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 .
Request for Suspension
Application on 03/16/2026 filed a request for suspension of action under 37 CFR § 1.103(c) for three months wherein the time has passed the suspension time till the June 25, 2026. The request filed 25 June 2026 is not acceptable because it was filed under 37 CFR § 1.103(c). If Applicants want to request an additional suspension, Applicants are advised to file a request for suspension of action under 37 CFR § 1.103(a) see MPEP § 709.
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 03/16/2026 has been entered.
Status of the Claims
The amendment filed 03/16/2026 has been entered. Claims 1, 4, and 6-29 are pending and are examined in this office action.
Rejection that are withdrawn
The 35 USC § 112 indefiniteness rejection has been withdrawn in light of applicant’s amendment of claim 6 to depend on claim 4.
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.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Obvious over Baum and further in view of Aziz, Merlo and Folkers, Puigbo, and Pardo-Lopez.
Claims 1, 4, 7 and 11-29 are rejected under 35 U.S.C. 103 as being unpatentable over Baum et al. (US Patent publication number: US 2016/0108426A1, published on 04/21/2016); and further in view of Aziz et al. (2012),Comparative study of cry1D gene expressed in E. coli and Baculovirus expression system; Submitted (09-APR-2012); Department of Biology, Universiti Pendidikan Sultan Idris, Faculty of Science and Mathematics, Tanjong Malim, Perak 35900, Malaysia, further in view of, Merlo and Folkerts (US Patent number: 6,166,302, published on 12/26/2000), further in view of Puigbo et al. 2007.OPTIMIZER: A web server utility that optimize a DNA or Protein sequence. Nucleic Acids Research, 35:W126-W131 (see IDS filed on 03/15/2023), and further in view of Pardo-Lopez et al., 2009, Strategies to improve the insecticidal activity of Cry toxins from Bacillus thuringiensis. Peptides, 30(3), 589-595.
The claims are drawn to a codon optimized nucleic acid molecule consisting of SEQ ID NO:1 and encoding a CRY1DA consisting of SEQ ID NO: 3. Claims are further drawn to a nucleic acid construct comprising the nucleic acid molecule. A vector, a host cell, a plant cell, a transgenic plant, comprising the nucleic acid molecule. The claims are further drawn to a cell transformation method comprising introducing into the cell the nucleic acid molecule wherein the nucleic acid molecule integrates into the cell genome and regenerating the transgenic plant from the plant cell. The claims are drawn to a method of producing a transgenic plant comprising transforming the plant cell with the nucleic acid molecule and selecting the plant cell transformed with the nucleic acid molecule. The claims are further drawn to wherein the transgenic plant, a monocotyledonous plant for example maize, rice, sorghum etc., is resistant to crop pests, an insect of the order Lepidoptera and species Spodoptera frugiperda and Diatrea saccharalis. The claims are further drawn to a method of controlling invertebrate pests in crop plants comprising the nucleic acid molecule which comprises planting seeds obtained from the plant in an area of cultivation of crop plants susceptible to invertebrate pests.
Regarding claim 1, Baum et al. teaches about synthesis of genes and their derivatives encoding engineered insecticidal protein and scaffold protein for expression in plant by avoiding ATTA and A/T rich plant sequences and preserving original amino acid sequences (Paragraph 0120 and 0121, Example 4). Instant application uses nucleotide sequence, SEQ ID NO: 2 which is originally isolated from B. thurengiensis to optimize the codon in Optimizer software. The SEQ ID NO: 2 is 99.8% identical to SEQ ID NO: 1 of instant application (see alignment below) which is nucleotide sequence encoding a Cry1Da1 protein taught by Baum et al. (Page 3, Paragraph 0023) suggesting both instant application and Baum et al. started optimizing same native sequences wherein instant application optimized known truncated sequence of Aziz et al. Baum further teaches their disclosed insecticidal proteins for example SEQ ID NO: 2 can be in truncated forms wherein one or more amino acids are deleted from the N-terminal end, C-terminal end, the middle of the protein, or combinations thereof without a loss of insect inhibitory activity and these fragments should retain the insect inhibitory activity of the parent engineered insecticidal protein (page 7, paragraph 0080).
Baum et al. does not teach codon optimized nucleic acid molecule encoding Cry1Da protein that consist of SEQ ID NO: 3 which is a truncated version of Baum’s SEQ ID NO: 2 and the truncation is in C-terminal end.
Furthermore, it was known in the art before the effective date of filing invention that the truncation of protein can improve the insecticidal activity of Cry toxins from Bacillus thuringiensis. Pardo-Lopez et al. teaches deletion of small fragments from amino-terminal region led to improved toxicity or overcome resistance representing interesting alternatives for insect pest control (page 589, Abstract and page 593).
Aziz et al. teaches a locus AFK29089 which has amino acid sequence which has 100% sequence identity to SEQ ID NO: 3 of the instant application where both has same size of 625 amino acid sequences as truncated protein (see alignment below). Aziz et al. define the locus as an active core crystal toxin protein 1D, from B. thuringiensis (see DEFINITION). Furthermore Aziz et al. teaches the sequence has been disclosed in the comparative study of cry1D gene expressed in E. coli and Baculovirus expression system (see TITLE). Aziz et al. teaches isolation source of the protein is commercial Bt based insecticide. Aziz et al. teaches region from amino acid sequence position 48-250 include a delta endotoxin, N-terminal domain (Endotoxin N), and 460-592, a C-terminal domain (Endotoxin C) and 258-450, an Endotoxin M domain (see the description of the locus below).
Applicant describes Bt gene present in construct were synthesized based on: presence of C-terminal (Endotoxin C), central domain (Endotoxin M) and N-terminal domain (Endotoxin N), size of the protein active core along with In silico detection of cry1Da protoxin hydrolysis site with trypsin or chymotrypsin enzymes (Spec, page 33-34, paragraph 0122). Applicant describes codon of the active core was modified – residues from aa 1-625 /1875 bp nucleotide originally isolated from B. thuringiensis (SEQ ID NO: 2) (Spec, page 34, paragraph 0123).
However, Baum et al. and Aziz et al. do not expressly teach about codon optimizing initially isolated strain of BT 1132C with CG content of 37.91% to a CG content of 63.8% in SEQ ID NO: 1 to make it compatible with maize (Spec, Page 34, Example 2, Paragraph 0123).
