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
1. The Office acknowledges the receipt of Applicant's election with traverse of Group I, claims 1-7 and the corresponding sequences of SEQ ID NO: 1 and 7 in the reply filed on August 05, 2025 is acknowledged. Upon further consideration the restriction is withdrawn. Claims 1-14, are pending. Claims 1-14, are examined in the instant application.
Applicants are advised that if any claims including all the limitations of an allowable claim examined here are presented in a continuation or divisional application, such claims may be subject to provisional statutory and/or nonstatutory double patenting rejections over the claims of the instant application. Once the restriction requirement is withdrawn, the provisions of 35 U.S.C. §121 are no longer applicable. See In re Ziegler, 443 F.2d 1211, 1215, 170 USPQ 129, 131–32 (CCPA 1971); see also MPEP §804.01.
Priority
2. Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). The certified copy has been filed in parent Application No. SE2150182-0, filed on February 19, 2021.
The certified copy is out of order and starts on the last page. Applicant is advised to resubmit a new copy starting on page 1.
Information Disclosure Statement
3. Initialed and dated copy of Applicant’s information disclosure statement (IDS) filed on July 27, 2023 is attached to the instant Office Action. The submission is in compliance with the provisions of 37 CFR 1.97. Accordingly, the information disclosure statement is being considered by the examiner.
Specification
4. The disclosure is objected to because of the following:
In page 2, line 19, the recitation of “abovementioned” is misspelled. It is advised to amend to -- above mentioned --.
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
In page 8, line 2,
In page 13, line 7,
In page 15, line 32, and
In page 47, line 6.
Applicant is reminded of the proper content of an abstract of the disclosure.
A patent abstract is a concise statement of the technical disclosure of the patent and should include that which is new in the art to which the invention pertains. The abstract should not refer to purported merits or speculative applications of the invention and should not compare the invention with the prior art.
If the patent is of a basic nature, the entire technical disclosure may be new in the art, and the abstract should be directed to the entire disclosure. If the patent is in the nature of an improvement in an old apparatus, process, product, or composition, the abstract should include the technical disclosure of the improvement. The abstract should also mention by way of example any preferred modifications or alternatives.
Where applicable, the abstract should include the following: (1) if a machine or apparatus, its organization and operation; (2) if an article, its method of making; (3) if a chemical compound, its identity and use; (4) if a mixture, its ingredients; (5) if a process, the steps.
Extensive mechanical and design details of an apparatus should not be included in the abstract. The abstract should be in narrative form and generally limited to a single paragraph within the range of 50 to 150 words in length.
See MPEP § 608.01(b) for guidelines for the preparation of patent abstracts.
This application does not contain an abstract of the disclosure as required by 37 CFR 1.72(b).
Applicant’s Abstract is the cover of the WIPO document. An abstract on a separate sheet is required.
Claim Rejections - 35 USC § 101
5. 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.
6. Claims 1-4 and 6-14, are rejected under 35 U.S.C. 101 because the claimed invention is directed to non-statutory subject matter. The claim(s) do not fall within at least one of the four categories of patent eligible subject matter because the claimed invention is directed to a natural phenomenon without conveying a “markedly different” characteristic. As described in MPEP § 2106, subsection III, Step 2A of the Office’s eligibility analysis is the first part of the Alice/Mayo test, i.e., the Supreme Court’s "framework for distinguishing patents that claim laws of nature, natural phenomena, and abstract ideas from those that claim patent-eligible applications of those concepts." Alice Corp. Pty. Ltd. v. CLS Bank Int'l, 573 U.S. 208, 217-18, 110 USPQ2d 1976, 1981 (2014) (citing Mayo, 566 U.S. at 77-78, 101 USPQ2d at 1967-68).
Step 2A asks: Is the claim directed to a law of nature, a natural phenomenon (product of nature) or an abstract idea? In the context of the flowchart in MPEP § 2106, subsection III. Claims 1-4 and 6-14, are directed to a plant cell/plant comprising a modified amino acid, in this case a decrease or inactivated expression of said protein, resulting in increased pathogen resistance and/or abiotic stress tolerance, falls within the judicial exception of a natural phenomenon or product of nature. The relevant prior art UniProt (A0A4D6L3K7_VIGUN. 2025 (U)), specifically discloses A0A4D6L3K7_VIGUN having 98% sequence identity to Applicants SEQ ID NO: 5. This establishes that SEQ ID NO: 5 is a naturally occurring protein found in Vigna unguiculata (Cowpea), (see alignments below). This 98% sequence identity drives home the point that the naturally occurring protein A0A4D6L3K7_VIGUN comprises the modifications, since claim 1 only requires “at least one part of the amino acid sequence has at least 78%... sequence identity to SEQ ID NO: 5 and wherein the protein comprises less than 200 amino acids.” As for the increase in pathogen resistance and/or abiotic stress tolerance, it is an inherent property due to the structure, since it already comprises the “modifications”. The claimed plant cell/plant comprising a modified amino acid sequence, in this case a decrease or inactivated expression of said protein, resulting in increased pathogen resistance and/or abiotic stress tolerance, does not possess “markedly different” characteristics from this naturally occurring example, besides it just being a form of delivery, (See MPEP 2106.04(c) and isolated DNA, Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576, 589-91, 106 USPQ2d 1972, 1978-79 (2013)). Therefore, the claim is directed to a judicial exception.
