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 .
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 14 January 2026 has been entered.
Claim Status
Claims 40-57 are newly, presented, pending, and examined on the merits.
Claim Scope and Language
No clarification has been provided as to what can or cannot be considered a container. Applicant has failed to clarify whether a growth chamber comprising many petri dishes should be considered a container and if not, why such a scenario should be considered distinct from a 24 well plate being considered a container. This issue will still exist even is the claims are amended to be kit claims. Currently, the claims are simply drawn to containers and the additional recitations are just intended uses of the containers and are thus non-limiting.
The term “deconvoluting” does not have clear meaning the art as applied to populations of organisms. Given the lack of clear art accepted meaning, the specification must provide a clear meaning of the term. The specification fails to do so.
There is nothing in claim 50 and its dependent claims which requires that embryo explant of different genotypes be co-cultured together. The term “co-culture” in the claim is only in reference to the Agrobacterium being cultivated with the explant.
Claim 50 as claimed is little more than the standard method of Agrobacterium transformation of plant. Given the random nature of transformation, it is almost certain that each independent transgenic event with be genotypically distinct (see indefiniteness rejection below regarding “at least 4 distinct known genotypes”). Standard methods of selection of transformants and basic characterization of the transgenic events meet the limitations of the screening process. This means any graduate student working a lab generating transgenic plants using Agrobacterium transformation of embryo explants would be infringing the method as claimed.
Applicant is urged to consider the broadest reasonable interpretation of the claims when making amendments and consider their contribution over the prior art which is voluminous given the extreme breadth of the instant claims.
Response to Arguments – Indefiniteness
Applicant's arguments filed 14 January 2026 have been fully considered but they are not persuasive. The response failed to clarify what should or should not be considered a container other than to note claim 67 of the specification which does nothing to clarify what is and is not a container in the context of the instant claims. Further, the amendments have raised additional grounds of indefiniteness.
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 40-49, 51-52, and 54 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.
Claims 40-49 are drawn to “containers” comprising a mixture having an inoculum and a population of embryo explants. This raises several grounds of indefiniteness.
The specification fails to provide any specific definition for a “container.” This means that the plain meaning must be applied to the claims. The term is being interpreted as anything which is capable of containing subject matter recited in the claim is encompassed in the scope of claim. This alone does not raise concerns of indefiniteness, but the following issues do: 1) Multi-compartment culture plates. Below is an image of a 24-well culture plate. Would each well be considered a container or would the culture plate as whole be considered a “container?” This question can be applied to any divided apparatus which can contain explants or germplasm. 2) Is a growth chamber used to grow tissue culture a “container.” 3) Is a greenhouse a “container?” The question above make clear that where to draw the line as to what should and should not be considered a “container” in light of this application is not clear. As such, the metes and bounds of the claims cannot be determined.
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Embryo explants comprising “at least 4 distinct known genotypes” is recited in claims 40 and 50. The meaning and known and distinct are unclear in the context of the claims. How different must two plants be to be considered “distinct” genotypes? If they differ by a single allele but are otherwise identical, can they be considered distinct? This question is critical, because most prior art practicing genome editing are encompassed in such a scenario as there are often a variety of alleles generated by genome editing methods. Further, what does “known” mean in the context of the claim? At what point must the genotype be known? How knowledge regarding the genomic sequence of a plant must be determined for the genotype to be considered known? Must the entire genome be sequenced? Is knowledge differing alleles at a single locus sufficient? Because none of the questions have obvious answers, the metes and bounds of the claims cannot be determined.
Claims 41 recites “substantially homozygous.” It is unclear how much of the genome of a plant must be fixed to be deemed, “substantially homozygous.” As such, the metes and bounds of the claims cannot be determined.
Claims 51-52 recite “deconvoluting.” The meaning of this term is never clearly defined in the specification nor does it have a clear art accepted meaning. What is stated in the specification suggests that the term may have something to do with marker-assisted selection, but the statements in the specification never make clear what additional steps must be practiced to “deconvolute” a population of plants. The Examiner notes that usage of the word “deconvolute” appears to be applied to data set typically and not plant populations.
Claim 54 recites, “further comprising fingerprinting the at least 4 distinct known varieties before co-cultivating.” Tian et al (cited in obviousness rejection below) teach fingerprinting more than 20k maize varieties and creation of a database for contains the “fingerprints” of said varieties. If a person of skill in the art were practicing the method of claim 50 and used 4 of the more than 20k varieties in the fingerprint database of Tian et al, would they be considered infringing the method of claim 54? Or would a person working in the art have to generate fingerprint for the variety de novo to infringe the claim? Given the lack of clarity of this issue, the metes and bounds of the claim cannot be determined.
Failure to Further Limit
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.
Claims 41-49 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. The additional recitations in claims 41-49 are intended uses of the container of claim 40 and thus they do not further limit claim 40. Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
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) 40-49 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Hosseini et al 2014 (Journal of Applied Biotechnology Reports 1:1, p.17-21).
The claims are drawn to “containers.”
“a recitation of the intended use of the claimed invention must result in a structural difference between the claimed invention and the prior art in order to patentably distinguish the claimed invention from the prior art. If the prior art structure is capable of performing the intended use, then it meets the claim.” (MPEP ¶ 7.37.09).
