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 .
Continued Examination Under 37 CFR 1.114
A request for continued examination under 37 CFR 1.114, including the fee set forth in 37 CFR 1.17(e), was filed in this application after final rejection. Since this application is eligible for continued examination under 37 CFR 1.114, and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114. Applicant's submission filed on 09/10/2026 has been entered.
Claim Status
Claims 4, 6, 9-15, 17, and 18 are pending. Claims 5, 7 and 8 are canceled. Claims 4, 6, 9-15, 17, and 18 have been amended. Claims 4, 6, 9-15, 17, and 18 are examined on the merits.
Response to Amendment
The previous rejection under 35 U.S.C. §103 is withdrawn in view of amendment to the claims.
A new rejection of claim 4 under 35 U.S.C. 112(b) is set forth below based on the amended claim language.
New rejections of claims 4, 6, 9-15, 17, and 18 under 35 U.S.C. 112(a) are also set forth below.
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.
This rejection is new.
Claim 4 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 4 recites an “an inhibitory RNA(RNAi) nucleic acid molecule having at least 25 nucleotides in length of the sequence shown in SEQ ID NO:1 operably linked to a promoter functional in rice plants”.
It is unclear whether the RNAi molecule itself is operably linked to the promoter, or whether a nucleic acid molecule encoding the RNAi molecule is intended to be operably linked to the promoter. The Specification describes a transgene encoding an RNAi molecule (pa0080) and expression of the RNAi molecule using a plant expression vector (pa0082). Therefore, the scope of claim 4 is unclear.
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.
Written Descriptions
This rejection is new.
Claim 4 is 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.
The Federal Circuit has clarified the application of 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.
The claims are rejected for lacking adequate written description support regarding the broad scope of the following.
Claim 4 is directed to a transgenic rice plant transformed with an inhibitory RNA (RNAi) nucleic acid molecule having at least 25 nucleotides in length of the sequence shown in SEQ ID NO:1 operably linked to a promoter functional in rice plants, wherein the transgenic rice plant exhibits increased grain weight and/or grain number per plant. Thus, the claim encompasses RNAi molecules directed to different portions of SEQ ID NO: 1 and requires the functional results of increased grain weight and/or grain number per plant. Claim 4 does not limit these results to high nighttime temperature (HNT) conditions and therefore encompasses the claimed phenotype under non-HNT conditions.
The Specification provides only general disclosure concerning RNAi. Specifically, Paragraph 0080 states the LOG1 expression can be reduced using inhibitory RNAs and that a transgenic plant may contain a transgene encoding an RNAi molecule that silences an endogenous nucleic acid molecule such as SEQ ID NO: 1 or 3. Paragraph 0081 generally describes RNAi molecules ranging from about 18 to about 700 nucleotides, and Paragraph 0082 states that an RNAi molecule typically is at least 25 nucleotides in length and has at least 91% sequence identity to SEQ ID NO: 1 or 3, or hybridizes thereto under stringent conditions. Paragraph 0083 then states that regenerated transgenic plants can be screened for an increase in grain weight and/or grain number.
However, the Specification does not provide an actual working example of an RNAi molecule directed to LOG1, demonstrate a particular degree of RNAi-mediated LOG1 suppression sufficient to produce the claimed phenotype, or demonstrate an RNAi-transformed rice plant having increased grain weight and/or grain number. The relevant uncertainty concerns whether RNAi-mediated suppression of LOG1 produces the claimed grain phenotype beyond the disclosed HNT context, rather than whether one skilled in the art can design an RNAi molecule specific to LOG1.
