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 .
Claim Status
Claims 1-3, 5-6, 10-17, 21-22, 24-34 are pending.
Claims 29-34 are newly added by the Applicant. However, claims 30-34 are withdrawn as the recited SEQ ID NOs do not read on to the elected SEQ ID NOs (i.e., SEQ ID NOs: 123-124) (Applicant’s response on 3/19/2026, p.8, para 1, line 1-2; and response on 8/25/2026, p.10, para 5).
Claims 13-17, 21-22, 24-28 and 30-34 are withdrawn as being part of non-elected Groups and/or non-elected species.
Claims 1-3, 5-6, 10-12 and 29 are being examined.
Claim Objections
Claims 1, 5, 11 and 29 are objected to because of the following informalities:
It is suggested to add the prhase “that is” between “a sequence” and “at least” in line 3 of claim 1, in line 2 of claim 5, and in line 4 in claim 11.
Claim 29 recites, “… Zea may…”. It is suggested to replace “may” to “mays”.
Appropriate correction is required.
Claim Rejections - 35 USC § 112(b)
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 5, 6, 10, 11 are 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 5 depends from claim 1 and recites “mutating a native promoter or a gene”. It is not clear to the Examiner what the Applicant implies by “… (i) mutating a native promoter or a gene encoding SEQ ID NO: 124 or a sequence at least 90% identical thereto; (ii) replacing said native promoter or said gene; or (iii) replacing a portion of said promoter or said gene”. Does the Applicant imply any native promoter of any gene or the native promoter of the gene encoding the protein consisting of at least 90% sequence identity to instant SEQ ID NO: 124? Claim 1 does not recite any promoter or gene.
Claim Rejections - 35 USC § 112(d)
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 5, 6, 10, 11 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 5 depends from claim 1 and recites “… mutating a native promoter or a gene …”. Claim 1 does not recite any promoter or a gene but recites only the protein coding part of the gene while reciting “… a nucleic acid sequence encoding SEQ ID NO: 124 or a sequence at least 90% identical thereto… “. Thus, claim 5 does not restrict instant claim 1 but expands its scope.
The Applicant may cancel the claim, amend the claim to place the claim in proper dependent form, rewrite the claim in independent form, or present a sufficient showing that the dependent claim complies with the statutory requirements.
Claim Rejections - 35 USC § 112(a)
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.
Written Description
Claims 1-3, 5-6, 10-12 and 29 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 contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention. This is a new rejection necessitated by claim amendments.
Claim 1 recites, “… at least 90% identical…” to instant SEQ ID NO: 124.
The Applicant describes identification of AtExo970 (AtExo970 cDNA- SEQ ID NO: 123; AtExo970 protein- SEQ ID NO: 124) and alleged “homologs” from other crop and vegetable species using publicly available whole genome sequences at https://phytozome.jgi.doe.gov (spec, page 65, para 5-6). Homologs of AtExo970 from 6 plant species such as canola, soybean, corn, wheat, Brachypodium and rice have been identified and used as examples in the invention. (page 65, para 6, line 3-6).
Several Arabidopsis genome sequencing and/or genome annotation projects have identified the gene and the protein having 100% sequence identity throughout the entire length of the protein (SEQ ID NO: 124) which is now named “AtExo970” by the Applicant. One such example (GenBank accession number: ACF16171) identifies the protein as “C2H2 Zinc finger” protein and “RNA exonuclease 4”. Apparently, the name AtExo970 appears in this application for the first time in the art. It is fair to say that the current status of the art does not describe any AtExo970 gene or protein.
Mutating up to 10% of the amino acids in 483 amino acid long SEQ ID NO:124 allows a skilled artisan to mutate up to 48 amino acids.
The Applicant does not describe representative examples of the broad genus comprising a sequence having less than 100% identity to SEQ ID NO: 124 obtained from a single plant species including in Arabidopsis. Polypeptide sequences having less than 90% sequence identities obtained from different plant species are also designated as Exo970 homologues by the Applicant (spec, p. 45, para 2, line 3-4; p.46, para 5, line 1-3). The Applicant does not describe expressing any homologue of AtEXO970 comprising at least one to up to 10% mutant amino acids (i.e., up to 48 amino acids) to obtain the claimed gain-of-functions of “increasing of tolerance to water and/or nutrient deficiency in a plant”. The Applicant also does not describe expressing a mutated AtEXO970 comprising at least one to up to 48 amino acids in Arabidopsis either.