A0A4D6L3K7_VIGUN
ID A0A4D6L3K7_VIGUN Unreviewed; 145 AA.
AC A0A4D6L3K7;
DT 03-JUL-2019, integrated into UniProtKB/TrEMBL.
DT 03-JUL-2019, sequence version 1.
DT 02-APR-2025, entry version 10.
DE SubName: Full=Uncharacterized protein {ECO:0000313|EMBL:QCD83091.1};
GN ORFNames=DEO72_LG2g3434 {ECO:0000313|EMBL:QCD83091.1};
OS Vigna unguiculata (Cowpea).
OC Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC rosids; fabids; Fabales; Fabaceae; Papilionoideae; 50 kb inversion clade;
OC NPAAA clade; indigoferoid/millettioid clade; Phaseoleae; Vigna.
OX NCBI_TaxID=3917 {ECO:0000313|EMBL:QCD83091.1, ECO:0000313|Proteomes:UP000501690};
RN [1] {ECO:0000313|EMBL:QCD83091.1, ECO:0000313|Proteomes:UP000501690}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC TISSUE=Leaf {ECO:0000313|EMBL:QCD83091.1};
RA Xia Q., Zhang R., Dong Y.;
RT "An improved genome assembly and genetic linkage map for asparagus bean,
RT Vigna unguiculata ssp. sesquipedialis.";
RL Submitted (APR-2019) to the EMBL/GenBank/DDBJ databases.
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DR EMBL; CP039346; QCD83091.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A4D6L3K7; -.
DR EnsemblPlants; Vigun03g180800.1.v1.2; Vigun03g180800.1.v1.2; Vigun03g180800.v1.2.
DR Gramene; Vigun03g180800.1.v1.2; Vigun03g180800.1.v1.2; Vigun03g180800.v1.2.
DR OrthoDB; 785928at2759; -.
DR Proteomes; UP000501690; Chromosome vu03.
DR PANTHER; PTHR37182; F24J8.11 PROTEIN; 1.
DR PANTHER; PTHR37182:SF2; F24J8.11 PROTEIN; 1.
PE 4: Predicted;
FT REGION 1..63
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 86..145
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1..10
FT /note="Pro residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 11..35
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 39..50
FT /note="Low complexity"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 123..132
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
SQ SEQUENCE 145 AA; 15698 MW; 775F69FF21F070FD CRC64;
Query Match 98.4%; Score 63; Length 145;
Best Local Similarity 92.9%;
Matches 13; Conservative 1; Mismatches 0; Indels 0; Gaps 0;
Qy 1 AKVLASKRRKEAMK 14
||:|||||||||||
Db 112 AKILASKRRKEAMK 125
Step 2B asks: to determine if the claim as a whole amounts to significantly more than the exception itself? The claim does not recite additional elements that amount to significantly more that the natural phenomenon itself. The human intervention of isolating the gene and now placing it in a new form of delivery does not transform the exception into a patent-eligible application. The naturally occurring protein was disclosed comprising 98% sequence identity, therefore comprises modifications, structure, and inherent function. Furthermore, merely making minor, routine changes such as simple “addition, deletion, or substitution” to a naturally occurring product like said protein does not transform the exception into a patent-eligible application. The claimed elements merely provide a generic context for embodying the natural phenomenon without adding an inventive concept, (see MPEP 210604 (b) and (d)). Therefore, taking this approach the claim is directed to a naturally occurring product, that is not patent-eligible pursuant to the Supreme Court decision in Funk Bros. Seed Co. v. Kalo Inoculant Co.
In regard to claim 2, the claim is open for the amino acid sequence having at least 70% sequence identity to SEQ ID NO: 13 with the additional limitation of claim 1. UniProt teaches on A0A4D6L3K7_VIGUN which has at least 80% sequence identity to Applicants SEQ ID NO: 13, (see alignment below). Therefore, this natural protein the claim is directed to a naturally occurring product, that is not patent-eligible pursuant to the Supreme Court decision in Funk Bros. Seed Co. v. Kalo Inoculant Co.
