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 1-12 are pending and examined. Claims 13-15 have been cancelled.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code (e.g., see p. 24, line 20). Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Rejections - 35 USC § 112
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.
Claim 1 is drawn to a plant comprising inactive 2-oxa-acid dependent dioxygenase (ALK) protein comprising a mutation compared to SEQ ID NO: 1 wherein the plant is Brussels sprout.
The metes and bounds of the claim are indefinite it is not clear whether the comparison is to a Brussels sprout plant comprising SEQ ID NO: 1 or if the plant comprising the mutated ALK is Brussels sprout and the comparison is to SEQ ID NO: 1.
Claims 2, 3 and 5 present the same issue and are therefore rejected for the same reason as provided for claim 1.
Claim 6 and 12 and drawn to a gene encoding an ALK protein obtained from or present in a plant from seed deposited under NCIMB 44053.
The metes and bounds of the claim are indefinite because it is not clear how the gene encoding the ALK protein can have multiple structures and/or mutations when the plant deposited from the seed has a genome that is fixed and thus cannot have multiple different mutations or structures.
Claims 4 and 7-11 are rejected for depending upon a rejected base claim and for failing to remedy the issues of indefiniteness.
Claims 1-12 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for using the guide RNA sequences of SEQ ID NO: 19-23 to produce mutations in SEQ ID NO: 1, does not reasonably provide enablement for making and using the genus of plants comprising mutations in a gene encoding an inactive ALK protein as broadly claimed. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and/or use the invention commensurate in scope with these claims.
In In re Wands (8 USPQ2d 1400 (CAFC 1988)), the CAFC considered the issue of enablement in molecular biology. The CAFC summarized eight factors to be considered in a determination of "undue experimentation". These factors include: (a) the quantity of experimentation; (b) the amount of guidance presented; (c) the presence or absence of working examples; (d) the nature of the invention; (e) the state of the prior art; (f) the predictability of the prior art; (g) the breadth of the claims; and (h) the relative skill in the art. The factors are analyzed in turn for the instant case as follows:
The instant claims are drawn broadly to any plant species that does not substantially comprise sinigrin and progoitrin wherein the plant comprises a gene encoding an enzymatically inactive ALK protein comprising a mutation as compared to SEQ ID NO: 1 wherein the plant is Brussels sprout, wherein the mutation is an insertion, deletion, substitution or truncation in SEQ ID NO: 1, wherein the inactive ALK protein has an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 16, wherein the gene is homozygously present, wherein the plant does not comprise an enzymatically active ALK protein of SEQ ID NO: 1, wherein the gene is obtained from a plant deposited under deposit number NCIMB 44053, wherein the plant is a hybrid, a method for providing a plant comprising introducing a mutation into an ALK protein, wherein the mutation is introduced using CRISPR Cas or mutagenesis, a method of providing said plant by crossing a plant comprising said mutation with another plant and wherein the gene is obtained from a plant deposited under deposit number NCIMB 44053.
The specification teaches crossing a Brassica line containing a non-functional ALK gene and an inbred line with the final selected backcross plant recurrent for all chromosomes but containing a small introgression with the non-functional ALK gene. This plant was inbred and a plant homozygous for the novel introgression was selected. Seeds were harvested and the new line was morphologically identical to the original Brussels sprouts line in a field trial with the exception that the newly created Brussels sprout was not bitter (p. 8, Example 1).
All lines lacked progoitrin and sinigrin (see Table 5). Additionally, the specification teaches knockout of ALK using CRISPR/Cas9 in a Brussels sprout plant comprising SEQ ID NO: 1 with guide RNAs targeting SEQ ID Nos: 19 to 23. These plants without an active ALK gene showed the expected phenotype (p. 27, Example 3).
However, the specification fails to teach structures conferring ALK function such that one would be unable to predictably mutate said gene to inactivate it resulting in a plant that substantially does not, or does not, comprise sinigrin and progoitrin.
Here, the claims encompass plants comprising a vast genus of structures encoding ALK proteins so long as they comprise mutation leading to inactive protein, yet the specification fails to teach structures commensurate in scope with what is claimed and further fails to provide working examples of plants comprising the genus of ALK structures as broadly claimed.
