DETAILED CORRESPONDENCE
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA (America Invents Act). As a result, Applicant is encouraged to review the AIA in the MPEP. Applicant should also note that the wording, requirements, and statutes may have some subtle changes from actions and requirements prior to AIA .
Preliminary Amendment
The preliminary amendments to the claims are acknowledged and are entered.
Applicant has cancelled claims 3-5, 7, 9-10, 14-15, 17-18, 21-27, 31, 33-35 and 41-45.
Restriction Election
Applicant’s election without traverse of Group I in the reply filed on 5 May 2026 is acknowledged.
Claims 16, 19-20, 28-30, 32, 36-40 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 5 May 2026.
Claims Pending
Claims 1-2, 6, 8, 11-13 and 46 will be examined on the merits.
Priority
The present application filed on 28 February 2025 claims the benefit of U.S. Provisional application number of 63/559,014 on 28 February 2024.
Drawings
The drawings, filed on 28 February 2025, have been approved.
Information Disclosure Statement
The Information Disclosure Statement filed on 5 May 2026 has been considered.
Claim Objection
Claim 12 is objected to because of the following informalities: line 2 discloses “PIL6” which conflicts with claim 1 “(PILS6)”. Appropriate correction is required.
Claim Rejections - 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.
Claim 1 is rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial
exception (i.e., a law of nature, a natural phenomenon, or an abstract idea) without significantly
more.
The statutory categories of invention under 35 U.S.C. 101 are processes, machines,
manufactures, and compositions of matter. However, certain members of these categories
constitute judicial exceptions, i.e., the courts have determined that these entities are not
patentable subject matter. These judicial exceptions include abstract ideas, laws of nature, and
natural phenomena. The Office released guidance on December 16, 2014 for the examination of
claims reciting natural products under 35 U.S.C. 101 in light of the recent Supreme Court
decisions in Association for Molecular Pathology V. Myriad Genetics, Inc. (569 U.S._ , 133 S.
Ct. 2107, 2116, 106 USPQ2d 1972 (2013)) and Mayo Collaborative Services v. Prometheus
Laboratories (566 U.S.__, 132 S. Ct. 1289, 101 USPQ2d 1961 (2012)), Diamond v.
Chakrabarty, 447 U.S. 303 (1980)) and Funk Brothers Seed Co. V. Kalo Inoculant Co. - 333 U.S. 127 (1948)). (inter alia).
Claims 1 is drawn to a “PIN-likes 6 (PILS6)” gene in a plant or plant cell of the Poaceae family.
The rejection is made to interpret the gene expression PIN-likes 6 (PILS6) which is inherently in the plant. The claim is drawn to a method specifically of altering crown root architecture, lateral root formation and/or stalk height in a Poaceae plant by reducing or eliminating expression of a PIN-likes 6 (PILS6) gene.
The application of the expression of the gene occurs naturally in Zea mays and considered a natural process as disclosed in Yue et al. (“Genome-Wide Identification and Expression Profiling Analysis of ZmPIN, ZmPILS, ZmLAX and ZmABCB Auxin Transporter Gene Families in Maize (Zea mays L.) under Various Abiotic Stresses,” PLOS ONE 10(3) March 5 2015). Yue et al. discloses that the PILS6 gene is occurs naturally in Zea mays as shown in Fig. 3. Therefore, the claim is not meaningfully limited and does not amount to significantly more than each product and process of nature by itself. The claimed mixture is like the cloned mammals of Roslin, which were held ineligible because, as claimed, the cloned mammals lacked markedly different characteristics from their naturally occurring counterparts. In re Roslin Institute (Edinburgh), 750 F.3d 1333, 1339 (2014). For the reasons described above, the claimed extracts are not markedly different from their closest naturally occurring counterparts and thus are product of nature judicial exceptions.
The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because the claims do not recite any additional elements beyond the claimed compositions themselves. Therefore, the claim does not recite something significantly more than a judicial exception and are thus deemed patent ineligible subject matter.
Claim Rejections - 35 USC § 102
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.
Claim(s) 1, 2 and 8 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Li et al. (OsSPL14 acts upstream of OsPIN1b and PILS6b to modulate axillary bud outgrowth by fine-tuning auxin transport in rice,” The Plant Journal (2022) 111, 1167-1182).
The claims are broadly drawn to a method of altering crown root architecture, lateral root formation, and/or stalk height in a Poaceae plant by reducing or eliminating expression of a PIN-likes 6 (PILS6) gene in a plant or a plant cell of the Poaceae family where reducing or eliminating is effective to reduce crown root architecture, lateral root formation, and/or stalk height in the plant or a plant produced from the plant cell, as compared to a wild type plant and the gene introducing a loss-of-function mutation into a coding sequence and/or regulatory sequence of a PILS6 gene and the plant or plant cell in the Poaceae is from maize, rice, wheat, barley, sugarcane, sorghum, millet, switchgrass, rye, oats, bamboo, Bermuda grass, fescue, elephant grass, ryegrass, or Kentucky bluegrass.
