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
Applicant’s election without traverse of SEQ ID NO: 1276 in the reply filed on 3 June 2026 is acknowledged.
Claims 7, 13-14, 20, 26-28, 35, and 37-38 are pending are examined herein.
Improper Markush Grouping Rejection
Claim 7, 13-14, 20, 26-28, 35, and 37-38 are rejected on the basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations. First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of the amino acid sequences recited in independent clams 7 and 37 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use.
The claimed amino acid sequence alternatives include sequences with very little structural similarity. For example, an alignment of SEQ ID NOs: 1276 and 609 shows that they only have 2.9% sequence similarity.
Query Match 2.9%; Score 72; DB 1; Length 415;
Best Local Similarity 19.8%;
Matches 70; Conservative 40; Mismatches 134; Indels 110; Gaps 15;
Qy 177 VKQALATMDATQLFDTFGTHYVSEVLVGGRADYVATTKTSAFSSSTSISVAAEASFQSIA 236
| :| :||:| || : : | || | |||:|:
Db 2 VDRAEFMQSSTQVFQFFGISFGMSFPI----------KKLMFSFDT--------SFQAIS 43
Qy 237 GGEVSPESKVL-------AEMLRENSSTRLYALGGSALPNITDPAT-------------- 275
|| :: || | | : :| | :: :| |
Db 44 GGRQEIKAAVLQVESYSRRSFFRNNLALQLNPTLVQDLNSLPEPPTITAHRHDWRNHENF 103
Qy 276 -------------YNAWLE---------------------------SIDTIPVFCGFTQN 295
| :|: : | | ||
Db 104 LRKWGSHYMTEVRYGSWMRQFTSAASTETYSEIEMKANACARLFGGKLSKIGACAGITQQ 163
Qy 296 SLKSIS----ELADSAQRRDALAKASQSYIPSYVTRPAVVGLEVIISDSNSE-----SPP 346
: : | | : :| | || | : :| :|| :|
Db 164 QINANSNLRVRLTTEVRGGNAQTAAQLRRIP--VQESVIESFKVEGRNSNEAVVYHFAPI 221
Qy 347 YGYTRIDYDLN----RNA---KGKYI-FLCYN-QQKISVAGSPADPTPITALYVASGDDD 397
: : | : | | : |: || :: |:| || ::|| : : |:
Db 222 WQAIKARYSVQTRQWRQADALESFYVGFLAFDCPQRILNTGSSSEPTTLLQQFRRRGEKF 281
Qy 398 HPYVPLGYTRINSDLN-----EGAGGKYIY--LCYTKDPA----AIPSDEDGLP 440
| : | | || | | | | | || : | ||
Db 282 QCVRHCVGCRRSKDCNFHTTGNGAPGCYCYGNSCLVAQGAESRIAIQTRRDNLP 335
SEQ ID NO: 609 has similarly low similarity to SEQ ID NOs: 2 and 56 (3.4% and 2.2%, respectively; alignments not included here)
Furthermore, while Applicant states that plant derived perforins comprise a MACPF domain and that IDP079 polypeptides are plant derived perforins with insecticidal activity and “sufficient homology to SEQ ID NO: 2 or 56”, it appears that this is structural feature does appear to not sufficient for insecticidal activity, as explained below in the claim rejections under 35 U.S.C. 112(a). Additionally, it appears that at least some of these claimed polypeptides are chimeric polypeptides, though this is not clear from the disclosure of the specification.
The peptides do not seem to have a common use as broadly claimed. The specification does not disclose any information regarding the function of most of the polypeptides claimed by Applicant. At least the following polypeptides have no activity against the pests that they were tested against: 4, 6, 80, 90, 92, 94, 110, 1277, and 1278 (page 124, lines 1-5; page 125, lines 1-11; page 142, lines 18-28; page 143, Table 11).
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 13 and 38 is rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
Claim 13 recites an “agriculturally important crop.” “Important” is relative term that renders the claim indefinite. Because the phrase “agriculturally important crop” is not defined by the claim and the specification does not provide a standard for ascertaining the requisite degree, the metes and bounds of claim 13 are unclear.
Claim 38 is drawn to “A method of engineering the chimeric polypeptide of claim 37”. The claim is drawn to a process but does not set forth any active method steps. Therefore, the metes and bounds of the claims are unclear.
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.
Claims 7, 13-14, 20, 26-28, 35 and 37-38 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 claims contain 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.
Claims 7, 12-14, 20, 26-28, and 35 are broadly drawn to a polynucleotide encoding an insecticidal polypeptide comprising an amino acid sequence having as little as 80% identity to the amino acid sequence of SEQ ID NO: 1276 wherein the polynucleotide is operably linked to a heterologous regulatory element, DNA constructs comprising said polynucleotide, transgenic plants comprising said DNA constructs, and methods of using said polypeptides and compositions comprising said polypeptides to control Coleopteran insect pests.
Claim 37 is broadly drawn to a chimeric insecticidal polypeptide wherein the chimeric polypeptide comprises at least two portions, wherein each one of the portions comprises a fragment of an insecticidal polypeptide comprising an amino acid sequence with at least 80% identity to an amino acid sequence of SEQ ID NO: 1276. Claim 38 is drawn to any method of engineering these chimeric polypeptides. Examiner notes that the claim does not require that the chimeric polypeptide comprises two or more fragments from proteins encoded by different genes, nor does the specification provide a definition limiting a chimeric protein to a protein comprising fragments from proteins encoded by different genes. There is no limitation regarding the size of the fragments.