Title: US-18-263-146-13
Perfect score: 183
Sequence: 1 EKKDPNVSGVLAKVLASKRRKEAMKESIAKLREKGKPV 38
Scoring table: BLOSUM62
Gapop 10.0 , Gapext 0.5
Searched: 1 seqs, 145 residues
Total number of hits satisfying chosen parameters: 1
Minimum DB seq length: 0
Maximum DB seq length: inf
Post-processing: Minimum Match 0%
Maximum Match 100%
Listing first 1 summaries
Database : AASEQ2_11132025_131005.pep:*
SUMMARIES
%
Result Query
No. Score Match Length DB ID Description
----------------------------------------------------------------------------
1 148 80.9 145 1 AASEQ2_11132025_131005
ALIGNMENTS
RESULT 1
AASEQ2_11132025_131005
Query Match 80.9%; Score 148; DB 1; Length 145;
Best Local Similarity 76.3%;
Matches 29; Conservative 5; Mismatches 4; Indels 0; Gaps 0;
Qy 1 EKKDPNVSGVLAKVLASKRRKEAMKESIAKLREKGKPV 38
|||||:||||:||:|||||||||||| : ||| :|| |
Db 101 EKKDPSVSGVMAKILASKRRKEAMKEEVEKLRARGKTV 138
In regard to claim 3, the claim is open for the amino acid sequence having at least 30% sequence identity to SEQ ID NO: 1 with the additional limitation of claims 1 and 2. UniProt teaches on A0A4D6L3K7_VIGUN which has at least 71% to Applicants SEQ ID NO: 1, (see alignment below). Therefore, this natural protein the claim is directed to a naturally occurring product, that is not patent-eligible pursuant to the Supreme Court decision in Funk Bros. Seed Co. v. Kalo Inoculant Co.
Title: US-18-263-146-1
Perfect score: 285
Sequence: 1 AARRPPPPPPTSEEKKDPNM..........MKESIAKLREKGKPVKEPSQ 56
Scoring table: BLOSUM62
Gapop 10.0 , Gapext 0.5
Searched: 1 seqs, 145 residues
Total number of hits satisfying chosen parameters: 1
Minimum DB seq length: 0
Maximum DB seq length: inf
Post-processing: Minimum Match 0%
Maximum Match 100%
Listing first 1 summaries
Database : AASEQ2_11132025_132325.pep:*
SUMMARIES
%
Result Query
No. Score Match Length DB ID Description
----------------------------------------------------------------------------
1 203 71.2 145 1 AASEQ2_11132025_132325
ALIGNMENTS
RESULT 1
AASEQ2_11132025_132325
Query Match 71.2%; Score 203; DB 1; Length 145;
Best Local Similarity 75.5%;
Matches 40; Conservative 6; Mismatches 5; Indels 2; Gaps 1;
Qy 1 AARRPPPPPPTSEEKKDPNMSGVMAKVLASKRRKEAMKESIAKLREKGKPVKE 53
||||||||||| |||||::||||||:|||||||||||| : ||| :|| | :
Db 90 AARRPPPPPPT--EKKDPSVSGVMAKILASKRRKEAMKEEVEKLRARGKTVNK 140
In regard to claim 7, since the naturally occurring modifications to the sequence falls in scope with the Applicant’s claims therefore the phenotype/function of increased pathogen resistance to Phytophthora infestans, Dickeya dadantii, and Alternaria solani, and wherein the abiotic stress tolerance comprises tolerance towards at least one abiotic stress selected from the group consisting of salt and drought, is inherent to the structure.
Claim Rejections - 35 USC § 112(a)(Written description)
7. 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.
8. Claims 1-14, 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.
Applicant’s disclosure is as follows.
