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 1-4, 9-10, 13, 15-16, 25, 33, 39-41, 49-55, and 60-65 are pending and examined on the merits.
Claims 1, 3, 9, 13, 39, 49, 51, 54, and 64-65 are currently amended.
The Objections and Rejections of Record are Withdrawn Unless Repeated Below
The claims objections and rejection of record are withdrawn due to amendments made to the claims in the claim set submitted 4 June 2026.
Claim Rejections - 35 USC § 112
Indefiniteness
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.
Claim 15 is rejected and claims 39-41, 49-55, and 60-64 remain 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 pre-AIA the applicant regards as the invention.
Claim 13 has been amended to recite, “wherein said expression cassette is operably linked to a heterologous sequence.” Claim 15 which depends from claim 13 recites, “where said expression cassette further comprises at least one polynucleotide of interest being operatively linked to the transcription regulating nucleotide sequence.” It is unclear how the “at least one polynucleotide of interest” is supposed to be interpreted when claim 13 already requires, “wherein said expression cassette is operably linked to a heterologous sequence.” As such, the metes and bounds of the claim cannot be determined.
Regarding Claims 39-41, 54-55, and 60-63: claims 39 and 54 recite at least one k-mer associated with the desired gene expression. It is unclear what is intended by the word associated in this context. Even if one assumes a relatively narrow interpretation meaning that the k-mer is linked on the chromosome, the boundaries are unclear as to how close the k-mer must be to the start of the CDS to be deemed “associated.” As such, the metes and bounds of the claims cannot be determined. Claims 40-41, 55, and 59-63 are rejected for depending from indefinite claims and failing to recite additional limitations that would render the claim definite.
Response to Arguments - Indefiniteness
Applicant's arguments filed 4 June 2026 have been fully considered but they are not persuasive.
The rejection regarding the “functional fragment” language has been overcome by Applicant’s statements screen captured below, which makes clear that functional fragment recitation only applies to the SEQ ID NOs recited and not variants of the SEQ ID NOs having less than 100% identity to the recited SEQ ID NOs.
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Applicant urges that the meaning of “associated” is clear. Applicant recites the screen capture below.
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This argument is not persuasive, because Applicant appears to want to have it both ways. On one hand by citing paragraph 33, they want it interpreted as synonymous with “operably linked to.” On the other hand, they want it to be read in terms of functional influence, which would seem to suggest that trans elements would also seem to be encompassed. This second broader interpretation, greatly increases the burden of providing adequate written description to such an enormous. In fact, such a broad scope seems to be a potentially unreasonable interpretation of the claims. Given that two very disparate interpretations of the claims are suggested, the metes and bounds of the claims cannot be determined.
Lack of Written Description
The following is a quotation 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.
Claims 1-4, 9-10, 13, 15-16, 25, 33, 39-41, 49-55, and 60-65 remain rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
Many of the claims are product-by-process claims. For examination purposes, the process by which something is made is only considered if it materially affects the final structure of the claimed product. These claims have the further difficulty that no claims have a distinct point of comparison. This results in the claims having no real structural limitations. Even method claims do not limit the proximity of the k-mer to CDS as there is no upper bound recited in the claims. Claims 39-41, 49-55, and 60-65 have no structural limitations. The claims that are limited are still quite broad as they encompass functional fragments without a minimum length of SEQ ID NOs:1-6 and variants of SEQ ID NOs: 1-6 with as little as 60% identity to said SEQ ID NOs.
The instant disclosure describes variants of the native promoters set forth in SEQ ID NOs: 2, 3, and 5 which have been modified to remove the GATCTG motifs. The variants were able to more uniformly drive expression of a luciferase gene in a transient expression system in tobacco (Example 1). They also describe that the native promoter set forth in SEQ ID NO:2 can drive expression of the AHAS herbicide tolerance gene when stably transformed in soybean. Examples 2-4 are prophetic so they do not add substantially to the written description provided.
These descriptions are insufficient, because they fail to describe the limitlessly broad and amorphous claims in the case of claims 39-41, 49-55, and 60-65. The instant disclosure fails to describe any truncations or variants of SEQ ID NOs: 1, 4, or 6 functionally (working examples).
Given the broad scope of the claimed genus, the lack of working examples and the failure to describe the structures required to confer the claimed function, one of skill in the art would not have recognized that Applicant was in possession of the claimed genus at the time of filing.
Response to Arguments – Lack of Written Description
Applicant's arguments filed 4 June 2026 have been fully considered but they are not persuasive.