Claims 7, 12-14, 20, 26 and 37-38 do not limit the insecticidal activity to any specific pest, and as such are interpreted to encompass the claimed polypeptides, polynucleotides encoding said polypeptide, transgenic plants comprising said polynucleotides, and methods of using said polypeptides, comprising insecticidal activity against any insect pest.
Claims 27-28 and 35 require insecticidal activity against any Coleopteran pests.
Applicant does not describe the genus of insecticidal polypeptides, polynucleotides, transgenic plants and compositions encompassed by the claims.
Applicant describes SEQ ID NO: 1276 as a chimeric protein comprising fragments from two different IPD079 proteins: an N-terminal portion from IPD079Ea (i.e. instant SEQ ID NO: 56) and a C-terminal portion from IPD079Aa (i.e. SEQ ID NO: 2), with a crossover at residue I352 (page 142, lines 18-28; page 143, Table 11). Applicant discloses that SEQ ID NO: 1276 has insecticidal activity against Diabrotica virgifera (Western Corn Root Worm; hereafter WCRW).
Applicant describes SEQ ID NO: 56 as an IPD079 protein, specifically IPD079Ea, isolated from the fern Ophioglossum pendulum L. (page 118-119, Example 4). Applicant discloses that SEQ ID NO: 56 has insecticidal activity against Diabrotica barberi (Northern Corn Rootworm; hereafter NCRW), Diabrotica undecimpunctata howardi (Southern Corn Rootworm; hereafter SCRW) and Diabrotica virgifera (Western Corn Root Worm; hereafter WCRW) (Page 121, Table 3; Page 122, Table 4).
Applicant describes SEQ ID NO: 2 as an IPD079 protein, specifically IPD079Aa, isolated from the fern Huperzia phlegmaria (L.) Roth. (page 114-115, Example 1). Applicant discloses that SEQ ID NO: 2 has insecticidal activity against Diabrotica barberi (Northern Corn Rootworm; hereafter NCRW) and Diabrotica virgifera (Western Corn Root Worm; hereafter WCRW) (Page 121, Table 3; Page 122, Table 4).
Applicant describes SEQ ID NO: 1278, which has 94.1% sequence identity to SEQ ID NO: 1276 and which is also a chimera comprising an N-terminal portion from IPD079Ea (i.e. instant SEQ ID NO: 56) and a C-terminal portion from IPD079Aa (i.e. SEQ ID NO: 2), but with a crossover at residue P286. SEQ ID NO: 1278 does not have activity against WCRW, the only pest that it was tested against.
Applicant describes SEQ ID NO: 1277 which has 74.2% sequence identity to SEQ ID NO: 1276 and which is also a chimera, but comprising an N-terminal portion from IPD079Aa (i.e. SEQ ID NO: 2) and a C-terminal portion from IPD079Ea (i.e. instant SEQ ID NO: 56), with a crossover at residue T147 (in other words, SEQ ID NO: 1277 is a chimera of SEQ ID NOs: 2 and 56, like SEQ ID NOs: 1276 and 1278, but with the arrangement of fragments reversed and a different crossover position). SEQ ID NO: 1277 does not have activity against WCRW, the only pest that it was tested against.
Applicant describes 32 polypeptides with at least 82-87% sequence identity to SEQ ID NO: SEQ ID NO: 1276. Four of these polypeptides were not tested for insecticidal activity (SEQ ID NO:s 62, 68, 70 and 532); one was tested against WRCW and did not have activity (SEQ ID NO: 110); and the remaining 27 polypeptides have insecticidal activity against WCRW, the only pest that they were tested against (page 126, lines 15-20, Table 6; page 127, lines 26-36; page 128, Table 7; see also Search Results of 28 August 2026, SEQ ID NO: 1276 queried against Published Applications Database). All of the polypeptides with confirmed activity against WRCW were isolated from Ophioglossum pendulum, except for SEQ ID NO: 58, which was isolated from Platycerium bifurcatum.
Applicant discloses that SEQ ID NOs: 2 and 56 have no activity against Lepidopteran pests (page 122, lines 17-21).
Applicant does not describe any polypeptides with between 80-81% and 88-99% sequence identity to SEQ ID NO: 1276 and which have insecticidal activity.
Applicant does not describe any polypeptides with activity against any and all Coleopteran pests (an extremely diverse order of insects that may comprise thousands of species considered to be “pests”)—applicant only describes polypeptides with insecticidal activity against WRCW, NRCW and/or SRCW.
Applicant does not describe any insecticidal polypeptides with activity against non-Coleopteran pests, such as Lepidopteran pests.
Applicant does not describe any insecticidal chimeric polypeptides, aside from SEQ ID NO: 1276.
Polypeptides with as little as 80% identity to the 486 amino acid long sequence of SEQ ID NO: 1276, would encompass polypeptides with 97 substitutions, or over 2097 (1.58 x 10126) unique amino acid sequences. This is an extremely vast genus of polypeptides
The genus of polypeptides that is encompassed by chimeric polypeptides comprising at least two portions, wherein each of the portions comprises a fragment (of any size and in any arrangement) of an insecticidal polypeptide comprising an amino acid sequence with at least 80% identity to SEQ ID NO: 1276 would be equally vast.