The possible involvement of other LOG homologs under non-HNT conditions also bears on whether the claimed grain phenotype can be predicted from LOG1 suppression. Paragraph 0086 expressly identifies LOG7 as the closest homolog of LOG1 in rice and provides the LOG 7 coding and protein sequence as SEQ ID NO : 3 and 4. An alignment of the cDNA nucleotide sequences corresponding to the LOC numbers for LOG1 and LOG7, corresponding to SEQ ID NO 1 and 3 (LOC_Os01g51210 and LOC_Os05g46360), respectively, shows approximately 79.58% overall nucleotide sequence identity and identities a continuous 27-nucleotide region having 100% sequence identity, as identified in the sequence alignment made of record (see below for alignment result),
Accordingly, because claim 4 encompasses inhibitory RNA molecules having at least 25 nucleotides of SEQ ID NO: 1, its scope includes an RNAi sequence selected from a region of LOG1 cDNA that is not unique to LOG1. Although a LOG1-specific RNAi molecule can be designed using ordinary skill, the Specification does not establish whether suppression of LOG1 alone would produce the claimed grain phenotype under non-HNT conditions, whether other homologs such as LOG7 would contribute to that phenotype under those conditions, or whether RNAi targeting a region shared by LOG1 and LOG7 would produce the same result as LOG1-specific suppression. The shared region therefore bears on the possible biological consequence of targeting different portions of SEQ ID NO: 1, rather than on an inability to design gene-specific RNAi.
The state of the art further demonstrates that LOG/LOGL family membership does not establish a predictable grain phenotype. Chen (Lei Chen et. al., Plant Biotechnology Journal (2022): 20(4):625–645) reports that rice contains multiple LOG/LOGL family members having different tissue-expression patterns (Abstract). For example, the review reports that OsLOG is expressed in all examined tissues, LOGL7 is expressed in all examined tissues and strongly in the shoot apex and immature inflorescence, whereas LOGL1 is barely detectable and only in the inflorescence meristem (p626, right column, pa2). Chen further explains that homologous LOG enzymes have different functions and summarizes different yield-related consequences resulting from manipulation of different LOG/LOGL members (p636, right column, pa1).
The actual working examples of the present Specification are directed to CRISPR-Cas9 genomic modification rather than RNAi. Paragraph 0094 describes three LOG1 knockout lines, one generated from sg1 and two generated from sg2, that were selected for downstream experiments, followed by sequence confirmation and phenotypic evaluation of homozygous plants. These particular genomic modification do not constitute representative RNAi species and do not identify which portions of SEQ ID NO: 1 can be targeted by RNAi to produce the required phenotype.
Further, Paragraph 0104 specifically identities KO #2 as having significantly higher single-grain weight under control conditions relative to WT and OE plants, higher per-plant grain weight, and favorable performance compared with the other two LOG1 KO lines under HNT stress. Thus, even among the particular LOG1-edited lines actually generated, Applicant identifies a particular mutation line as having especially favorable performance, further failing to establish a structure-function relationship applicable to the full range of RNAi target sequence encompassed by claim 4.
Finally, the environmental scope of claim 4 is substantially broader than the principal discovery and experimental focus disclosed in the Specification. The title of the application is directed to rice sequences involved in grain weight under high-temperature conditions. Consistently, Paragraph 0003 states that the disclosure related to nucleic acid sequences involved in rice grain weight under high-temperature conditions; Paragraph 0004 identifies high night temperature (HNT) stress as limiting rice yields; and Paragraph 0005 identifies the discovery as a correlation between higher LOGL1 transcript abundance and lower grain weight under HNT and higher gran weight of logl1 mutants relative to WT under HNT.
The experimental study likewise expressly compared WT, OE, and KO plants under control and HNT temperatures (pa0032), and Paragraph 0104 concludes that LOGL1 is a key regulator of single-grain weight in rice plants exposed to warmer nighttime temperatures during grain development. Although KO #2 also exhibited favorable results under control conditions, the Specification specifically identifies that particular edited line as potentially useful under optimal temperature conditions.
Claim 4, however, contains no high-temperature of HNT limitation and broadly requires that an RNAi-transformed rice plant exhibit increased grain weight and/or grain number per plant. Moreover, no RNAi working example is demonstrated under either HNT or control conditions.
Accordingly, the Specification does not provide a representative number of RNAi species or structural characteristics by which one skilled in the art could identify which RNAi molecules within the scope of claim 4 will specifically reduce LOG1 and produce the required increase in grain weight and/or grain number across the claimed scope. The specification therefore does not reasonably convey possession of the full scope of claim 4.
Scope of Enablement
This rejection is new.
Claims 4, 6, 9-15 and 17-18 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while providing working examples of CRISPR editing of the LOGL1 gene using sg1 and sg2; does not reasonably provide enablement for the full scope of the claimed RNAi-mediated suppression of LOGL1, including RNAi constructs targeting different portions of SEQ ID NO: 1 to produce the recited phenotype. 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.
