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 .
Priority
Acknowledgment is made of applicant’s claim for foreign priority under 35 U.S.C. 119 (a)-(d). Receipt is acknowledged of certified copies of papers required by 37 CFR 1.55.
Status of the Claims
Claims 8-16, 18-27 are pending.
Claims 8-16, 18-27 are examined herein.
Claim Objections
Claim 8 is objected to because of the following informalities:
Claim 8 recites the acronyms RPGMS and Ghpsm5. Where acronyms first appear in the claims, they should be enclosed by parentheses and preceded by the non-abbreviated term.
Claims 9 and 10 recite in part “wherein a method for the regulating and/or changing”. The article “a” before method should be changed to “the”.
It is noted that similar incorrect articles, wherein a previously recited limitation is repeated in dependent claims is identified by an “a” or “an” instead of the proper “the” are found throughout the claims.
Appropriate correction is required.
Claim Interpretation
Claim 8 recites: “A method for preparing an RPGMS plant material, comprising regulating and/or changing an activity and/or expression pattern of a cotton recessive photoperiod-sensitive genic male sterile (RPGMS) gene Ghpsm5,wherein an amino acid sequence of a protein encoded by the RPGMS gene Ghpsm5 comprises the sequence set forth in SEQ ID NO:2, or a sequence that has more than 75% identity with the amino acid sequence set forth in SEQ ID NO:2, or wherein a nucleotide sequence of the RPGMS gene Ghpsm5 comprises the nucleotide sequence set forth in SEQ ID NO:1, or a nucleotide sequence of a derivate protein with the function of regulating anther dehiscence obtained by replacing and/or deleting and/or adding one or more amino acid residues to the protein set forth in SEQ ID NO:2.”
The limitation “the function of regulating anther dehiscence obtained by replacing and/or deleting and/or adding one or more amino acid residues to the protein set forth in SEQ ID NO:2” is interpreted to only apply to the “regulating” step and not apply to “changing an activity and/or expression pattern”. This interpretation is reasonable in view of the structure of the dependent claims, which appear to allow for other modes of gene expression regulation that do not involve mutating a gene sequence. It is noted though, that the lack of any limitations on the step of “changing an activity and/or expression pattern” renders the step very broadly claimed.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claims 8 and 19 are rejected under 35 U.S.C. 101 because the claimed invention is directed to a judicial exception, here a natural phenomenon, without significantly more. The claim recites “A method for preparing an RPGMS plant material, comprising regulating and/or changing an activity and/or expression pattern of a cotton recessive photoperiod-sensitive genic male sterile (RPGMS) gene Ghpsm5,wherein an amino acid sequence of a protein encoded by the RPGMS gene Ghpsm5 comprises the sequence set forth in SEQ ID NO:2, or a sequence that has more than 75% identity with the amino acid sequence set forth in SEQ ID NO:2, or wherein a nucleotide sequence of the RPGMS gene Ghpsm5 comprises the nucleotide sequence set forth in SEQ ID NO:1, or a nucleotide sequence of a derivate protein with the function of regulating anther dehiscence obtained by replacing and/or deleting and/or adding one or more amino acid residues to the protein set forth in SEQ ID NO:2.” The claim is directed to a natural phenomenon because the claim encompasses any changing an activity and/or expression pattern of a cotton recessive photoperiod-sensitive genic male sterile (RPGMS) gene, which includes naturally occurring changes to expression of the gene. This judicial exception is not integrated into a practical application because nothing is done with the gene other than changing its activity or expression. The claims do not include additional elements that are sufficient to amount to significantly more than the judicial exception because the cotton psm5 gene appears to be a UDP-galactose transporter. Reyes, Francisca, et al. "AtUTr1, a UDP-glucose/UDP-galactose transporter from Arabidopsis thaliana, is located in the endoplasmic reticulum and up-regulated by the unfolded protein response." Journal of Biological Chemistry 281.14 (2006): 9145-9151 teaches that plant UDP-galactose transporters are subject to regulation of expression including upregulation by the unfolded protein response. (whole article).
Claim Rejections - 35 USC § 112
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 8-16, 18-27 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention.