Further, in view codon optimization to GC content of 63.8% is known in the art. Merlo and Folkerts et al. teaches about optimizing another B. thuringiensis (BT) gene, Cry1A(c) and its truncated versions (Col. 23, lines 14-30), and teaches optimizing by changing of native codons with CG content of 37% to the maize genes of the GC content range of 45-75% where it teaches the range for expressing structural proteins is 48.6-70.5% with mean of 63.6% (Col 8, line 42-47, Table 1). Their optimized codons were 71% homologous to native BT nucleotide sequence encoding insecticidal plant protein (Col. 2, line 35-37) showing substantial changes. They further described the method they disclosed enables one skilled in the art to modify gene(s) that are foreign to a particular plant so that genes are optimally expressed in plants (Col 3, line 22-26).
Baum et al. does not teach about optimizing codon using freely available software “Optimizer”. Puigbo et al. teaches about the web server utility that optimizes a DNA or protein sequence. Puigbo et al. further teaches that "optimizer" software can be used to design any new genes that confer new metabolic capabilities in a given species (Page W130, first paragraph).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to optimize or adapt nucleotide constitution of CRY1DA gene taught by Baum et al. for content of GC and AT that is suitable for expression of protein in plants with teaching, suggestion, or motivation from prior arts (Aziz et al., Merlo and Folkerts et al. and Puigbo et al.). It would have led one of the ordinary skill to optimize the sequence based on suggestions provided by Baum et al. for sequence encoding native CRY1DA and their engineered derivatives. Pardo-Lopez further motivates to use a truncated protein for improving toxicity or overcome insect resistance as alternatives for insect pest control. Thus someone skilled in the art would use the known truncated protein with disclosed by Aziz et al. with its disclosed N, C and central domain information as active core crystal toxin protein 1D choosing from finite number of truncated proteins with such active core, upload it in the freely available software “OPTIMIZER” taught by Puigbo et al. for optimizing codons and optimizing genes conferring to express new metabolic capabilities that can efficiently expresses in plants based on the teaching of most suitable GC content of about 63% suggested by Merlo and Folkerts to obtain the predictable result of codon optimized CRY1DA nucleic acid molecule encoding a Cry1Da protein consisting of SEQ ID NO: 3, comprising a nucleic acid sequence of SEQ ID NO: 1.
Regarding claim 4, Baum et al. teaches the polynucleotide construct that encodes one or more of their engineered insect inhibitory proteins (Paragraph 0003, Line 7-9).
Baum et al. teaches the recombinant DNA constructs where the polynucleotide molecule is operably linked to genetic expression elements such as promoter (Paragraph 0084, line 3-9).
Regarding claim 7, Baum et al. teaches about the construct where a 3' UTR sequence is provided 3' of the coding sequence to facilitate termination of transcription. (Paragraph 0123, line 2-26).
Regarding claim 11, Baum et al. teaches the recombinant DNA construct is operably linked to regulatory sequences (Paragraph 0084, line 3-9).
Regarding claim 12, Baum et al. teaches the recombinant DNA construct which has plant multi-gene expression system, each expressing a different protein (i.e., construct comprising multiple nucleotide sequence for example a nucleotide sequence which is at least 70% identical to SEQ ID NO: 1 and SEQ ID No:10) (Paragraph 0086).
Regarding claim 13, Baum et al. teaches a transformation vector containing expression cassettes comprise a polynucleotide sequence designed for use in plant (Paragraph 0125, Example 6).
Regarding claim 14, Baum et al. teaches the plant or bacterial host cell comprising of optimized polynucleotide of SEQ ID NO:33, 35, 37 and 39 (Page 2, Paragraph 0012) (Page 120, claim 9).
Regarding claim 15, Baum et al. teaches the plant (e.g. corn, cotton) cells comprising of optimized SEQ ID NO:39 expressing engineered insect inhibitory protein Cry1Da1_7.nno (Page 14, Paragraph 0128, Paragraph 0132, claim 16).
Regarding claim 16, Baum et al. teaches the transgenic plant comprising of optimized nucleic acid sequence SEQ ID NO:39 expressing engineered insect inhibitory protein Cry1Da1_7.nno (Page 14, Paragraph 0128, Paragraph 0132, claim 16).
Regarding claim 17, Baum et al. teaches a method of transforming host cell which expresses the optimized polynucleotide encoding the insecticidal protein (Page 14, Example 6, Paragraph 0124, 0125, 0126).
Regarding claim 18, Baum et al. teaches the corn, cotton and soybean plant where the optimized polynucleotide encoding engineered insect inhibitory protein are integrated into genome resulting in increased resistance to lepidopteran insects in insect activity test (Page 14-15, Example 7, 8 and 9, Table 6,7, 8 and 9).
Regarding claim 19, Baum et al. teaches a method of producing transgenic plant which expresses the engineered polynucleotide encoding the insecticidal protein (Page 14, Example 6, Paragraph 0124, 0125, 0126).
Regarding claim 20, Baum et al. teaches method of selecting transformed events expressing engineered protein Cry1Da1_7.nno (Page 14, Paragraph 0133; Page 13, Paragraph 0136).
Regarding claim 21, Baum et al. teaches a method of making transgenic plants that comprised the engineered polynucleotide encoding insecticidal protein, where plant are derived from the plant cell by regeneration. (Page 8, Paragraph 0089).
Regarding claim 22, Baum et al. teaches crops (e.g. corn, cotton and soybean) where the engineered polynucleotide are integrated into genome resulting in increased resistance to lepidopteran insects (Page 14-15, Example 7, 8 and 9, Table 6,7, 8 and 9).
Regarding claim 23, Baum et al. teaches method of producing host cell comprising the engineered polynucleotide where host cell includes monocots (Page 2, Paragraph 0012). Baum et al further give example of method of generation of transgenic plant of maize (i.e., corn) which is monocot (Page14, Example 7).
Regarding claim 24, Baum et al. teaches method of generation of transgenic plant of maize which is monocot (Page14, Example 7) and further give example for method can be carried out in sugarcane (Paragraph 0007), sorghum, wheat or grass (i.e., Brachiaria) (Paragraph 0088).
Regarding claim 25, Baum et al. teaches method produces the transgenic plants resistant to insect crop pests (Page 14-15, Example 7, 8 and 9).
Regarding claim 26, Baum et al. teaches method produces the transgenic plants resistant to insect pests from order Lepidoptera (Page 14-15, Example 7, 8 and 9).
Regarding claim 27, Baum et al. teaches the encoded protein are active against Spodoptera frugiperda (Page 5, Paragraph 0073).
Regarding claim 28, Baum et al. teaches the encoded protein are active against Diatrea saccharalis. (Page 5, Paragraph 0073).
