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 of group I drawn to claims 1-12 in the reply filed on 06/04/2025 is acknowledged. Because applicant did not distinctly and specifically point out the supposed errors in the restriction requirement, the election has been treated as an election without traverse (MPEP § 818.01(a)).
Claim Status
Claims 1-20 are pending.
Claims 13-20 are withdrawn as drawn to an unelected invention.
Claims 1-12 are examined on the merits.
Response to Amendment
The amendment to the claims filed on 6/12/2023 does not comply with the requirements of 37 CFR 1.121(c) because there are two sets of claims, a first set dated 03/27/2023 and a second set dated 06/12/2023. The second set (06/12/2023) appears to be an amended set, having been submitted after the first, however the claims are not marked as original, amended, or cancelled and the claimset itself is not labeled as amended. Amendments to the claims filed on or after July 30, 2003 must comply with 37 CFR 1.121(c) which states:
(c) Claims. Amendments to a claim must be made by rewriting the entire claim with all changes (e.g., additions and deletions) as indicated in this subsection, except when the claim is being canceled. Each amendment document that includes a change to an existing claim, cancellation of an existing claim or addition of a new claim, must include a complete listing of all claims ever presented, including the text of all pending and withdrawn claims, in the application. The claim listing, including the text of the claims, in the amendment document will serve to replace all prior versions of the claims, in the application. In the claim listing, the status of every claim must be indicated after its claim number by using one of the following identifiers in a parenthetical expression: (Original), (Currently amended), (Canceled), (Withdrawn), (Previously presented), (New), and (Not entered).
(1) Claim listing. All of the claims presented in a claim listing shall be presented in ascending numerical order. Consecutive claims having the same status of “canceled” or “not entered” may be aggregated into one statement (e.g., Claims 1–5 (canceled)). The claim listing shall commence on a separate sheet of the amendment document and the sheet(s) that contain the text of any part of the claims shall not contain any other part of the amendment.
(2) When claim text with markings is required. All claims being currently amended in an amendment paper shall be presented in the claim listing, indicate a status of “currently amended,” and be submitted with markings to indicate the changes that have been made relative to the immediate prior version of the claims. The text of any added subject matter must be shown by underlining the added text. The text of any deleted matter must be shown by strike-through except that double brackets placed before and after the deleted characters may be used to show deletion of five or fewer consecutive characters. The text of any deleted subject matter must be shown by being placed within double brackets if strike-through cannot be easily perceived. Only claims having the status of “currently amended,” or “withdrawn” if also being amended, shall include markings. If a withdrawn claim is currently amended, its status in the claim listing may be identified as “withdrawn—currently amended.”
(3) When claim text in clean version is required. The text of all pending claims not being currently amended shall be presented in the claim listing in clean version, i.e., without any markings in the presentation of text. The presentation of a clean version of any claim having the status of “original,” “withdrawn” or “previously presented” will constitute an assertion that it has not been changed relative to the immediate prior version, except to omit markings that may have been present in the immediate prior version of the claims of the status of “withdrawn” or “previously presented.” Any claim added by amendment must be indicated with the status of “new” and presented in clean version, i.e., without any underlining.
(4) When claim text shall not be presented; canceling a claim.
(i) No claim text shall be presented for any claim in the claim listing with the status of “canceled” or “not entered.”
(ii) Cancellation of a claim shall be effected by an instruction to cancel a particular claim number. Identifying the status of a claim in the claim listing as “canceled” will constitute an instruction to cancel the claim.
(5) Reinstatement of previously canceled claim. A claim which was previously canceled may be reinstated only by adding the claim as a “new” claim with a new claim number.
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.
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 1-12 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.
Claims 1, 8 and 11 recite “ZmDA2” indicating that they refer to the ZmDA2 protein while claims 2, 4-5, 7 and 9-10 recite “ZmDA2 gene”. These recitations render the claims indefinite because the names appear to be arbitrary and the specification does not specifically define the metes and bounds of these terms. While the specification discloses features that may be associated with the named gene and protein, no specific definitions have been provided for each.
Further, this term does not appear to be known in the art because while DA2 is a name given to a protein found in Arabidopsis thaliana, it is not clear which specific sequence this refers to in maize, especially given that there are several members of the E3 ubiquitin ligases comprising RING finger proteins including GAIN WIDTH AND WIEGHT2 (GW2) which was identified in rice (Li, Page 1, Abstract; Li, Page 15, Paragraph 0269). Therefore, given that there is a rice gene named GW2 which encodes an E3 ubiquitin ligase and an Arabidopsis gene named DA2 that encodes a ubiquitin ligase it is unclear which E3 ubiquitin ligase sequences in maize correspond to GW2 or DA2 and therefore the scope of the term ZmDA2 (Zea mays DA2) is unclear because the metes and bounds of the structure imparted by that term is not clear.