An “analysis of whether a particular claim is supported by the disclosure in an application requires a determination of whether that disclosure, when filed, contained sufficient information regarding the subject matter of the claims as to enable one skilled in the pertinent art to make and use the claimed invention.” MPEP 2164.01. “A conclusion of lack of enablement means that. . . the specification, at the time the application was filed, would not have taught one skilled in the art how to make and/or use the full scope of the claimed invention [i.e. commensurate scope] without undue experimentation.” In re Wright, 999 F.2d 1557,1562, 27 USPQ2d 1510, 1513 (Fed. Cir. 1993); MPEP 2164.01.
In In re Wands, 858 F.2d 731,8 USPQ2d 1400 (Fed. Cir. 1988), several factors implicated in determination of whether a disclosure satisfies the enablement requirement and whether any necessary experimentation is “undue” are identified. These factors include, but are not limited to:
(A) The breadth of the claims;
(B) The nature of the invention;
(C) The state of the prior art;
(D) The level of one of ordinary skill;
(E) The level of predictability in the art;
(F) The amount of direction provided by the inventor;
(G) The existence of working examples; and
(H) The quantity of experimentation needed to make or use the invention based on the content of the disclosure. In re Wands, 858 F.2d 731,737, 8 USPQ2d 1400, 1404 (Fed. Cir. 1988). No single factor is independently determinative of enablement; rather “[i]t is improper to conclude that a disclosure is not enabling based on an analysis of only one of the above factors while ignoring one or more of the others.” MPEP 2164.01. Likewise, all factors may not be relevant to the enablement analysis of any individual claim.
This rejection is new.
With respect to claim 4, the claim broadly encompasses an inhibitory RNA molecule having at least 25 nucleotides of SEQ ID NO: 1 and functionally requires that the resulting transgenic rice plant exhibit increased grain weight and/or grain number per plant. The claim does not specify a particular RNAi target location, particular RNAi sequence, degree of LOG suppression, or environmental condition under which the claimed phenotype must occur.
The RNAi disclosure at Paragraph 0080-0083 provides general methods for RNAi construction, expression, transformation, and subsequent phenotypic screening, but does not provide an actual LOG1 RNAi working example or identify and RNAi sequence experimentally demonstrated to produce the claimed phenotype. Moreover, Paragraph 0086 identifies LOG7 as the closest LOG1 homolog. An alignment of the cDNA nucleotide sequences corresponding to the LOC numbers for LOG1 and LOG7, corresponding to SEQ ID NO 1 and 3 (LOC_Os01g51210 and LOC_Os05g46360), respectively, shows approximately 79.58% overall nucleotide sequence identity and identities a continuous 27-nucleotide region having 100% sequence identity. Because this identical region exceeds the 25-nucleotide threshold recited by claim 4, at least a portion of the claimed LOG1 RNAi target space is not unique to LOG1. The specification provides no guidance establishing which regions provide sufficient LOG1 specificity while also producing the required grain phenotype.
This uncertainty is consistent with the state of the art. Chen reports that rice contains multiple LOG/LOGL family members having different tissue-expression patterns (Abstract). functions of homologous LOG enzymes have differentiated and summarizes different yield-related consequences resulting from manipulation of different LOG/LOGL members (p636, right column, pa1). Thus, potential cross-silencing of another homolog cannot simply be assumed to produce the same phenotype as reduction of LOG1.
Wang (Changgui Wang et. al., Plant Molecular Biology (2020) 102:373–388) further demonstrate unpredictability even within a single rice LOG-family gene. Six different CRISPR-edited variants of OsLOGL5 produced nonuniform phenotypes. Wang directly reports that Edit-B and Edit-F increased panicle number whereas Edit-D and Edit-E decreased panicle number (Abstract). The edited lines were evaluated under well-watered , drought, normal-nitrogen, and low-nitrogen field conditions at multiple geographical locations, and their phenotypic effects were not uniform across edits and environments (Abstract; p374, right column, pa2).