Regarding claim 29, Baum et al. teaches a method of producing a seed comprising optimized polynucleotide encoding engineered insecticidal protein, the method comprise planting seeds (Page 3, Paragraph 0017). Baum et al. discloses the method for controlling a Lepidopteran insect, comprising exposing the pest to the transgenic plant (Page 2, Paragraph 0016).
Obvious over Baum and further in view of Aziz, Gelvin, Merlo and Folkerts, Puigbo
Claims 1, 4, and 6-10 are rejected under 35 U.S.C. 103 as being unpatentable over Baum et al., and further in view of Aziz et al., further in view of Gelvin et al. (US Patent publication number: US 2004/0152197A1, Application number: US/14884432, published in 08/05/2004)), further in view of Merlo and Folkerts; further in view of Puigbo et al.
Claims are drawn to a codon optimized CRY1DA nucleic acid molecule comprising a nucleic acid molecule defined as SEQ ID NO.1 which encodes a Cry1Da protein consisting of SEQ ID NO: 3. Claims are further drawn to a nucleic acid construct that comprises of a maize ubiquitin gene promotor sequence, a 3’ UTR terminator sequence called nopaline synthase gene terminator sequence, a selection gene, a duplicated CaMV 35S gene promotor sequence and Tvsp gene terminator.
Regarding claim 4, Baum et al. teaches the polynucleotide construct that encodes one or more of the engineered insect inhibitory proteins (Paragraph 0003, Line 7-9).
Baum et al. teaches the recombinant DNA constructs where the polynucleotide molecule is operably linked to genetic expression elements such as promoter (Paragraph 0084, line 3-9).
Regarding claim 6, Baum et al. teaches about the recombinant DNA constructs where the polynucleotide molecule is operably linked to genetic expression elements such as promoter (Paragraph 0084, line 3-9).
Baum et al. does not expressly teach that the promotor sequence is maize ubiquitin gene promotor sequence.
Further in view, Gelvin et al. teaches about using maize ubiquitin promoter for expression of genes in recombinant construct (Page 9, paragraph 0098). It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use maize ubiquitin promoter in their construct taught by Gelvin et al. to obtain predictable result of enhanced plant cell transformation optimized for plants.
Regarding claim 7, Baum et al. teaches about the construct where a 3' UTR sequence is provided 3' of the coding sequence to facilitate termination of transcription. (Paragraph 0123, line 2-26).
Regarding claim 8, Baum et al. teaches the construct comprises transcriptional termination sequences (Paragraph 0123).
Baum et al. does not expressly teach that the terminator sequence is nopaline synthase gene terminator sequence.
Gelvin et al. teaches about a recombinant construct which include nopaline synthase terminator, a 3'NOS fused to the 3' region (Page 5, Paragraph 0069) for enhanced plant cell transformation).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use nopaline synthase terminator in their construct taught by Gelvin et al. to obtain predictable result of enhanced plant cell transformation optimized for plants.
Regarding claim 9, Baum et al. teaches the construct comprises multiple promoter element, enhancer elements or other expression elements known to those of ordinary skill in the art operably linked to boost the expression of the transgenes and terminator sequences (Paragraph 0123). It further teaches for making transgenic plants requires selecting a plant derived from the plant cell that expresses an insect or lepidoptera - inhibitory amount of engineered insecticidal protein (Paragraph 0089, line 3-11).
Baum et al. does not expressly teach that the construct comprises a selection gene. Gelvin et al. teaches a kanamycin resistance gene (Page 5, Paragraph 0068) and hygromycin resistance gene (Page 5, paragraph 0069) for plant selection linked to the recombinant construct. It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use selection genes taught by Gelvin et al. to obtain predictable result of efficiently selecting the integrated transgene.
Regarding claim 10, Baum et al. teaches the construct comprises multiple promoter elements (Paragraph 0123).
Baum et al. does not expressly teach that the construct comprises duplicated CaMV 35S gene promoter sequence and Tvsp gene terminator sequence.
Gelvin et al. teaches about the CaMV 35S promotor (double promotor region) in the construct to drive the screenable markers and reporter gene. (Page 9, paragraph 0103). Gelvin et al. further teaches the Tvsp gene terminator which encodes for soybean vegetative storage protein is included in the recombinant construct (Page 10, paragraph 0103, Page 4, Paragraph 0058, FIG. 10).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to use duplicated CaMV 35S gene promoter sequence and Tvsp gene terminator sequence taught by Gelvin et al. to obtain predictable result of enhanced plant cell transformation optimized for plants.
Sequence alignment with SEQ ID NO: 3 to Uniprot database:
I3RS06_BACTU
ID I3RS06_BACTU Unreviewed; 625 AA.
AC I3RS06;
DT 05-SEP-2012, integrated into UniProtKB/TrEMBL.
DT 05-SEP-2012, sequence version 1.
DT 25-MAY-2022, entry version 34.
DE RecName: Full=Crystaline entomocidal protoxin {ECO:0000256|ARBA:ARBA00029653};
DE Flags: Fragment;
OS Bacillus thuringiensis.
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus cereus group.
OX NCBI_TaxID=1428 {ECO:0000313|EMBL:AFK29089.1};
RN [1] {ECO:0000313|EMBL:AFK29089.1}
RP NUCLEOTIDE SEQUENCE.
RC STRAIN=Aizawai {ECO:0000313|EMBL:AFK29089.1};
RA Abdul Aziz H., Wei Hong L., Yusoff K.;
RT "Comparative study of cry1D gene expressed in E. coli and Baculovirus
RT expression system.";
RL Submitted (APR-2012) to the EMBL/GenBank/DDBJ databases.
CC -!- SIMILARITY: Belongs to the delta endotoxin family.
CC {ECO:0000256|ARBA:ARBA00007819}.
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DR EMBL; JQ910166; AFK29089.1; -; Genomic_DNA.
DR SMR; I3RS06; -.
DR GO; GO:0005102; F:signaling receptor binding; IEA:InterPro.
DR GO; GO:0090729; F:toxin activity; IEA:UniProtKB-KW.
DR GO; GO:0001897; P:cytolysis by symbiont of host cells; IEA:InterPro.
DR GO; GO:0030435; P:sporulation resulting in formation of a cellular spore; IEA:UniProtKB-KW.
DR Gene3D; 1.20.190.10; -; 1.
DR Gene3D; 2.100.10.10; -; 1.
DR InterPro; IPR008979; Galactose-bd-like_sf.
DR InterPro; IPR038979; Pest_crys.
DR InterPro; IPR005638; Pest_crys_C.