Applicant urges that the disclosure describes the method used to identify putative promoters and that this method can be used to identify any promoter within the scope of the claims. Applicant also urges that the disclosure describes the working examples of SEQ ID NOs:1, 4, and 6. Applicant also urges that breadth of the claim is not a test for written description but the question is whether or not the specification conveys possession of the claimed invention.
Of course, breadth of the claim must be determined to assess satisfaction of the written description requirement. How could person assess that someone was in possession of something with knowing what that something is? There is no reasonable person of ordinary skill in the art that would consider Applicant to be possession of the scope of claims 39-41, 49-55, and 60-65. They have no structural limitations required. Regarding the other rejected claims, the instant disclosure fails to describe any truncations or variants of SEQ ID NOs: 1, 4, or 6 functionally (working examples). With no working examples and no description in the prior art to provide guidance on the functionally required domains of the claimed promoter, a person of ordinary skill also would not have recognized as Applicant being possession of the broad scope of the claims.
Scope of Enablement
Claims 1-4, 49-53, and 60 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 transcriptional regulating sequences in operable linkage with a DNA sequence that is intended to be transcribed, does not reasonably provide enablement for using a transcriptional regulating sequence not in operable linkage with another sequence. 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.
The claims encompass segments of DNA with potential promoter activity not operably linked to a segment of DNA to be transcribed. In the absence of such fusion, the specific use of these segments of DNA is unclear. As such, claims 1-4, 13, 49-53, 60, and 66 are rejected under 35 U.S.C. 112(a) for lacking enablement throughout the scope of the claims.
Response to Arguments – Scope of Enablement
Applicant's arguments filed 4 June 2026 have been fully considered but they are not persuasive.
Applicant urges that the scope of the claims no longer encompass promoter fragments in isolation.
This argument is not persuasive, because claims 1-4, 49-53, and 60 still do not require that the promoter/transcription regulating nucleotide sequence be in operable linkage with a sequence that is transcribed. Without such a requirement, a significant scope of the claim encompasses embodiments which a person of ordinary skill would not know how to use. All enabled embodiments within the scope of the rejected claims are of the promoter/transcription regulating nucleotide sequence be in operable linkage with a sequence that is transcribed; thus, the claims should be limited as such.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 1-4, 13, 49-53, and 60-61 remain rejected under 35 U.S.C. 101 because the claimed invention is directed to products of nature without significantly more. The claim(s) encompass genomic fragments of DNA that are indistinguishable from the products of nature. The claimed regulatory sequences can be achieved by truncating full-length promoters from which they are derived.
This rejection could be overcome by requiring that the transcriptional regulatory sequences are in operable linkage with a heterologous sequence.
Response to Arguments - 35 USC § 101 – Products of Nature
Applicant's arguments filed 4 June 2026 have been fully considered but they are not persuasive.
Applicant urges that the claims are not merely directed to a naturally occurring sequence as found in nature, because they require that at least one occurrence of GATCTG has been eliminated from the sequence.
This argument is not persuasive, because genomic segments are still encompassed in the scope of the claims. This is the case, because promoters that are made via truncating a genomic sequence to eliminate the GATCTG motif are still indistinguishable from the genomic segment in the native chromosome. In Ass’n for Molecular Pathology v. Myriad Genetics, Inc., 569 U.S. 576, 589-91, 106 USPQ2d 1972, 1978-79 (2013), the Courts found that simply isolating DNA does not render it patent eligible. The example of the truncation discussed above is nothing more that isolated DNA. SEQ ID NO:1 of Zhang et al is an actual example of such an isolated promoter made via truncation.
Claims 39-41 remain rejected under 35 U.S.C. 101 because the claimed invention is directed to a method that amounts to no more than mental processes without significantly more. The claim(s) recite(s) (a) analyze RNA sequence expression datasets across tissue types from a plant species; (b) identify at least one k-mer associated with the desired gene expression; (c) identify a CDS having said k-mer upstream of said CDS; (d) select at least 100bp…nucleotide sequence upstream from said CDS: thereby identifying a promoter sequence. This judicial exception is not integrated into a practical application, because no application is required by the claims. These can all be done as mental steps.
Note that claim 54 which has the additional step of modifying the sequence to remove a k-mer is not rejected in this rejection, because the claim has a material step that actually requires manipulation of a molecule.
Response to Arguments – 35 USC § 101 – Abstract Process
Applicant's arguments filed 4 June 2026 have been fully considered but they are not persuasive.
Applicant urges that the claims amount to more than mental steps. Applicant further urges that the method is not directed to an abstract idea in the absence of technological context but a bioinformatic method for identifying promoter sequences from biological datasets, wherein the identified promoter can be used for downstream genetic engineering.