Therefore, practicing the full scope of claim 4 would require selection of RNAi target regions, construction and expression of the corresponding RNAi molecules, determination of LOG1 suppression, evaluation of potential effects on homologous LOG-family transcripts, determination of the digress of suppression necessary for the phenotype, generation of transgenic rice plants, and phenotypic screening for increased grain weight and/or grain number.
Claims 6 and 9 present a related but district breadth issue. Claim 6 encompasses a genomic mutation in an endogenous nucleic acid encoding SEQ ID NO: 2, wherein the mutation reduces expression and results in increased grain weigh and /or grain number. Claim 9 further encompasses insertion, deletion, and substitution mutations. The Specification broadly states that mutations may be random or targeted and may include point mutations, insertions, deletions, substitutions, or combinations thereof, and that such mutations may alter LOG1 expression or activity( pa0064-0066). Paragraph 0072 then generally states that plants can be screened for mutations or for increased grain with and/or grain number and states that such increases may occur, e.g., under temperature stress.
However, the actual LOG1 working examples are considerably narrower. Paragraph 0094 describes three selected CRISPR LOG1 knockout lines generated using two sgRNA target sites. Paragraph 0104 specifically singles out KO #2 as having significantly increased single-grain weight under control conditions, higher per-plant grain weight, and favorable performance relative to the other LOG1 KO lines under HNT. Thus, the experimental disclosure does not establish the broad range of insertions, deletions, substitutions, and degrees of recued LOG1 expression encompassed by claim 6 and 9 predictably produce increased grain weight and/or grain number.
Claims 10-14 similarly encompass methods based upon identifying a LOG1 mutation producing increased grain weight and/or grain number. Claim 10 is not limited to the particular experimentally demonstrated CRISPR mutations or to a particular degree of reduced LOG1 expression. Claims 11-14 depend on therefrom and do not cure this deficiency.
The state of the art reinforces this lack of predictability. Wang demonstrates that different diets within OsLOGL5 produced differing yield-component phenotypes, including opposite effects on panicle number and among particular edits (Abstract). Chen similarly reports differentiated functions and expression patterns among LOG-family members and summarizes differing phenotypic consequences among LOG/LOGL manipulations (Abstract; p636, right column, pa1) . Accordingly, a skilled artisan could not reasonably extrapolate from a limited number of specific LOG1 knockout line to every mutation that reduces expression satisfies the functional result recited by claims 6 and 9-14 without empirical testing.
Finally, claims 4, 6, and 10, and their respective dependent claims at issue, are not limited to high-temperature of HNT conditions. This is significant because the Specification identifies this technical field as rice grain weight under high-temperature conditions (pa0003), identifies HNT as the problem addressed (pa0004), and states that the underlying discovery is the relationship between LOGL1 expression and grain weight under HNT (pa0005). The experimental design likewise compares the relevant genotypes under control and HNT conditions (pa0032), and concludes that LOGL1 is a key regulator of single-grain weight in plants exposed to warmer nighttime temperatures (pa0104).
The Specification does provide evidence for the particular KO #2 line under control conditions, and therefore the rejection is not based on an absence of any evidence outside HNT. Rather, the issue is that a favorable control-condition phenotype of one particular CRISPR-edited line does not establish that the broad classes of RNAi molecules and genomic mutations encompassed by claims 4, 6, and 9-14 will predictably produce increased grain weight and /or grain number across the claimed range of modifications and relevant growth conditions. The environmental variability reported for OsLOGL5 in Wang further demonstrates the unpredictability of such extrapolation.
Considering the breadth of the claims; the absence of an RNAi working example for claim 4; the lack of guidance identifying LOG1-specific and phenotypically effective RNAi regions; the sequence homology with LOG7; the broad range of genomic mutations encompassed by claims 6, and 9-14; the limited number and variable performance of the demonstrated LOG1 CRISPR lines; the differentiated function and phenotypes reported for LOG/LOGL family members in the art; and the environmental dependence of yield-related effects, practicing the full scope of claims 4, 6, and 9-14 would require substantial trail-and-error experimentation. The Specification therefore does not enable the full scope of claims 4, 6, and 9-14 without undue experimentation.
Claims 15, 17, and 18 are rejected because the Specification does not enable the full scope of the recited “nighttime or daytime temperature stress” limitation without undue experimentation.
