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 1-5, 7, 9-17 and 19-30 are pending.
Claims 1-2, 4-5, 7, 9-17, 19-23 and 26-28 are newly amended.
Claims 29-30 are newly added.
Claims 6, 8 and 18 are newly cancelled.
Claims 1-5, 7, 9-17 and 19-30 are rejected.
Response to Applicant Arguments - Claim Objections
In response to Applicant’s arguments and amendments dated 06/11/2025 the claim objections due to improper multiple dependencies of record are withdrawn.
Response to Applicant Arguments - 35 USC § 112 (Indefiniteness)
In response to Applicant’s arguments and amendments dated 06/11/2025 the indefiniteness rejections of record are withdrawn. However, applicant’s amendments to the claims require new indefiniteness rejections.
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 12-15 and 29-30 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.
A broad range or limitation together with a narrow range or limitation that falls within the broad range or limitation (in the same claim) may be considered indefinite if the resulting claim does not clearly set forth the metes and bounds of the patent protection desired. See MPEP § 2173.05(c). In the present instance, claims 12-15 and 29-30 recite the broad recitation of banana gene id numbers (Ma numbers), which are immediately followed by specific sequence identification numbers in parenthesis which is the narrower statement of the range/limitation. The claim(s) are considered indefinite because there is a question or doubt as to whether the feature introduced by such narrower language is (a) merely exemplary of the remainder of the claim, and therefore not required, or (b) a required feature of the claims.
In order to ensure compact prosecution the claims are interpreted to be drawn to the genes corresponding to the Ma numbers.
Response to Applicant Arguments - 35 USC § 103)
Applicant’s arguments and amendments to the claims dated 06/11/2025 have been fully considered and are not found to be persuasive.
Applicant’s arguments are drawn to the following theme:
Obviousness rejections of the claimed invention based on the teachings of Slaymaker require impermissible hindsight because Slaymaker is not drawn to CRISPR editing of plant cells and because Slaymaker does not teach or suggest editing banana to increase shelf life, let alone provide a practical disclosure of banana editing.
To support this applicant provides the following details:
Slaymaker only suggests manipulation of 1-aminocyclopropane-1-carboxylic acid synthase (ACS) and 1-aminocyclopropane-1-carboxylic acid oxidase (ACO) by inserting an antisense or truncated copy of the gene into the genome. This is in stark contrast to the claimed invention which is drawn to methods of inducing a loss of function mutation in a banana nucleic acid sequence.
Slaymaker simply recites banana in an alphabetical list of over one hundred plants and the office has provided no reasoning as to why one of skill in the art would specifically select banana as a target plant from the disclosure of Slaymaker.
The disclosure of Slaymaker does not provide any practical guidance that would allow one of skill to arrive at the pending claims.
With respect to 1. above, applicant’s argument is not found to be persuasive because given applicant’s definition of loss of function mutation in the specification, the gene silencing approaches described in Slaymaker appear to be considered loss of function mutations.
Specifically, the instant specification states that “As used herein “loss of function” mutation refers to a genomic aberration which results in reduced ability (i.e., impaired function) or inability of the component of the ethylene biosynthesis pathway to facilitate in the synthesis of ethylene or precursor thereof” (Specification, Page 27, Lines 8-10).
Given this definition, Slaymaker’s teachings of the insertion of an antisense or truncated copy of the target gene is inserted into the plant’s genome to suppress ACC synthase gene expression appear to be the introduction of a loss of function mutation into the target genes. This is because Slaymaker teaches a genomic aberration (insertion of a mirror-image or truncated copy of the synthase gene) which results in reduced ACC gene expression. Slaymaker teaches that ACC synthase is the enzyme responsible for catalyzing the second to last step in ethylene biosynthesis and as such this gene must be expressed and the mRNA translated to produce the protein. Slaymaker teaches hindered expression of ACS which would result in decreased protein and reduced ability of ACS to facilitate in the synthesis of ethylene or a precursor thereof.
Therefore, Slaymaker teaches a genomic aberration which results in reduced ability of ACS to facilitate the synthesis of ethylene. Further, Slaymaker teaches that these same approaches can be used to down regulate ACC oxidase expression.
Applicant’s arguments are not found to be persuasive because as demonstrated in the analysis above Slaymaker’s teachings of the insertion of antisense and truncated genes corresponding to target genes clearly fall within the scope of a “loss of function mutation” as defined in the specification.
With respect to 2 above, applicant’s arguments are not found to be persuasive . Applicant urges that given the disclosure of Slaymaker the ordinary artisan would not have been motivated to select banana as a target plant for the methods of using Cas9 to affect fruit-ripening taught in Slaymaker. This is not found to be persuasive because while Slaymaker states in paragraph 1192 that “In particular embodiments, the plant is a tomato plant” Slaymaker begins paragraph 1191 by saying that “Ripening is a normal phase in the maturation process of fruits and vegetables. Only a few days after it starts it renders a fruit or vegetable inedible. This process brings significant losses to both farmers and consumers”. This statement provides motivation to modify the ripening process in all plants.
Further, following the recitation of plants to which the CAS9 based methods apply, Slaymaker states the following: “The methods for genome editing using the CRISPR/Cas9 system described herein can be used to confer desired traits on essentially any plant” demonstrating that the method of affecting fruit ripening is not limited to any one species or group.