Li et al. teach relationships between OsSPL14, PILS6b and auxin regulation in rice plants (entire document). Li et al. teach that pathways related to auxin synthesis, transport, and signaling have been extensively studied and the PIN-FORMED (PIN) protein family has been identified to be pivotal for polar auxin transport (PAT) and distribution and that the PIN proteins are central to auxin-regulated growth processes (page 1168, left col., para.1). Li et al. teach that PIN family member play an essential role in mediating PAT and plant architecture, particularly branch and root development (page 1168, left col., para.1). Li et al. teach that PILS proteins are another major family of auxin efflux carriers in plants and have been identified to be located in the endoplasmic reticulum and sequester auxin in there, thereby regulating auxin availability for nuclear auxin signaling (page 1168, left col., para.2). Li et al. teach that OsSPL14 (IDEAL PLANT ARCHITECTURE1 or WEATHY FARMER’S PANICLE) directly binds to PILS6b to modulate expression and thereby regulating the outgrowth of axillary buds and tiller number by fine-tuning auxin transport in rice (page 1168, left col., para. 2). Li et al. teach that OsSPL14 is a target gene of miR156 and miR529 and that enhanced miR529/miR156 expression led to a bushy phenotype caused by the accelerated outgrowth of axillary buds in the transgenic plants (page 1169, right col., para. 2; Figure S2). Li et al. teach overexpression (OE) and RNA interference (RNAi) transgenic lines (designated as OsSPL14-OE and OsSPL14-RNAi, respectively) and characterized their plant architecture (page 1169, left column, para. 1; Fig. 1; Fig. S1). Figure S1 shows that OsSPL14-RNAi (which triggers reducing or eliminating expression of a PIN-like (PILS6) gene; which reads on introducing a loss-of-function mutation into the regulatory sequence of a PILS6 gene) results in a compact. busy phenotype with a reduction in stalk height as compared to the wild type (WT) (Fig. S1). Li et al. teach that OsSPL14 positively regulates OsPIN1b and PILS6b expression (page 1170, right col. para.2). Li et al. constructed the CRISPR/Cas9 knockout plasmids for PILS6b in rice (pg. 1170, right col., 1st para; Fig. 3). In contrast to the negative control plants, pils6B-cri mutant plant exhibited an increase in tiller number which in turn produced bushy plants (page 1170, right col. para. 2; Fig. 3). Li et al. teach that a decrease in the expression of OsPIN1b and PILS6b accelerated the outgrowth of axillary buds (i.e. bushy phenotype) and that the expression of OsPIN1b and PILS6b is negatively correlated with axillary bud development in rice (page. 1170, right col. para. 2). Li et al. found that overexpression of OsSPL14 resulted in enhanced expression in axillary buds, leaves, leaf sheaths and roots of OsSPL-14 plants, but suppressed expression in OsSPL14-RNAi (which in turn resulted in a suppressed expression of PILS6b) plants and that the OsSPL14-RNAi plants exhibited an increase in tiller number relative to the wild type (paragraph bridging pages 1170-1172; Fig. 4).
The teachings of Li et al. meet the limitations of claim 1 and thus anticipates 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 (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 of this title, 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.
Claims 1-2, 6, 8, 11-13 and 46 are rejected under 35 U.S.C. 103 as being unpatentable over Li et al. (“OsSPL14 acts upstream of OsPIN1b and PILS6b to modulate axillary bud outgrowth by fine-tuning auxin transport in rice,” The Plant Journal (2022) 111, 1167-1182) and Li and Ll et al. (Nov. 2015. US 2015/0315605 A1).