While applicant has described numerous polypeptides with activity against WCRW having at between 82-87 identity to SEQ ID NO: 1276, applicant has not provided comparable disclosure of species with 80-81% and 88-99% identity to SEQ ID NO: 1276 and which have the required insecticidal function. The decision in AbbVie Deutschland GmbH & Co. v. Janssen Biotech, Inc. 111 USPQ2d 1780 (Fed. Cir. 2014) seems to be germane to the instant case. In AbbVie, an analogy is drawn between a claimed genus and a plot of land (see pages 1789-1791). Using this analogy, the Court offered that “[I]f the disclosed species only abide in a corner of the genus, one has not described the genus sufficiently to show that the inventor invented, or had possession of, the genus. He only described a portion of it.”
Thus, the disclosed species are not sufficiently representative of the full scope of the broadly claimed genus.
It is noted that a definition by function alone “does not suffice” to sufficiently describe a coding sequence “because it is only an indication of what the gene does, rather than what it is.” Eli Lilly, 119 F.3 at 1568, 43 USPQ2d at 1406. See also Fiers, 984 F.2d at 1169-71, 25 USPQ2d at 1605-06 (discussing Amgen Inc. v. Chugai Pharm. Co., 927 F.2d 1200, 18 USPQ2d 1016 (Fed. Cir. 1991)).
Applicant does not describe the structures that are necessary and sufficient for the required insecticidal function of the claimed polypeptides.
Applicant discloses that IPD079 polypeptides “show homology” to membrane attack complex/perforin (MACPF) domain proteins (page 136, lines 31-34). Applicant further discloses that plant derived perforins comprise a MACPF domain and that IDP079 polypeptides are plant derived perforins with insecticidal activity and “sufficient homology to SEQ ID NO: 2 or 56” (page 28, line 30, to page 29, line 1).
While MACPF appears to be necessary for insecticidal activity, it does not appear to be sufficient for said activity.
Anderluh et al (2014, MACPF/CDC Proteins - Agents of Defence, Attack and Invasion, Subcellular Biochemistry 80: 7-30) discloses that the MACPF protein family is characterized by a variety of functions that may not always be linked to pore formation or membrane association, including the neuronal and embryo development and protein secretion and nutrient uptake (page 16, first complete paragraph).
Anderluh et al further discloses that not all MACPF proteins have lytic functions and are perhaps more accurately described as housekeeping genes (pages 23-24, bridging paragraph; page 24, second paragraph).
Morita-Yamamuro et al (2005, Plant and Cell Physiology, 46: 902-912) disclose that CAD1 is an Arabidopsis protein containing a MACPF domain that acts as a negative regulator of plant immunity (page 903, paragraph bridging left and right columns). Morita-Yamamuro also discloses that under conditions of no pathogen infection, CAD1 represses the programmed cell death (PCD) pathway. However, upon pathogen infection recognition, the regulatory function of CAD1 is inhibited, leading to activation of the PCD pathway (page 908, paragraph bridging left and right columns). Morita-Yamamuro et al further discloses that plants lacking a functional CAD1 show spontaneously activated expression of pathogenesis related genes and CAD1 appears to be a negative regulator of immune response in Arabidopsis (page 908, column 1, paragraph 1; page 909, paragraph bridging column 1 and 2).
Chen et al (2021, Frontiers in Plant Science 12: 684227) discloses that MACPF genes are involved in growth, development, and response to abiotic stress in sorghum, rice and maize (page 2, column 1, paragraph 3 and references therein). Chen at el further discloses that a MACPF gene in Gossypium, GhMACPF26, is involved in response to cold stress—silencing of the gene enhanced plant cold tolerance (page 9, paragraph bridging columns 1-2).
Boeckman et al (2022, Journal of Economic Entomology, 115(5): 1531-1538) discloses that only 3 out of 11 Coleopteran’s tested showed biologically relevant sensitivity to IPD079Ea (i.e., SEQ ID NO: 56, which is one of the two IPD079 polypeptides, along with SEQ ID NO:2, used to create the chimeric polypeptide of SEQ ID NO: 1276; sensitive pests were WCRW, SCRW and Mexican bean beetle; page 1531, Abstract; Table 2; page 1536, column 2, paragraphs 3-4). The art appears silent on the insecticidal activity of IPD079Aa (i.e. SEQ ID NO: 2).
Thus, the disclosures of the references cited above, taken as a whole, suggest variability in the function of MACPF domain containing proteins. Furthermore, the activity of IPD079Ea appears limited to a few members of Coleoptera.
Regarding claims 37 and 38, Examiner notes that there appears to be substantial variability among the insecticidal activity of even related chimeric polypeptides. All three of the disclosed chimeric polypeptides, i.e. SEQ ID NOs: 1276-1278, are constructed using fragments of SEQ ID NO: 2 and SEQ ID NO: 56, yet only one, SEQ ID NO: 1276, has insecticidal function. Thus, it appears that both the amino acid sequence of the fragments selected as well as the arrangement of these fragments in the chimeric polypeptide affects the insecticidal activity.
Applicant has not described any motifs or domains necessary and sufficient for insecticidal activity in insecticidal polypeptides with at as little as 80% identity to SEQ ID NO: 1276, and by extension, the claimed chimeric polypeptides.