Contrary to applicant’s arguments a person having ordinary skill in the art at the time of filing would understand that the CRISPR/Cas9 based methods of Slaymaker are applicable to all plants. They would also understand that modifying fruit ripening can prevent crop loss to farmers and prevent food spoilage to consumers, a significant motivation which is of intrinsic agronomic and economic value. The ordinary artisan would understand that Banana fruits ripen and spoil.
Given these teachings from Slaymaker, the ordinary artisan would have been motivated to modify bananas to produce banana fruits having modified ripening. This would allow for enhanced crop yields for farmers and delayed fruit ripening would allow for longer shelf life and prevent food spoilage.
Such a modified banana would be marketable and allow for the purveyor of that variety to charge more. It is this motivation that would have driven the ordinary artisan at the time of filing to apply the method of affecting fruit ripening of Slaymaker to Banana plants.
Additionally, combining the teachings of Slaymaker to arrive at the instantly claimed invention would have been obvious because it is simply combining prior art elements according to known methods to yield predictable results.
Specifically, applicants claim a banana plant comprising a loss of function in a gene encoding an ACS or an ACC oxidase and Slaymaker teaches methods of making loss of function mutations (those mutations that lead to impaired function of the target gene, see applicants definition on Page 27 in lines 8-10 of the specification and teach that these methods are applicable to any plant and include bananas in a list of applicable plants. Therefore, the prior art includes each element claimed with the only different being the lack of actual combination of the claimed elements.
Slaymaker teaches that the versatility of CRISPR/Cas9 based methods and teaches that they can be applied to any plant. This demonstrates that one of ordinary skill in the art could have combined the elements of a loss of function mutation in an ACS or ACO gene and banana plants as the target plant.
These results would have been predictable because applicant’s include protoplast cells in their definition of a plant (Instant Specification, Page 19, Lines 21-23) and methods of generating and transforming protoplast cells are routine, predictable and well known in the art (Slaymaker, Page 386, Paragraph 1131) and further Slaymaker teaches that CRISPR systems can be used to perform efficient and cost effective gene or genome interrogation or editing in plants (Slaymaker, Page 374, Paragraph 1099). Thus combining the elements of Slaymaker would be predictable given that a key characteristic of CRISPR systems is their versatility and applicability to a variety of different organisms and that these systems have been shown to work in plants, particularly in protoplasts.
Therefore, given the above factual inquiries combining the teachings of Slaymaker to arrive at the claimed invention is obvious because it is simply combining prior art elements according to known methods to yield predictable results (MPEP 2143 I. A.) and therefore applicant’s argument that it would not be obvious to choose banana plants given the teachings of Slaymaker are not persuasive.
With respect to applicant’s arguments summarized in 3. above, applicant’s arguments are not found to be persuasive because Slaymaker provides practical guidance on the transformation and gene editing of plant protoplasts that would allow the ordinary artisan to arrive at the instantly claimed invention.
First, applicant has defined plant to include “whole plant(s), a grafted plant, ancestors and progeny of the plants and plant parts, including seeds, fruits, shoots, stems, roots (including tubers), rootstock, scion, and plant cells, tissues and organs” and then states that “The plant may be in any form including suspension cultures, protoplasts, embryos, meristematic regions, callus tissues, leaves, gametophytes, sporophytes, pollen and microspores” (Specification, Page 25, Lines 18-23).
Additionally, as noted above, applicant’s define loss of function mutation as any genomic aberration that results in reduced ability of the component of the ethylene biosynthesis pathway to facilitate in the synthesis of ethylene or precursor thereof.
Therefore, the broadest reasonable interpretation of independent claim 1 includes any banana plant protoplast comprising any genomic aberration in an ACS or ACO gene which results in reduced ability of ACS or ACO to facilitate in the synthesis of ethylene or an ethylene precursor.
The teachings of Slaymaker provide guidance on the generation, transformation and gene editing of protoplast cells and generating protoplasts from a variety of plants is well known and routine practice in the art (Slaymaker, Page 376, Paragraph 1103; Slaymaker, Page 386, Paragraph 1130; Slaymaker, Page 386, Paragraph 1131; Slaymaker, Page 391, Paragraph 1147; and Slaymaker, Page 391, Paragraph 1150).
Therefore, because Slaymaker provides sufficient guidance on the generation, transformation and gene editing of protoplasts applicant arguments that there is no practical guidance in the art for a person of ordinary skill in the art to arrive at the claimed invention is not found to be persuasive.
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.
Due to Applicant’s amendment of the claims, the rejection is modified from the rejection as set forth in the Office action mailed 2/12/2025 as applied to claims 1-4, 9 and 27. Applicant’s arguments filed on 6/11/2025 have been fully considered but they are not persuasive, see above.
Claims 1-4, 9 and 27 remain rejected and claims 5,7, 10-11, 16, 23-26 and 28 are newly rejected under 35 U.S.C. 103 as being unpatentable over Slaymaker (WO 2016/205613 Al).
The obviousness rejections below are grouped based on shared fact pattern and analysis even though they all rely on the same prior art references.