Applicant transforms a plant cell by agrobacterium with pK2GW7 containing the full-length protein 72, (SEQ ID NO: 2, Amino acid) also known as thylakoid proteins, (see page 3 lines 5-24 and page 12 example 1). Transformed plants resulted in “transient overexpression of the 72 protein in the leaf tissue has thus made the leaf tissue more susceptible, i.e., less resistant, to infection by the pathogen P. infestans.”, (see page 14 lines 4-6). Applicant shows that silencing protein 72 “provided the leaf with increased resistance to P. infestans.”, (see example 1 page 15 lines 19-20). In example 2, Applicant shows that silencing of 72 protein (SEQ ID NO: 2 full-length amino acid) in Nicotiana benthamiana resulted in increased ROS production, (see page 14 lines 26-30). In example 3, Applicant shows a sequence alignment of SEQ ID NO: 5 being a common motif shared by other plants, (see pages 16-41). In example 3B, Applicant shows a sequence alignment of SEQ ID NO: 13 being a common motif shared by other plants, (see pages 42-43). In example 4, Applicant shows that silencing of 72 protein (SEQ ID NO: 2 full-length amino acid) in Nicotiana benthamiana resulted in increased resistance to Pseudomonas syringae, (see page 43 lines 9-24). In example 5, Applicant shows deletion of 72 protein (SEQ ID NO: 15 full-length amino acid) in Arabidopsis thaliana and Solanum tuberosum resulting in increased ROS production, (see page 44). In example 6, Applicant shows that silencing of 72 protein (SEQ ID NO: 2 full-length amino acid) in Nicotiana benthamiana resulted in increased resistance to Dickeya dadantii 3937 Soft rot bacteria, (see page 44 lines 26-30). In examples 7-9, Applicant shows that silencing of 72 protein (SEQ ID NO: 15 full-length amino acid) in Solanum tuberosum resulted in increased resistance to P. infestans late blight, Alternaria solani, and salt tolerance,(see pages 45-46).
Any gene with at least 78% sequence identity or fragment – Only shown full length sequences SEQ ID NO: 2 and 15.
The claimed invention lacks adequate written description for the following reasons. Claims 1 and 9, are directed to a plant cell and or plant comprising SEQ ID NO: 5 (also known as a motif of 72 protein), that was isolated from the natural occurring Nicotiana benthamiana plant which at least one part of the amino acid sequence has at least 78%, such as at least 85%, more preferably at least 90% sequence identity to SEQ ID NO: 5, and wherein the protein comprises less than 200 amino acids. Applicant shows a sequence alignment of SEQ ID NO: 5 being a common motif shared by other plants, (see pages 16-41). However, the Applicant only shows transforming and silencing the full-length sequence of 72 protein that results in said phenotype. Furthermore, Applicant has not adequately described what part or the size of said part, which can mean only a fragment of two amino acids. From the disclosure of SEQ ID NO: 5 one skilled in the art cannot predict the structures of other genes from other sources and their allelic variants or fragments having increased pathogen resistance and/or abiotic stress tolerance activity. Additionally, the 78%, 85%, and 90% sequence identity to SEQ ID NO: 5 encompasses genes obtained from sources other than Nicotiana benthamiana, whereby their structures and identities are not disclosed, so long as they share at least 78%, 85%, or 90% sequence identity to a portion of SEQ ID NO: 5 and having less than 200 amino acids. The claims encompass mutants, derivatives, fragments, and allelic variants of SEQ ID NO: 5 and thus imply that structural variants exist in nature, yet no structural variant has been disclosed having similar activity. The implication is that there is a gene and a protein other than that disclosed which exists in nature, but the structure thereof is not known, which also include polypeptides as small as dipeptides. Thus, there are insufficient relevant identifying characteristics to allow one skilled in the art to predictably determine such allelic variants or fragments of other 72 protein genes, that would result in similar phenotype especially given that SEQ ID NO: 5 is just a motif and not the full-length sequence, absent further guidance. Taken into consideration of BRI the fragments may be any size as small as a dipeptide only requiring at least one part of the amino acid sequence having at least 78% of SEQ ID NO: 5. Applicant has not adequately described or shown examples of said fragments effectively increased pathogen resistance and/or abiotic stress tolerance. Therefore, this suggests that 72 protein variants or fragments, may function differently if sequence and structure changes, showing the unpredictability of all variants or fragments at the time of filling. Applicant failed to disclose a representative number of species within the scope of the genus.
Moreover, while one skilled in the art can generate a population of sequences having at least 78%, 85%, or 90% sequence identity to SEQ ID NO: 5, it is unpredictable which species within the population would also have 72 protein activity, specifically fragments, where polypeptides structurally change resulting in a non-working polypeptide or functionally different. Especially since majority of the identified sequences in pages 16-41 are all uncharacterized showing that the state of the prior art at the time of filing has not been adequately described to allow on skilled in the art to replicate and produce a functional plant with said disclosure. For example, Hamel et al. (The Chloroplastic Protein THF1 Interacts with the Coiled-Coil Domain of the Disease Resistance Protein N' and Regulates Light-Dependent Cell Death. 2016. Plant physiology vol. 171,1: 658-74. doi:10.1104/pp.16.00234 (V)), teaches on Thylakoid Formation1 (THF1) protein which is known “to be involved in plant-pathogen interactions, as it is a direct target of the phytotoxin ToxA, a cell death-inducing protein of the necrotroph Pyrenophora tritici-repentis”, (see page 659 right column middle section). Hamel mentions that “the CC domains of I2-5, I2-28, and the L proteins did not induce strong cell death and did not affect THF1 levels more than Tm-2aCC, which did not induce cell death.”, (see page 664 and figure 6). Suggesting that not all thylakoid fragments induce disease resistance. Since it would cause undue burden to identify all sequence with 78% sequence identity or fragments with less than 200 amino acids it would not allow one skilled in the art to predictably produce a gene with said phenotype.
