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and the fee set forth in 37 CFR 1.17(e) has been timely paid, the finality of the previous Office action has been withdrawn pursuant to 37 CFR 1.114.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 May 5, 2025, has been entered.
Election/Restrictions
Applicant has elected group II, drawn to a fertile homozygous mutated female fish, crustacean, or mollusk for producing a sterile fish, crustacean, or mollusk (claims 11, 41-42, and 49-51).
Furthermore, Applicant has elected a mutation in a cis-acting 5’ or 3’ UTR regulatory sequence pf a primordial germ cell (PGC) development gene.
Applicant has elected nanos3 as the mutated PGC Development gene.
Claims 1-10, 21-40, and 43-51 are pending but withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, there being no allowable generic or linking claim.
Election of Applicant’s invention(s) was made with traverse in the reply filed
on February 7, 2024.
DETAILED ACTION
The amended claims filed on May 5, 2025, have been acknowledged.
Claims 12-20 were cancelled. Claims 1-11 and 21-51 are pending. Claims 1-10, 21-40, and 43-48 are pending but withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a non-elected invention, there being no allowable generic or linking claim. Claims 11, 41-42, and 49-51 are pending and examined on the merits.
Information Disclosure Statement
The information disclosure statements (IDS) submitted on January 20, 2025, May 5, 2025, and August 14, 2025, have been considered.
Withdrawn Nucleotide and/or Amino Acid Sequence Disclosures
The prior objection to the sequence disclosures associated with Figures 9B, Figure 32B-C, Figure 33A, 34B-C, 35A-B, and 36B-C is withdrawn in light of Applicant’s amendments to the specification identify the residues associated with each partial sequences of the full sequence in the Sequence Listing.
Maintained 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 11, 41-42, and 49-51 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 claims contain 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.
Claim 11 and 49 recites the functional limitation “wherein the mutation disrupts the post- transcriptional regulation of a primordial germ cell (PGC) development gene to reduce the maternal-effect of the PGC development gene, and wherein the mutation that disrupts the post-transcriptional regulation of a PGC development gene does not impair somatic (claim 11)/zygotic (claim 49) function of the gene, wherein the mutation is in a cis-acting 5' or 3' UTR regulatory sequence of nanos3.” Applicant does not teach any mutations in a cis-acting 5' UTR regulatory sequence of nanos3 that lead to fertile homozygous mutated female fish for producing a sterile fish. Furthermore, Applicant only teaches one example of a mutation in a cis-acting 3' UTR regulatory sequence of nanos3 by mutating nucleotides near the miR-430 binding site.
Claims 41 and 50 recite the limitation “wherein the mutation is a nucleotide insertion or a nucleotide deletion that cause a frameshift mutation,” while Applicant does not teach any mutation that cause a frameshift mutation.
However, the applicant does not describe a structure capable of performing these functions. Vas-cath Inc. v. Mahurkar, 19USPQ2d 1111, clearly states that Applicant must convey with reasonable clarity to those skilled in the art that, as of the filing date sought, he or she was in possession of the invention. The invention is, for purposes of the ‘written description’ inquiry, whatever is now claimed.'' (See page 1117). The specification should “clearly allow persons of ordinary skill in the art to recognize that (he or she) invented what is claimed.'' (See Vas-cath at page 1116).
In analyzing whether the written description requirement is met for genus claims, it is first determined whether a representative number of species have been described by their complete structure. To provide adequate written description and evidence of possession of a claimed genus, the specification must provide sufficient distinguishing identifying characteristics of the genus. The factors to be considered include disclosure of complete or partial structure, physical and/or chemical properties, functional characteristics, structure/function correlation, methods of making the claimed product, or any combination thereof. The disclosure of a single species is rarely, if ever, sufficient to describe a broad genus, particularly when the specification fails to describe the features of that genus, even in passing. (see In re Shokal 113USPQ283(CCPA1957); Purdue Pharma L.P. vs Faulding Inc. 56 USPQ2nd 1481 (CAFC 2000).
Applicant teaches one example of a mutation in a cis-acting 3' UTR regulatory sequence of nanos3 that lead to fertile homozygous mutated female fish for producing a sterile fish. Applicant does not teach any mutations in a cis-acting 5' UTR regulatory sequence of nanos3 that lead to fertile homozygous mutated female fish for producing a sterile fish. As such, applicant provides limited examples of mutations in the 5’ or 3’ UTR of nanos3 that result in fertile homozygous mutated female fish for producing a sterile fish (paragraph 00134). Applicant does not provide any examples of a mutation in the 3’ or 5’ UTR that causes a frameshift mutation as these are untranslated regions and do not code for a protein.
The applicant has provided limited description or reduction to practice of mutations that lead to fertile homozygous mutated female fish for producing a sterile fish. Based on the applicant's specification, the skilled artisan cannot envision the detailed mutations that would allow for fertile homozygous mutated female fish for producing a sterile fish.
The limited number of recited mutations specifically disclosed that lead to a fertile homozygous mutated female fish for producing a sterile fish are not representative of the genera because the genera are highly variant. Kedde et al. (Cell 131: 1273-1286. 2007) teaches that 4 of 5 mutations of the 3’ UTR of nanos1 (also known as nanos3) did not cause a reduction in expression of nanos1. As such, the site of the mutations within the nanos3 3’ UTR region is important for producing fertile homozygous mutated female fish for producing a sterile fish. As these results show, only certain mutation sites can lead to fertile homozygous mutated female fish for producing a sterile fish.