Obviousness rejection against claim 1.
Claim 1 is drawn to a banana plant comprising a loss of function mutation in nucleic acid sequence encoding a 1-aminocyclopropane-1-carboxylate synthase (ACS) or an ACC Oxidase (ACO).
Applicant defines two important terms in the specification.
First, applicant defines “plant” on page 25 in lines 18-22 as follows:
“As used herein “plant” refers to whole plant(s), a grafted plant, ancestors and progeny of the plants and plant parts, including seeds, fruits, shoots, stems, roots (including tubers), rootstock, scion, and plant cells, tissues and organs.
The plant may be in any form including suspension cultures, protoplasts, embryos, meristematic regions, callus tissue, leaves, gametophytes, sporophytes, pollen, and microspores”.
Applicant also defines “loss of function mutation” on page 27 in lines 8-10 as follows:
“As used herein “loss of function” mutation refers to a genomic aberration which results in reduced ability (i.e., impaired function) or inability of the component of the ethylene biosynthesis pathway to facilitate in the synthesis of ethylene or precursor thereof”.
Given these definitions, when viewing the claims in light of the specification the broadest reasonable interpretation of the claims is drawn to the following: any single banana cell, including a protoplast comprising any genomic aberration which results in reduced ability of either ACS or ACO to facilitate in the synthesis of ethylene or a precursor thereof.
With respect to claim 1, Slaymaker teaches plant cells comprising genomic modifications (Slaymaker, Page 411, Paragraph 1192). Slaymaker teaches introducing genomic modifications (aberrations) using CRISPR/Cas9, specifically Slaymaker teaches introducing an antisense or truncated copy of the target ACS or ACO gene (Slaymaker, Page 410, Paragraph 1191). This hinders enzyme expression, impairing the ability of the enzyme (Slaymaker, Page 411, Paragraph 1191). In the case of the ACS and ACO enzymes, this results in impaired ability of these enzymes to facilitate in the synthesis of ethylene or a precursor thereof.
Slaymaker also teaches that parts of a plant including plant cells and protoplasts can be treated according to the methods of the invention of Slaymaker (Slaymaker, Page 381, Paragraphs 1114-1115).
Further, Slaymaker teaches the generation, transformation and gene editing of protoplast cells and generating protoplasts and further teaches that these methods are well known and routine practice in the art (Slaymaker, Page 376, Paragraph 1103; Slaymaker, Page 386, Paragraph 1130; Slaymaker, Page 386, Paragraph 1131; Slaymaker, Page 391, Paragraph 1147; and Slaymaker, Page 391, Paragraph 1150).
Finally, Slaymaker teaches that the methods described by Slaymaker use the CRISPR/Cas9 system and can be used to confer desired traits on essentially any plant including those from the Musa family and in the previous paragraph Slaymaker makes clear that the term plants refers to a variety of different species including Banana (Slaymaker, Pages 380-381, Paragraphs 1111-1112; Slaymaker, Page 379, Paragraph 1110).
With respect to claim 1, Slaymaker does not teach each and every element as set forth in the claim. Specifically, Slaymaker teaches generic methods of using CRISPR/Cas9 systems to modify plants including Banana and then in a separate embodiment teaches methods of using Crispr/Cas9 systems to affect fruit ripening by suppression of ACC synthase gene expression in plants including tomato.
As such, Slaymaker does not disclose a method of using CRISPR/Cas9 systems to target ACC synthase in Banana plants to affect fruit ripening.
At the time of filing given the teachings of Slaymaker it would have been obvious to one of ordinary skill in the art to arrive at the claimed invention because it is simply combining prior art elements according to known methods to yield predictable results.
Specifically, applicants claim a banana plant comprising a loss of function in a gene encoding an ACS or an ACC oxidase and Slaymaker teaches methods of making loss of function mutations (those mutations that lead to impaired function of the target gene, see applicants definition on Page 27 in lines 8-10 of the specification, and teaches that these methods are applicable to any plant and include bananas in a list of applicable plants. Therefore, the prior art includes each element claimed with the only different being the lack of actual combination of the claimed elements.
Slaymaker teaches the versatility of CRISPR/Cas9 based methods and teaches that they can be applied to any plant. This demonstrates that one of ordinary skill in the art could have combined the elements of a loss of function mutation in an ACS or ACO gene and banana plants as the target plant.
These results would have been predictable because applicant’s include protoplast cells in their definition of a plant (Instant Specification, Page 19, Lines 21-23) and methods of generating and transforming protoplast cells are routine, predictable and well known in the art (Slaymaker, Page 386, Paragraph 1131) and further Slaymaker teaches that CRISPR systems can be used to perform efficient and cost effective gene or genome interrogation or editing in plants (Slaymaker, Page 374, Paragraph 1099). Thus combining the elements of Slaymaker would be predictable given that a key characteristic of CRISPR systems is their versatility and applicability to a variety of different organisms and that these systems have been shown to work in plants, particularly in protoplasts.
Therefore, given the above factual inquiries, combining the teachings of Slaymaker to arrive at the claimed invention is obvious because it is simply combining prior art elements according to known methods to yield predictable results (MPEP 2143 I. A.).
