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 .
Claims 1-13 are pending and examined on their merit herein.
Claim Objections
Claims 9 -11 are objected to because of the following informalities: Claim 9, and claim 10, both recite two step (ii)s. Similarly, claim 11 at item (c1) recites two step (ii)s. In addition, claim 11 at (b) lacks a step (iii) between (ii) and (iv). It is suggested Applicant correct the numbering of the steps. Appropriate correction is required.
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 1-10 and 12-13 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 rejected for being indefinite because of the recitation of “regenerating intact individual plants from the cells of one or more selected subgroup(s) of step (c)”, in step (c). It is unclear whether it is referring to the subgroups selected in step (b), or there is another step/process of further selection of subgroups in step (c).
Dependent claims 2-10 and 12-13 are included in this rejection for failure to correct the deficiency of claim 1 above.
Claim 3 is rejected as being indefinite because it is unclear if the entire “wherein the population of plant cells comprising regenerative cells is first divided into subgroups and then, each subgroup is tested for the concentration of the desired nucleic acid sequence in said subgroup” is merely a repetition of step (a) of claim 1 (in that case, claim 3 fails to further limit the base claim, see rejection below), or there is a further subgroup dividing step required.
Claim 6 recites the limitation "the cells, tissues or plants" in lines 1-2. There is insufficient antecedent basis for this limitation in the claim.
Claim Rejections - 35 USC § 112
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claim 3 is rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claim 3 depends on claim 1. Claim 1 is directed to a method comprising the step (a) which reads:
“a) dividing a population of plant cells comprising regenerative cells, that comprises a subpopulation of cells comprising a desired nucleic acid sequence, into subgroups, quantifying the concentration of the desired nucleic acid sequence for each subgroup, each subgroup representing a subset of the populations genotype, and identifying one or more subgroups with the highest concentration of the desired nucleic acid sequence,”
Claim 3 is directed to the method of claim 1, “wherein the population of plant cells comprising regenerative cells is first divided into subgroups and then, each subgroup is tested for the concentration of the desired nucleic acid sequence in said subgroup.”.
It appears that claim 3 merely recite part of step (a) of claim 1 without adding any more limitation. Therefore, claim 3 either fails to further narrow the scope of claim 1 or actually broadens the scope.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Claim Rejections - 35 USC § 102
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.
(a)(2) the claimed invention was described in a patent issued under section 151, or in an application for patent published or deemed published under section 122(b), in which the patent or application, as the case may be, names another inventor and was effectively filed before the effective filing date of the claimed invention.
Claims 1-13 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by CARLSBERG (WO2021069614A1, published on April 15, 2021, priority filing date October 10, 2019).
Claim 1 is drawn to a method for the production of plants comprising a desired nucleic acid sequence from a population of plant cells comprising regenerative cells comprising a subpopulation of cells comprising the desired nucleic acid sequence, wherein the method comprises the steps of:
a) dividing a population of plant cells comprising regenerative cells, that comprises a subpopulation of cells comprising a desired nucleic acid sequence, into subgroups, quantifying the concentration of the desired nucleic acid sequence for each subgroup, each subgroup representing a subset of the populations genotype, and identifying one or more subgroups with the highest concentration of the desired nucleic acid sequence,
b) culturing cells from the one or more sub-group(s) with the highest concentration of the desired nucleic acid sequence, dividing the cells, into subgroups, quantifying the concentration of the desired nucleic acid sequence in each subgroup, each subgroup representing a subset of the population's genotype, and selecting one or more subgroups with the highest concentration of the desired nucleic acid sequence, and
c) regenerating intact individual plants from the cells of one or more selected subgroup(s) with the desired nucleic acid sequence.
CARLSBERG discloses a method for identifying a mutant plant of a predefined species carrying one or more mutation(s) in nucleotide(s) of interest [NOI(s)], in a predetermined target sequence (Claim 1). The recited “mutation in a nucleotide of interest in a predetermined target” reads on the instantly claimed “desired nucleic acid sequence”.