In regard to claims 2 and 10, and for the same reasons explained above Applicant has not adequately described an amino acid sequence in which at least one part of the amino acid sequence having at least 70%, 80%, or 90% sequence identity to SEQ ID NO: 13. Applicant has only shown knock-out of the full-length sequences having said phenotype.
In regard to claim 3, and for the same reasons explained above Applicant has not adequately described an amino acid sequence in which at least one part of the amino acid sequence having at least 30%, 40%, or 47% sequence identity to SEQ ID NO: 1. Applicant has only shown knock-out of the full-length sequences having said phenotype.
In regard to claims 4 and 11, and for the same reasons explained above Applicant has not adequately described an amino acid sequence in which at least one part of the amino acid sequence has at least 90%, 95%, or 99% sequence identity to SEQ ID NO: 7. Applicant has only shown knock-out of the full-length sequences having said phenotype.
Accordingly, there is lack of adequate description to inform a skilled artisan that Applicant was in possession of the claimed invention at the time of filing. See Written Description guidelines published in Federal Register/ Vol.66, No. 4/ Friday, January 5, 2001/ Notices; p. 1099-1111
Claim Rejections - 35 USC § 112(a)(Enablement)
9. Claims 1-14, are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for the Agrobacterium transformation and silencing a plant with SEQ ID NO: 2 or 15 (full-length 72 protein), resulting in Nicotiana benthamiana, Arabidopsis thaliana, and Solanum tuberosum having increased pathogen resistance against P. infestans, Pseudomonas syringae, Dickeya dadantii, and Alternaria solani, (see examples 1-2 and 4-9). Additionally, shown that knocking out the activity of 72 protein shows increase in ROS levels and increased salt tolerance. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
An “analysis of whether a particular claim is supported by the disclosure in an application requires a determination of whether that disclosure, when filed, contained sufficient information regarding the subject matter of the claims as to enable one skilled in the pertinent art to make and use the claimed invention.” MPEP 2164.01. “A conclusion of lack of enablement means that. . . the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed invention [i.e. commensurate scope] without undue experimentation.” In re Wright, 999 F.2d 1557,1562, 27 USPQ2d 1510, 1513 (Fed. Cir. 1993); MPEP 2164.01.
In In re Wands, 858 F.2d 731,8 USPQ2d 1400 (Fed. Cir. 1988), several factors implicated in determination of whether a disclosure satisfies the enablement requirement and whether any necessary experimentation is “undue” are identified. These factors include, but are not limited to:
(A) The breadth of the claims;
(B) The nature of the invention;
(C) The state of the prior art;
(D) The level of one of ordinary skill;
(E) The level of predictability in the art;
(F) The amount of direction provided by the inventor;
(G) The existence of working examples; and
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. In re Wands, 858 F.2d 731,737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988). No single factor is independently determinative of enablement; rather “[i]t is improper to conclude that a disclosure is not enabling based on an analysis of only one of the above factors while ignoring one or more of the others.” MPEP 2164.01. Likewise, all factors may not be relevant to the enablement analysis of any individual claim.
(1) The quantity of experimentation necessary, (3) The presence or absence of working examples, and (7) The predictability or unpredictability of the art
The claimed invention lacks adequate enabling experimentation for the following reasons. Claims 1-14, are directed to a plant or plant cell comprising SEQ ID NO: 5, 13, 1, or 7 conferring increased pathogen resistance and abiotic stress tolerance.
As stated in the written description rejection above, Applicant has provided enabling guidance for transforming Nicotiana benthamiana, Arabidopsis thaliana, and Solanum tuberosum plants with said SEQ ID NO: 2 and 15 and silencing SEQ ID NO: 2 and 15. Applicant has not adequately enabled or shown effectively transforming and/or silencing using having at least 78%, 85%, or 90% sequence identity to SEQ ID NO: 5, 70%, 80%, or 90% sequence identity to SEQ ID NO: 13, 30%, 40%, or 47% sequence identity to SEQ ID NO: 1, and/or 90%, 95%, 99% sequence identity to SEQ ID NO: 7 or fragments of said sequences.