It is a reasonable interpretation that the additional recitations are simply intended uses of the “containers.” Note that the Applicant could have claimed kits comprising a container and explants, but they did not. Further, note that the word “comprise” means to be made of. No containers are made of a mixture of explants, so only the intended use interpretation applied here makes sense (see indefiniteness rejection above).
Hosseini et al show petri dishes in figures 2 and 3. These are “containers” and as such anticipate and claims drawn to “a container.”
Claim(s) 50-53 and 55-56 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Omer et al 2013 (International Journal of Genetic Engineering 3:2 p. 7-14).
Omer discloses a composition of maize germplasm comprising thirteen different maize genotypes that Agrobacterium (introduced via an inoculation medium) was used to transform embryos of the thirteen varieties with a vector comprising the BAR gene selectable marker (Abstract and Methods). The Agrobacterium must be co-cultured with the plant tissue to achieve plant transformation. Further, they use a PCR assay as a marker to determine the presence of the BAR gene which is linked to the NPK1 transgene and thus if identifying plants having the BAR gene, they are also identifying plants having the NPK1 transgenic genotype (Figure 5). The ratio of genotypes used was predetermined by the number immature zygotic embryos present on one ear (left column, p. 8). Accordingly, claims 50-51, 53, and 55-56 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Omer.
Claim(s) 50-53 and 55-56 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Char et al 2017 (Plant Biotechnology Journal 15: p.257-268).
Char discloses the use of CRISPR/Cas gene editing to modify both the ZmAgo18a and ZmAgo18b loci in maize genotypes Hi-II and B104 (Abstract). They teach that genes encoding gRNAs were provided to direct the targeted modification and that genotyping primers (molecular markers) were used in the assessment of the mutations (these are genetic markers as recited in claim 34, Table S1). Note that the maize transformation used Agrobacterium-based transformation of embryo explants (See Experiment Procedures section). Each distinct mutation is a distinct genotype. Accordingly, claims 50-53 and 55-56 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Char.
Claim(s) 50-52, 55, and 57 rejected under 35 U.S.C. 102(a)(1) as being anticipated by Ko et al 2004 (Crop Science 44: p.1825-1831).
Ko et al disclose Agrobacterium-mediated transformation of 13 different soybean (dicot) cultivars. In this method, embryonic tissues (immature cotyledons) are co-cultured with the transforming Agrobacterium. Transformants were selected by both hygromycin resistance and GUS expression (can be considered two genetic markers for indication of the genomic insertion, a modification). The Examiner concludes that Applicant intended such a broad interpretation of “genetic markers” to be applied to the claims given that claim 53 states that “wherein screening comprises a molecular technique.” If a narrower reading of “genetic markers” was intended, then claim 53 would not further limit claim 50. Accordingly, claims 50-52, 55, and 57 are rejected as being anticipated by Ko et al.
Response to Arguments - Claim Rejections - 35 USC § 102
Regarding Boyd: Applicant's amendments filed 14 January 2026 have overcome the rejection of record. Namely, requiring that explants are necessary for the claims.
Regarding Hosseini: Applicant's arguments filed 14 January 2026 have been fully considered but they are not persuasive. The disclosure of Hosseini meets the limitations of the claims, because only a container is being claim all further recitations are simply intended uses of the containers.
Regarding Omer and Char: Applicant's arguments filed 14 January 2026 have been fully considered but they are not persuasive.
In response to applicant's argument that the references fail to show certain features of the invention, it is noted that the features upon which applicant relies (i.e., co-culture of embryo explants of distinct known genotypes) are not recited in the rejected claim(s). Although the claims are interpreted in light of the specification, limitations from the specification are not read into the claims. See In re Van Geuns, 988 F.2d 1181, 26 USPQ2d 1057 (Fed. Cir. 1993).
Further, it is noted that each independent transgenic event can be considered a distinct genotype. Note that the term “known” is indefinite in the context of the claims.
Contrary to Applicant’s assertion, Omer did in fact genotype the plants to a limited extent when they confirmed presence of the BAR gene (Item 2.3 in Omer et al).
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claim(s) 54 is/are rejected under 35 U.S.C. 103 as being unpatentable over Omer et al 2013 (International Journal of Genetic Engineering 3:2 p. 7-14) as applied to claims 50-51, 53, and 55-56 above, and further in view of Tian et al 2021 (Agriculture 11: p. 597-611).
Claim 54 is drawn to the method of claim 50 further comprising fingerprinting the at least 4 distinct known genotypes before co-cultivating.
Omer teaches all the limitations of claim 50. See anticipation rejection above.
Omer does not teach fingerprinting the different varieties before co-culturing.
Tian et al teach fingerprinting more than 20k maize varieties and creation of a database for contains the “fingerprints” of said varieties. They also teach the importance of a fingerprint of maize varieties for “maize variety management, market monitoring, and intellectual property protection.”
At the time filing, it would have been prima facie obvious for a person of ordinary generate a fingerprint for all their varieties given the teaching of Tian et al that the fingerprint allows for “maize variety management, market monitoring, and intellectual property protection.”
Response to Arguments - Claim Rejections - 35 USC § 103
Applicant's arguments filed 14 January 2026 have been fully considered but do not apply as the claim had been canceled.
Conclusion
No claims are allowed.
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