The prior art method comprises the steps of: a) Providing Np regenerative parts; b) subjecting said regenerative parts to a step of mutagenesis; c) growing said regenerative parts of generation M0 into mature plants of generation M1 and obtaining regenerative parts of generation M1 from said mature plants; e) dividing regenerative parts of a plurality of generation M1 or M(1 +X) plants into sub-pools, each sub-pool comprising regenerative parts representing a plurality of genotypes;
f) preparing DNA samples, such as gDNA samples or cDNA samples obtained from mRNA samples, from each sub-pool; g) identifying sub-pool(s) comprising DNA comprising the mutation(s) using sensitive detection means; h) identifying regenerative parts within said sub-pool comprising said mutation, thereby identifying said mutant plant. (Claim 1).
The method also comprises a step of reproduction of one or more of said plants or regenerative parts, within the pool or within a sub-pool of plants or regenerative parts. (p. 17, lines 11-13). The step of identifying a group of sub-pools comprising the mutation in the NOI may be performed at any useful time (P. 18, lines 17-19).
Once a sub-pool comprising regenerative parts with the DNA comprising the mutation(s) of interest has been identified, the methods in general comprise a step of identifying regenerative parts within said sub-pool comprising said mutation. (p. 59, lines 31-34);
Also, after step h, providing a sub-pool comprising a plurality of regenerative parts of a plant, wherein said sub-pool comprises regenerative parts comprising one or several mutation(s) of the NOI(s); dividing the regenerative parts of said sub-pool into secondary sub-pools; obtaining a sample from each regenerative part of the secondary sub-pools - in a manner leaving the regenerative parts sufficiently intact to develop into a plant - and combining all samples from all regenerative parts of each secondary sub pool; and identifying secondary sub-pool(s) comprising DNA comprising the mutation(s). (claim 17); a step of reproduction of the organisms, or regenerative parts thereof, within the pool, and wherein said step of reproducing may be performed simultaneously with, or subsequent to, step e) of dividing the organisms into sub-pools; and growing the regenerative part into plants (Item 55).
Therefore, claim 1 is anticipated by the prior art.
Regarding claims 2 and 12, CARLSBERG discloses the “regenerative parts” of a plant is a germline cell in a seed, an embryo, a vegetative tissue, or pollen, which may regenerate into a whole plant. (p. 14, lines 5-13; also Item 72.)
Regarding claim 3, the dividing into pools and subpools are disclosed above.
Regarding claims 4-5, CARLSBERG discloses the mutagenesis in step (b), and wherein the mutagenesis is “an irradiation-induced mutagenesis or a chemical mutagenesis performed with a mutagenizing chemical such as sodium azide (NalS ), ….. methanesulfonate (EMS) ” (Claim 4).
Claim 6 limits the method of claim 1 wherein the cells, tissues or plants are cultured in a medium or growing condition which is not selective for the presence of a desired nucleic acid sequence in the genome of the regenerative cells. Regarding claim 6, CARLSBERG discloses after mutagenesis the growing of the regenerative cells, without selective pressure.
Regarding claim 7, CARLSBERG discloses extracting (isolating) DNA from the pools and sub-pools, e.g., “ f) preparing DNA samples,” in Claim 1, also in claims 13, 14, 17, etc.
Regarding claims 8 and 13, CARLSBERG discloses identifying sub-pool(s) comprising DNA comprising the mutation(s) using sensitive detection means in Claim 1 cited above; e.g., performing one or more PCR amplifications, comprising the DNA sample from said fraction of the sub-pool, one or more set(s) of primers each set flanking the target sequence and PCR reagents, thereby amplifying the target sequence(s); detecting PCR amplification product(s) comprising the target sequence(s) comprising the one or more mutation(s) in the NOI(s) (Item 41, for example); and such means including for example, ddPCR (p. 79, line 5).
Regarding claims 9-10, CARLSBERG discloses the steps, as cited above.
Regarding claim 11, CARLSBERG discloses the steps, as cited above; See Items 1-72.
Therefore, the claimed invention is anticipated by the prior art.