The dependent claims provide the following limitations on the independent claim:
Claim 6 provides the non-limiting recitation that the modified plants of claim 1 can comprise a polynucleotide sequence selected form a group of sequences, however given the language of the claim this sequence is not required to be modified ZmDA2 polypeptide or polynucleotide.
Claims 8, 10 and 12 are drawn to the modified plant of claims 1, 2 and 8, respectively, and provide a list of alternatives that further limit the modification. Several of these alternatives refer to the sequence of SEQ ID NO: 3 as a reference sequence but focus on a position with respect to that reference sequence and do not limit the scope of the claim to sequences having any other relationship to SEQ ID NO: 3 nor do they make clear the relationship between SEQ ID NO: 3 and ZmDA2 sequences.
Claim 11 is drawn to the modified plant of claim 8 and provides a list of alternatives that further limit the claim. One of these alternatives limits the plant to those that comprise a chromosomal sequence in the ZmDA2 gene that has at least 70% sequence identity to SEQ ID NO: 3 outside of the modification.
With respect to 1 and 2 above, while these claims recite a reference sequence, the relationship between this reference sequence and ZmDA2 sequences is not clear and therefore, despite this recitation this additional limitation does not clarify the metes and bounds of the structures associated with ZmDA2 and ZmDA2 gene.
With respect to 3 above, while claim 11 includes a further limitation which limits the scope of ZmDA2 sequences to a finite genus of sequences having specific bounds there are two aspects of this claim which prevent it from limiting the scope of the claim to definite subject matter.
First, claim 11 is drawn to the modified plant of claim 8 having one of four additional limitations which are offered as alternatives, therefore part ii) of the claim which includes the reference to SEQ IDNO: 3 is not required by the claim.
Second, part ii) of the claim uses the following language “comprises a chromosomal sequence in the ZmDA2 gene that has at least 70% ... sequence identity to SEQ ID NO: 3 in the regions outside of the modification”. SEQ ID NO: 3 is a polynucleotide sequence that is 4237 nucleotides in length and therefore sequences which share 70% sequence identity with SEQ ID NO: 3 can differ by 1271 and these differences can be insertions, deletions, and any substitution creating an extremely large and diverse pool of potential sequences. This is complicated by the language of the claim which indicates that it is the genomic ZmDA2 sequence outside of the modification that shares this level of identity with the reference sequence.
Claim 11 depends on claim 8, the broadest reasonable interpretation of claim 8 includes the plant of claim 1 wherein the modification comprises a deletion, an insertion, a substitution, an inversion, a duplication or any combination thereof. Therefore, the mutation can be nearly any mutation. Given that the mutation can be any mutation whatsoever the starting sequence which undergoes the modification to arrive at the sequence of claim 11 is not clear and therefore the relationship between ZmDA2 sequences and sequences which have undergone any mutation whatsoever and retain at least 70% sequence identity to SEQ ID NO: 3 is not clear.
Therefore, the metes and bounds of the structure conferred by the recitation of ZmDA2 and ZmDA2 gene are not clear and the additional limitations of the dependent claims fail to limit the claim scope to definite subject matter. Dependent claims are included.
Claim 1 recites, “a genomic modification that reduces or disrupts the activity of ZmDA2” as compared to a plant not comprising the modification. This limitation is unclear because the scope conferred by the term “disrupts” is not clear. The plain meaning of disrupted activity means reduced activity or reduced ability to perform its biological function, however, given that the claim presents reduced activity and disrupted activity as alternatives, these terms appear to confer distinct scopes to the claim. It is not clear how the scope imparted by these two terms differs. The specification provides no definition of “disrupt” or “disrupts” and appears to use this term interchangeable with “reduce” or “reduces”, thus the metes and bounds imparted on the claim by the recitation of “disrupted activity” are not clear and the claim is rejected as indefinite. All dependent claims are included.
Claims 10 and 12 depend on claim 2 and claim 8 respectively and add limitations drawn to modifications found within specific genomic regions of a reference sequence. Given the language of the claims it is unclear whether the broadest reasonable interpretation of the scope of each claim is drawn to a modified plant having a modification within the specified region of the exact sequence of SEQ ID NO: 3 or if instead the modification must be present within a region of any ZmDA2 sequence corresponding the specified sequence in reference sequence SEQ ID NO: 3.
This is unclear because of the use of the term “reference sequence SEQ ID NO: 3”. Including the term “reference” in the claim indicates that the sequence does not need to be the exact sequence of SEQ ID NO: 3, however because the claim omits the use of clear language such as “the modification is comprised within a genomic region corresponding to about position 1689 to about position 3733 of reference sequence SEQ ID NO: 3” it is unclear whether the claim scope is limited to plants comprising the exact sequence of SEQ ID NO: 3 which comprises a modification in the specified range or whether it is more broadly drawn to a ZmDA2 sequence having a modification in a region which corresponds to the specified regions in the reference sequence SEQ ID NO: 3.