In fact, the specification provides one working examples of using CRISPR/Cas9 to mutate one structure corresponding to SEQ ID NO: 1 encoding an ALK protein (e.g., see Example 3).
This guidance and working examples are critical in light of the state of the art, which teaches that not all genes encoding ALK proteins are capable of functional complementation of ALK mutants in so far as some show high level production of sinigrin whereas others do not (Zhang et al, 2015, Journal of Experimental Botany, 66(20):6205-6218; see p. 6211, col. 2, ¶ 1).
Therefore, in light of the breadth of the claims, the failure of the specification to provide a structure-function correlation for ALK, the lack of working examples and the state of the art, the skilled practitioner would be required to engage in impermissible trial and error screening which is tantamount to undue experimentation.
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.
Instant claims 1-12 are drawn broadly to any plant species that does not substantially comprise sinigrin and progoitrin wherein the plant comprises a gene encoding an enzymatically inactive ALK protein comprising a mutation as compared to SEQ ID NO: 1 wherein the plant is Brussels sprout, wherein the mutation is an insertion, deletion, substitution or truncation in SEQ ID NO: 1, wherein the inactive ALK protein has an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 16, wherein the gene is homozygously present, wherein the plant does not comprise an enzymatically active ALK protein of SEQ ID NO: 1, wherein the gene is obtained from a plant deposited under deposit number NCIMB 44053, wherein the plant is a hybrid, a method for providing a plant comprising introducing a mutation into an ALK protein, wherein the mutation is introduced using CRISPR Cas or mutagenesis, a method of providing said plant by crossing a plant comprising said mutation with another plant and wherein the gene is obtained from a plant deposited under deposit number NCIMB 44053.
The specification describes crossing a Brassica line containing a non-functional ALK gene and an inbred line with the final selected backcross plant recurrent for all chromosomes but containing a small introgression with the non-functional ALK gene. This plant was inbred and a plant homozygous for the novel introgression was selected. Seeds were harvested and the new line was morphologically identical to the original Brussels sprouts line in a field trial with the exception that the newly created Brussels sprout was not bitter (p. 8, Example 1).
All lines lacked progoitrin and sinigrin (see Table 5). Additionally, the specification teaches knockout of ALK using CRISPR/Cas9 in a Brussels sprout plant comprising SEQ ID NO: 1 with guide RNAs targeting SEQ ID Nos: 19 to 23. These plants without an active ALK gene showed the expected phenotype (p. 27, Example 3).
The written description requirement may be satisfied through sufficient description of a representative number of species by disclosing relevant and identifying characteristics such as structural or other physical and/or chemical properties, by disclosing functional characteristics coupled with a known or disclosed correlation between function and structure, or by a combination of such identifying characteristics, sufficient to show the applicant was in possession of the invention as claimed. See Eli Lilly,119 F.3d at 1568, 43 USPQ2d at 1406.
Here, the specification fails to describe structures conferring ALK function such that one would be unable to predictably mutate said gene to inactivate it resulting in a plant that substantially does not, or does not, comprise sinigrin and progoitrin.
Moreover, the claims encompass plants comprising a vast genus of structures of genes encoding ALK proteins so long as they comprise a mutation leading to inactive protein, yet the specification fails to describe structures commensurate in scope with what is claimed and further fails to provide working examples of plants comprising the genus of ALK structures as broadly claimed.
Additionally, the specification fails to describe a representative number of species from the genus of ALK structures as broadly claimed. In fact, the specification provides one working example of using CRISPR/Cas9 to mutate one structure corresponding to SEQ ID NO: 1 encoding an ALK protein (e.g., see Example 3).
An appropriate description of the gene encoding an ALK protein is critical in light of the state of the art, which describes that not all genes encoding ALK proteins are capable of functional complementation of ALK mutants in so far as some show high level production of sinigrin whereas others do not (Zhang et al, see p. 6211, col. 2, ¶ 1).