The claims are broadly drawn to a method of altering crown root architecture, lateral root formation, and/or stalk height in a Poaceae plant by comprising reducing or eliminating expression of a PIN-likes 6 (PILS6) gene in a plant or a plant cell of the Poaceae family where reducing or eliminating is effective to reduce crown root architecture, lateral root formation, and/or stalk height in the plant or a plant produced from the plant cell, as compared to a wild type plant. and the gene comprises introducing a loss-of-function mutation into a coding sequence and/or regulatory sequence of a PILS6 gene and wherein an insertion is between nucleotides of 777 and 778 of SEQ ID NO:1 or an insertion between nucleotides of 1227 and 1228 of SEQ ID NO:1 and where the plant or plant cell in the Poaceae is from maize, rice, wheat, barley, sugarcane, sorghum, millet, switchgrass, rye, oats, bamboo, Bermuda grass, fescue, elephant grass, ryegrass, or Kentucky bluegrass, wherein the PILS6 gene is ZmPILS6 and comprises a nucleotide sequence encoding an amino acid sequence of SEQ ID NO: 3 or an amino acid sequence having at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 3 and a method of increasing salt tolerance in a Poaceae plant by reducing or eliminating expression of a PIN-likes 6 (PILS6) gene in a plant or a plant cell of the Poaceae family by reducing or eliminating is effective to increase salt tolerance in the plant or a plant produced from the plant cell, as compared to a wild type plant.
The teachings of Li et al. are supra.
Although Li et al. do not specifically teach wherein the PILS6 gene expression in roots is reduced by at least 35% compared to PIL6 [sic] gene expression in roots of a wild type plant, it would naturally follow that this characteristic would be seen in plants where the PILS6 gene has reduced or silenced function. The mutations as taught by Li et al. introduce frameshift mutations that reduce or silence the function of PILS6 gene expression.
Although Li et al. do not specifically teach wherein the crown root total root length is reduced by at least 30% compared to the crown root total root length of a wild type plant, the lateral root primordia density is reduced by at least 30% compared to the lateral root primordia density of a wild type plant, and/or the stalk height is reduced by at least 20% compared to stalk height of a wild type plant, , it would naturally follow that these characteristics would be seen in plants where the PILS6 gene has reduced or silenced function. The mutations as taught by Li et al. introduce frameshift mutations that reduce or silence the function of PILS6 gene expression.
Although Li et al. do not teach wherein said reducing or eliminating is effective to increase salt tolerance in the plant as compared to a wild type plant, it would naturally follow that these characteristics would be seen in plants were the PILSS6 gene has reduced or silenced function. The mutation as taught by Li et al. introduce frameshift mutation that reduce or silence the function of PILS6 gene expression.
Li et al. do not specifically teach wherein said loss-of function mutation is an insertion is between nucleotides of 777 and 778 of SEQ ID NO:1 or an insertion between nucleotides of 1227 and 1228 of SEQ ID NO:1, wherein the PILS6 gene is ZmPILS6 and comprises a nucleotide sequence encoding an amino acid sequence of SEQ ID NO: 3 or an amino acid sequence having at least 95% sequence identity to the amino acid sequence of SEQ ID NO: 3 reducing or eliminating is effective to increase salt tolerance in a Poaceae plant or produced from the plant cell.
Li et al. and Ll et al. teach computational analysis of hundreds of RNA-seq libraries enabling the identification of novel transcripts in maize. Li et al. and LI et al. also teach methods using Clustal V method of alignments and methods of introduction nucleic acids that suppresses the level of an endogenous polypeptide (claim 1). Zea maize proteins comprising an amino acid sequence containing a deletion, substitution, insertion and/or addition of one or more amino acids in an amino acid sequence [0106]. Li et al. and Ll et al. also disclose the use of CRISPR/Cas9 (0087-0091). Li et al. and Ll et al. teach a Zea maize amino acid sequence showing a deletion event with 95.4% sequence identity with the amino acid sequence SEQ ID NO: 3.