For clarity, claim 12 includes distinct language in sections i) and ii). In section i) the claims states “with reference to sequence ID NO: 3” making clear that the claimed sequence only has to have the modification in the region which corresponds to the specified region in the reference. In contrast section ii) uses the language “of reference sequence SEQ ID NO: 3” and it is this language which is rejected as indefinite.
Written Description
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 1-12 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 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.
Applicant claims a modified corn plant, seed, plant part or plant cell comprising a genomic modification that reduces or disrupts the expression or activity of a ZmDA2 polypeptide as compared to an otherwise identical plant that lacks the mutation.
Claim 2 is drawn to the plant, seed, plant part or plant cell where the modification is in at least one allele of an endogenous ZmDA2 gene.
Claim 3 is drawn to the modified plant wherein the genomic modification is an endogenous ZmDA2 gene encoding a protein having at least 70% sequence identity to the sequence of SEQ ID NO: 2.
Claim 4 depends on claim 2 and is drawn to the modification being in a transcribable region or in a downstream region of a sequence coding for a RING domain in as ZmDA2 gene.
Claim 5 depends on claim 4 and is drawn to modifications where the modification is in the exon of the ZmDA2 gene, an intron of the ZmDA2 gene or an exon region and intron region of the ZmDA2 gene.
Claim 6 depends on claim 1 and is drawn to the plants that are heterozygous for the modification, homozygous for the modification, comprise a polynucleotide sequence selected from the group consisting of SEQ ID NOs: 9, 11-34, or exhibits increased yield, grain yield estimate per plant, grain yield estimate, as compared toa n otherwise identical plant that lacks the modification.
Claim 7 depends on claim 6 is drawn to plants that comprise a first modification in a first allele of the ZmDA2 gene and a second modification in a second allele of the ZmDA2 gene, the two modifications being different from one another.
Claim 8 depends on claim 1 and is drawn to modifications which comprise a deletion, insertion, a substitution, inversion, duplication or a combination thereof, is located about 1960 nucleotides or more downstream from the 5’ end of reference sequence SEQ ID NO: 3, is located at about 1473 nucleotides or more upstream from the 3’ end of reference sequence SEQ ID NO: 3, comprises a deletion, substitution, disrupts or alters the activity of ZmDA2, as compared to the activity of ZmDA2 in an otherwise identical plant that lacks the modification or confers an altered phenotype to the plant as compared to the phenotype of an otherwise identical plant that lacks the modification.
Claim 9 depends on claim 2 and is drawn to plants comprising one of a series of specific modifications in at least one allele of the ZmDA2 gene.
Claims 10 depends on claim 2 and is drawn to plants where the modification is comprised within a genomic region of about position 1689-3733, 1964-2765 or 2654-2676 of reference sequence SEQ ID NO: 3.
Claim 11 depends on claim 8 and is drawn to plants where the modification comprises a deletion of at least 1 consecutive nucleotide, the chromosomal sequence in the ZmDA2 gene has at least 70% sequence identity to SEQ ID NO: 3 in the regions outside the modification, the modification alters the ubiquitin ligase activity of ZmDA2, or the altered phenotype comprises an increase in yield or a specific group of yield related traits.
Claim 12 depends on claim 8 and is drawn to plants wherein the modification is comprises within a genomic region from about nucleotide position 1964 to about nucleotide position 1987 or from about nucleotide position 2665 to about nucleotide position 2765 of reference sequence SEQ ID NO: 3.
These claims include several areas which add breadth. First, the independent claim is drawn to a modified corn plant, plant seed, corn plant part, or corn plant cell. Therefore, any single cell from any corn plant, in planta, in culture, or in any other state falls within in the scope of the claim. This is the case even if the plant or plant cell has previously undergone extensive modification such as EMS mutagenesis or any other mutation or modification. Similarly this scope includes any non-modified plant that is considered to be a corn plant.
A second recitation in the independent claim which adds breadth is the recitation of “a genomic modification that reduces or disrupts the activity of ZmDA2, as compared to the activity of ZmDA2 in an otherwise identical corn plant”.
This phrase adds breadth in several different ways. The use of the term genomic modification is broad. The specification defines genomic modification as follows, “”genomic modification” (also referred to as “modification”) or “genomic edit” (also referred to as “edit”) refers to any modification to a genomic nucleotide sequence as compared to a wild-type or control plant. A genomic modification or genomic edit comprises a deletion, an insertion, a substitution, an inversion, a duplication, or any combination thereof” (Instant Specification, Page 47, Paragraph 0133). Thus, this scope includes changes to the order of the nucleotides but also includes any “modification to the sequence”. The broadest reasonable interpretation of modification to the sequence includes epigenetic modifications such as glycosylation’s or the additions of any other epigenetic marks, tags or any other possible modification to the target nucleotide sequence.