Therefore, in light of the breadth of the claims, the failure of the specification to describe a structure-function correlation for ALK, the failure to describe a representative number of structures from the genus of genes encoding ALK proteins as claimed, the lack of working examples and the state of the art, the skilled practitioner would not be of the opinion Applicant possesses the plants and methods as broadly claimed.
Claim Rejections - 35 USC § 102
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 the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claim(s) 1, 4 and 8-10 is/are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Hansen et al (2008, Plant Physiology, 148:2096-2108).
Instant claims 1, 4 and 8-10 are drawn broadly to a Brussels sprout plant that does not substantially comprise sinigrin and progoitrin wherein the plant comprises a gene encoding an enzymatically inactive ALK protein comprising a mutation as compared to SEQ ID NO: 1, wherein the gene is homozygously present, and a method for providing a plant comprising introducing a mutation into an ALK protein wherein the mutation is introduced by mutagenesis.
Here, it is noted that the only structural requirement of the plant of claim 1 is that a gene encoding an ALK protein comprises a mutation and is enzymatically inactive. Therefore, prior art that discloses this plant will be structurally indistinguishable from that as claimed and will necessarily not comprise sinigrin or progoitrin.
Hansen et al disclose a 2-oxoacid-dependent dioxygenase encoded by At2g25450 required for the formation of both 2R- and 2S-2-hydroxybut-3-enyl glucosinolate from the precursor 3-butenyl glucosinolate precursor and that naturally occurring null mutations and T-DNA insertional mutations in At2g25450 exhibit a complete absence of 2-hydroxybut-3-enyl glucosinolate accumulation (see Abstract; see also p. 2099, col. 2, ¶ 1; see p. 2100, col. 2, last ¶).
Therefore, a Brussels sprout plant that does not substantially comprise sinigrin and progoitrin wherein the plant comprises a gene encoding an enzymatically inactive ALK protein comprising a mutation as compared to SEQ ID NO: 1, wherein the gene is homozygously present, and a method for providing a plant comprising introducing a mutation into an ALK protein wherein the mutation is introduced by mutagenesis is anticipated by Hansen et al.
Claim Rejections - 35 USC § 103
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
Claim(s) 1-5 and 7-11 is/are rejected under 35 U.S.C. 103 as being unpatentable over Quiros et al (Patent No. US 7,250,559 B2).
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Instant claims 1-5 and 7-11 are drawn broadly to any plant species that does not substantially comprise sinigrin and progoitrin wherein the plant comprises a gene encoding an enzymatically inactive ALK protein comprising a mutation as compared to SEQ ID NO: 1 wherein the plant is Brussels sprout, wherein the mutation is an insertion, deletion, substitution or truncation in SEQ ID NO: 1, wherein the inactive ALK protein has an amino acid sequence having at least 90% sequence identity to SEQ ID NO: 16, wherein the gene is homozygously present, wherein the plant does not comprise an enzymatically active ALK protein of SEQ ID NO: 1, wherein the plant is a hybrid, a method for providing a plant comprising introducing a mutation into an ALK protein, wherein the mutation is introduced using or mutagenesis, a method of providing said plant by crossing a plant comprising said mutation with another plant.
Quiros et al claim a method of modifying the glucosinolate profile in a Brassica plant by introducing a GSL-ALK nucleic acid sequence comprising SEQ ID NO: 3 in the antisense orientation and wherein sinigrin is decreased (see claims 14 and 17). The nucleic acid of SEQ ID NO: 3 encodes the amino acid sequence of SEQ ID NO: 4 having 99% sequence identity to SEQ ID NO: 1 and 16 of the instant invention.
Quiros et al teach transformation with individual constructs followed by traditional plant breeding methods to obtain plants expressing both of the desired genes or when a construct is introduced into a hybrid species of plant. Thus, Quiros et al teach and suggest using hybrids as encompassed by instant claim 7.
Quiros et al teach invention includes increasing or decreasing the length, desaturation and hydroxylation of the glucosinolate content in a plant or plant cell in comparison to a non-transformed plant or plant cell by transforming a plant with nucleic acid encoding one or more enzymes from a glucosinolate biosynthesis pathway where the gene can be expressed in the antisense orientation to decrease sinigrin and gluconapin and progoitrin.