Claims 1-13 are rejected under 35 U.S.C. 102(a)(1) and (a)(2) as being anticipated by DING (CN108611364A, published on October 2, 2018, submitted by Applicant in IDS of October 2, 2024).
Regarding claims 1 and 11:
DING discloses a method for screening non-transgenic CRISPR-Cas9 mutant plants; comprising:
preparing non-transgenic CRISPR-Cas9 mutant plants by mutagenesis with a CRISPR-cas9 agent,
Transfer the explants after S4 co-cultivation to a medium suitable for regeneration without adding antibiotics, and induce callus and bud regeneration of the target plant;
The regenerated seedlings of independent strains obtained in S5 were randomly divided into several groups to be tested, and an equal amount of leaf tissue was taken from each regenerated seedling in each group to be tested, mixed, and DNA was extracted. The PCR amplification ….., and obtains the PCR product samples of each group …..;……to obtain the corresponding dilution group PCR product samples of each test group; High-throughput sequencing of the PCR product samples of each test group; the ratio of nucleotides identical to the wild-type sequence at each site in the PCR product samples of the test group, the wild group PCR product samples, and the diluted group PCR product samples were counted to obtain the frequency of non-variant nucleotides, and the frequency of variable nucleotides The total frequency of acid is 1-non-variant nucleotide frequency; compare the total frequency of variable nucleotides in each site in the test group, its corresponding dilution group and wild group samples; if a certain site variable nucleotide If the total frequency conforms to "test group >> dilution group ≥ wild group", it indicates that there is a mutation at this site; point, it shows that the test group contains the mutant plants in which the target gene is mutated, and the test group is a mutation group;
These parts read on the instantly claimed “dividing a population of plant cells comprising regenerative cells, that comprises a subpopulation of cells comprising a desired nucleic acid sequence, into subgroups, quantifying the concentration of the desired nucleic acid sequence for each subgroup, each subgroup representing a subset of the populations genotype, and identifying one or more subgroups with the highest concentration of the desired nucleic acid sequence”.
Further, the mutant group screened by the above is further divided into several subgroups to be tested, and an equal amount of leaf tissue is taken from each regenerated seedling in each subgroup to be tested, mixed, and DNA is extracted; the leaf tissue of the wild-type plant is taken, mixed, Extract DNA, and there is no special limit on the number of wild-type plant leaf samples; the subgroup to be tested and the wild group use the same primers specific to the region near the sgRNA target site to perform high-resolution melting curve PCR under the same conditions, if the subgroup to be tested The curves of the wild group are clearly separated from the curves of the wild group (the value statistical test P<0.001 of the two curves at the point of the difference), then the subgroup to be tested is a mutant subgroup; Equal amounts of leaf tissue were mixed 1:1, DNA was extracted, and high-resolution melting curve PCR was performed; if the obtained curve was significantly separated from the wild group, the independently regenerated seedlings were mutant plants with mutations in the target gene;
These reads on the instant claims for example, claim 1 (b).
And finally asexually propagate the non-transgenic mutant candidate plants obtained in the above, which reads on (c).
Regarding claims Regarding claims 2 and 12, DING teaches explants as explants such as leaves, hypocotyls, cotyledons, and callus.
Regarding claim 3, the dividing into pools and subpools are disclosed above.
Regarding claims 4-5, DING discloses the mutagenesis as CRISPR-mediated genome editing.
Regarding claims 4-5, DING discloses non-selective regeneration (see above).
Regarding claim 7, DING discloses extracting (isolating) DNA from the pools and sub-pools, see above.
Regarding claims 8 and 13, DING discloses identifying sub-pool(s) comprising DNA comprising the mutation(s) using e.g., PCR amplifications, and high-throughput sequencing (i.e., NGS)
Regarding claims 9-10, DING discloses the steps, as cited above.
Therefore, the claimed invention is anticipated by the prior art.
Conclusion
No claims are allowed.
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WEIHUA . FAN
Examiner
Art Unit 1663
/WEIHUA FAN/Primary Examiner, Art Unit 1663