Given the language recited above, the independent claim is broadly drawn to any genomic modification whatsoever that reduces or disrupts the activity of ZmDA2. Therefore, not only are genomic modifications in the ZmDA2 coding sequence included in this scope, any genomic modification whatsoever which reduces or disrupts the activity of ZmDA2 to any degree as compared to an otherwise identical corn plant that lacks the modification is included in the scope of the claim. To illustrate, this would include modifications that alter the expression of a transcription factor important in promoting the expression of the ZmDA2 gene, any modification which affects the activity or expression of any cofactor involved in ZmDA2 activity, or even any modification that affects the concentration of the materials required for ZmDA2 activity including those that reduce the concentration of ZmDA2 targets or those that reduce the materials ZmDA2 requires to carry out its activity.
Further, the independent claim recites “reduces or disrupts the activity of ZmDA2”. This broad recitation indicates that any function or activity of ZmDA2 can be reduced or disrupted. This includes canonical functions associated with DA2 genes but also any other function whatsoever carried out by that gene or protein. Additionally, the use of the term reduced indicates that the activity can be diminished to any degree.
Finally as discussed in the indefiniteness rejection above, the scope conferred by the term ZmDA2 is unclear but broad.
In contrast to this broad scope, Applicant describes designing gene editing vectors targeting the ZmDA2 coding sequence of SEQ ID NO: 1 (Specification, Page 49, Example 1, Paragraphs 0150-0151). Applicant describes generating corn plants comprising gene edited ZmDA2 alleles and devoid of editing T-DNA sequences, using the construct described earlier. These plants were outcrossed to produce hybrid plants (Specification, Page 51, Example 2). The plants were genotyped using amplicon sequencing, and plants with diverse edits were selected. These hybrid plants then underwent yield trails where ear size related traits were measured and analyzed (Specification, Page 52, Example 3).
Applicant describes the design of two other gene editing constructs targeting the ZmDA2 gene to produce novel variants which also target the same ZmDA2 gene downstream of the RING domain. One of these constructs targeted the same exact region as the construct described above, the other construct targeted a different exon (Specification, Page 53, Example 4, Paragraphs 0167-0168). The use of one of these constructs produced at least ten different modified plants having either heterozygous (one modified and one wild type allele) or biallelic (a different modification in each allele) modifications (Specification, Page 57, Table 6).
Applicant does not describe a representative number of species across the claimed genus of plants, seeds, plant parts, or plant cells comprising any modification whatsoever which reduces or disrupts the activity of a ZmDA2 polypeptide as compared to an otherwise identical plant, seed, plant part, or plant cell that lacks the modification. Applicant does not describe a structure-function relationship reduced to practice in a maize plant or plant cell wherein the expression or activity of a ZmDA2 polypeptide is reduced other than in the plants produced using their three gene editing constructs which target a single sequence and two of which targe the same region of that sequence. None of the plants including hybrid offspring plants produced using any of these three constructs was demonstrated to have altered ZmDA2 activity.
Instead, applicants genotyped plants in each target region by sequencing with one of these modifications described in table 3. Then applicants assessed kernel/ear/yield potential of plants with edited alleles. Applicant’s summarized the findings from this field trial data as follows: “The field trial data presented in this example demonstrates that targeted editing of the ZmDA2 gene leads to the improvement of key yield component traits in hybrid corn, suggesting that these genomic edits may produce a dominant effect on increased yield traits” (Specification, Page 53, Paragraph 0166). In applicant’s own words the genomic edits may produce a dominant effect on increased yield traits. There is no definite causal link between these edits and these traits rather a correlation between the presence of these edits in hybrid corn and certain yield components.
Importantly, while example 1 states that “The edited ZmDA2 gene can encode modified proteins with, reduced, disrupted, or altered activity” and “The modified ZmDA2 produced from the edited ZmDA2 gene may have reduced or disrupted activity, yet still be able to interact with other proteins” there are no other recitations in any of applicant’s examples of the word activity (Specification, Page 49, Paragraph 0150; Specification, Page 50, Paragraph 0152). There does not appear to be any assessment of the activity of ZMDA2 in any of applicant’s examples and there is no demonstration of any link between the edited ZmDA2 gene and reduce or disrupted activity other than yield phenotypes which may be a result of the targeted editing. Even if the editing is linked to these phenotypes there is no evidence to suggest that it is reduced activity of ZMDA2 that is responsible for the phenotype, rather the edit could result in the phenotype through some other mechanism not related to ZmDA2 activity.