Quiros et al teach of particular interest for practicing the invention are crop plants such as Brassica, especially Brassica oleracea plants including broccoli, cauliflower, cabbage, collard and brussels sprouts.
Thus, while Quiros et al reasonably teaches, suggests and provides motivation with a reasonable expectation of success for making a plant with inactive ALK that does not comprise sinigrin and progoitrin, the issue is whether one would have done so by using one or more mutations as opposed to antisense RNA.
Therefore, prior to the effective filing date of the instant invention it would have been prima facie obvious to one of ordinary skill in the art to modify the teachings of Quiros et al by instead using mutations as opposed to antisense RNA because Quiros et al teaches the regions of a glucosinolate biosynthesis gene encoding a polypeptide important for glucosinolate activity can be determined through routine mutagenesis where mutants can include deletions, insertions and point mutations, or combinations thereof.
Thus, one would readily appreciate based on the teachings of Quiros et al that using mutagenesis as opposed to antisense RNA would achieve the goal producing inactive ALK. One would have a reasonable expectation of success in producing a plant lacking sinigrin and progoitrin because expression of ALK leads to an increase in said product (col. 32, ¶ 1).
Conclusion
No claim is allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to JASON DEVEAU-ROSEN whose telephone number is (571)272-2828. The examiner can normally be reached 7:30am - 4pm.
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Bratislav Stankovic can be reached at (571)270-0305. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/JASON DEVEAU ROSEN/Primary Examiner, Art Unit 1662
ATTACHMENT A
Alignment of SEQ ID NO: 4 from Quiros et al with SEQ ID NO: 1 of the instant invention
Patent No. 7250559
GENERAL INFORMATION
APPLICANT: Quiros, Carlos
APPLICANT: Li, Genyi
APPLICANT: The Regents of the University of California
TITLE OF INVENTION: Nucleic Acids Encoding Glucosinolate Biosynthesis
TITLE OF INVENTION: Enzymes and Methods of Their Use
FILE REFERENCE: 02307O-124410PC
CURRENT APPLICATION NUMBER: US/10/482,951
CURRENT FILING DATE: 2004-01-05
PRIOR APPLICATION NUMBER: PCT/US02/21408
PRIOR FILING DATE: 2002-07-05
PRIOR APPLICATION NUMBER: US 60/303,310
PRIOR FILING DATE: 2001-07-05
NUMBER OF SEQ ID NOS: 41
SEQ ID NO 4
LENGTH: 439
TYPE: PRT
ORGANISM: Brassica oleracea (viridis group)
FEATURE:
OTHER INFORMATION: BoGSL-ALK from collard
Query Match 99.4%; Score 2253; Length 439;
Best Local Similarity 99.3%;
Matches 436; Conservative 1; Mismatches 2; Indels 0; Gaps 0;
Qy 1 MGADTPQLPVIYLSDQTLKPGGEKWVEVRSDVRKALEDYGAFEVSYDRVSEELKKSVLDA 60
||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Db 1 MGADTPQLPVIYLSDQTLKPGSEKWVEVRSDVRKALEDYGAFEVSYDRVSEELKKSVLDA 60
Qy 61 MIELFELPVEAKQRNVSPKPYTGYSTHNGLSESLGIQDSNVLEKVNEFTQLLRPDCEGNK 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 MIELFELPVEAKQRNVSPKPYTGYSTHNGLSESLGIQDSNVLEKVNEFTQLLRPDCEGNK 120