DR InterPro; IPR005639; Pest_crys_N.
DR InterPro; IPR036716; Pest_crys_N_sf.
DR InterPro; IPR001178; Pest_cryst_cen_dom.
DR InterPro; IPR036399; Pest_cryst_cen_dom_sf.
DR PANTHER; PTHR37003; PTHR37003; 1.
DR Pfam; PF03944; Endotoxin_C; 1.
DR Pfam; PF00555; Endotoxin_M; 1.
DR Pfam; PF03945; Endotoxin_N; 1.
DR SUPFAM; SSF49785; SSF49785; 1.
DR SUPFAM; SSF51096; SSF51096; 1.
DR SUPFAM; SSF56849; SSF56849; 1.
PE 3: Inferred from homology;
KW Sporulation {ECO:0000256|ARBA:ARBA00022969};
KW Toxin {ECO:0000256|ARBA:ARBA00022656};
KW Virulence {ECO:0000256|ARBA:ARBA00023026}.
FT DOMAIN 48..250
FT /note="Endotoxin_N"
FT /evidence="ECO:0000259|Pfam:PF03945"
FT DOMAIN 258..450
FT /note="Endotoxin_M"
FT /evidence="ECO:0000259|Pfam:PF00555"
FT DOMAIN 460..592
FT /note="Endotoxin_C"
FT /evidence="ECO:0000259|Pfam:PF03944"
FT NON_TER 625
FT /evidence="ECO:0000313|EMBL:AFK29089.1"
SQ SEQUENCE 625 AA; 70313 MW; 1408C676E64E4C3D CRC64;
Query Match 100.0%; Score 3242; DB 106; Length 625;
Best Local Similarity 100.0%;
Matches 625; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MEINNQNQCVPYNCLSNPKEIILGEERLETGNTVADISLGLINFLYSNFVPGGGFIVGLL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MEINNQNQCVPYNCLSNPKEIILGEERLETGNTVADISLGLINFLYSNFVPGGGFIVGLL 60
Qy 61 ELIWGFIGPSQWDIFLAQIEQLISQRIEEFARNQAISRLEGLSNLYKVYVRAFSDWEKDP 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ELIWGFIGPSQWDIFLAQIEQLISQRIEEFARNQAISRLEGLSNLYKVYVRAFSDWEKDP 120
Qy 121 TNPALREEMRIQFNDMNSALITAIPLFRVQNYEVALLSVYVQAANLHLSILRDVSVFGER 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TNPALREEMRIQFNDMNSALITAIPLFRVQNYEVALLSVYVQAANLHLSILRDVSVFGER 180
Qy 181 WGYDTATINNRYSDLTSLIHVYTNHCVDTYNQGLRRLEGRFLSDWIVYNRFRRQLTISVL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 WGYDTATINNRYSDLTSLIHVYTNHCVDTYNQGLRRLEGRFLSDWIVYNRFRRQLTISVL 240
Qy 241 DIVAFFPNYDIRTYPIQTATQLTREVYLDLPFINENLSPAASYPTFSAAESAIIRSPHLV 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 DIVAFFPNYDIRTYPIQTATQLTREVYLDLPFINENLSPAASYPTFSAAESAIIRSPHLV 300
Qy 301 DFLNSFTIYTDSLARYAYWGGHLVNSFRTGTTTNLIRSPLYGREGNTERPVTITASPSVP 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 DFLNSFTIYTDSLARYAYWGGHLVNSFRTGTTTNLIRSPLYGREGNTERPVTITASPSVP 360
Qy 361 IFRTLSYITGLDNSNPVAGIEGVEFQNTISRSIYRKSGPIDSFSELPPQDASVSPAIGYS 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 IFRTLSYITGLDNSNPVAGIEGVEFQNTISRSIYRKSGPIDSFSELPPQDASVSPAIGYS 420
Qy 421 HRLCHATFLERISGPRIAGTVFSWTHRSASPTNEVSPSRITQIPWVKAHTLASGASVIKG 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 HRLCHATFLERISGPRIAGTVFSWTHRSASPTNEVSPSRITQIPWVKAHTLASGASVIKG 480
Qy 481 PGFTGGDILTRNSMGELGTLRVTFTGRLPQSYYIRFRYASVANRSGTFRYSQPPSYGISF 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 PGFTGGDILTRNSMGELGTLRVTFTGRLPQSYYIRFRYASVANRSGTFRYSQPPSYGISF 540
Qy 541 PKTMDAGEPLTSRSFAHTTLFTPITFSRAQEEFDLYIQSGVYIDRIEFIPVTATFEAEYD 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 PKTMDAGEPLTSRSFAHTTLFTPITFSRAQEEFDLYIQSGVYIDRIEFIPVTATFEAEYD 600
Qy 601 LERAQKVVNALFTSTNQLGLKTDVT 625
|||||||||||||||||||||||||
Db 601 LERAQKVVNALFTSTNQLGLKTDVT 625
Sequence alignment to SEQ ID NO: 1 to published application database:
US-14-884-432-1; Sequence 1, Application US/14884432
; Patent No. 10059959
; GENERAL INFORMATION
; APPLICANT: Monsanto Technology LLC
; APPLICANT:Baum, James A.
; APPLICANT:Cerruti, Thomas
; APPLICANT:Flasinski, Stanislaw
; APPLICANT:Fu, Xiaoran
; APPLICANT:Howe, Arlene R.
; APPLICANT:Salvador, Sara
; TITLE OF INVENTION: Lepidopteran-Active Cry1Da1 Amino Acid Sequence Variant Proteins
; FILE REFERENCE: P34223US02
; CURRENT APPLICATION NUMBER: US/14/884,432
; CURRENT FILING DATE: 2015-10-15
; PRIOR APPLICATION NUMBER: US 62/064,994
; PRIOR FILING DATE: 2014-10-16
; PRIOR APPLICATION NUMBER: US 62/065,017
; PRIOR FILING DATE: 2014-10-17
; NUMBER OF SEQ ID NOS: 44
; SOFTWARE: PatentIn version 3.5
; SEQ ID NO 1
; LENGTH: 3498
; TYPE: DNA
; ORGANISM: Bacillus thuringiensis
; FEATURE:
; NAME/KEY: misc_feature
; LOCATION: (1)..(3498)
; OTHER INFORMATION: Nucleotide sequence used for expression in a bacterial cell
; OTHER INFORMATION:encoding Cry1Da1.