Claim 1 remains rejected as obvious in view of the teachings of Slaymaker.
Obviousness rejection against claim 2.
Claim 2 is drawn to a method of increasing the shelf-life of banana comprising:
subjecting any banana plant cell including protoplasts to a DNA editing agent directed at a nucleic acid sequence encoding an ACS or ACO enzyme to produce a mutation which results in impaired function of the ACS or ACO and regenerating a plant from said plant cell.
This broad genus of methods includes the introduction of mutations which reduce the expression of ACS and ACO as lack of expression would impair the function of the gene/enzyme in producing ethylene, see applicant definitions of plant and loss of function mutation at the beginning of the anticipation rejections above.
With respect to claim 2, Slaymaker teaches methods using Cas9 to affect fruit-ripening in plants (Slaymaker, Page 410, Paragraph 1191 and Section Title). Slaymaker teaches methods of using the CRISPR/Cas9 DNA editing agent system to ensure the introduction of one or more directed modifications of the genome of a plant cell (Slaymaker, Page 411, Paragraph 1192).
Specifically, Slaymaker teaches introducing genomic modifications (aberrations) using CRISPR/Cas9, where the genomic modifications are the introduction of an antisense or truncated copy of the target ACS or ACO gene (Slaymaker, Page 410, Paragraph 1191). These modifications hinder enzyme expression, impairing the ability of the enzyme and therefore represent loss of function mutations (Slaymaker, Page 411, Paragraph 1191). In the case of the ACS and ACO enzymes, this results in impaired ability of these enzymes to facilitate in the synthesis of ethylene or a precursor thereof.
Slaymaker also teaches that parts of a plant including plant cells and protoplasts can be treated according to the methods of the invention of Slaymaker (Slaymaker, Page 381, Paragraphs 1114-1115).
Further, Slaymaker teaches the generation, transformation and gene editing of protoplast cells and generating protoplasts and further teaches that these methods are well known and routine practice in the art (Slaymaker, Page 376, Paragraph 1103; Slaymaker, Page 386, Paragraph 1130; Slaymaker, Page 386, Paragraph 1131; Slaymaker, Page 391, Paragraph 1147; and Slaymaker, Page 391, Paragraph 1150).
Additionally, Slaymaker teaches that the methods described by Slaymaker use the CRISPR/Cas9 system and can be used to confer desired traits on essentially any plant including those from the Musa family and in the previous paragraph Slaymaker makes clear that the term plants refers to a variety of different species including Banana (Slaymaker, Pages 380-381, Paragraphs 1111-1112; Slaymaker, Page 379, Paragraph 1110).
Finally, Slaymaker teaches regenerating an edited plant cell to produce a plant therefrom (Slaymaker, Page 411, Paragraph 1192).
With respect to claim 2, Slaymaker does not teach each and every element as set forth in the claim. Specifically, Slaymaker teaches generic methods of using CRISPR/Cas9 systems to modify plants including Banana and then in a separate embodiment teaches methods of using Crispr/Cas9 systems to affect fruit ripening by suppression of ACC synthase gene expression in plants including tomato.
As such, Slaymaker does not disclose a method of using CRISPR/Cas9 systems to target ACC synthase in Banana plants to affect fruit ripening.
At the time of filing given the teachings of Slaymaker it would have been obvious to one of ordinary skill in the art to arrive at the claimed invention because it is simply combining prior art elements according to known methods to yield predictable results.
Specifically, applicants claim a method of modifying fruit ripening in a banana plant by using a targeted DNA editing agent to introduce a loss of function mutation in a gene encoding an ACS or an ACC oxidase and Slaymaker teaches methods of making loss of function mutations (those mutations that lead to impaired function of the target gene, see applicants definition on Page 27 in lines 8-10 of the specification, and teaches that these methods are applicable to any plant and include bananas in a list of applicable plants. Therefore, the prior art includes each element claimed with the only different being the lack of actual combination of the claimed elements.
Slaymaker teaches the versatility of CRISPR/Cas9 based methods and teaches that they can be applied to any plant. This demonstrates that one of ordinary skill in the art could have combined the elements of the introduction of a loss of function mutation in an ACS or ACO gene and banana plants as the target plant.
These results would have been predictable because applicant’s include protoplast cells in their definition of a plant (Instant Specification, Page 19, Lines 21-23) and methods of generating and transforming protoplast cells are routine, predictable and well known in the art (Slaymaker, Page 386, Paragraph 1131) and further Slaymaker teaches that CRISPR systems can be used to perform efficient and cost effective gene or genome interrogation or editing in plants (Slaymaker, Page 374, Paragraph 1099). Thus combining the elements of Slaymaker would be predictable given that a key characteristic of CRISPR systems is their versatility and applicability to a variety of different organisms and that these systems have been shown to work in plants, particularly in protoplasts.
Therefore, given the above factual inquiries, combining the teachings of Slaymaker to arrive at the claimed invention is obvious because it is simply combining prior art elements according to known methods to yield predictable results (MPEP 2143 I. A.).
Claim 2 remains rejected as obvious in view of the teachings of Slaymaker.
Obviousness rejections against claims 3-5, 7, 10-11, 16, 23-26 and 28.