Claim 15 requires the first rice plant to exhibit higher grain weight under “nighttime or daytime temperature stress” and further requires progeny exhibiting higher grain weight under “nighttime or daytime temperature stress”. Claims 17 and 18 depend therefrom.
The Specification provides substantial disclosure directed to high nighttime temperature (HNT). Paragraph 0003 identifies the technical field as rice grain weight under high-temperature conditions; Paragraph 0004 specifically identifies rising nighttime temperatures and HNT stress as the problem affecting rice yield; and Paragraph 0005 reports that high LOG L1 transcript abundance correlates with lower grain weight under HNT and that logl1 mutants have higher grain weight than wild type under HNT. The experimental design likewise exposed WT, LOG1-overexpression, and LOG1 knockout plant to control or HNT treatment (pa 0032, and 0104) concludes that LOG L1 is a key regulator of single-grain weight in rice plants exposed to warmer nighttime temperatures during grain development.
Thus, the working examples provide experimental support for the nighttime-temperature-stress embodiments. However, the presently identified experimental disclosure does not demonstrate the claimed phenotype under daytime-temperature stress or establish that the LOG1 response observed under HNT can be extrapolated predictably to daytime-temperature stress.
The distinction is particularly relevant because the disclosed discovery concerns the response of LOG1 to warmer nighttime conditions, and the Specification itself identifies the relationship between LOGL1 expression and grain weight specifically under HNT. Moreover, the state of the art demonstrates that the phenotypic effects of LOG/LOGL modification can vary with environment conditions. Wang (2020), for example, evaluated OsLOGL5-edited lines under well-watered, drought, normal nitrogen, and low-nitrogen conditions and reported nonuniform phenotypic responses among particular edits and environments. Accordingly, environmental responses of a LOG-family modification cannot simply be presumed to extend form one stress contention to another.
Therefore, while the Specification provides experimental guidance concerning nighttime-temperature stress, it does not provide sufficient working examples or other guidance demonstrating that the claimed LOG1 mutation and breeding method will produce higher grain weight under the separately recited daytime-temperature-stress alternative. Determining whether particular LOG1 mutations produce the required phenotype under daytime-temperature stress would require additional empirical testing.
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Conclusion
No claims are allowed.
The closest prior art of record includes Kurakawa (Takashi Kurakawa et. al., NATURE (2007) Vol 445, pp652-655), Wang (2020), and Chen (2022).
Kurakawa identifies member of the rice LOG/LOGL gene family, including the sequence corresponding to the presently claimed LOG1 sequence. However, Kurakawa does not teach or suggest an RNAi molecule direct to the claimed LOG1 sequence that results in increased grain weight and/or grain number, not does it teach that mutation or educed expression of the presently claimed LOG1 sequence produces the claimed grain phenotype.
Wang (2020) teaches CRISPR-dieted variants of a different rice LOG-family member, OsLOGL5, and reports increased grain yield under certain field and stress conditions. However, Wang does not teach modification of the presently claimed LOG1 sequence. Further, the different OsLOGL5 edits produced different phenotypic effects; for example, Edit-B and Edit-F increased panicle number, whereas Edit-D and Edit-E decreased panicle number.
Chen (2022) review the LOG gene family and reports that LOG-family members exhibit differing expression patterns and that LOG transgenics and mutations in rice variously affect yield. Thus, Chen provides evidence that the phenotypic effect of altering one LOG/LOGL family member cannot necessarily be predicted for another family member.
Accordingly, although the prior art establishes that LOG/LOGL genes are involved in cytokinin regulation and can affect yield-related traits, the prior art of record does not teach or reasonably suggest the presently claimed LOG1 RNAi or LOG1 mutation resulting in the recited increase in grain weight and/or grain number, including the claimed phenotype under nighttime or daytime temperature stress. Therefore, the prior art of record is insufficient to support an anticipation or obviousness rejection of the presently amended claims.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to YANXIN SHEN whose telephone number is (571)272-7538. The examiner can normally be reached Monday-Friday.
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/YANXIN SHEN/Examiner, Art Unit 1663
/WEIHUA FAN/Primary Examiner, Art Unit 1663
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