US-14-884-432-1
Query Match 99.8%; Score 1873.8; DB 1; Length 3498;
Best Local Similarity 99.9%;
Matches 1875; Conservative 0; Mismatches 2; Indels 0; Gaps 0;
Qy 1 ATGGAAATAAATAATCAAAACCAATGTGTGCCTTACAATTGTTTAAGTAATCCTAAGGAG 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 ATGGAAATAAATAATCAAAACCAATGTGTGCCTTACAATTGTTTAAGTAATCCTAAGGAG 60
Qy 61 ATAATATTAGGCGAGGAAAGGCTAGAAACAGGGAATACTGTAGCAGACATTTCATTAGGG 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ATAATATTAGGCGAGGAAAGGCTAGAAACAGGGAATACTGTAGCAGACATTTCATTAGGG 120
Qy 121 CTTATTAATTTTCTATATTCTAATTTTGTACCAGGAGGAGGATTTATAGTAGGTTTACTA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 CTTATTAATTTTCTATATTCTAATTTTGTACCAGGAGGAGGATTTATAGTAGGTTTACTA 180
Qy 181 GAATTAATATGGGGATTTATAGGGCCTTCGCAATGGGATATTTTTTTAGCTCAAATTGAG 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 GAATTAATATGGGGATTTATAGGGCCTTCGCAATGGGATATTTTTTTAGCTCAAATTGAG 240
Qy 241 CAATTGATTAGTCAAAGAATAGAAGAATTTGCTAGGAATCAGGCAATTTCAAGATTGGAG 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 CAATTGATTAGTCAAAGAATAGAAGAATTTGCTAGGAATCAGGCAATTTCAAGATTGGAG 300
Qy 301 GGGCTAAGCAATCTTTATAAGGTCTATGTTAGAGCGTTTAGCGACTGGGAGAAAGATCCT 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 GGGCTAAGCAATCTTTATAAGGTCTATGTTAGAGCGTTTAGCGACTGGGAGAAAGATCCT 360
Qy 361 ACTAATCCTGCTTTAAGGGAAGAAATGCGTATACAATTTAATGACATGAATAGTGCTCTC 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 ACTAATCCTGCTTTAAGGGAAGAAATGCGTATACAATTTAATGACATGAATAGTGCTCTC 420
Qy 421 ATAACGGCTATTCCACTTTTTAGAGTTCAAAATTATGAAGTTGCTCTTTTATCTGTATAT 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 ATAACGGCTATTCCACTTTTTAGAGTTCAAAATTATGAAGTTGCTCTTTTATCTGTATAT 480
Qy 481 GTTCAAGCCGCAAACTTACATTTATCTATTTTAAGGGATGTTTCAGTTTTCGGAGAAAGA 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 GTTCAAGCCGCAAACTTACATTTATCTATTTTAAGGGATGTTTCAGTTTTCGGAGAAAGA 540
Qy 541 TGGGGATATGATACAGCGACTATCAATAATCGCTATAGTGATCTGACTAGCCTTATTCAT 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 TGGGGATATGATACAGCGACTATCAATAATCGCTATAGTGATCTGACTAGCCTTATTCAT 600
Qy 601 GTTTATACTAACCATTGTGTGGATACGTATAATCAGGGATTAAGGCGTTTGGAAGGTCGT 660
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 601 GTTTATACTAACCATTGTGTGGATACGTATAATCAGGGATTAAGGCGTTTGGAAGGTCGT 660
Qy 661 TTTCTTAGCGATTGGATTGTATATAATCGTTTCCGGAGACAATTGACAATTTCAGTATTA 720
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 661 TTTCTTAGCGATTGGATTGTATATAATCGTTTCCGGAGACAATTGACAATTTCAGTATTA 720
Qy 721 GATATTGTTGCGTTTTTTCCAAATTATGATATTAGAACATATCCAATTCAAACAGCTACT 780
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 721 GATATTGTTGCGTTTTTTCCAAATTATGATATTAGAACATATCCAATTCAAACAGCTACT 780
Qy 781 CAGCTAACGAGGGAAGTCTATCTGGATTTACCTTTTATTAATGAAAATCTTTCTCCTGCA 840
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 781 CAGCTAACGAGGGAAGTCTATCTGGATTTACCTTTTATTAATGAAAATCTTTCTCCTGCA 840
Qy 841 GCAAGCTATCCAACCTTTTCAGCTGCTGAAAGTGCTATAATTAGAAGTCCTCATTTAGTA 900
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 841 GCAAGCTATCCAACCTTTTCAGCTGCTGAAAGTGCTATAATTAGAAGTCCTCATTTAGTA 900
Qy 901 GACTTTTTAAATAGCTTTACCATTTATACAGATAGTCTGGCACGTTATGCATATTGGGGA 960
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 901 GACTTTTTAAATAGCTTTACCATTTATACAGATAGTCTGGCACGTTATGCATATTGGGGA 960
Qy 961 GGGCACTTGGTAAATTCTTTCCGCACAGGAACCACTACTAATTTGATAAGATCCCCTTTA 1020
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 961 GGGCACTTGGTAAATTCTTTCCGCACAGGAACCACTACTAATTTGATAAGATCCCCTTTA 1020
Qy 1021 TATGGAAGGGAAGGAAATACAGAGCGCCCCGTAACTATTACCGCATCACCTAGCGTACCA 1080
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1021 TATGGAAGGGAAGGAAATACAGAGCGCCCCGTAACTATTACCGCATCACCTAGCGTACCA 1080
Qy 1081 ATATTTAGAACACTTTCATATATTACAGGCCTTGACAATTCAAATCCTGTAGCTGGAATC 1140
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1081 ATATTTAGAACACTTTCATATATTACAGGCCTTGACAATTCAAATCCTGTAGCTGGAATC 1140
Qy 1141 GAGGGAGTGGAATTCCAAAATACTATAAGTAGAAGTATCTATCGTAAAAGCGGTCCAATA 1200
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1141 GAGGGAGTGGAATTCCAAAATACTATAAGTAGAAGTATCTATCGTAAAAGCGGTCCAATA 1200
Qy 1201 GATTCTTTTAGTGAATTACCACCTCAAGATGCCAGCGTATCTCCTGCAATTGGGTATAGT 1260
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1201 GATTCTTTTAGTGAATTACCACCTCAAGATGCCAGCGTATCTCCTGCAATTGGGTATAGT 1260
Qy 1261 CACCGTTTATGCCATGCAACATTTTTAGAACGGATTAGTGGACCAAGAATAGCAGGCACC 1320
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1261 CACCGTTTATGCCATGCAACATTTTTAGAACGGATTAGTGGACCAAGAATAGCAGGCACC 1320
Qy 1321 GTATTTTCTTGGACACACCGTAGTGCCAGCCCTACTAATGAAGTAAGTCCATCTAGAATT 1380
|||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Db 1321 GTATTTTCTTGGACACACCGTAGTGCCAGCCCTACTAACGAAGTAAGTCCATCTAGAATT 1380
Qy 1381 ACACAAATTCCATGGGTAAAGGCGCATACTCTTGCATCTGGTGCCTCCGTCATTAAAGGT 1440
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1381 ACACAAATTCCATGGGTAAAGGCGCATACTCTTGCATCTGGTGCCTCCGTCATTAAAGGT 1440