Further and importantly, applicants provide only examples in what appears to be a single inbred corn plant line which target a single specific sequence which is in stark contrast to the claims which read broadly on any corn plant with any modification which reduces or disrupts ZmDA2 activity.
Given the breadth of the genera encompassed by the claims, the described species are not sufficiently representative. The Applicant has not set forth the structure-function relationship for the claimed genus such that one of ordinary skill in the art would be able to recognize which members of the vast and functionally recited genus of mutants at any location of the genome in any corn plant species would have reduced or disrupted activity of the ZmDA2 polypeptide.
Given the breadth of dependent claims the additional limitations do not overcome the lack of description for the scope of the claimed invention. Even in those dependent claims (Claims 2-5 and 9-10) were applicant has limited the plants to those which have the modification in an endogenous ZmDA2 gene, applicant has not described a representative number of species across the genus of the ZmDA2 genes and proteins such that the ordinary artisan would be able to determine if a sequence was a ZmDA2 sequence, even claim 3, drawn to a ZmDA2 protein having at least 70% sequence identity to SEQ ID NO: 2 (431 amino acids in length) includes sequences which differ from the sequence of SEQ ID NO: 2 by 129 amino acids, creating a genus which remains broad and diverse.
Further, even in claim 9 which limits the modified sequences to specific sequences the claims remain broadly drawn to any corn plant cell whatsoever which comprises one of these sequences as long as these cells have ZMDA2 activity which is reduced or disrupted. Again, it is not clear how to identify if ZmDA2 activity is reduced or disrupted and therefore the ordinary artisan would not be able to determine if they were in possession of the claimed invention without a structure function relationship between a specific modification in a specific target sequence in a corn plant cell and the function of reduced or disrupted activity of ZmDA2.
The prior art does not provide resolution for the lack of description provided by Applicant. Specifically, there is insufficient teaching in the art for the ordinary artisan to be able to determine if the broad genus of any modification in any sequence in the genome would result in reduced ZmDA2 activity. Therefore, the specification fails to sufficiently describe the claimed invention in such full, clear, concise, and exact terms that a skilled artisan would recognize that Applicant was in possession of the invention as broadly claimed at the time of filing.
Claim Rejections - 35 USC § 112 (Enablement)
Claims 1-12 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 enablement requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to enable one skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention.
Applicant claims a modified corn plant, seed, plant part or plant cell comprising a genomic modification that reduces or disrupts the expression or activity of a ZmDA2 polypeptide as compared to an otherwise identical plant that lacks the mutation.
Claim 2 is drawn to the plant, seed, plant part or plant cell where the modification is in at least one allele of an endogenous ZmDA2 gene.
Claim 3 is drawn to the modified plant wherein the genomic modification is an endogenous ZmDA2 gene encoding a protein having at least 70% sequence identity to the sequence of SEQ ID NO: 2.
Claim 4 depends on claim 2 and is drawn to the modification being in a transcribable region or in a downstream region of a sequence coding for a RING domain in as ZmDA2 gene.
Claim 5 depends on claim 4 and is drawn to modifications where the modification is in the exon of the ZmDA2 gene, an intron of the ZmDA2 gene or an exon region and intron region of the ZmDA2 gene.
Claim 6 depends on claim 1 and is drawn to the plants that are heterozygous for the modification, homozygous for the modification, comprise a polynucleotide sequence selected from the group consisting of SEQ ID NOs: 9, 11-34, or exhibits increased yield, grain yield estimate per plant, grain yield estimate, as compared toa n otherwise identical plant that lacks the modification.
Claim 7 depends on claim 6 is drawn to plants that comprise a first modification in a first allele of the ZmDA2 gene and a second modification in a second allele of the ZmDA2 gene, the two modifications being different from one another.
Claim 8 depends on claim 1 and is drawn to modifications which comprise a deletion, insertion, a substitution, inversion, duplication or a combination thereof, is located about 1960 nucleotides or more downstream from the 5’ end of reference sequence SEQ ID NO: 3, is located at about 1473 nucleotides or more upstream from the 3’ end of reference sequence SEQ ID NO: 3, comprises a deletion, substitution, disrupts or alters the activity of ZmDA2, as compared to the activity of ZmDA2 in an otherwise identical plant that lacks the modification or confers an altered phenotype to the plant as compared to the phenotype of an otherwise identical plant that lacks the modification.
Claim 9 depends on claim 2 and is drawn to plants comprising one of a series of specific modifications in at least one allele of the ZmDA2 gene.
Claims 10 depends on claim 2 and is drawn to plants where the modification is comprised within a genomic region of about position 1689-3733, 1964-2765 or 2654-2676 of reference sequence SEQ ID NO: 3.
