event, this teaching is not considered adequate to amount to an anticipation of the instantly claimed invention, the claim is also obvious over Fischer in view of Pennell.
Fischer’s teaching is set forth, above. Fischer does not reduce to practice a rice grain comprising an antisense construct targeting the endogenous ROS1a gene.
Pennell teaches inhibition of endogenous DNA methyltransferases to cause an increase in seed weight (Pennell abstract). Pennell teaches a transgenic plant comprising a recombinant nucleic acid construct effective for reducing levels of DNA methylation (Id. claim 57) including wherein the plant is a monocotyledonous plant (Id. claim 65). Pennell reduces to practice this invention in Arabidopsis, and they analyze homozygous plants to demonstrate an increase in seed weight (Id. 11 Table 1). Pennell teaches the use of an RNAi construct to inhibit expression of an endogenous rice gene and achieved inhibition of gene expression resulting in transcript levels between 2% and 53% of the levels in control plants (Id. 13 ¶ 119).
At the time the instant application was filed, it would have been obvious and within the scope of one of ordinary skill in the art to make a transgenic rice plant transformed with an antisense or RNAi construct to inhibit the endogenous rice gene encoding the protein Fischer refers to as SEQ ID NO: 17 and Fischer labels as a demethylation (DMT) polypeptide. One would have been motivated to do so because Fischer specifically suggests rice as one of the plants for their invention and they specifically provide the rice sequence in their sequence listing along with the genomic sequence encoding it (SEQ ID NO: 19). Furthermore, Pennell even went so far as generating transgenic rice transformed with an RNAi construct to target one of rice’s endogenous DMT genes, and the sequence taught by Fischer that encodes SEQ ID NO: 17 is an obvious variation over the DMT sequence taught by Pennell.
One would have expected to achieve partial inhibition of expression resulting in reduced expression compared to wild-type plants such as the 2% - 53% levels of expression achieved by Pennell. One would have expected the result to be enhanced endosperm production and increased average seed weight, because those are the characteristics taught by Fischer and Pennell for a plant with decreased expression of an endogenous DMT gene.
Rejection Under 35 USC § 103
Claim(s) 5 is/are rejected under 35 U.S.C. 103 as being unpatentable over Fischer et al (US Pre-Grant Publication US 2003/0135890) in view of Pennell et al (US Pre-Grant Publication US 2005/0081261) as applied to claim 1 above, and further in view of Haughn et al. (Floriculture, ornamental and plant biotechnology (2006) Vol. 1 Global Science Books, UK; pp. 476-482).
The claim is directed to a rice grain comprising an aleurone, a starchy endosperm, and a means for reducing the activity of at least one ROS1a gene in the rice grain relative to a corresponding wild-type rice grain; wherein the means for reducing the activity comprises a means for causing ROS1a polypeptide in the grain to be reduced in DNA glycosylase activity relative to the DNA glycosylase activity of a wild-type ROS1a polypeptide in a corresponding wild-type rice grain.
Fischer in view of Pennell teach a rice grain comprising an aleurone, a starchy endosperm, and a means for reducing the activity of at least one ROS1a gene in the rice grain relative to a corresponding wild-type rice grain (see obviousness rejection, above). Pennell teaches the use of an RNAi construct to inhibit expression of an endogenous rice gene and achieved inhibition of gene expression resulting in transcript levels between 2% and 53% of the levels in control plants (Pennell 13 ¶ 119).
Fischer in view of Pennell do not teach a means for reducing the DNA glycosylase activity of a ROS1a protein.
Haughn teaches Targeting Induced Local Lesions IN Genomes (TILLING) as a genetic technique in plants (Haughn 476, abstract). Haughn teaches TILLING as an alternative approach that can be used for obtaining loss of gene function in plants similar to RNAi (Id. 478). Haughn teaches the use of ethylmethane sulfonate (EMS) to induce primarily loss-of-function mutations at a high mutation frequency to generate mutants that can be screened using the TILLING method (Id.). Haughn teaches that the TILLING technique is unique because it can deliver a higher level of allelic diversity compared to the other known techniques (Id. 479).
At the time the instant application was filed, it would have been obvious and within the scope of one of ordinary skill in the art to substitute TILLING for the RNAi or antisense taught by Fischer in view of Pennell. One would have been motivated to do so because Haughn teaches TILLING can provide a high level of allelic diversity in the target gene(s). Using TILLING, one of ordinary skill would have found multiple point mutations within the ROS1a gene, and this mutant population would have necessarily included some mutations that reduce the ROS1a activity such as nonsense mutations that introduce early stop codons and result in truncated protein or missense mutations that cause amino acid substitutions (Haughn 479). One would have had an expectation of success because Haughn teaches that TILLING can be used universally in virtually any organism (Id.). Given the teachings of Fischer and Pennell, one of ordinary skill would have expected the result of a loss of function mutation to be enhanced endosperm development and increased seed weight.
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.
Nonstatutory Double Patenting over US Patent No. 11,452,252
Claims 1 and 5 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-9 of U.S. Patent No. 11,452,272. Although the claims at issue are not identical, they are not patentably distinct from each other because the ‘272 claims are directed to a rice grain that has a particular amino acid substitution in the native ROS1a protein, and this is a species that falls within the genus of rice grains being claimed in the instant claims.
Nonstatutory Double Patenting over US Patent No. 12,178,174
Claims 1 and 5 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-20 of U.S. Patent No. 12,178,174. Although the claims at issue are not identical, they are not patentably distinct from each other because the ‘174 claims are directed to a method that would necessarily produce a rice grain that has a particular amino acid substitution in the native ROS1a protein, and this is a species that falls within the genus of rice grains being claimed in the instant claims.
It is noted that the Examiner informed Applicant that this nonstatutory double patenting was likely to be made in an interview while prosecuting the application that resulted in the ‘174 patent (interview summary mailed on Sept. 5, 2024, in Application No. 17/842,998)
Summary
No claim is allowed.
Examiner’s Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CATHY KINGDON whose telephone number is (571)272-8784. The examiner can normally be reached on M-F 9:00 - 5:30 EST.
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CATHY KINGDON
Primary Examiner
Art Unit 1663
/CATHY KINGDON/Primary Examiner, Art Unit 1663