This argument is not persuasive, because the claimed methods are nothing more than observing natural phenomena all of which can done as mental processes. Computers typically are used to aid in processing the large amount of data, but the claimed methods are still simply observations of natural processes. As noted above, claim 54 which has the additional step of modifying the sequence to remove a k-mer is not rejected in this rejection, because the claim has a material step that actually requires manipulation of a molecule. Claim 54 requires an application of the observed natural phenomena, hence, it is patent eligible.
Claim Rejections - 35 USC § 102
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 49-53 and 60-65 remain rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kumar-Sahoo et al 2015 (Plant Mol Biol Rep 33: p. 178-199).
Kumar-Sahoo teach a constitutive DaDVFLt4- promoter from Dahlia mosaic virus which they characterized. When they cloned this promoter from the DaMV genome, they truncate the region such that two GATCTG elements were removed. Note that the isolated promoter region is between the vertical bars below and the GATCTG elements are underlined. The DaDVFLt4- promoter was fused to GFP and GUS coding sequence in the Agrobacterium vectors pKDaMVFLt4-GFP and pKDaMVFLt4-GUS and transformed into Agrobacterium strains (p. 180-183). The transformed strains were used to transform Arabidopsis. Being that this DaDVFLt4- is demonstrated to support a greater expression level than the well-studied 35S CaMV promoter in dicots, it is expected that DaDVFLt4- will also support constitutive expression in soybean and thus can be considered a soybean promoter. As such, claims 49-53 and 60-65 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kumar-Sahoo et al.
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Response to Arguments – 35 USC § 102 – Kumar-Sahoo
Applicant's arguments filed 4 June 2026 have been fully considered but they are not persuasive.
Applicant urges that the claims have been amended to overcome the rejection.
This argument is not persuasive, because the products disclosed by Kumar-Sahoo are still encompassed in the broad scope of the claims. The only structural limitations to the still rejected claims are that one instance of GATCTG has been deleted. The promoter Kumar-Sahoo meets this requirement.
Claim(s) 39-41, 49-55, and 60-64 remain rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zhang (US 20150376643 A1) as evidenced by Schmutz et al 2025 (Genbank NC_016090.4).
Zhang et al disclose constitutive promoter set forth in SEQ ID NO:1 which was identified of analysis of soybean expression data across tissues (Example 1). Analysis of the chromosomal contig (Schmutz et al) from which SEQ ID NO:1 was isolated found that a GATCTG motif was 8183bp upstream of the SEQ ID NO:1 sequence. In isolating SEQ ID NO:1, this upstream GATCTG motif was removed (deleted). They teach expression cassettes (operably linked to heterologous nucleotides including herbicide tolerance gene, vectors, Agrobacterium, and transformed plants (of species including soybean) all comprising SEQ ID NO:1 (claims and Examples). As such, claims 1-2, 4, 9-10, 13, 15-16, 25, 33, 39-41, and 49-55, and 60-64 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zhang as evidenced by Schmutz et al.
Response to Arguments – 35 USC § 102 - Zhang
Applicant's arguments filed 4 June 2026 have been fully considered but they are not persuasive.
Applicant urges that just because at GATCTG motif 8183 bp upstream of SEQ ID NO:1 was “removed” when SEQ ID NO:1 was isolated that does not amount to anticipation of the claims. Applicant also urges that the claimed methods require analysis of RNA expression datasets across tissues, identification of the GATCTG associated with desired gene expression, identification of a CDS, and selection of an upstream region to identify the promoter sequence.
This argument is not persuasive, because the claims are still broad enough to be encompass the disclosures of Zhang et al. The Examiner made clear in the “Claim Interpretation” section of the non-final office action mailed 12/05/2025 that the claims are very broad because there is no upper limit as to the size of upstream region selected for the promoter. Applicant failed to heed this guidance.
In regard to the rejected method claims, Zhang et al disclosed the following:
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Accordingly, claims 39-41, 49-55, and 60-64 remain rejected as being anticipated by Zhang as evidenced by Schmutz et al.
Conclusion
No claims are 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).
Applicant is encouraged to cancel claims 49-53 and 60-65 as there no way that product claims without any structural limitations can be allowed.
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 extension fee 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 date of this final action.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to MATTHEW R KEOGH whose telephone number is (571)272-2960. The examiner can normally be reached M-Th 7-4:30, half day on Fridays.
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/MATTHEW R KEOGH/Primary Examiner, Art Unit 1663
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