Claim 11 depends on claim 8 and is drawn to plants where the modification comprises a deletion of at least 1 consecutive nucleotide, the chromosomal sequence in the ZmDA2 gene has at least 70% sequence identity to SEQ ID NO: 3 in the regions outside the modification, the modification alters the ubiquitin ligase activity of ZmDA2, or the altered phenotype comprises an increase in yield or a specific group of yield related traits.
Claim 12 depends on claim 8 and is drawn to plants wherein the modification is comprises within a genomic region from about nucleotide position 1964 to about nucleotide position 1987 or from about nucleotide position 2665 to about nucleotide position 2765 of reference sequence SEQ ID NO: 3.
These claims include several areas which add breadth. First, the independent claim is drawn to a modified corn plant, plant seed, corn plant part, or corn plant cell. Therefore, any single cell from any corn plant, in planta, in culture, or in any other state falls within in the scope of the claim. This is the case even if the plant or plant cell has previously undergone extensive modification such as EMS mutagenesis or any other mutation or modification. Similarly this scope includes any non-modified plant that is considered to be a corn plant.
A second recitation in the independent claim which adds breadth is the recitation of “a genomic modification that reduces or disrupts the activity of ZmDA2, as compared to the activity of ZmDA2 in an otherwise identical corn plant”.
This phrase adds breadth in several different ways. The use of the term genomic modification is broad. The specification defines genomic modification as follows, “”genomic modification” (also referred to as “modification”) or “genomic edit” (also referred to as “edit”) refers to any modification to a genomic nucleotide sequence as compared to a wild-type or control plant. A genomic modification or genomic edit comprises a deletion, an insertion, a substitution, an inversion, a duplication, or any combination thereof” (Instant Specification, Page 47, Paragraph 0133). Thus, this scope includes changes to the order of the nucleotides but also includes any “modification to the sequence”. The broadest reasonable interpretation of modification to the sequence includes epigenetic modifications such as glycosylation’s or the additions of any other epigenetic marks, tags or any other possible modification to the target nucleotide sequence.
Given the language recited above, the independent claim is broadly drawn to any genomic modification whatsoever that reduces or disrupts the activity of ZmDA2. Therefore, not only are genomic modifications in the ZmDA2 coding sequence included in this scope, any genomic modification whatsoever which reduces or disrupts the activity of ZmDA2 to any degree as compared to an otherwise identical corn plant that lacks the modification is included in the scope of the claim. To illustrate, this would include modifications that alter the expression of a transcription factor important in promoting the expression of the ZmDA2 gene, any modification which affects the activity or expression of any cofactor involved in ZmDA2 activity, or even any modification that affects the concentration of the materials required for ZmDA2 activity including those that reduce the concentration of ZmDA2 targets or those that reduce the materials ZmDA2 requires to carry out its activity.
Further, the independent claim recites “reduces or disrupts the activity of ZmDA2”. This broad recitation indicates that any function or activity of ZmDA2 can be reduced or disrupted. This includes canonical functions associated with DA2 genes but also any other function whatsoever carried out by that gene or protein. Additionally, the use of the term reduced indicates that the activity can be diminished to any degree.
Applicant provides enabling guidance on designing gene editing vectors targeting the ZmDA2 coding sequence of SEQ ID NO: 1 (Specification, Page 49, Example 1, Paragraphs 0150-0151). Applicant also provides guidance on generating corn plants comprising gene edited ZmDA2 alleles and devoid of editing T-DNA sequences, using the construct described earlier. These plants were outcrossed to produce hybrid plants (Specification, Page 51, Example 2). The plants were genotyped using amplicon sequencing, and plants with diverse edits were selected. These hybrid plants then underwent yield trails where ear size related traits were measured and analyzed (Specification, Page 52, Example 3).
Applicant provides guidance on the design of two other gene editing constructs targeting the ZmDA2 gene to produce novel variants which also target the same ZmDA2 gene downstream of the RING domain. One of these constructs targeted the same exact region as the construct described above, the other construct targeted a different exon (Specification, Page 53, Example 4, Paragraphs 0167-0168). The use of one of these constructs produced at least ten different modified plants having either heterozygous (one modified and one wild type allele) or biallelic (a different modification in each allele) modifications (Specification, Page 57, Table 6).
The breadth of the claim includes plants, seeds, plant parts, or plant cells comprising any modification whatsoever which reduces or disrupts the activity of a ZmDA2 polypeptide as compared to an otherwise identical plant, seed, plant part, or plant cell that lacks the modification. Applicant does not describe a structure-function relationship reduced to practice in a maize plant or plant cell wherein the expression or activity of a ZmDA2 polypeptide is reduced other than in the plants produced using their three gene editing constructs which target a single sequence and two of which targe the same region of that sequence. None of the plants including hybrid offspring plants produced using any of these three constructs was demonstrated to have altered ZmDA2 activity.