Therefore, applicant has not adequately described the structure-function relationship such that one of ordinary skill in the art would recognize which members of the claimed genus possess the recited insecticidal function.
Given the size of the genus of polypeptides encompassed by the claims, the species described are not sufficiently representative. In addition, Applicant has failed to set forth any structural features that would allow one having ordinary skill in the art to visualize which members of the claimed genus of proteins will have the recited insecticidal activity and which do not.
For these reasons, it does not appear that, at the time of filing, Applicant was in possession of the invention as broadly claimed.
Scope of Enablement
Claims 7, 12-14, 20, 26-28, 35 and 37-38 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 11 (pre-AIA ), first paragraph, because the specification, while being enabling for polynucleotides encoding an insecticidal polypeptide comprising the SEQ ID NO: 1276 , DNA constructs comprising said polynucleotide, transgenic plants comprising said DNA constructs, methods of using said polypeptides and compositions comprising said polypeptides to control insect pests in the genus Diabrotica, and methods of making said polypeptides, does not reasonably provide enablement for polynucleotides encoding an insecticidal polypeptide comprising an amino acid sequence having as little as 80% identity to the amino acid sequence of SEQ ID NO: 1276; DNA constructs comprising said polynucleotide, transgenic plants comprising said DNA constructs, and methods of using said polypeptides and compositions comprising said polypeptides to control any insect pests nor does it reasonable provide enablement for chimeric polypeptide comprises at least two portions, wherein each one of the portions comprises a fragment of an insecticidal polypeptide comprising an amino acid sequence with at least 80% identity to an amino acid sequence of SEQ ID NO: 1276 and methods of making said chimeric polypeptide. 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 or use the invention commensurate in scope with these claims.
In re Wands, 858 F.2d 731 (Fed. Cir. 1988) lists the following eight factors for determining whether undue experimentation would be required to practice an invention: (1) quantity of experimentation necessary; (2) amount of direction or guidance supplied; (3) presence or absence of working examples; (4) nature of the invention; (5) state of the prior art; (6) relative skill of those in the art; (7) predictability or unpredictability or the prior art; (8) breadth of the claims.
Claims 7, 12-14, 20, 26-28, and 35 are broadly drawn to a polynucleotide encoding an insecticidal polypeptide comprising an amino acid sequence having as little as 80% identity to the amino acid sequence of SEQ ID NO: 1276 wherein the polynucleotide is operably linked to a heterologous regulatory element, DNA constructs comprising said polynucleotide, transgenic plants comprising said DNA constructs, and methods of using said polypeptides and compositions comprising said polypeptides to control Coleopteran insect pests.
Claim 37 is broadly drawn to a chimeric insecticidal polypeptide wherein the chimeric polypeptide comprises at least two portions, wherein each one of the portions comprises a fragment of an insecticidal polypeptide comprising an amino acid sequence with at least 80% identity to an amino acid sequence of SEQ ID NO: 1276. Claim 38 is drawn to any method of engineering these chimeric polypeptides. Examiner notes that the claim does not require that the chimeric polypeptide comprises two or more fragments from proteins encoded by different genes, nor does the specification provide a definition limiting a chimeric protein to a protein comprising fragments from proteins encoded by different genes. There is no limitation regarding the size of the fragments.
Claims 7, 12-14, 20, 26 and 37-38 do not limit the insecticidal activity to any specific pest, and as such are interpreted to encompass the claimed polypeptides, polynucleotides encoding said polypeptide, transgenic plants comprising said polynucleotides, and methods of using said polypeptides, comprising insecticidal activity against any insect pest.
Claims 27-28 and 35 require insecticidal activity against any Coleopteran pests.
Applicant teaches that SEQ ID NO: 1276 is a chimeric protein comprising fragments from two different IPD079 proteins: an N-terminal portion from IPD079Ea (i.e. instant SEQ ID NO: 56) and a C-terminal portion from IPD079Aa (i.e. SEQ ID NO: 2), with a crossover at residue I352 (page 142, lines 18-28; page 143, Table 11). Applicant teaches that SEQ ID NO: 1276 has insecticidal activity against Diabrotica virgifera (Western Corn Root Worm; hereafter WCRW).
Applicant teaches that SEQ ID NO: 56 is an IPD079 protein, specifically IPD079Ea, isolated from the fern Ophioglossum pendulum L. (page 118-119, Example 4). Applicant teaches that SEQ ID NO: 56 has insecticidal activity against Diabrotica barberi (Northern Corn Rootworm; hereafter NCRW), Diabrotica undecimpunctata howardi (Southern Corn Rootworm; hereafter SCRW) and Diabrotica virgifera (Western Corn Root Worm; hereafter WCRW) (Page 121, Table 3; Page 122, Table 4).
Applicant teaches that SEQ ID NO: 2 is an IPD079 protein, specifically IPD079Aa, isolated from the fern Huperzia phlegmaria (L.) Roth. (page 114-115, Example 1). Applicant teaches that SEQ ID NO: 2 has insecticidal activity against Diabrotica barberi (Northern Corn Rootworm; hereafter NCRW) and Diabrotica virgifera (Western Corn Root Worm; hereafter WCRW) (Page 121, Table 3; Page 122, Table 4).
Applicant teaches that SEQ ID NOs: 2 and 56 have no activity against Lepidopteran pests (page 122, lines 17-21).