The Applicant also does not describe any structure function relationship between the structure of AtEXO970 or its “homologues” with the claims function(s) of “increasing of tolerance to water and/or nutrient deficiency in a plant”. The Applicant also does not describe any structure function relationship of the protein sequence of SEQ ID NO: 124 with the claimed gain-of-function(s) of increased tolerance to water and/or nutrient deficiency in a plant that the mutated protein needs to retain/achieve. The Applicant does not describe, and it is not known which amino acid must not be mutated and/or which amino acid(s) would tolerate what type of mutation(s) while retaining/achieving the claimed function(s).
Current status of the art also does not describe any structure function relationship that would enable a skilled artesian to mutate up to 10% of SEQ ID NO: 124 anywhere in the entire length of the protein while retaining/achieving the recited function(s) while being overexpressed. These are all naturally occurring polypeptides that were selected through the course of evolution in the respective plants. Current status of the art does not indicate how a specific polypeptide sequence with specific mutation(s) would function in another plant in the context of the claimed function(s).
Regarding claim 29, the applicant describes several proteins from canola, soybean, corn, wheat, Brachypodium and rice which are identified by sequence identity to AtEXO970 (SEQ ID NO: 124). Some of these native proteins have significantly less sequence identity to instant SEQ ID NO: 124; e.g., TaExo506 (66%), TaExo220 (70%) (spec, p.44, para 2, line 1-2), BdExo960 (69%) (spec, p.45, para 2, line 3-4), GmExo690 and GmExo740 (70%) (spec, p.35, last para, line 1-6), and ZmExo807 (73%) (spec, p.40, para 3, line 3-5). Nonetheless, the Applicant does not overexpress any of these native proteins or a mutated version of the protein comprising at least one to up to 10% amino acid mutation(s) in the same species to obtain the claimed function(s).
Considering the breadth of the claims, lack of representative species of the broad genus claimed, lack of structure function relationship of the broad genus claimed, the Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
Scope of Enablement
Claims 1-3, 5-6, 10-12 and 29 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for overexpressing a nucleic acid sequence encoding a protein comprising 100% sequence identity to SEQ ID NO: 124, does not reasonably provide enablement for overexpressing a nucleic acid sequence encoding a protein having at least 90% sequence identity to SEQ ID NO: 124. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
This is a new rejection necessitated by claim amendments.
The Applicant describes identification of AtExo970 (AtExo970 cDNA- SEQ ID NO: 123; AtExo970 protein- SEQ ID NO: 124) and “homologs” from other crop and vegetable species using publicly available whole genome sequences at https://phytozome.jgi.doe.gov (spec, page 65, para 5-6) based on sequence homology/identity. Homologs of AtExo970 from 6 species such as canola, soybean, corn, wheat, Brachypodium and rice have been identified and used as examples in the invention. (page 65, para 6, line 3-6).
Several Arabidopsis genome sequencing and/or genome annotation projects have identified the gene and the protein having 100% sequence identity to the entire length protein recited as “AtExo970”. One such example (GenBank accession number: ACF16171) identifies the protein as “C2H2 Zinc finger” protein and “RNA exonuclease 4”. Apparently, the name AtExo970 appears in this application for the first time in the art. It is fair to say that the current status of the art does not describe any AtExo970 gene or protein.
Mutating up to 10% of the amino acids in 483 amino acid long SEQ ID NO:124 allows a skilled artisan to mutate up to 48 amino acids.
The Applicant does not provide any guidance for a skilled artisan to mutate up to 48 amino acids to SEQ ID NO: 124 obtained from a single (same) plant species including Arabidopsis while obtaining the claimed functions. Polypeptide sequences having less than 100% or even 90% sequence identities (to SEQ ID NO: 124) obtained from different plant species are also designated as AtExo970 homologues by the Applicant (spec, p. 45, para 2, line 3-4; p.46, para 5, line 1-3). These are all naturally occurring protein sequences that were selected through the course of evolution in the respective plants. The Applicant does not describe expressing any homologue of AtEXO970 from either Arabidopsis or other plant species comprising at least 1 to up to 10% mutant amino acid residues while obtaining the claimed function(s).