Qy 1441 CCTGGATTTACAGGTGGAGATATTCTGACTAGGAATAGTATGGGCGAGCTGGGGACCTTA 1500
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1441 CCTGGATTTACAGGTGGAGATATTCTGACTAGGAATAGTATGGGCGAGCTGGGGACCTTA 1500
Qy 1501 CGAGTAACCTTCACAGGAAGATTACCACAAAGTTATTATATACGTTTCCGTTATGCTTCG 1560
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1501 CGAGTAACCTTCACAGGAAGATTACCACAAAGTTATTATATACGTTTCCGTTATGCTTCG 1560
Qy 1561 GTAGCAAATAGGAGTGGTACATTTAGATATTCACAGCCACCTTCGTATGGAATTTCATTT 1620
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1561 GTAGCAAATAGGAGTGGTACATTTAGATATTCACAGCCACCTTCGTATGGAATTTCATTT 1620
Qy 1621 CCAAAAACTATGGACGCAGGTGAACCACTAACATCTCGTTCGTTCGCTCATACAACACTC 1680
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1621 CCAAAAACTATGGACGCAGGTGAACCACTAACATCTCGTTCGTTCGCTCATACAACACTC 1680
Qy 1681 TTCACTCCAATAACCTTTTCACGAGCTCAAGAAGAATTTGATCTATACATCCAATCGGGT 1740
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1681 TTCACTCCAATAACCTTTTCACGAGCTCAAGAAGAATTTGATCTATACATCCAATCGGGT 1740
Qy 1741 GTTTATATAGATCGAATTGAATTTATACCGGTTACTGCAACATTTGAGGCAGAATATGAT 1800
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1741 GTTTATATAGATCGAATTGAATTTATACCGGTTACTGCAACATTTGAGGCAGAATATGAT 1800
Qy 1801 TTAGAAAGAGCGCAAAAGGTGGTGAATGCCCTGTTTACGTCTACAAACCAACTAGGGCTA 1860
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1801 TTAGAAAGAGCGCAAAAGGTGGTGAATGCCCTGTTTACGTCTACAAACCAACTAGGGCTA 1860
Qy 1861 AAAACAGATGTGACGTA 1877
||||||||||||||| |
Db 1861 AAAACAGATGTGACGGA 1877
Sequence alignment with SEQ ID NO: 3 to published application database for full length amino acid sequence.
RESULT 6
US-14-884-432-2
; Sequence 2, Application US/14884432
; Publication No. US20160108426A1
; GENERAL INFORMATION
; APPLICANT: Monsanto Technology LLC
; APPLICANT:Baum, James A.
; APPLICANT:Cerruti, Thomas
; APPLICANT:Flasinski, Stanislaw
; APPLICANT:Fu, Xiaoran
; APPLICANT:Howe, Arlene R.
; APPLICANT:Salvador, Sara
; TITLE OF INVENTION: Lepidopteran-Active Cry1Da1 Amino Acid Sequence Variant Proteins
; FILE REFERENCE: P34223US02
; CURRENT APPLICATION NUMBER: US/14/884,432
; CURRENT FILING DATE: 2015-10-15
; PRIOR APPLICATION NUMBER: US 62/064,994
; PRIOR FILING DATE: 2014-10-16
; PRIOR APPLICATION NUMBER: US 62/065,017
; PRIOR FILING DATE: 2014-10-17
; NUMBER OF SEQ ID NOS: 44
; SOFTWARE: PatentIn version 3.5
; SEQ ID NO 2
; LENGTH: 1165
; TYPE: PRT
; ORGANISM: Bacillus thuringiensis
; FEATURE:
; NAME/KEY: MISC_FEATURE
; LOCATION: (1)..(1165)
; OTHER INFORMATION: Amino acid sequence of the protein Cry1Da1.
US-14-884-432-2
Query Match 100.0%; Score 3242; DB 14; Length 1165;
Best Local Similarity 100.0%;
Matches 625; Conservative 0; Mismatches 0; Indels 0; Gaps 0;
Qy 1 MEINNQNQCVPYNCLSNPKEIILGEERLETGNTVADISLGLINFLYSNFVPGGGFIVGLL 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MEINNQNQCVPYNCLSNPKEIILGEERLETGNTVADISLGLINFLYSNFVPGGGFIVGLL 60
Qy 61 ELIWGFIGPSQWDIFLAQIEQLISQRIEEFARNQAISRLEGLSNLYKVYVRAFSDWEKDP 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 ELIWGFIGPSQWDIFLAQIEQLISQRIEEFARNQAISRLEGLSNLYKVYVRAFSDWEKDP 120
Qy 121 TNPALREEMRIQFNDMNSALITAIPLFRVQNYEVALLSVYVQAANLHLSILRDVSVFGER 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TNPALREEMRIQFNDMNSALITAIPLFRVQNYEVALLSVYVQAANLHLSILRDVSVFGER 180
Qy 181 WGYDTATINNRYSDLTSLIHVYTNHCVDTYNQGLRRLEGRFLSDWIVYNRFRRQLTISVL 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 WGYDTATINNRYSDLTSLIHVYTNHCVDTYNQGLRRLEGRFLSDWIVYNRFRRQLTISVL 240
Qy 241 DIVAFFPNYDIRTYPIQTATQLTREVYLDLPFINENLSPAASYPTFSAAESAIIRSPHLV 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 DIVAFFPNYDIRTYPIQTATQLTREVYLDLPFINENLSPAASYPTFSAAESAIIRSPHLV 300
Qy 301 DFLNSFTIYTDSLARYAYWGGHLVNSFRTGTTTNLIRSPLYGREGNTERPVTITASPSVP 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 DFLNSFTIYTDSLARYAYWGGHLVNSFRTGTTTNLIRSPLYGREGNTERPVTITASPSVP 360
Qy 361 IFRTLSYITGLDNSNPVAGIEGVEFQNTISRSIYRKSGPIDSFSELPPQDASVSPAIGYS 420
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 361 IFRTLSYITGLDNSNPVAGIEGVEFQNTISRSIYRKSGPIDSFSELPPQDASVSPAIGYS 420
Qy 421 HRLCHATFLERISGPRIAGTVFSWTHRSASPTNEVSPSRITQIPWVKAHTLASGASVIKG 480
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 421 HRLCHATFLERISGPRIAGTVFSWTHRSASPTNEVSPSRITQIPWVKAHTLASGASVIKG 480
Qy 481 PGFTGGDILTRNSMGELGTLRVTFTGRLPQSYYIRFRYASVANRSGTFRYSQPPSYGISF 540
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 481 PGFTGGDILTRNSMGELGTLRVTFTGRLPQSYYIRFRYASVANRSGTFRYSQPPSYGISF 540
Qy 541 PKTMDAGEPLTSRSFAHTTLFTPITFSRAQEEFDLYIQSGVYIDRIEFIPVTATFEAEYD 600
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 541 PKTMDAGEPLTSRSFAHTTLFTPITFSRAQEEFDLYIQSGVYIDRIEFIPVTATFEAEYD 600
Qy 601 LERAQKVVNALFTSTNQLGLKTDVT 625
|||||||||||||||||||||||||
Db 601 LERAQKVVNALFTSTNQLGLKTDVT 625
Response to Arguments
Applicant's arguments filed 03/16/2026 have been fully considered but they are not persuasive.