Applicant teaches SEQ ID NO: 1278, which has 94.1% sequence identity to SEQ ID NO: 1276 and which is also a chimera comprising an N-terminal portion from IPD079Ea (i.e. instant SEQ ID NO: 56) and a C-terminal portion from IPD079Aa (i.e. SEQ ID NO: 2), but with a crossover at residue P286. SEQ ID NO: 1278 does not have activity against WCRW, the only pest that it was tested against.
Applicant teaches SEQ ID NO: 1277 which has 74.2% sequence identity to SEQ ID NO: 1276 and which is also a chimera, but comprising an N-terminal portion from IPD079Aa (i.e. SEQ ID NO: 2) and a C-terminal portion from IPD079Ea (i.e. instant SEQ ID NO: 56), with a crossover at residue T147 (in other words, SEQ ID NO: 1277 is a chimera of SEQ ID NOs: 2 and 56, like SEQ ID NOs: 1276 and 1278, but with the arrangement of fragments reversed and a different crossover position). SEQ ID NO: 1277 does not have activity against WCRW, the only pest that it was tested against.
Applicant teaches 32 polypeptides with at least 82-87% sequence identity to SEQ ID NO: SEQ ID NO: 1276. Four of these polypeptides were not tested for insecticidal activity (SEQ ID NO:s 62, 68, 70 and 532); one was tested against WRCW and did not have activity (SEQ ID NO: 110); and the remaining 27 polypeptides have insecticidal activity against WCRW, the only pest that they were tested against (page 126, lines 15-20, Table 6; page 127, lines 26-36; page 128, Table 7; see also Search Results of 28 August 2026, SEQ ID NO: 1276 queried against Published Applications Database). All of the polypeptides with confirmed activity against WRCW were isolated from Ophioglossum pendulum, except for SEQ ID NO: 58, which was isolated from Platycerium bifurcatum.
Applicant further teaches an additional 36 IPD079 proteins isolated from Huperzia carinata, H. goebelii, H. nummulariifolia, and H. salvinioides (page 124, Table 5; page 128, Table 7). Of these approximately a quarter are insoluble or have no activity against the tested species (SEQ ID NOs: 4, 6, 8, 10, 12, 24, 80, 90, 92, and 94), while the others have activity against WCRW (page 124, lines 1-5; page 125, lines 1-11; page 127, lines 26-36). Examiner notes that none of the IPD079 proteins isolated from Huperzia have at least 90% identity to SEQ ID NO: 1276.
Applicant teaches a single insecticidal polypeptide isolated from Selaginella victoriae (SEQ ID NO: 144) which has activity against NCRW and WCRW (page 120, lines 19-23; page 121, Table 3; Page 122, Table 4. SEQ ID NO: 144 does not have 80% identity to SEQ ID NO: 1276.
Applicant teaches insecticidal polypeptides from a total of 8 species of plants in 4 genera (all ferns or lycophytes), none of which have any disclosed insecticidal activity outside of the genus Diabrotica.
Applicant teaches that IPD079 polypeptides “show homology” to membrane attack complex/perforin (MACPF) domain proteins (page 136, lines 31-34). Applicant further teaches that plant derived perforins comprise a MACPF domain and that IDP079 polypeptides are plant derived perforins with insecticidal activity and “sufficient homology to SEQ ID NO: 2 or 56” (page 28, line 30, to page 29, line 1)
Applicant does not teach any polypeptides with between 80-81% and 88-99% sequence identity to SEQ ID NO: 1276 and which have insecticidal activity.
Applicant does not teach any polypeptides with activity against any and all Coleopteran pests (an extremely diverse order of insects that may comprise thousands of species considered to be “pests”)—applicant only teaches polypeptides with insecticidal activity against WRCW, NRCW and/or SRCW.
Applicant does not teach any insecticidal polypeptides with activity against non-Coleopteran pests, such as Lepidopteran pests.
Applicant does not teach any insecticidal chimeric polypeptides, aside from SEQ ID NO: 1276.
Applicant does not teach the structures that are necessary and sufficient for the required insecticidal function of the claimed polypeptides
Applicant does not teach how to predictably make or use the vast genus of insecticidal polypeptides encompassed by the claims, polynucleotides encoding said polypeptides, or transgenic plants and compositions comprising said insecticidal polypeptides.
Polypeptides with as little as 80% identity to the 486 amino acid long sequence of SEQ ID NO: 1276, would encompass polypeptides with 97 substitutions, or over 2097 (1.58 x 10126) unique amino acid sequences. This is an extremely vast genus of polypeptides
The genus of polypeptides that is encompassed by chimeric polypeptides comprising at least two portions, wherein each of the portions comprises a fragment (of any size and in any arrangement) of an insecticidal polypeptide comprising an amino acid sequence with at least 80% identity to SEQ ID NO: 1276 would be equally vast.
There are several hundred thousand species of plants and over 10,000 species of ferns. Anderluh et al (2014, MACPF/CDC Proteins - Agents of Defence, Attack and Invasion, Subcellular Biochemistry 80: 7-30) discloses that approximately 1300 unique MACPF domain proteins are known in public databases from all domains of life (page 10, first paragraph). Anderluh et al does not disclose any activity associated with said proteins, however. Moreover, it does not appear that plants in general, or more specifically ferns, have been broadly surveyed for the presence or absence of insecticidal perforins.