The Federal Circuit has clarified the written description requirement. The court stated that a written description of an invention "requires a precise definition, such as by structure, formula, [or] chemical name, of the claimed subject matter sufficient to distinguish it from other materials". University of California v. Eli Lilly and Co., 119 F.3d 1559, 1568; 43 USPQ2d 1398, 1406 (Fed. Cir. 1997). The court also concluded that "naming a type of material generally known to exist, in the absence of knowledge as to what that material consists of, is not description of that material". Id. Further, the court held that to adequately describe a claimed genus, Patent Owner must describe a representative number of the species of the claimed genus, and that one of skill in the art should be able to "visualize or recognize the identity of the members of the genus". Id.
Applicant claims a method for preparing an RPGMS plant material, comprising regulating and/or changing an activity and/or expression pattern of a cotton recessive photoperiod-sensitive genic male sterile (RPGMS) gene Ghpsm5,wherein an amino acid sequence of a protein encoded by the RPGMS gene Ghpsm5 comprises the sequence set forth in SEQ ID NO:2, or a sequence that has more than 75% identity with the amino acid sequence set forth in SEQ ID NO:2, or wherein a nucleotide sequence of the RPGMS gene Ghpsm5 comprises the nucleotide sequence set forth in SEQ ID NO:1, or a nucleotide sequence of a derivate protein with the function of regulating anther dehiscence obtained by replacing and/or deleting and/or adding one or more amino acid residues to the protein set forth in SEQ ID NO:2.
Applicant further claims a method for preparing a cotton RPGMS material comprising editing a cotton RPGMS gene and/or a promoter that regulates the expression of the cotton RPGMS gene Ghpsm5 with gene editing technology, wherein an amino acid sequence of a protein encoded by the RPGMS gene Ghpsm5 comprises the sequence set forth in SEQ ID NO:2, or a sequence that has more than 75% identity with the amino acid sequence set forth in SEQ ID NO:2, or wherein a nucleotide sequence of the RPGMS gene Ghpsm5 comprises the nucleotide sequence set forth in SEQ ID NO:1, or a nucleotide sequence of a derivate protein with the function of regulating anther dehiscence obtained by replacing and/or deleting and/or adding one or more amino acid residues to the protein set forth in SEQ ID NO:2;wherein the nucleotide sequence of the promoter comprises any one of 1) - 3):
1) a DNA molecule with the nucleic acid sequence set forth in SEQ ID NO:3;
2) a genomic DNA molecule with 75% or more identity with the nucleotide sequence in 1); or 3) a DNA molecule that is inversely complementary to the DNA molecule in 1) or 2).
Applicant describes editing the cotton psm5 gene by CRISPR techniques to generate the RPGMS cotton line. (Specification p. 2). Applicant describes the sequence of the psm5 coding sequence in cotton, the encoded polypeptide and a promoter as SEQ ID Nos: 1-3.
Applicant does not describe the genus of psm5 polypeptides having as little as 75% identity with SEQ ID NO:2 or derivative polypeptides wherein the polypeptide will cause a photoperiod-sensitive genic male sterile phenotype when the expression is altered. The recited genus of polypeptides encompassed by the claims includes polypeptides with up to 85 substitutions, deletions or additions relative to the 341 amino acid residues of SEQ ID NO:2. “derivative” polypeptides that confer the same function encompass a vast number of polypeptides with no meaningful structural limitations.
A sequence search using SEQ ID No:2, the sequence of the psm5 gene from cotton, shows that psm5 appears to be a UDP-rhamnose/UDP-galactose transporter. Regarding the state of the art, Rautengarten, Carsten, et al. "The Golgi localized bifunctional UDP-rhamnose/UDP-galactose transporter family of Arabidopsis." Proceedings of the National Academy of Sciences 111.31 (2014): 11563-11568 teaches that despite being essential for polysaccharide biosynthesis in the Golgi apparatus, sugar transporters have historically been poorly characterized. (p. 11566 left col. ¶ 2). Rautengarten teaches that plants, such as Arabidopsis thaliana, can encode several UDP-galactose transporters in their genomes. The Arabidopsis genome encodes at least 6 such transporters that are closely interrelated with one another, sharing high identity between members (see Supplemental Table S1). Rautengarten teaches that despite overlapping functions in vitro, plant sugar transporters seem to have more restricted functions in vivo. Rautengarten teaches that despite having similar expression patterns and in-vitro functionality, one Arabidopsis UDP-rhamnose/UDP-galactose transporter causing reduction in the amount of seed mucilage, when mutated and another affecting leaf cell wall galactose content. (p. 11567 left col. ¶ 4). As such, structural identification of a polypeptide as a UDP-rhamnose/UDP-galactose transporter and even expression analysis of said encoding gene does not appear to be sufficient to determine if mutating said gene/polypeptide or otherwise changing its expression levels will produce the recited function of male sterility. It is noted that a sequence search using SEQ ID NO:2 reveals over 50 matches at over 75% in Gossypium hirsutum as well as other closely related cotton species. It cannot be determined from mere sequence identity which polypeptides would produce the required function when mutated from the teachings of the prior art and the instant disclosure fails to remedy this deficiency. The single species of a mutated psm5 gene from cotton fails to describe the recited genus by virtue of example.