Applicant argues as previously explained, Aziz does not disclose or suggest that (1) this particular truncated Cry1Da protein will have commercially useful insecticidal activity, and (2) that optimizing the nucleotide sequence encoding this particular protein would allow one to successfully express it in a plant and achieve said increased insecticidal activity (Response to rejection, page 7, paragraph 1).
Applicant argues the Examiner appears to ignore the teachings of Baum which would have led one of ordinary skill in the art away from using the protein of SEQ ID NO: 3. Applicant argues Baum teaches that the wild type Cry1Da is not commercially useful. Applicant argues Baum states: "Because of its narrow insecticidal spectrum and its inability to provide commercial-level protection against a range of important Lepidopteran agricultural pests such as CEW, the Cry1Da1 insecticidal protein has limited value as a transgenic plant insect control trait." Paragraph [0005] of Baum (Response to Rejection, page 7, paragraph 2).
Applicant argues In paragraph [0080] cited by the Examiner, Baum states that "[f]ragments of the engineered insecticidal proteins described herein can be truncated forms wherein one or more amino acids are deleted from the N-terminal end, C-terminal end, the middle of the protein, or combinations thereof without a loss of insect inhibitory activity." Applicant argues thus, truncated fragments are only expected to "retain the insect inhibitory activity of the parent engineered insecticidal protein," which in itself is not commercially useful according to Baum. Applicant argues Truncation is not expected to enhance the toxicity or range of target pests of the native protein (Response to Rejection, page 7, paragraph 3).
Applicant argues Baum teaches using the full-length amino acid sequence of variants of Cry1Da1 or a chimeric protein named TIC844, which comprises the Cry1Da1 N-terminal domain and the Cry1Ab3 protoxin C-terminal domain. See paragraph [0008] of Baum. Applicant argues Baum teaches that using said variants, which all require a C-terminal protoxin domain either from CrylDal or Cry1Ab3, would "exhibit markedly improved activity (compared to the CrylDal native toxin) towards H. zea." Paragraph [0007] of Baum (Response to Rejection, pages 7 and 8, last and first paragraphs).
Applicant argues Baum teaches a person skilled in the art to not use C-terminally truncated sequences such as SEO ID NO: 3. Applicant argues the claims recite a codon-optimized nucleic acid molecule consisting of a specific nucleotide sequence, i.e., the nucleotide sequence of SEQ ID NO: 1. Applicant argues as set forth in Dr. Lirette's Declaration filed July 14, 2025, it is clear that the cited references would not have led a person skilled in the art aiming at expressing a CrylDa protein in maize to obtain the nucleotide sequence of SEQ ID NO: 1. Applicant argues the Examiner has failed to explain why a person skilled in the art would be motivated to provide this specific nucleotide sequence and the cited references do not support the Examiner's assertions (Response to Rejection, pages 8, paragraphs 2 and 4).
Applicant argues as explained in Dr. Lirette' s Declaration, using "Optimizer" software of Puigbo to optimize the native Bt Cry1Da nucleotide sequence for expression in maize does not result in the sequence of SEQ ID NO: 1 recited in the present claims. Applicant argues as further explained in the Declaration, Merlo does not cure the deficiencies of Puigbo. Applicant argues in fact, Merlo teaches away from SEQ ID NO: 1 because it discloses several preferred codons that are different from those used in SEQ ID NO: 1. See pages 4-5 of the Declaration (Response to Rejection, page 8, last paragraph).
Applicant argues Examiner did not set forth any explanation as to how one of ordinary skill in the art would have obtained SEQ ID NO: 1 based on the disclosure of the cited references and despite the fact that Merlo teaches different preferred codons than those used in SEQ ID NO: 1 (Response to Rejection, pages 9, first paragraph).
Applicant’s argument were fully considered but they are not found persuasive since:
Regarding Aziz’s does not disclose or suggest the truncated Cry1Da protein will have commercially useful insecticidal activity was not found persuasive since finding specific toxicity and dose of a known protein taught by Aziz et al. is routine procedure for a skilled in the art. Aziz et al. teaches the isolation source of their disclosed locus AFK29089 is from commercial Bt based insecticide (see description in “source of the locus AFK29089). Furthermore, there is no indication that the applicants have applied any inventive step that has changed the toxicity and dose of the disclosed protein by Aziz et al.
Furthermore, having a higher toxicity for the fragment compared to the full-length protein is not surprising or unexpected because this trend/characteristic was already known in the prior art Pardo-Lopez et al. (see analysis above), and the specific amount of activity for SEQ ID NO: 3 is an inherent property of SEQ ID NO: 3 which is specifically taught by Aziz et al. Furthermore, the activity of LC50 concentrations against Spodoptera frugiperda, D. sacharalis, and Helicoverpa zea at 0.13. 0.15, and 0.92 ug/cm2, respectively would have been inherent property of the toxin disclosed by Aziz et al.