As explained above in the Written Description rejection, the state-of-the-art is such that one of skill in the art cannot rely on the presence of a MACPF domain alone to predict insecticidal function. As also explained in the Written Descriptions rejection, Applicant has not taught which structural features or amino acid residues are necessary and sufficient for the claimed insecticidal function such that one would not be able to reasonably predict which of members of the claimed genus would have insecticidal function. Applicant fails to provide guidance for which amino acids of can be altered and to which other amino acids, and which amino acids must not be changed, to maintain the insecticidal activity of the polypeptide.
Further, one of skill in the art could not rely on sequence alignments to identity insecticidal polypeptides with as little as 80% identity to the 486 amino acid long sequence of SEQ ID NO: 1276. Anderluh et al teaches that “low sequence conservation presents a great challenge in discovering novel MACPF-containing proteins, as is highlighted by the fact that the original discovery of MACPFs in mammals and of CDCs in Gram-positive bacteria hid their deep evolutionary relationship until their structures were solved” (page 10-11, bridging paragraph).
Even within a genus of plants known to comprise insecticidal MACPF domain polypeptides, such as Huperzia, identifying said polypeptides is unpredictable. Applicant teaches several polypeptides which lack insecticidal activity (SEQ ID NOs: 4, 6, 8, 10, 12, 24, 80, 90, 92, and 94) that were isolated using the same primers used to isolate SEQ ID NO: 2, which has insecticidal activity (page 124, lines 1-5; page 125, lines 1-11; page 127, lines 26-36). Thus, even within the genus Huperzia, the skilled artisan would be unable to discern a plant derived perforin with insecticidal activity from those that do not have said activity from sequence similarity alone.
Regarding the chimeric polypeptides of claims 37 and 38, Applicant’s own admission provides evidence of unpredictability. All three of the chimeric polypeptides taught by Applicant, i.e. SEQ ID NOs: 1276-1278, are constructed using fragments of SEQ ID NO: 2 and SEQ ID NO: 56, yet only one, SEQ ID NO: 1276, has insecticidal function. Thus, it appears that both the amino acid sequence of the fragments selected as well as the arrangement of these fragments in the chimeric polypeptide affects the insecticidal activity. Applicant has not provided guidance on which fragments of IPD079 polypeptides are necessary and sufficient to provide insecticidal activity in a chimeric protein.
Thus, the skilled artisan would have required extensive teachings of those regions found in the insecticidal polypeptides taught by applicant, aside from MACPF, that are responsible for insecticidal activity make or use the genus as is currently claimed. Lacking said guidance, one of skill in the art would have to rely on trial-and-error experimentation to isolate and assay the vast genus of encompassed polynucleotides to identify those with the required insecticidal function. Therefore, undue trial and error experimentation would be required for one of skill in the art to make and use the claimed invention.
Thus, given the breadth of the claims; the lack of guidance; the unpredictability in the art; the state-of-the-art as discussed above, and the undue experimentation required, the invention is not enabled throughout the broad scope of the claims.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
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Claims 7, 13-14, 20, and 26-28 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1 and 5-10 of U.S. Patent No. 11, 198, 709 B2 (hereafter ‘709). Although the claims at issue are not identical, they are not patentably distinct from each other.
Claims 7, 13-14, 20, and 26-28 are broadly drawn to a polynucleotide encoding an insecticidal polypeptide comprising an amino acid sequence having as little as 80% identity to the amino acid sequence of SEQ ID NO: 1276 wherein the polynucleotide is operably linked to a heterologous regulatory element, DNA constructs comprising said polynucleotide, transgenic plants comprising said DNA constructs, and methods of using said polypeptides and compositions comprising said polypeptides to control Coleopteran insect pests.
The claims of ‘709 are drawn to an insecticidal polypeptide comprising an amino acid sequence having as little as 95% identity to the amino acid sequence of SEQ ID NO: 56, polynucleotides encoding said polypeptide, transgenic plants comprising said polynucleotides, and methods of using polypeptides and compositions to control insect pests.