With respect to claim 3, Slaymaker teaches all of the limitations of claim 2, see above. Importantly, Slaymaker teaches regenerating an edited plant cell to produce a plant therefrom (Slaymaker, Page 411, Paragraph 1192).
With respect to claim 4, Slaymaker teaches all of the limitations of claims 2, see above. Further, Slaymaker teaches that CRISPR systems can be self-cleaving in that cleavage of both ends of a CRISPR/Cas cassette can be used to generate transgene-free T0 plants with biallelic mutations without having to perform a crossing or segregating step in T1 plants, this would be beneficial in plants like banana which are not normally sexually propagated (Slaymaker, Page 425, Paragraph 1228).
With respect to claim 5, Slaymaker teaches all of the limitations of claim 2, see above. Importantly, Slaymaker teaches that the CRISPR/Cas9 system produces homozygous mutations in plants (Slaymaker, Page 376, Paragraph 1104).
With respect to claim 7, Slaymaker teaches all of the limitations of claim 2, see above. Importantly, as noted above, Slaymaker teaches the insertion of antisense or truncated copies of the target genes (Slaymaker, Page 410, Paragraph 1191).
With respect to claims 10-11, Slaymaker teaches all of the limitations of claim 2, see above. Importantly, Slaymaker teaches the use of the CRISPR/Cas9 system (Slaymaker, Pages 410-411, Paragraphs 1191-1192).
With respect to claim 16, Slaymaker teaches all of the limitations of claim 2, see above. Importantly, Slaymaker teaches that not only can CRISPR be used to insert antisense or truncated copies of target genes for gene silencing approaches, CRISPR can be used to induce insertion, deletion or substitution mutations of a target polynucleotide (Slaymaker, Page 115, Paragraph 416).
Additionally, Slaymaker teaches that Cas9CRISPR complexes can be designed to allow targeted mutation of multiple genes in plants (Slaymaker, Pages 408-409, Paragraph 1187).
Finally, Slaymaker teaches that in some cases, a single control element could therefore be used to control the transcription of multiple genes simultaneously (Slaymaker, Page 368, Paragraph 1083).
Therefore, Slaymaker teaches DNA editing agents which are directed at multiple target genes either directly or by targeting specific coordinates that then regulate multiple secondary targets.
With respect to claims 23-25, Slaymaker teaches all of the limitations of claim 1, see above.
With respect to claim 26, Slaymaker teaches all of the limitations of claim 1, see above. Importantly, Slaymaker teaches that the CRISPR/Cas9 system can be introduced into plant protoplasts which are then regenerated to plant cells which are then grown and regenerated into plants (Slaymaker, Page 392, Paragraph 1152).
With respect to claim 28, Slaymaker teaches all of the limitations of claim 1, see above. Importantly, Slaymaker teaches the use of the CRISPR/Cas9 system to make genetically modified non-transgenic plants by transiently expressing the CRISPR/Cas9 components in plant protoplasts where the DNA encoding the gene editing system is not integrated into the genome (Slaymaker, Pages 392-393, Paragraphs 1153-1155).
With respect to claims 3-5, 7, 10-11, 16, 23-26 and 28, Slaymaker does not teach each and every element as set forth in the claim. Specifically, Slaymaker teaches generic methods of using CRISPR/Cas9 systems to modify plants including Banana and then in a separate embodiment teaches methods of using Crispr/Cas9 systems to affect fruit ripening by suppression of ACC synthase gene expression in plants including tomato.
As such does not disclose a method of using CRISPR/Cas9 systems to target ACC synthase in Banana plants to affect fruit ripening nor does Slaymaker teach harvesting Banana fruits from the edited plants.
At the time of filing given the teachings of Slaymaker it would have been obvious to one of ordinary skill in the art to arrive at the claimed invention because it is simply combining prior art elements according to known methods to yield predictable results with the obvious addition of harvesting fruit from plants which have been modified to have enhanced fruit ripening characteristics.
Specifically, applicants claim a method of modifying fruit ripening in a banana plant by using a targeted DNA editing agent to introduce a loss of function mutation in a gene encoding an ACS or an ACC oxidase and Slaymaker teaches methods of making loss of function mutations (those mutations that lead to impaired function of the target gene, see applicants definition on Page 27 in lines 8-10 of the specification, and teaches that these methods are applicable to any plant and include bananas in a list of applicable plants. Therefore, the prior art includes each element claimed with the only different being the lack of actual combination of the claimed elements.
Slaymaker teaches the versatility of CRISPR/Cas9 based methods and teaches that they can be applied to any plant. This demonstrates that one of ordinary skill in the art could have combined the elements of the introduction of a loss of function mutation in an ACS or ACO gene and banana plants as the target plant.
These results would have been predictable because applicant’s include protoplast cells in their definition of a plant (Instant Specification, Page 19, Lines 21-23) and methods of generating and transforming protoplast cells are routine, predictable and well known in the art (Slaymaker, Page 386, Paragraph 1131) and further Slaymaker teaches that CRISPR systems can be used to perform efficient and cost effective gene or genome interrogation or editing in plants (Slaymaker, Page 374, Paragraph 1099). Thus combining the elements of Slaymaker would be predictable given that a key characteristic of CRISPR systems is their versatility and applicability to a variety of different organisms and that these systems have been shown to work in plants, particularly in protoplasts.