Qy 121 TMSETIQKFSEKLAELDVMVRRMVIESFGIENYFDEHLKSTNYRLRLMKYVAPPDVDANV 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TMSETIQKFSEKLAELDVMVRRMVIESFGIENYFDEHLKSTNYRLRLMKYVAPPDVDANV 180
Qy 181 AVSTKDSVDGANTNTTANADAGDIANGIAKVHIDDDANAKGDVCTGVGTNHNGDDVNTGD 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 AVSTKDSVDGANTNTTANADAGDIANGIAKVHIDDDANAKGDVCTGVGTNHNGDDVNTGD 240
Qy 241 CANVKSNVDVGTNVSAKSSVGADVNIGTIADVKANTGTRTSATVGVSDSVKANGGADDEE 300
|||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Db 241 CANVKSNVDVGTNVSAKSSVGADVNIGTIADVKANTGTRTSANVGVSDSVKANGGADDEE 300
Qy 301 KKLGLPSHTDKNLLTVLYQYEIEGLEVLTKDEKWIRLKPSHNSFVVMAGDSLYALMNGRL 360
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 301 KKLGLPSHTDKNLLTVLYQYEIEGLEVLTKDEKWIRLKPSHNSFVVMAGDSLYALMNGRL 360
Qy 361 SRPFHRVRVTERKKTRYSIALFSTPNGDYIIEPPKELVDEKHPRLFKPFTFVDLMSFYHT 420
||||||||||||||||||||||||||||||||||||||||||||||||||:|||||||||
Db 361 SRPFHRVRVTERKKTRYSIALFSTPNGDYIIEPPKELVDEKHPRLFKPFTYVDLMSFYHT 420
Qy 421 EAGRRPRSTLHAYCAVSGA 439
|||||||||||||||||||
Db 421 EAGRRPRSTLHAYCAVSGA 439
Alignment of SEQ ID NO: 4 from Quiros et al with SEQ ID NO: 16 of the instant invention
Patent No. 7250559
GENERAL INFORMATION
APPLICANT: Quiros, Carlos
APPLICANT: Li, Genyi
APPLICANT: The Regents of the University of California
TITLE OF INVENTION: Nucleic Acids Encoding Glucosinolate Biosynthesis
TITLE OF INVENTION: Enzymes and Methods of Their Use
FILE REFERENCE: 02307O-124410PC
CURRENT APPLICATION NUMBER: US/10/482,951
CURRENT FILING DATE: 2004-01-05
PRIOR APPLICATION NUMBER: PCT/US02/21408
PRIOR FILING DATE: 2002-07-05
PRIOR APPLICATION NUMBER: US 60/303,310
PRIOR FILING DATE: 2001-07-05
NUMBER OF SEQ ID NOS: 41
SEQ ID NO 4
LENGTH: 439
TYPE: PRT
ORGANISM: Brassica oleracea (viridis group)
FEATURE:
OTHER INFORMATION: BoGSL-ALK from collard
Query Match 99.3%; Score 1519; Length 439;
Best Local Similarity 99.3%;
Matches 297; Conservative 0; Mismatches 2; Indels 0; Gaps 0;
Qy 1 MGADTPQLPVIYLSDQTLKPGGEKWVEVRSDVRKALEDYGAFEVSYDRVSEELKKSVLDA 60
||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Db 1 MGADTPQLPVIYLSDQTLKPGSEKWVEVRSDVRKALEDYGAFEVSYDRVSEELKKSVLDA 60
Qy 61 MIELFELPVEAKQRNVSPKPYTGYSTHNGLSESLGIQDSNVLEKVNEFTQLLRPDCEGNK 120
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 MIELFELPVEAKQRNVSPKPYTGYSTHNGLSESLGIQDSNVLEKVNEFTQLLRPDCEGNK 120
Qy 121 TMSETIQKFSEKLAELDVMVRRMVIESFGIENYFDEHLKSTNYRLRLMKYVAPPDVDANV 180
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 121 TMSETIQKFSEKLAELDVMVRRMVIESFGIENYFDEHLKSTNYRLRLMKYVAPPDVDANV 180
Qy 181 AVSTKDSVDGANTNTTANADAGDIANGIAKVHIDDDANAKGDVCTGVGTNHNGDDVNTGD 240
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 181 AVSTKDSVDGANTNTTANADAGDIANGIAKVHIDDDANAKGDVCTGVGTNHNGDDVNTGD 240
Qy 241 CANVKSNVDVGTNVSAKSSVGADVNIGTIADVKANTGTRTSATVGVSDSVKANGGADDE 299
|||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||
Db 241 CANVKSNVDVGTNVSAKSSVGADVNIGTIADVKANTGTRTSANVGVSDSVKANGGADDE 299
Prosecution Insights