SEQ ID NO: 56 has 87.3% sequence identity to instant SEQ ID NO: 1276:
Query Match 87.3%; Score 2169; Length 478;
Best Local Similarity 88.9%;
Matches 432; Conservative 16; Mismatches 30; Indels 8; Gaps 3;
Qy 1 MEPNKGGAPAMKNVAKPSTKRLIPSSIAASSQTSANALTEPLPGSDAIGQSYDAFGFFAN 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MEPNKGGAPAMKNVAKPSTKRLIPSSIAASSQTSANALTEPLPGSDAIGQSYDAFGFFAN 60
Qy 61 PRSIMKELFEFSPQEEIVVEGNTWLLSSDFVYTAIRDTETSTVSRRTKDDYSKELAVKVK 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 PRSIMKELFEFSPQEEIVVEGNTWLLSSDFVYTAIRDTETSTVSRRTKDDYSKELAVKVK 120
Qy 121 LSGSYGYFSASVESDFSQSISDATDTTYTSVRTHVNKWRLSLKDDVGALRSKLLPGVKQA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 LSGSYGYFSASVESDFSQSISDATDTTYTSVRTHVNKWRLSLKDDVGALRSKLLPGVKQA 180
Qy 181 LATMDATQLFDTFGTHYVSEVLVGGRADYVATTKTSAFSSSTSISVAAEASFQSIAGGEV 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 LATMDATQLFDTFGTHYVSEVLVGGRADYVATTKTSAFSSSTSISVAAEASFQSIAGGEV 240
Qy 241 SPESKVLAEMLRENSSTRLYALGGSALPNITDPATYNAWLESIDTIPVFCGFTQNSLKSI 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 SPESKVLAEMLRENSSTRLYALGGSALPNITDPATYNAWLESIDTIPVFCGFTQNSLKSI 300
Qy 301 SELADSAQRRDALAKASQSYIPSYVTRPAVVGLEVIISDSNSESPPYGYTRIDYDLNRNA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 SELADSAQRRDALAKASQSYIPSYVTRPAVVGLEVIISDSNSESPPYGYTRIDYDLNRNA 360
Qy 361 KGKYIFLCYNQQKISVAGSPADPTPITALYVASGDDDHPYVPLGYTRINSDLNEGAGGKY 420
|||:|||| |: ||| | | || : | |:| :| || |||:|: ||| ||||||
Db 361 GGKYVFLCYKQKNISVGG---DADAITDVLVVYGNDRNPSVPSGYTKIDKDLNSGAGGKY 417
Qy 421 IYLCYTKDPAAIPSDEDGLPIRGIRVIGNEKVENVVTPYGFTKIDKDLNEGAGGDYIFVC 480
|| ||:|| |:||||||:||:| | ||||:||| ||| |||||:|::|
Db 418 IYFCYSKDKR---KQEEGLPIRGLRVVGPHPTS--VAPYGFSKIDIDLNMGAGGDFIYLC 472
Qy 481 FSRHLD 486
||||:
Db 473 KSRHLE 478
Thus, the methods and products of claims 1, and 5-10 of ‘709 are a subgenus of the genus claimed by the instant application and, therefore, anticipate instant claims 7, 13-14, 20, and 26-28.
Claims 7, 13, 14, and 20 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 8-13, 16-23 and 48-51 of U.S. Patent No. 12,371,707 B2 (hereafter ‘707). Although the claims at issue are not identical, they are not patentably distinct from each other.
The claims of the instant application are broadly drawn to an insecticidal polypeptide comprising an amino acid sequence having as little as 80% identity to the amino acid sequence of SEQ ID NO: 1276, polynucleotides encoding said polypeptide, and transgenic plants comprising said polynucleotides.
The claims of ‘707 are drawn to a corn plant comprising event DP-915635-4, plant parts, cells, extracts and DNA samples thereof.
Event DP-915635-4 was produced by transforming a maize plant with plasmid PHP83175, which comprises a IPD079Ea polynucleotide encoding the polypeptide of SEQ ID NO: 5 (page 2, lines 23-32; page 24-25, Table 1).
SEQ ID NO: 5 has 87.3% sequence identity to instant SEQ ID NO: 1276:
Query Match 87.3%; Score 2169; Length 478;
Best Local Similarity 88.9%;
Matches 432; Conservative 16; Mismatches 30; Indels 8; Gaps 3;
Qy 1 MEPNKGGAPAMKNVAKPSTKRLIPSSIAASSQTSANALTEPLPGSDAIGQSYDAFGFFAN 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MEPNKGGAPAMKNVAKPSTKRLIPSSIAASSQTSANALTEPLPGSDAIGQSYDAFGFFAN 60
Qy 61 PRSIMKELFEFSPQEEIVVEGNTWLLSSDFVYTAIRDTETSTVSRRTKDDYSKELAVKVK 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 PRSIMKELFEFSPQEEIVVEGNTWLLSSDFVYTAIRDTETSTVSRRTKDDYSKELAVKVK 120
Qy 121 LSGSYGYFSASVESDFSQSISDATDTTYTSVRTHVNKWRLSLKDDVGALRSKLLPGVKQA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 LSGSYGYFSASVESDFSQSISDATDTTYTSVRTHVNKWRLSLKDDVGALRSKLLPGVKQA 180
Qy 181 LATMDATQLFDTFGTHYVSEVLVGGRADYVATTKTSAFSSSTSISVAAEASFQSIAGGEV 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 LATMDATQLFDTFGTHYVSEVLVGGRADYVATTKTSAFSSSTSISVAAEASFQSIAGGEV 240
Qy 241 SPESKVLAEMLRENSSTRLYALGGSALPNITDPATYNAWLESIDTIPVFCGFTQNSLKSI 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 SPESKVLAEMLRENSSTRLYALGGSALPNITDPATYNAWLESIDTIPVFCGFTQNSLKSI 300
Qy 301 SELADSAQRRDALAKASQSYIPSYVTRPAVVGLEVIISDSNSESPPYGYTRIDYDLNRNA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 SELADSAQRRDALAKASQSYIPSYVTRPAVVGLEVIISDSNSESPPYGYTRIDYDLNRNA 360
Qy 361 KGKYIFLCYNQQKISVAGSPADPTPITALYVASGDDDHPYVPLGYTRINSDLNEGAGGKY 420
|||:|||| |: ||| | | || : | |:| :| || |||:|: ||| ||||||
Db 361 GGKYVFLCYKQKNISVGG---DADAITDVLVVYGNDRNPSVPSGYTKIDKDLNSGAGGKY 417
Qy 421 IYLCYTKDPAAIPSDEDGLPIRGIRVIGNEKVENVVTPYGFTKIDKDLNEGAGGDYIFVC 480
|| ||:|| |:||||||:||:| | ||||:||| ||| |||||:|::|
Db 418 IYFCYSKDKR---KQEEGLPIRGLRVVGPHPTS--VAPYGFSKIDIDLNMGAGGDFIYLC 472
Qy 481 FSRHLD 486
||||:
Db 473 KSRHLE 478
Thus, the corn plants, plant parts, cells, extracts and compositions thereof claimed in patent ‘707 are a species of the genus claimed by the instant application and, therefore, anticipate instant claims 7, 14, 20.