Hence, Applicant has not, in fact, described the claimed invention within the full scope of the claims, and the specification fails to provide an adequate written description of the claimed invention.
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 9-16, 18, 20-25 and 27 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 12 recites in part “A method for preparing a cotton RPGMS material comprising editing a cotton RPGMS gene and/or a promoter that regulates the expression of the cotton RPGMS gene Ghpsm5 with gene editing technology, wherein the editing the cotton RPGMS gene Ghpsm5 and/or the promoter comprises: A) ligating a DNA fragment containing gRNAs set forth in SEQ ID NO:1-4”. SEQ ID Nos:1-3 are not sequences that can be reasonably understood to be gRNAs. SEQ IDs Nos 1 and 3 are lengthy nucleic acid sequences and SEQ ID NO:2 is an amino acid sequence. As such, the metes and bounds of the claim are unclear. For purposes of examination, the gRNAs in Claim 12 are interpreted to mean SEQ ID NO:4, which at least is a sequence that could be reasonably interpreted to be a gRNA. This interpretation does not relieve Applicant of the duty to amend the claims to address the cited deficiency.
Claim 9 recites “the method according to claim 8, wherein a method for the regulating and/or changing comprises one or more of gene editing, RNAi, antisense RNA and DNA methylation.” It is unclear how RNAi, antisense or DNA methylation can achieve “replacing and/or deleting and/or adding one or more amino acid residues to the protein set forth in SEQ ID NO:2” as set forth in Claim 8, limiting the term “regulating”. As such, the metes and bounds of the claim are unclear. For purposes of examination, the claim is interpreted to encompass gene editing, which can achieve the recited deletion. This interpretation does not relieve Applicant of the duty to amend the claims to address the cited deficiency.
Similarly, Claim 10 is directed to the method of regulating and/or changing in Claim 8 by constructing an expression vector to express genes similar to the psm5 gene of the instant invention. It is unclear how constructing an expression vector can achieve “replacing and/or deleting and/or adding one or more amino acid residues to the protein set forth in SEQ ID NO:2” as set forth in Claim 8, limiting the term “regulating”. As such, the metes and bounds of the claim are unclear. For purposes of examination, the claim is interpreted to be limited to changing expression of the psm5 gene. This interpretation does not relieve Applicant of the duty to amend the claims to address the cited deficiency.
Similarly, Claim 20 is directed to the method of regulating and/or changing in Claim 8 by constructing an expression vector to express genes similar to the psm5 gene of the instant invention. It is unclear how constructing an expression vector can achieve “replacing and/or deleting and/or adding one or more amino acid residues to the protein set forth in SEQ ID NO:2” as set forth in Claim 8, limiting the term “regulating”. As such, the metes and bounds of the claim are unclear. For purposes of examination, the claim is interpreted to be limited to changing expression of the psm5 gene. This interpretation does not relieve Applicant of the duty to amend the claims to address the cited deficiency.
Claims that depend from a claim rejected as indefinite without further clarifying the deficiency are also rejected as indefinite.
Conclusion
No claims are allowed.
The claims appear to be free of the prior art. The closest prior art is Kovalik et al. (US 20070061916). While Kovalik teaches a sequence from cotton having over 98% identity to the instant SEQ ID NO:2 (Kovalik SEQ ID NO:62856), and methods of overexpressing said polypeptide in plants, it does not teach mutating the encoding polypeptide or otherwise changing expression such that the resulting plant would exhibit the required photoperiod-sensitive genic male sterile phenotype (which appears to require some degree of inactivation from the teachings of the instant disclosure).
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CHARLES A LOGSDON whose telephone number is (571)270-0282. The examiner can normally be reached M-F 8:30 - 5:00 pm.
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/CHARLES LOGSDON/ Primary Examiner, Art Unit 1662
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