Therefore, applicant does not provide any enabled guidance on how to determine if the activity of ZmDA2 has been reduced or disrupted.
Instead, applicants describe genotyping plants in each target region by sequencing with one of these modifications described in table 3. Then applicants assessed kernel/ear/yield potential of plants with edited alleles. Applicant’s summarized the findings from this field trial data as follows: “The field trial data presented in this example demonstrates that targeted editing of the ZmDA2 gene leads to the improvement of key yield component traits in hybrid corn, suggesting that these genomic edits may produce a dominant effect on increased yield traits” (Specification, Page 53, Paragraph 0166). In applicant’s own words the genomic edits may produce a dominant effect on increased yield traits. There is no definite causal link between these edits and these traits rather a correlation between the presence of these edits in hybrid corn and certain yield components.
Importantly, while example 1 states that “The edited ZmDA2 gene can encode modified proteins with, reduced, disrupted, or altered activity” and “The modified ZmDA2 produced from the edited ZmDA2 gene may have reduced or disrupted activity, yet still be able to interact with other proteins” there are no other recitations in any of applicant’s examples of the word activity (Specification, Page 49, Paragraph 0150; Specification, Page 50, Paragraph 0152). There does not appear to be any assessment of the activity of ZMDA2 in any of applicant’s examples and there is no demonstration of any link between the edited ZmDA2 gene and reduce or disrupted activity other than yield phenotypes which may be a result of the targeted editing. Even if the editing is linked to these phenotypes there is no evidence to suggest that it is reduced activity of ZMDA2 that is responsible for the phenotype, rather the edit could result in the phenotype through some other mechanism not related to ZmDA2 activity.
Further and importantly, applicants provide only examples in what appears to be a single inbred corn plant line which target a single specific sequence which is in stark contrast to the claims which read broadly on any corn plant with any modification which reduces or disrupts ZmDA2 activity.
Therefore, one of ordinary skill in the art would be unable to make and use or predictably practice the methods of the claimed invention without undue experimentation, i.e., it would be necessary to test every possible mutation at every possible locus in any corn plant cell of any background with the exception of the modifications produced by targeting the two regions within the single target gene in the single genetic background described by Applicant.
The prior art does not provide resolution for the lack of description provided by Applicant. Specifically, there is insufficient teaching in the art for the ordinary artisan to be able to determine if the broad genus of any modification in any sequence in the genome would result in reduced ZmDA2 activity. Therefore, the specification fails to provide sufficient enabled guidance such that a skilled artisan would be able to make and use the full scope of the claimed invention at the time of filing. The lack of predictability in the art and the lack of guidance provided by Applicant would not have enabled one of ordinary skill in the art to predictably make and use the full scope of the claimed invention without undue experimentation.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
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.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-6, 8 and 11 are rejected under 35 U.S.C. 103 as being unpatentable over Li, US 2016/0194651 A1, published July 7, 2016.
With respect to claim 1, Li teaches a plant (Arabidopsis thaliana) comprising a genomic modification (T-DNA insertion mutants) that reduces or disrupts the activity of a DA2 protein (Li, Page 16, Paragraph 0284; Li, Page 18, Paragraph 0297), as compared to the activity of DA2 in an otherwise identical plant (Wild-type plants and seeds), that lacks the modification (Li, Page 16, Paragraph 0284). Li teaches that these mutant plants demonstrate a mutant phenotype of larger and heavier seeds, increased seed number per silique and increased seed yield (Li, Page 16, Paragraph 0284).
Further, Li teaches that DA2 polypeptides and nucleotides can be identified in any plant species of interest in particular crop plants such as maize (Li, Page 5, Paragraph 0080). Li also teaches that the methods herein are not limited to particular plant species and expression or activity of DA2 may be reduced in any plant species of interest (Li, Page 8, Paragraph 0141) and further teaches that suitable plants for use in accordance with the invention of Li include maize (Li, Page 14, Paragraph 0246).
With respect to claim 1, Li does not explicitly teach a maize plant comprising a genomic modification that reduces or disrupts the activity of a DA2 protein, as compared to the activity of DA2 in an otherwise identical plant.
At the time of filing it would have been obvious to the ordinary artisan to modify the plants and methods of Li in order to generate a modified maize plant comprising homologous mutations to those found in the Arabidopsis thaliana DA2 mutant plants of Li, in order to produce modified maize plants having enhanced seed size, seed number and seed yield.