Regarding argument that Aziz does not teach or suggest the truncated protein would be commercially useful, the rationale to modify or combine the prior art of Baum et al. does not have to be expressly stated in the prior art; the rationale may be expressly or impliedly contained in the prior art or it may be reasoned from knowledge generally available to one of ordinary skill in the art, established scientific principles, or legal precedent established by prior case law. In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988); In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992); see also In re Kotzab, 217 F.3d 1365, 1370, 55 USPQ2d 1313, 1317 (Fed. Cir. 2000). Furthermore, “Obviousness does not require absolute predictability of success.” Id. at 903, 7 USPQ2d at 1681., but at least some degree of predictability is required. The fact that the Aziz’s locus AFK29089 being truncated protein of Baum et al. and Aziz et al.’s definition as “active core crystal toxin protein 1D” would have scientifically predictable to have insecticidal activity.
Furthermore, Aziz discloses the information is dated 03/2018 before the effective date of filling of the invention in https://www.researchgate.net/publication/323627747_Bacillus_thuringiensis_strain_aizawai_active_core_crystal_toxin_protein_1D_gene_partial_cds_ACCESSION_JQ910166, accessed 03/07/2025 that their data showed the active core cry1D gene sequence from genomic DNA of Bacillus thuringiensis subsp. Aizawai and the gene coded for the active form of Cry1D crystal protein and has been proven toxic to its specific targeted-insect pests which were Spodoptera litura and Spodoptera exigua (see enclosed snippet and the entered accession JQ910166.1 included with the website included in the office action previously presented). The attached locus of the ResearchGate website JQ910166.1 encodes SEQ ID NO:3. For this reason it was known to have effect to insects from genus Spodoptera.
Regarding argument on Baum teaching away, Aziz et al. teaches truncated protein of Baum and Baum teaches their disclosed insecticidal proteins for example SEQ ID NO: 2 can be truncated forms wherein one or more amino acids are deleted from the N-terminal end, C-terminal end, the middle of the protein, or combinations thereof without a loss of insect inhibitory activity and these fragments should retain the insect inhibitory activity of the parent engineered insecticidal protein (page 7, paragraph 0080). Baum teaches engineered toxic protein contain amino acids substitution addition or deletions as compared to Baum’s SEQ ID NO: 2 which have showed unexpectedly improved insecticidal activity and enhanced insecticidal spectrum against Lepidopteran insect pests including H. zea (page 1, paragraph 0008). The deletion is a form of truncation. Furthermore, applicant is basing the argument on single art when the obviousness is determined by combination of arts for example Pardo-Lopez et al. teaches deletion of small fragments from amino-terminal region led to improved toxicity or overcome resistance representing interesting alternatives for insect pest control (page 589, Abstract and page 593).
Furthermore, as previously discussed evidence in prior office action that use of truncated protein in increasing insecticidal activity is known in the art. See for example Koziel et al., 1993, Field performance of elite transgenic maize plants expressing an insecticidal protein derived from Bacillus thuringiensis. Bio/technology, 11(2), 194-200; teaches expression of insecticidal proteins from Bacillus thuringiensis have been difficult when the native genes from B. thuringiensis were used requiring the use of truncated version of the native lepidopteran active genes for measurable protein and insecticidal activity in the transgenic plant. Koziel further teaches use of a native δ-endotoxin coding region, which has a high A-T content, appears to lead to abnormally low gene expression in plants. Koziel teaches plants in general have a higher G-C content than that found in the δ-endotoxins (page 194, left paragraph 2). Koziel teaches modifying the coding sequence to increase the G-C content of the native gene results in a dramatic increase in expression of the insecticidal protein (page 194, right paragraph 1). Koziel teaches about field performance of maize plant containing synthetic gene encoding truncated version of the CryIA(b) protein derived from B. thuringiensis which was affected by use of CaMV 35S promoter from maize where the transgenic plant produced higher levels of insecticidal protein (page 194, right paragraph 2).
Furthermore, Deist et al., 2014, Bt toxin modification for enhanced efficacy. Toxins, 6(10), 3005-3027; teaches truncation of Bt toxins has proven to be a useful option for enhancing Bt toxin activity by circumventing the toxin activation step resulting in improved toxicity against target pests and such toxin and truncation also improves expression levels in planta (page 3008, paragraph 4). Deist teaches higher insecticidal activity of truncated Cry1A over Cry1A protoxin for Mandusca sexta and it was not toxic to the plants (page 3009, paragraph 5). Deist further provides Table 1 (page 3018) which shows truncation as a modification for improved efficiency citing various references for different Bt toxin and different insect species. Hence applicant’s arguments are not persuasive.
Regarding argument on narrow insecticidal spectrum stated in paragraph 0005, the argument was not found persuasive since for example paragraph 0006 states despite narrow insecticidal spectrum, Cry1Da1 is an interesting insecticidal protein which uses an alternative mode of action for controlling certain Lepidopteran pests that are resistance to for example Cry1Ac and it has distinct action compared to Cry1Ac, Cry1Ab, Cry1A.105 etc. and can be used for broad spectrum insect resistance for insect resistance management.
Regarding argument on cited references do not teach the codon-optimized nucleic acid molecule of SEQ ID NO: 1, the argument is not found persuasive since codon optimization is routine procedure to express a gene across different species and it would produce the same protein disclosed by Aziz et al. it is not an inventive step. Furthermore, Puigbo teaches about the web server utility that optimizes a DNA or protein sequence. Puigbo further teaches that "optimizer" software can be used to design any new genes that confer new metabolic capabilities in a given species (Page W130, first paragraph).
The codon optimization is a routine procedure to produce the already known protein taught by Aziz et al. as having insecticidal activity, although the protein is not produced by optimizing codon. The claim's patentability hinges on the novelty of the product itself, not the process. The feely available website accessed at http://genomes.urv.es/OPTIMIZER/, access at 09/04/2025 as taught by Puigbo et al. showed Optimizer is an on-line PHP application that optimizes the codon usage of a DNA sequence to increase its expression level. Therefore increase in expression is expected. Furthermore, the codon usage database showed it clearly provides codon usage for the maize, for example see the usage table showed below accessed from the linked codon usage database in website.
PNG
media_image1.png
403
568
media_image1.png
Greyscale
Therefore, the arguments are not persuasive and 103 rejection is maintained.
However, Applicant’s reply is considered to be a bona fide attempt at a response and is being accepted as a complete response.
Conclusion
No claims are allowed.
Examiner’s Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to SANTOSH SHARMA whose telephone number is (571)272-8440. The examiner can normally be reached Mon-Fri 8:00 AM - 5:00 PM.
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/SANTOSH SHARMA/Examiner, Art Unit 1663
/DAVID H KRUSE/Primary Examiner, Art Unit 1663
Prosecution Insights