The claimed invention lacks adequate enabling guidance for the following reasons. Claims 1 and 9, are directed to a plant cell and or plant comprising SEQ ID NO: 5 (also known as a motif of 72 protein), that was isolated from the natural occurring Nicotiana benthamiana plant which at least one part of the amino acid sequence has at least 78%, such as at least 85%, more preferably at least 90% sequence identity to SEQ ID NO: 5, and wherein the protein comprises less than 200 amino acids. Applicant shows a sequence alignment of SEQ ID NO: 5 being a common motif shared by other plants, (see pages 16-41). However, the Applicant only shows transforming and silencing the full-length sequence of 72 protein that results in said phenotype. Furthermore, Applicant has not adequately described what part or the size of said part, which can mean only a fragment of two amino acids. From the disclosure of SEQ ID NO: 5 (14 amino acids) one skilled in the art cannot predict the structures of other genes from other sources and their allelic variants or fragments having increased pathogen resistance and/or abiotic stress tolerance activity. Additionally, the 78%, 85%, and 90% sequence identity to SEQ ID NO: 5 encompasses genes obtained from sources other than Nicotiana benthamiana, whereby their structures and identities are not disclosed, so long as they share at least 78%, 85%, or 90% sequence identity to a portion of SEQ ID NO: 5 and having less than 200 amino acids. The claims encompass mutants, derivatives, fragments, and allelic variants of SEQ ID NO: 5 and thus imply that structural variants exist in nature, yet no structural variant has been disclosed having similar phenotypic activity. The implication is that there is a gene and a protein other than that disclosed which exists in nature, but the structure thereof is not known, which also include polypeptides as small as dipeptides. Thus, there are insufficient relevant identifying characteristics to allow one skilled in the art to predictably determine such allelic variants, sequences having at least 78%, 85%, or 90% sequence identity, or fragments of other 72 protein genes, that would result in similar phenotype especially given that SEQ ID NO: 5 is just a motif and not the full-length sequence, absent further guidance. Taken into consideration of BRI the fragments may be any size as small as a dipeptide only requiring at least one part of the amino acid sequence having at least 78% of SEQ ID NO: 5. Applicant has not adequately enabled or shown examples of said fragments effectively increased pathogen resistance and/or abiotic stress tolerance. Therefore, this suggests that 72 protein variants or fragments, may function differently if sequence and structure changes, showing the unpredictability of all variants or fragments at the time of filling. Applicant failed to disclose a representative number of species within the scope of the genus.
Moreover, while one skilled in the art can generate a population of sequences having at least 78%, 85%, or 90% sequence identity to SEQ ID NO: 5, it is unpredictable which species within the population would also have 72 protein activity, specifically fragments, where polypeptides structurally change resulting in a non-working polypeptide or functionally different. Especially, since majority of the identified sequences in pages 16-41 are all uncharacterized showing that the state of the prior art at the time of filing has not been adequately enabled to allow on skilled in the art to replicate and produce a functional plant with said disclosure. For example, Hamel et al. (The Chloroplastic Protein THF1 Interacts with the Coiled-Coil Domain of the Disease Resistance Protein N' and Regulates Light-Dependent Cell Death. 2016. Plant physiology vol. 171,1: 658-74. doi:10.1104/pp.16.00234 (V)), teaches on Thylakoid Formation1 (THF1) protein which is known “to be involved in plant-pathogen interactions, as it is a direct target of the phytotoxin ToxA, a cell death-inducing protein of the necrotroph Pyrenophora tritici-repentis”, (see page 659 right column middle section). Hamel mentions that “the CC domains of I2-5, I2-28, and the L proteins did not induce strong cell death and did not affect THF1 levels more than Tm-2aCC, which did not induce cell death.”, (see page 664 and figure 6). Suggesting that not all thylakoid fragments induce disease resistance. Since it would cause undue burden to identify all sequence with 78% sequence identity or fragments with less than 200 amino acids it would not allow one skilled in the art to predictably produce a gene with said phenotype, especially with SEQ ID NO: 5 that only contains 14 amino acids.
In regard to claims 2 and 10, and for the same reasons explained above Applicant has not adequately enabled an amino acid sequence in which at least one part of the amino acid sequence has at least 70%, 80%, or 90% sequence identity to SEQ ID NO: 13. Applicant has only shown knock-out of the full-length sequences having said phenotype.
In regard to claim 3, and for the same reasons explained above Applicant has not adequately enabled an amino acid sequence in which at least one part of the amino acid sequence has at least 30%, 40%, or 47% sequence identity to SEQ ID NO: 1. Applicant has only shown knock-out of the full-length sequences having said phenotype.
In regard to claims 4 and 11, and for the same reasons explained above Applicant has not adequately enabled an amino acid sequence in which at least one part of the amino acid sequence has at least 90%, 95%, or 99% sequence identity to SEQ ID NO: 7. Applicant has only shown knock-out of the full-length sequences having said phenotype.