RESULT 4
US-14-628-469-66351
Sequence 66351, US/14628469
Publication No. US20150315605A1
GENERAL INFORMATION
APPLICANT: EI DuPont de Nemours
APPLICANT: Li, Bailin
APPLICANT: Thatcher, Shawn
TITLE OF INVENTION: NOVEL TRANSCRIPTS AND USES THEREOF FOR IMPROVEMENT OF AGRONOMIC
TITLE OF INVENTION: CHARACTERISTICS IN CROP PLANTS
FILE REFERENCE: BB2384USNP
CURRENT APPLICATION NUMBER: US/14/628,469
CURRENT FILING DATE: 2015-02-23
PRIOR APPLICATION NUMBER: US 61/942,846
PRIOR FILING DATE: 2014-02-21
NUMBER OF SEQ ID NOS: 72254
SEQ ID NO 66351
LENGTH: 413
TYPE: PRT
ORGANISM: Zea Mays
Query Match 94.4%; Score 2096; Length 413;
Best Local Similarity 95.4%;
Matches 413; Conservative 0; Mismatches 0; Indels 20; Gaps 1;
Qy 1 MMERSLLEVLATAAQGGTEGTSVLSMLKYAVLPIAKVFTVCFMGFLMASKYVNILQPNGR 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MMERSLLEVLATAAQGGTEGTSVLSMLKYAVLPIAKVFTVCFMGFLMASKYVNILQPNGR 60
Qy 61 KLLNGLVFSLLLPCLIFSQLGRAITIEKMIQWWYIPVNIVVGAVSGSLIGFVVASIIRPP 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 KLLNGLVFSLLLPCLIFSQLGRAITIEKMIQWWYIPVNIVVGAVSGSLIGFVVASIIRPP 120
Qy 121 YPYFKFTVIHIGIGNIGNIPLVLIAALCRDPSNPFGDSDKCNQDGNAYISFGQWVGAIIV 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 YPYFKFTVIHIGIGNIGNIPLVLIAALCRDPSNPFGDSDKCNQDGNAYISFGQW------ 174
Qy 181 YTYVFKMLAPPPGQTFDGSEEDGIPIKASGENTVPQVGKYPMNTNSSTVPENEPLLSAGE 240
||||||||||||||||||||||||||||||||||||||||||||||
Db 175 --------------TFDGSEEDGIPIKASGENTVPQVGKYPMNTNSSTVPENEPLLSAGE 220
Qy 241 VQKERATSVGTKIMGYVKCVVKFLKDKQLLQPPIIASAFAIA IGVIPFLKNFVLTDDAPL 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 221 VQKERATSVGTKIMGYVKCVVKFLKDKQLLQPPIIASAFAIA IGVIPFLKNFVLTDDAPL 280
Qy 301 FFFTDSCLILGEAMIPCILLAVGGNLVDGPGEGSKRLGVRTTVAIIFARLVLVPLAGVGI 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 281 FFFTDSCLILGEAMIPCILLAVGGNLVDGPGEGSKRLGVRTTVAIIFARLVLVPLAGVGI 340
Qy 361 TMLVDKLGFIPEGDRMFKFVLLLQHSMPTSVLSGAVANLRGCGKESAAILFWVHIFAVFS 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 341 TMLVDKLGFIPEGDRMFKFVLLLQHSMPTSVLSGAVANLRGCGKESAAILFWVHIFAVFS 400
Qy 421 MAGWIIFYLSLLF 433
|||||||||||||
Db 401 MAGWIIFYLSLLF 413
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention was made to utilize the CRISPR method to knockout, decrease, suppress or silence the function of a specific type of gene to produce agronomic plant traits of interest. It would have been obvious to use the CRISPR method, specifically in the PILS6 gene region, to reduce or eliminate the function of the PILS6 gene to obtain the claimed invention and produce plants with increased tiller formation. Substitution of one mutation conferring function of a PILS6 gene for another mutation is merely a design choice. One would have been motivated to reduce the function of PILS6 gene thereby increasing tiller number to increase the production of grain-bearing panicles and thereby increasing yield of rice.
Moreover, by the teachings of the cited references, it is apparent that one of ordinary skill in the art would have a reasonable expectation of success in using the methods as taught in the cited references as it was commonly known in the art to use the CRISPR method to reduce or eliminate the expression of PIN-likes 6 (PILS6) gene. Furthermore, the teachings of Li et al. produce PILSb mutants that exhibited an increase in tiller number (page 1170, right col., para. 2; Fig. 3).
Furthermore, given that genome of corn has been well-studied, documented and has searchable databases, it would have been obvious to one of ordinary skill in the art before the effective filing data of the claimed invention to introduce a mutation in the PILS6 gene of Zea maize conferring reduced or silenced expression of the gene produce plants with increase tiller number. It would have been obvious to use the CRISPR method, specifically in the PILS6 gene region, to reduce or eliminate the function of the PILS6 gene to obtain plants with increased tiller formation. Substitution of one mutation conferring function of a PILS6 gene for another mutation is merely a design choice. One would have been motivated to reduce the function of PILS6 gene in corn thereby increasing tiller number to increase the production of grain-bearing stalks and thereby increasing yield of corn. Searching known databases for orthologs is well known and commonly practiced by the skilled artesian. Introducing frameshift mutations in gene coding sequences is well known to reduce or silence gene expression. One would have had a reasonable expectation of success introducing a frameshift mutation into a known gene, PILS6, using CRISPR to produce a plant with reduced or silenced gene expression.
Thus, the invention, as a whole, would be clearly prima facie obvious to one of ordinary skill in the art at the time the invention was made.
Summary
No claim is allowed.
Correspondence
Any inquiry concerning this communication or earlier communications from the Examiner should be directed to SUSAN MCCORMICK EWOLDT whose telephone number is (571)272-0981. The Examiner can normally be reached on M-TH 5:30-4.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, Applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
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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/SUSAN MCCORMICK EWOLDT/Primary Examiner, Art Unit 1661
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