Therefore, given the above factual inquiries, combining the teachings of Slaymaker to arrive at the claimed invention is obvious because it is simply combining prior art elements according to known methods to yield predictable results (MPEP 2143 I. A.).
Claims 3-4 remain rejected and claims 5, 7, 10-11, 16, 23-26 and 28 are newly rejected as obvious in view of the teachings of Slaymaker.
Obviousness rejection against claim 9.
With respect to claim 9, Slaymaker teaches nucleic acid constructs encoding the CRISPR/Cas9 genome editing system (Slaymaker, Page 380, Paragraph 1111). Additionally, in Slaymaker teaches the use of the CRISPR/Cas9 gene editing system to affect fruit-ripening by reducing ethylene production by targeting ethylene biosynthesis ACS and ACO synthase gene expression in plants including Banana (Slaymaker, Pages 410-411, Paragraphs 1191-1192; Slaymaker, Page 379, Paragraph 1110). In this embodiment ethylene production is reduced through the use of CRISPR/Cas9 to suppress 1-aminocyclopropane-1-carboxylic acid synthase (ACC synthase) gene expression and then regenerating a plant and therefore the gene editing system of Slaymaker is directed modulating ACS and ACO expression (Slaymaker, Page 411, Paragraph 1192) .
With respect to claim 9, Slaymaker does not teach each and every element as set forth in the claim. Specifically, Slaymaker teaches generic nucleic acid constructs comprising generic CRISPR/Cas9 systems to modify plants including Banana and then in a separate embodiment teaches methods of using Crispr/Cas9 systems to affect fruit ripening by suppression of ACC synthase gene expression in plants including tomato.
As such, Slaymaker does not disclose nucleic acid constructs encoding DNA editing agents directed at a nucleic acid sequence encoding a component in an ethylene biosynthesis pathway of a banana.
With respect to claim 9, it would have been obvious given the teachings of Slaymaker to modify the nucleic acid constructs of Slaymaker to target ACC synthase in Banana plants in order to reduce ethylene biosynthesis in Banana plants and delay fruit ripening in fruits of those plants. This would have been obvious because Slaymaker teaches that modifying ethylene biosynthesis is useful in plants that produce fruits or vegetables because it will slow fruit ripening, Slaymaker teaches that Banana plants can be improved using CRISPR/Cas9 systems and finally Slaymaker teaches generic nucleic acid constructs comprising CRISPR/Cas9 gene editing system.
The ordinary artisan would have been motivated to produce these nucleic acid constructs in order to use them to target ACC synthase in Banana plants to produce and harvest Banana fruits having delayed ripening because these constructs can be used to produce Banana fruits having improved shelf life which would have economic and agronomic advantages over Banana fruits without this enhanced characteristic. Therefore, claim 9 remains rejected as obvious under Slaymaker.
Obviousness rejection against claim 27.
With respect to claim 27, Slaymaker teaches the application of the Cas9-CRISPR system to plants and yeasts and provides a broad list of applicable plants including banana plants (Slaymaker, Page 379, Paragraph 1110). In the next paragraph Slaymaker teaches that this system can be used to confer desired traits onto essentially any plant (Slaymaker, Page 379, Paragraph 1111).
Additionally, later in a separate embodiment Slaymaker teaches the use of CRISPR/Cas9 to suppress the ethylene biosynthetic enzyme, 1-aminocyclopropane-1-carboxylic acid synthase (ACC synthase) gene expression in a target plant and then regenerating a plant (Slaymaker, Page 410, Paragraph 1191). In this section Slaymaker notes that in particular embodiments, the methods comprise the CRISPR/Cas9 system to ensure modifications of plant cells which in particular embodiments are tomato plants.
Therefore, with respect to claim 27, Slaymaker does not teach each and every element as set forth in the claim. Specifically, Slaymaker teaches generic methods of using CRISPR/Cas9 systems to modify plants including Banana and then in a separate embodiment teaches methods of using Crispr/Cas9 systems to affect fruit ripening by suppression of ACC synthase gene expression in plants including tomato. As such, Slaymaker does not disclose a method of using CRISPR/Cas9 systems to target ACC synthase in Banana plants to affect fruit ripening nor does Slaymaker disclose processing of modified Banana fruits to produce a product.
With respect to claim 27, it would have been obvious given the teachings of Slaymaker to use the CRISPR/Cas9 system to target ACC synthase to reduce ethylene biosynthetic enzyme in Banana plants. This would have been obvious because Slaymaker teaches that this method is useful in plants that produce fruits or vegetables because it will slow fruit ripening and Slaymaker also teaches that Banana plants can be improved using CRISPR/Cas9 systems. It would also have been obvious to process the fruits having these enhanced traits in order to produce a processed banana product having increased value as compared to unprocessed bananas. The ordinary artisan would have been motivated to use this method in Banana plants in order to produce Banana fruits having delayed ripening which would improve shelf life and then process these fruits into products retaining this enhanced property of increased shelf life because of the economic and agronomic advantages of a product with longer shelf life. Therefore, claim 27 remains rejected as obvious under Slaymaker.