The Applicant does not provide any guidance for a skilled artisan to mutate up to 48 amino acid residues anywhere in SEQ ID NO: 124 in AtExo970 protein Arabidopsis while retained the recited function(s) when overexpressed. Moreover, the Applicant describes overexpression of apparently an unrelated (to AtExo970) gene, AtKin960, encoding a protein (SEQ ID NO: 422) having only 21.2% sequence identity to instant SEQ ID NO: 124 (data not shown) also improved draught tolerance, albeit “mildly” (spec, p.23, para 1, last 4 lines).
Current status of the art also does not provide any guidance to mutate up to 10% of SEQ ID NO: 124 anywhere in the entire length of the protein while retaining/achieving the claimed function(s) while being overexpressed.
Undue trial and error experimentations would be needed to mutate up to 10% of SEQ ID NO: 124 anywhere in the entire length of the protein while retaining/achieving the claimed function(s) while being overexpressed.
Based on breadth of the claims, lack of any working example, lack of guidance in the instant description or in prior art, the specification at the time of the application filed would not have taught one skilled in the art how to make and use the full scope of the claimed invention without performing undue experiments.
Claims 5-6 remain rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for replacing the native promoter or the native gene (which includes the native promoter) encoding said AtExo970 protein, does not reasonably provide enablement for all other mutations of the native promoter or the gene encoding said AtExo970, homolog or ortholog thereof, that does not abolish or overexpress the expression of the native protein AtExo970 or the homolog or ortholog thereof. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the invention commensurate in scope with these claims.
The Applicant describes screening about 27,000 Arabidopsis T-DNA activation tag lines and thee d200 mutant lines to identify plants in which silique (pod) length is not dramatically affected by the stress (spec, page 20, para 5, line 10-13). Subsequent analysis with a mutant line (d200) with water stress condition help identifying the At3g27970 gene, which is annotated as “zinc ion binding exonuclease family protein possibly involved in ribosomal RNA (rRNA) processing” and named AtExo970 in the instant invention (P. 22, para 4, line 1-3). Constitutive overexpression of AtExo970 improves drought tolerance and productivity (p. 25, para 7).
Constitutive overexpression of AtExo970 improves drought tolerance and productivity (p. 25, para 7). All the “homologs” (based on sequence homology/identity) of AtExo970 from different plant species, as described, are cloned in plant expression vector(s) under the control of a constitutive promoter (e.g. 35S CaMV) and used to transform different plants (page 28-45). A loss of function mutation is achieved for AtExo970 via CRISPR based gene editing (page 54, last para). However, the Applicant does not describe any result in terms of its phenotype/trait especially in relation to water and/or nutrient deficiency.
The Applicant does not provide any guidance regarding how myriad different mutations including in the promoter and or the gene outside the protein coding region(s) would affect tolerance to water and/or nutrient deficiency in a plant. Current status of the art also does not provide any guidance regarding how different modifications of the native promoter(s) and/or the gene(s) itself of AtExo970 gene or its homologs or orthologs would affect the tolerance to water and/or nutrient deficiency in a plant.
Undue trial and error experimentations would be needed to determine what modifications/mutations of the native promoter AtExo970 gene or the gene itself outside the protein coding exons of homologs or orthologs, would increase tolerance to water and/or nutrient deficiency in a plant. There can be myriad of such mutations including specific indel and/or substitution mutation(s) in the native promoters(s), terminator and/or intron(s). Even overexpression of the gene may not result in increasing tolerance to water and/or nutrient deficiency if the mutated gene encodes functionally a very different protein with altered activity or no functional activity at all, in terms of tolerance to water and/or nutrient deficiency.
Based on breadth of the claims, lack of any working example, lack of guidance in the instant description or in prior art, the specification at the time of the application filed would not have taught one skilled in the art how to make and use the full scope of the claimed invention without performing undue experiments.