This would have been obvious because Li teaches Arabidopsis thaliana mutant plants carrying T-DNA insertions in the DA2 gene which resulted in the mutant phenotype of larger and heavier seeds, increased seed number per silique and increased seed yield. Further, Li states explicitly that the methods taught in Li are applicable in any plant species, with maize plants listed as a specific example of plants suitable for use in accordance with any aspect of the invention.
The ordinary artisan would have been motivated to generate these mutations in the maize plants in order to increase the yield in maize plants by recapitulating the seed related phenotypes demonstrated in the model plant Arabidopsis thaliana, specifically, larger, heavier seeds, more seeds per fruit and increased seed yield per plant. This would have been motivating because it represents a maize plant having increased yield, with these plants farmers could increase yields without making any other changes. The farmers would be motivated to buy these seed and seed producers would be motivated to generate these seeds.
Therefore, claim 1 is rejected as obvious under Li.
With respect to claim 2, Li teaches all of the limitations of claim 1 taught above, see above. Further, Li teaches that the DA2 polypeptide may expressed endogenously in a plant cell (Li, Page 14, Paragraph 0262).
With respect to claim 3, Li teaches all of the limitations of claim 1 taught above, see above. Further, Li teaches that in some preferred embodiments a DA2 polypeptide may comprise a RING domain having an amino acid sequence of residues 65-107 of SEQ ID NO: 30 which is annotated as Zm_GI-220961719.pro (Li, Page 4, Paragraph 0066). This suggests that SEQ ID NO: 30 is DA2 from maize (Zea mays or Zm). SEQ ID NO: 30 from Li shares 98.8 percent sequence identity with instant SEQ ID NO: 2 (See Figure 1 below).
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Figure 1: Description of alignment of instant SEQ ID NO: 2 and SEQ ID NO: 30 of Li.
With respect to claim 4, Li teaches all of the limitations of claim 2 taught above, see above. Further, Li teaches a T-DNA insertion into a transcribable region of the DA2 gene, specifically Li teaches an insertion into the seventh exon of the Arabidopsis thaliana DA2 gene (Li Page 17, Paragraph 0295).
With respect to claim 5, Li teaches all of the limitations of claim 4 taught above, see above. Further, as noted above, Li teaches a T-DNA insertion into the seventh exon of the Arabidopsis thaliana DA2 gene (Li Page 17, Paragraph 0295).
With respect to claim 6, Li teaches all of the limitations of claim 1 taught above, see above. Further, Li teaches homozygous da2-1 mutants produce seed size changes (Li, Page 17, Paragraph 0290).
With respect to claim 8, Li teaches all of the limitations of claim 1 taught above, see above. Importantly, Li teaches T-DNA insertions into the DA2 gene (Li, Page 16, Paragraph 0284).
With respect to claim 11, Li teaches all of the limitations of claim 8 taught above, see above. Further, Li teaches that da2 mutant plants demonstrate an altered mutant phenotype of larger and heavier seeds, increased seed number per silique and increased seed yield (Li, Page 16, Paragraph 0284).
With respect to claims 2-6, 8 and 11, Li does not explicitly teach a maize plant comprising a genomic modification that reduces or disrupts the activity of a DA2 protein, as compared to the activity of DA2 in an otherwise identical plant.
At the time of filing it would have been obvious to the ordinary artisan to modify the plants and methods of Li in order to generate a modified maize plant comprising homologous mutations to those found in the Arabidopsis thaliana DA2 mutant plants of Li, in order to produce modified maize plants having enhanced seed size, seed number and seed yield.
This would have been obvious because Li teaches Arabidopsis thaliana mutant plants carrying T-DNA insertions in the DA2 gene which resulted in the mutant phenotype of larger and heavier seeds, increased seed number per silique and increased seed yield. Further, Li states explicitly that the methods taught in Li are applicable in any plant species, with maize plants listed as a specific example of plants suitable for use in accordance with any aspect of the invention.
The ordinary artisan would have been motivated to generate these mutations in the maize plants in order to increase the yield in maize plants by recapitulating the seed related phenotypes demonstrated in the model plant Arabidopsis thaliana, specifically, larger, heavier seeds, more seeds per fruit and increased seed yield per plant. This would have been motivating because it represents a maize plant having increased yield, with these plants farmers could increase yields without making any other changes. The farmers would be motivated to buy these seed and seed producers would be motivated to generate these seeds.
Therefore, claims 2-6, 8 and 11 are rejected as obvious under Li.
Conclusion
All examined claims are rejected.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to BRIAN JAMES SULLIVAN whose telephone number is (571)272-0561. The examiner can normally be reached on 7:30 to 5:00.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Amjad Abraham can be reached on (571)270-7058. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/BRIAN JAMES SULLIVAN/Examiner, Art Unit 1663
/Amjad Abraham/SPE, Art Unit 1663
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