Claims 12-15, 17, 19-22 and 29-30 are newly rejected under 35 U.S.C. 103 as being unpatentable over Slaymaker (WO 2016/205613 Al) in view of Jourda, New Phytologist (2014) as evidenced by Liu, Journal of experimental botany 72.20 (2021): 7078-7091.
Obviousness rejections against claims 12-15.
Claims 12-15 are drawn to the method of claim 2 where the target gene is selected from a group including either Ma04_g35640 or Ma01_g11540. Liu demonstrates inherent characteristics of these sequences, specifically that they have other common names beyond the gene ID numbers (Liu, Journal of experimental botany 72.20 (2021). Specifically, Liu discloses that Ma04_g35640 is ACS7 and that Ma01_g11540 is ACO1 from red banana (Musa acuminata) (Liu, Page 7084, Column 1, After reference to supplementary table S3; Liu, Page 7078, Abstract).
Therefore, claims 12-15 are drawn to the method of claim 2, wherein the target ACS or ACO is ACS7 or ACO1.
With respect to claims 12-15, Slaymaker teaches all of the limitations of claim 2, see above.
With respect to claims 12-15, Slaymaker does not teach targeting MaACS7 or MaACO1.
With respect to claims 12-15, Jourda teaches that there are 11 ACS genes in banana including MaACS7 (Jourda, Page 989, Column 1, First Paragraph; Jourda, Page 990, Column 1, First Paragraph).
Additionally, Jourda teaches that several ACO genes are expressed in the fruits including MaACO1 which is the most highly expressed (Jourda, Page 993, Column 1, Last Paragraph). Slaymaker also states that MaACO1 is a previously known ethylene- and ripening-induced genes and that there are 12 ACO genes in banana (Jourda, Page 993, Column 2; Jourda, Page 994, Figure 4).
Given the teaches of Slaymaker and Jourda, at the time of filing it would have been obvious to one of ordinary skill in the art to arrive at the claimed methods. At the time of filing it would have been obvious to try the methods Slaymaker with all of the ACS and ACO genes in banana.
This would have been obvious because of the following:
Slaymaker demonstrates at the time of filing that there was a need to modify fruit ripening in order to delay that process. This is because fruit ripening renders fruits or vegetables inedible only a few days after it starts and brings significant losses to both farmers and consumers (Slaymaker, Page 410, Paragraph 1191)
The combined teachings of Slaymaker (See 103 analysis against claim 2 above), teach targeting ACS and ACO genes in banana to delay fruit ripening and Jourda teaches that there are 11 ACS and 12 ACO genes in banana. Therefore, there is a finding that there had been a number of finite predictable solutions to the recognized problem.
Given the teachings of Slaymaker, it appears that one of ordinary skill in the art could have made gRNAs to target all of the ACO and ACS genes in banana protoplasts with a reasonable chance of success given the versatility and ease of use of the CRISPR/Cas9 system.
Given the above factual inquiries it is clear that it would have been obvious to try to use the method of Slaymaker, see above, to target all of the ACO and ACS genes including MaACS7 and MaACO1.
Therefore claims 12-15 are newly rejected as obvious under Slaymaker in view of Jourda as evidenced by Liu.
Obviousness rejections against claims 17 and 19-22.
Claims 17 and 19-22 are drawn to method of claim 2 wherein the DNA editing agent comprises a nucleic acid sequence of one or more of SEQ ID NOs: 47-54 in certain specific combinations. The specification describes these sequences as guide RNAs in lines 25-28 on page 9.
With respect to claims 17 and 19-22, Slaymaker teaches all of the limitations of claim 2, see above. Further, Slaymaker teaches direct targeted mutagenesis of target genes in plants (Slaymaker, Page 409, Paragraph 1188). Later, Slaymaker teaches that the use of multiple guide RNAs may increase the cutting frequency and hinder the evolution of drive resistant alleles in some target species (Slaymaker, 431, Paragraph 1248).
Slaymaker also teaches the use of multiple guide RNAs to target a target locus (Slaymaker, Page 86, Paragraph 312).
Finally, Slaymaker teaches that the guide RNAs which target the Cas9 enzyme to the target cut site have intrinsic design parameters which limit the structure of these molecules and also the sites within the genome which they can target (Slaymaker, Pages 139-140, Paragraph 484).
With respect to claims 17 and 19-22, Slaymaker does not teach the use of the exact guide RNAs of SEQ ID NOs: 47-54.
With respect to claims 17 and 19-22, Jourda teaches that there are 11 ACS genes in banana including MaACS7 (Jourda, Page 989, Column 1, First Paragraph; Jourda, Page 990, Column 1, First Paragraph).
Additionally, Jourda teaches that several ACO genes are expressed in the fruits including MaACO1 which is the most highly expressed (Jourda, Page 993, Column 1, Last Paragraph). Slaymaker also states that MaACO1 is a previously known ethylene- and ripening-induced genes and that there are 12 ACO genes in banana (Jourda, Page 993, Column 2; Jourda, Page 994, Figure 4).
Given the teaches of Slaymaker and Jourda, at the time of filing it would have been obvious to one of ordinary skill in the art to arrive at the claimed methods. At the time of filing it would have been obvious to try the methods Slaymaker with all of the ACS and ACO genes in banana.