Further It would be obvious to codon optimize the nucleotide of event DP-915635-4 to improve expression in an agriculturally important crop, such as maize, as claimed by instant claim 13 as this is routinely practiced by those of skill in the art to optimize expression of heterologous proteins.
Claims 7, 13-14, and 20 are provisionally rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-3, 8-13, 16-23 and 50-53 of copending Application No. 19/250,376 (reference application). Although the claims at issue are not identical, they are not patentably distinct from each other.
The claims of the instant application are broadly drawn to an insecticidal polypeptide comprising an amino acid sequence having as little as 80% identity to the amino acid sequence of SEQ ID NO: 1276, polynucleotides encoding said polypeptide, and transgenic plants comprising said polynucleotides.
The claims of the reference application are drawn to a corn plant comprising event DP-915635-4, plant parts, cells, extracts and DNA samples thereof.
Event DP-915635-4 was produced by transforming a maize plant with plasmid PHP83175, which comprises a IPD079Ea polynucleotide encoding the polypeptide of SEQ ID NO: 5 (page 2, lines 23-32; page 24-25, Table 1).
SEQ ID NO: 5 has 87.3% sequence identity to instant SEQ ID NO: 1276:
Query Match 87.3%; Score 2169; Length 478;
Best Local Similarity 88.9%;
Matches 432; Conservative 16; Mismatches 30; Indels 8; Gaps 3;
Qy 1 MEPNKGGAPAMKNVAKPSTKRLIPSSIAASSQTSANALTEPLPGSDAIGQSYDAFGFFAN 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 1 MEPNKGGAPAMKNVAKPSTKRLIPSSIAASSQTSANALTEPLPGSDAIGQSYDAFGFFAN 60
Qy 61 PRSIMKELFEFSPQEEIVVEGNTWLLSSDFVYTAIRDTETSTVSRRTKDDYSKELAVKVK 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 PRSIMKELFEFSPQEEIVVEGNTWLLSSDFVYTAIRDTETSTVSRRTKDDYSKELAVKVK 120
Qy 121 LSGSYGYFSASVESDFSQSISDATDTTYTSVRTHVNKWRLSLKDDVGALRSKLLPGVKQA 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 LSGSYGYFSASVESDFSQSISDATDTTYTSVRTHVNKWRLSLKDDVGALRSKLLPGVKQA 180
Qy 181 LATMDATQLFDTFGTHYVSEVLVGGRADYVATTKTSAFSSSTSISVAAEASFQSIAGGEV 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 LATMDATQLFDTFGTHYVSEVLVGGRADYVATTKTSAFSSSTSISVAAEASFQSIAGGEV 240
Qy 241 SPESKVLAEMLRENSSTRLYALGGSALPNITDPATYNAWLESIDTIPVFCGFTQNSLKSI 300
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 241 SPESKVLAEMLRENSSTRLYALGGSALPNITDPATYNAWLESIDTIPVFCGFTQNSLKSI 300
Qy 301 SELADSAQRRDALAKASQSYIPSYVTRPAVVGLEVIISDSNSESPPYGYTRIDYDLNRNA 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 SELADSAQRRDALAKASQSYIPSYVTRPAVVGLEVIISDSNSESPPYGYTRIDYDLNRNA 360
Qy 361 KGKYIFLCYNQQKISVAGSPADPTPITALYVASGDDDHPYVPLGYTRINSDLNEGAGGKY 420
|||:|||| |: ||| | | || : | |:| :| || |||:|: ||| ||||||
Db 361 GGKYVFLCYKQKNISVGG---DADAITDVLVVYGNDRNPSVPSGYTKIDKDLNSGAGGKY 417
Qy 421 IYLCYTKDPAAIPSDEDGLPIRGIRVIGNEKVENVVTPYGFTKIDKDLNEGAGGDYIFVC 480
|| ||:|| |:||||||:||:| | ||||:||| ||| |||||:|::|
Db 418 IYFCYSKDKR---KQEEGLPIRGLRVVGPHPTS--VAPYGFSKIDIDLNMGAGGDFIYLC 472
Qy 481 FSRHLD 486
||||:
Db 473 KSRHLE 478
Thus, the corn plants, plant parts, cells, extracts and compositions thereof claimed in the reference application are a species of the genus claimed by the instant application and, therefore, anticipate instant claims 7, 14, 20.
Further it would be obvious to codon optimize the nucleotide of event DP-915635-4 to improve expression in an agriculturally important crop, such as maize, as claimed by instant claim 13 as this is routinely practiced by those of skill in the art to optimize expression of heterologous proteins.
This is a provisional nonstatutory double patenting rejection because the patentably indistinct claims have not in fact been patented.
Conclusion
No claims are allowed.
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/ALEKSANDAR RADOSAVLJEVIC/ Examiner, Art Unit 1662
/BRENT T PAGE/ Primary Examiner, Art Unit 1663
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