Regarding claim 29, the applicant describes several proteins from canola, soybean, corn, wheat, Brachypodium and rice which are identified by sequence identity to AtEXO970 (SEQ ID NO: 124). Some of these native proteins have significantly less sequence identity to instant SEQ ID NO: 124; e.g., TaExo506 (66%), TaExo220 (70%) (spec, p.44, para 2, line 1-2), BdExo960 (69%) (spec, p.45, para 2, line 3-4), GmExo690 and GmExo740 (70%) (spec, p.35, last para, line 1-6), and ZmExo807 (73%) (spec, p.40, para 3, line 3-5). It is note that the Applicant does not define what qualifies as “homolog” (of AtExo970), as recited in claim 29.
Undue trial and error experimentations would be needed to mutate up to 48 amino acid residues anywhere in SEQ ID NO: 124 while retaining/achieving the claimed function(s) while being overexpressed. Undue trial and error experimentations would also be needed to identify specific homolog(s) in specific plant species including Glycine max, Zea may (mays), Triticum aestivum, Brachypodium distachyon, or Oryza sativa whose overexpression would result in the recited gain-of-function trait(s), as recited in claim 29.
Based on breadth of the claims, lack of any working example, lack of guidance in the instant description or in prior art, the specification at the time of the application filed would not have taught one skilled in the art how to use the full scope of the claimed invention without performing undue experiments.
Response to Applicant’s Arguments
Applicant’s arguments dated 8/25/2026 regarding claim rejections are fully considered
but not found persuasive.
Regarding 35 USC 112(a) written description rejections, all of the arguments by the Applicant boil down to “Applicant has amended claim 1 to recite a nucleic acid sequence encoding SEQ ID NO: 124 or a sequence at least 90% identical thereto. Dependent claims have been amended accordingly” (response, p.11, last para). The Applicant argues that “contrary to the Examiner's assertion, Applicant has provided multiple examples of orthologs of AtExo970 exhibiting the same function of increasing tolerance to water and/or nutrient deficiency” (response, p.11, para 4). The Applicant mentions, “multiple working examples of various orthologs overexpressed in plants increasing tolerance to water and/or nutrient deficiency are described. See for instance, Example 8.1 of the specification, where overexpression of canola ortholog BnExo317 improved biomass, water-use efficiency, and drought tolerance; Examples 9.1, 9.2, and 10 of the specification, where overexpression of soybean orthologs GmExo090 and GmExo0740 improved drought tolerance, water-use efficiency, and increased root biomass under low nitrogen and phosphorus conditions; Examples 11.1 and 11.2, where overexpression of corn ortholog ZmExo846 improved drought tolerance, water-use efficiency, and increased shoot and root biomass under low nitrogen and phosphorus conditions. See also Example 16 (Brachypodium ortholog) and Example 17.2 (additional soybean example)” (response, p.11, para 5).
Regarding 112(a) scope of enablement rejections, all of the arguments by the Applicant boil down to claim amendments.
The Examiner disagrees. Regarding 112(a) written description rejections, the Applicant does not describe expressing a single homolog of AtEXO970 polypeptide comprising at least one to up to 10% mutant amino acids (i.e., up to 48 amino acids) to obtain the claimed gain-of-functions of “increasing of tolerance to water and/or nutrient deficiency in a plant” when overexpressed. The Applicant does not describe overexpressing even a mutated AtEXO970 comprising at least one to up to 48 amino acids in Arabidopsis either to obtain the claimed gain-of-functions of “increasing of tolerance to water and/or nutrient deficiency in a plant”. Thus, the examples of the “homologs” of AtExo970 are not interpreted as representative examples of sequences having at least 90% sequence identity to instant SEQ ID NO: 124.
Regarding 112(a) scope of enablement rejections, Applicant’s arguments are fully considered but not found persuasive, as described above.
Conclusion
No claim is allowed.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any nonprovisional extension fee (37 CFR 1.17(a)) pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the mailing date of this final action.
Contact Detail
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JAY CHATTERJEE whose telephone number is (703)756-1329. The examiner can normally be reached (Mon - Fri) 8.30 am to 5.30 pm..
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J.C.
/Jay Chatterjee/Examiner, Art Unit 1662
/BRATISLAV STANKOVIC/ Supervisory Patent Examiner, Art Units 1661 & 1662
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