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, 8-10, 13, 15-16, 25, 33, 39-41, 49-55, and 59-66 are pending and examined on the merits.
Claims 3, 8-9, 15-16, 25, 33,40-41, 51-53, and 59-60 are currently amended.
Claim Interpretation
The claims have few to no structural limitations. As they are product-by-process claims with no strict point of comparison in any of the claims which would limit the final product that is claimed. This means that the scope of most of the claims encompasses a significant amount of prior art and products of nature which are not patent eligible. It should further be noting that there is large body of “promoter bashing” studies from the 90s and 00s which are encompassed in the scope of the claims. Note that for method claims 39-41 and 54-55, there is no upper limit as to the size of upstream region selected for the promoter. Please consider this when making amendments.
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.
Claims 1-4, 8-10, 13, 15-16, 25, 33, 39-41, 49-55, and 59-66 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 pre-AIA the applicant regards as the invention.
The claims all directly or indirectly recite “Motif,” “k-mer,” or “GATCTG.” Claim 59 recites: “wherein the at least one k-mer is GATCTG.” Claims 64-66 recite, “the k-mer GATCTG.” The specification directly says that “Motif,” “k-mer,” or “GATCTG” are interchangeable, but claim 59 suggests that they are not. If they are interchangeable, claim 59 fails to further limit claim 54. The use of the phrase “k-mer GATCTG,” because if these terms are interchangeable, “k-mer GATCTG” is redundant. Given the conflict between what the specification says about interchangeability of the terms and how the claims use the terms, the metes and bounds of the claims cannot be determined.
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Claims 8 and 13 recite, “nucleotide sequence having at least 60%, 65%..to any one of the nucleic acid sequences set forth in in SEQ ID NO:1, SEQ ID NO:2… SEQID NO:6, or a functional fragment thereof.” It is unclear if the functional fragment thereof is referring to the only the SEQ ID NOs recited in the claims or if functional fragment of polynucleotide sequences at least 60% identical to the SEQ ID NOs recited in the claims are also intended to be encompassed by the claims. As such, the metes and bounds of the claims cannot be determined.
Claims 9-10, 13, 25, 33, 64 require to “expression cassette.” Yet, dependent claims 15-16 and 65 further require that the “expression cassette” be in operable linkage to a polynucleotide of interest. What is an expression cassette without operable linkage to a sequence that is transcribed? If it unclear what structural limitations are intended to be imparted by the phrase “expression cassette,” given that the claim drafter does not believe that an “expression cassette” requires a transcriptional regulating sequence be in operable linkage to a polynucleotide of interest. As such, the metes and bounds of the claim cannot be determined.
Regarding Claims 39-41, 54-55, and 59-63: 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.
Claim 66 recites “A soybean promoter…” It is unclear if a promoter element originating from soybean or a promoter element that is able to support expression in soybean is being claimed. Claims 50-51 have the problem.
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, 8-10, 13, 15-16, 25, 33, 39-41, 49-55, and 59-66 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for 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.
The instant disclosure describes variants of the native promoters set forth in SEQ ID NOs: 2, 4, 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.
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.
Scope of Enablement
Claims 1-4, 8-10, 13, 49-53, 60, and 66 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 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, 8-10, 13, 49-53, 60, and 66 are rejected under 35 U.S.C. 112(a) for lacking enablement throughout the scope of the claims.
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, 8-10, 13, 15, 49-53, 60-61, and 64-66 are 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.
Claims 39-41 are 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.
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) 1-4, 8-10, 13, 15, 25, 33, 49-53, and 60-66 is/are 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. Note that give the indefinite language regarding “functional fragments” of the SEQ ID NOs recited in the claims, these claim limitations are also met by Kumar-Sahoo. As such, claims 1-4, 8-10, 13, 15, 25, 33, 49-53, and 60-66 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Kumar-Sahoo et al.
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Claim(s) 1-2, 4, 8-10, 13, 15-16, 25, 33, 39-41, and 49-64 is/are 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:! 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, 8-10, 13, 15-16, 25, 33, 39-41, and 49-64 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Zhang as evidenced by Schmutz et al.
Conclusion
No claims are allowed.
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/MATTHEW R KEOGH/Primary Examiner, Art Unit 1663