Any type of modification – Only shown agrobacterium and virus-induced gene silencing (VIGS).
The claims are directed to any form of modification. The term “modifying the genome” is overly broad and could include any method of down-regulating or suppressing expression of an endogenous plant gene. The specification, however, provides guidance only for Agrobacterium-mediated and virus-induced gene silencing approaches targeting SEQ ID NO: 2 (the “72 protein”). Given the limited disclosure and the broad sequence identity ranges, the specification does not enable the full scope of the claimed invention.
There is insufficient written description and guidance. An unnecessary amount of undue experimentation would be needed to effectively transforming and/or silencing using having at least 78%, 85%, or 90% sequence identity to SEQ ID NO: 5, 70%, 80%, or 90% sequence identity to SEQ ID NO: 13, 30%, 40%, or 47% sequence identity to SEQ ID NO: 1, and/or 90%, 95%, 99% sequence identity to SEQ ID NO: 7 or fragments of said sequences, without enabling a representative number of variant species.
(4)The nature of the invention
The nature of the claimed invention is are directed to a plant or plant cell comprising SEQ ID NO: 5, 13, 1, or 7 conferring increased pathogen resistance and abiotic stress tolerance. Applicant has only enabled for transforming Nicotiana benthamiana, Arabidopsis thaliana, and Solanum tuberosum plants with said SEQ ID NO: 2 and 15 and silencing SEQ ID NO: 2 and 15. Applicant is not enabled transforming and/or silencing using having at least 78%, 85%, or 90% sequence identity to SEQ ID NO: 5, 70%, 80%, or 90% sequence identity to SEQ ID NO: 13, 30%, 40%, or 47% sequence identity to SEQ ID NO: 1, and/or 90%, 95%, 99% sequence identity to SEQ ID NO: 7 or fragments of said sequences.
(8) The breadth of the claims
The breadth of the claims encompass any sequence having at least having at least 78%, 85%, or 90% sequence identity to SEQ ID NO: 5, 70%, 80%, or 90% sequence identity to SEQ ID NO: 13, 30%, 40%, or 47% sequence identity to SEQ ID NO: 1, and/or 90%, 95%, 99% sequence identity to SEQ ID NO: 7 or fragments of said sequences that may be any size as small as a dipeptide. Applicant has only enabled for transforming Nicotiana benthamiana, Arabidopsis thaliana, and Solanum tuberosum plants with said SEQ ID NO: 2 and 15 and silencing SEQ ID NO: 2 and 15.
Given the lack of sufficient guidance, examples of operable embodiments, the state of the prior art, and unpredictability in the art, one skilled in the art cannot make and use the claimed invention as commensurate in scope with the claims without excessive burden and undue experimentation.
For at least this reason, the Specification does not teach a person with skill in the art how to make and/or use the subject matter within the full scope of these Claims.
Claim Rejections - 35 USC § 102
10. 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.
11. 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.
12. Claims 1-14, are rejected under 35 U.S.C. 102(a)(1) as being anticipated by La Rosa et al. (US 2004/0031072 A1(A)).
In regard to claims 1, 5, and 9, La Rosa teaches on a method of producing a plant/plant cell having increased disease resistance, (see claim 3 section d), and/or drought tolerance, (see claim 3 section c), using SEQ ID NO: 282493, (see Table 1 and claim 2), having 100% sequence identity to Applicants SEQ ID NO: 5 (Protein 72, Parakletos, or thylakoid protein), (see below). Furthermore, La Rosa teaches using site-directed mutagenesis, (see paragraphs [0030] and [0090]-[0091]), to reduce activity or expression, (see paragraphs [0030] and [0080]).
AFQ91316
ID AFQ91316 standard; protein; 155 AA.
XX
AC AFQ91316;
XX
DT 18-OCT-2007 (first entry)
XX
DE Glycine max protein SEQ ID NO:282493.
XX
KW plant; cold tolerance; heat tolerance; drought resistance;
KW herbicide resistance; pathogen resistance; pesticide resistance;
KW disease-resistance; crop improvement; insect resistance;
KW nitrogen fixation; plant growth regulation; plant disease;
KW stress tolerance; seed oil; transgenic.
XX
OS Glycine max.
XX
CC PN US2004031072-A1.
XX
CC PD 12-FEB-2004.
XX
CC PF 28-APR-2003; 2003US-00424599.
XX
PR 06-MAY-1999; 99US-00304517.
PR 05-NOV-2001; 2001US-00985678.
XX
CC PA (LROS/) LA ROSA T J.
CC PA (ZHOU/) ZHOU Y.
CC PA (KOVA/) KOVALIC D K.
CC PA (CAOY/) CAO Y.