Further it would have been obvious to target sites early in the coding region of these target genes and given that the method of Slaymaker uses the CRISPR/Cas9 system and that the gRNAs from that system have certain design limitations it would have been obvious to generate gRNAs having the sequences of SEQ ID NOs: 47-54 and to use more than one gRNA to target a specific locus in the target genes given that Slaymaker teaches that multiple the use of gRNAs may improve cutting efficiency.
This would have been obvious because of the following:
Slaymaker demonstrates at the time of filing that there was a need to modify fruit ripening in order to delay that process. This is because fruit ripening renders fruits or vegetables inedible only a few days after it starts and brings significant losses to both farmers and consumers (Slaymaker, Page 410, Paragraph 1191)
The combined teachings of Slaymaker (See 103 analysis against claim 2 above), teach targeting ACS and ACO genes in banana to delay fruit ripening and Jourda teaches that there are 11 ACS and 12 ACO genes in banana. Therefore, there is a finding that there had been a number of finite predictable solutions to the recognized problem.
Given the teachings of Slaymaker, it appears that one of ordinary skill in the art could have made gRNAs to target all of the ACO and ACS genes in banana protoplasts with a reasonable chance of success given the versatility and ease of use of the CRISPR/Cas9 system.
Given the above factual inquiries it is clear that it would have been obvious to try to use the method of Slaymaker, see above, to target all of the ACO and ACS genes including MaACS7 and MaACO1.
Given these teachings the ordinary artisan would naturally have arrived a the claimed gRNA sequences and given the motivation in Slaymaker to use multiple gRNAs the claimed methods are obvious.
Therefore claims 17and 19-22 are newly rejected as obvious under Slaymaker in view of Jourda as evidenced by Liu.
Obviousness rejections against claims 29-30.
Claims 29-30 are drawn to the plants of claim 1 (Claim 29) and the method of claim 2 (Claim 30) where the target gene is selected from a loss of function mutation between exons 1 and 3 in Ma04_g35640 or a loss of function mutation between exons 1 and 4 in Ma01_g11540. Liu demonstrates inherent characteristics of these sequences, specifically that they have other common names beyond the gene ID numbers (Liu, Journal of experimental botany 72.20 (2021). Specifically, Liu discloses that Ma04_g35640 is ACS7 and that Ma01_g11540 is ACO1 from red banana (Musa acuminata) (Liu, Page 7084, Column 1, After reference to supplementary table S3; Liu, Page 7078, Abstract).
With respect to claims 29-30, Slaymaker teaches all of the limitations of claims 1-2, see above.
Additionally, Slaymaker teaches that the CRISPR/Cas9 system can be used for the direct targeted mutagenesis of target genes in plants (Slaymaker, Page 409, Paragraph 1108).
With respect to claims 29-30, Slaymaker does not teach targeting MaACS7 or MaACO1.
With respect to claims 29-30, Jourda teaches that there are 11 ACS genes in banana including MaACS7 (Jourda, Page 989, Column 1, First Paragraph; Jourda, Page 990, Column 1, First Paragraph).
Additionally, Jourda teaches that several ACO genes are expressed in the fruits including MaACO1 which is the most highly expressed (Jourda, Page 993, Column 1, Last Paragraph). Slaymaker also states that MaACO1 is a previously known ethylene- and ripening-induced genes and that there are 12 ACO genes in banana (Jourda, Page 993, Column 2; Jourda, Page 994, Figure 4).
Given the teaches of Slaymaker and Jourda, at the time of filing it would have been obvious to one of ordinary skill in the art to arrive at the claimed methods. At the time of filing it would have been obvious to try the methods Slaymaker to use direct targeted mutagenesis to generate modifications early in the coding sequences of all of the ACS and ACO genes in banana.
This would have been obvious because of the following:
Slaymaker demonstrates at the time of filing that there was a need to modify fruit ripening in order to delay that process. This is because fruit ripening renders fruits or vegetables inedible only a few days after it starts and brings significant losses to both farmers and consumers (Slaymaker, Page 410, Paragraph 1191)
The combined teachings of Slaymaker (See 103 analysis against claim 2 above), teach targeting ACS and ACO genes in banana to delay fruit ripening and Jourda teaches that there are 11 ACS and 12 ACO genes in banana. Therefore, there is a finding that there had been a number of finite predictable solutions to the recognized problem.
Given the teachings of Slaymaker, it appears that one of ordinary skill in the art could have made gRNAs to target all of the ACO and ACS genes in banana protoplasts with a reasonable chance of success given the versatility and ease of use of the CRISPR/Cas9 system.
Given the above factual inquiries it is clear that it would have been obvious to try to use the method of Slaymaker, see above, to target all of the ACO and ACS genes including MaACS7 and MaACO1.
Further, it would have been obvious to generate mutations in the early exons of these genes as these modifications are more likely to produce an early stop codon and a null mutant.
Therefore, claims 29-30 are newly rejected as obvious under Slaymaker in view of Jourda as evidenced by Liu.
Conclusion
Claims 1-5, 7, 9-17 and 19-30 are rejected.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a).
A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is maile