XX
CC PI La Rosa TJ, Zhou Y, Kovalic DK, Cao Y;
XX
DR WPI; 2004-168999/16.
XX
CC PT New recombinant DNA construct, useful in producing plants with desired
CC PT properties, e.g. increased cold, heat or drought tolerance or tolerance
CC PT to herbicides, extreme osmotic conditions or pathogens and improved plant
CC PT growth and development.
XX
CC PS Claim 2; SEQ ID NO 282493; 15pp; English.
XX
CC The invention relates to a recombinant DNA construct, polynucleotides or
CC polypeptides which are useful in improving plant cold, heat or drought
CC tolerance or tolerance to herbicides, extreme osmotic conditions,
CC pathogens or pests, in improving yield by modification of photosynthesis
CC or of carbohydrate, nitrogen or phosphorus use and/or uptake, in
CC manipulating growth rate in plant cells by modification of the cell cycle
CC pathway, in providing increased resistance to plant disease and improved
CC plant growth and development under at least one stress condition, in
CC producing galactomannan, plant growth regulators and lignin, in
CC increasing the rate of homologous recombination in plants, in modifying
CC seed oil yield and/or content and seed protein yield and/or content and
CC in encoding a plant transcription factor. The present sequence represents
CC a Glycine max protein of the invention. Note: This sequence is not shown
CC in the specification but was obtained in electronic format directly from
CC USPTO at seqdata.uspto.gov/sequence.html.
XX
SQ Sequence 155 AA;
Query Match 100.0%; Score 64; Length 155;
Best Local Similarity 100.0%;
Matches 14; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 AKVLASKRRKEAMK 14
||||||||||||||
Db 117 AKVLASKRRKEAMK 130
In regard to claims 2 and 10, La Rosa teaches using SEQ ID NO: 282493 having at least 80% sequence identity to Applicants SEQ ID NO: 13, (see alignment below).
Query Match 86.3%; Score 158; Length 155;
Best Local Similarity 84.2%;
Matches 32; Conservative 3; Mismatches 3; Indels 0; Gaps 0;
Qy 1 EKKDPNVSGVLAKVLASKRRKEAMKESIAKLREKGKPV 38
|||||||||| ||||||||||||||| :|:| |:||||
Db 106 EKKDPNVSGVQAKVLASKRRKEAMKEEVARLIERGKPV 143
In regard to claim 3, La Rosa teaches using SEQ ID NO: 282493 having at least 74% sequence identity to Applicants SEQ ID NO: 1, (see alignment below).
Query Match 74.0%; Score 211; Length 155;
Best Local Similarity 82.4%;
Matches 42; Conservative 4; Mismatches 3; Indels 2; Gaps 1;
Qy 1 AARRPPPPPPTSEEKKDPNMSGVMAKVLASKRRKEAMKESIAKLREKGKPV 51
||||||||||| ||||||:||| ||||||||||||||| :|:| |:||||
Db 95 AARRPPPPPPT--EKKDPNVSGVQAKVLASKRRKEAMKEEVARLIERGKPV 143
In regard to claims 4 and 11, since Applicant states “preferably having at least 90%” it is not required for the sequence to have at least 90% sequence identity to SEQ ID NO: 7. Therefore, La Rosa teaches on SEQ ID NO: 139651 having at least 26% sequence identity to Applicants SEQ ID NO: 7.
In regard to claims 6 and 14, La Rosa teaches using “alfalfa, barley, millet, rice, tobacco, fruit and vegetable crops, and turf grass”, (see page 3 paragraphs [0021] and [0067]).
In regard to claims 7 and 12, La Rosa does not specifically teach on specifically having disease resistance to Phytophthora infestans, Dickeya dadantii, and Alternaria solani, and wherein the abiotic stress tolerance comprises tolerance towards at least one abiotic stress selected from the group consisting of salt and drought. However, the impact on pathogens and abiotic stress is inherent to the structure. Therefore, since it is known to improve disease resistance and abiotic stress it would inherently improve for both disease resistance to Phytophthora infestans, Dickeya dadantii, and Alternaria solani, and wherein the abiotic stress tolerance comprises tolerance towards at least one abiotic stress selected from the group consisting of salt and drought.
In regard to claims 8 and 13, La Rosa teaches on producing a plant, (see abstract and claim 3), and further states that “[t]ransformed plant cells comprising such exogenous genetic material may be regenerated to produce whole transformed plants”, (see paragraph [0067]).
Conclusion
13. No claims are allowed.
14. Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHRISTIAN JOSE ORDAZ whose telephone number is (703)756-1967. The examiner can normally be reached 8:30 am-5:00 pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad A Abraham can be reached on (571) 270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/C.J.O./Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663