Furthermore, claims 11, 41, and 49-50 are claiming a genus of mutations based on the function of the mutations. This claim would encompass novel mutations not yet described in the literature. Additionally, while maternal-effect mutations were known, not all mutations, let alone maternal-effect mutations, result in the functional properties of claims 11 and 49. As an example, Kishimoto et al. (Mechanisms of Development 121: 79-89. 2004) teaches that their acytokinesis mutations are a maternal-effect mutation that causes sterility as embryos die during development (abstract and Figure 2).
Without a correlation between structure and function, the claim does little more than define the claimed invention by function. That is not sufficient to satisfy the written description requirement. See Eli Lilly, 119 F.3d at 1568, 43 USPQ2d at 1406 (“definition by function … does not suffice to define the genus because it is only an indication of what the gene does, rather than what it is”).
Therefore, conception is not achieved until reduction to practice has occurred. See Fiers v. Revel, 25 USPQ2d 1602 at 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016. One cannot describe what one has not conceived. See Fiddes v. Baird, 30 USPQ2d 1481, 1483. In Fiddes, claims directed to mammalian FGF's were found to be unpatentable due to lack of written description for that broad class. The specification provided only the bovine sequence.
As such, there is a wide variety of mutations encompassed by the scope of claims 11 and 49. Accordingly, given that the specification only teaches one species of the broadly-defined genera of mutations that produce sterile offspring as recited in claims 11 and 49, this limited information is not deemed sufficient to reasonably convey to one skilled in the art that the applicant is in possession of the required starting materials, that is a fertile homozygous mutated female fish for producing a sterile fish, at the time the application was filed. Regarding claims 41 and 50, Applicant has not provided any examples of a frameshift mutation in the 5’ or 3’ UTR of nanos3 that produce the recited function. As such, the Applicant is not deemed to be in possession of the required starting materials, that is a fertile homozygous mutated female fish for producing a sterile fish with the requisite mutation, at the time the application was filed
Thus, for the reasons outlined above, it is concluded that the claims do not meet the requirements for written description under 35 U.S.C. 112, first paragraph.
Applicant is reminded that MPEP 2163 - 35 U.S.C. 112(a) and the first paragraph of pre-AIA 35 U.S.C. 112 require that the “specification shall contain a written description of the invention ....” This requirement is separate and distinct from the enablement requirement. Ariad Pharm., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1340, 94 USPQ2d 1161, 1167 (Fed. Cir. 2010) (en banc).
The court explained that “reading a claim in light of the specification, to thereby interpret limitations explicitly recited in the claim, is a quite different thing from ‘reading limitations of the specification into a claim,’ to thereby narrow the scope of the claim by implicitly adding disclosed limitations which have no express basis in the claim.” The court found that applicant was advocating the latter, i.e., the impermissible importation of subject matter from the specification into the claim.). See also In re Morris, 127 F.3d 1048, 1054-55, 44 USPQ2d 1023, 1027-28 (Fed. Cir. 1997).
The claims fail to recite, and the specification fails to disclose, a nexus between the required fertile homozygous mutated female fish for producing a sterile fish and the corresponding recited functional properties of “wherein the mutation disrupts the post- transcriptional regulation of a primordial germ cell (PGC) development gene to reduce the maternal-effect of the PGC development gene, and wherein the mutation that disrupts the post-transcriptional regulation of a PGC development gene does not impair somatic (claim 11)/zygotic (claim 49) function of the gene, wherein the mutation is in a cis-acting 5' or 3' UTR regulatory sequence of nanos3.” Applicant does not teach any mutations in a cis-acting 5' UTR regulatory sequence of nanos3 that lead to fertile homozygous mutated female fish for producing a sterile fish. Furthermore, Applicant only teaches one example of a mutation in a cis-acting 3' UTR regulatory sequence of nanos3 by mutating nucleotides near the miR-430 binding site.
Claims 41-42 are also rejected because they fail to fix the 112(a) issues associated with claim 11. Claims 50-51 are also rejected because they fail to fix the 112(a) issues associated with claim 49.
Response to Arguments
Applicant's arguments filed May 5, 2025, are acknowledged.
Applicant argues that the specification provides multiple representative species, well defined structural motifs and assays that correlate structure with function and explicit teachings that the homozygous carriers are fertile while their offspring are sterile.
First, Applicant references the Δ8 and Δ32 deletions within conserved motif 1 of the nanos 3’ UTR, and the conserved motifs in the 3’ UTR of dnd1 and Elavl2 as being sufficient to show multiple representative species.
Second, Applicant cites to Motif 1 and the methodology of identifying equivalent motifs by MEME analysis and miRNA seed mapping as providing sufficient structural boundaries.
Third, Applicant cites to eight different frameshit mutations that they tested as providing possession of the frameshift genus.
Fourth, Applicant argues that paragraph 0086 teaches mutating the 5’ UTR and that one can use the mapping protocol of Example 17 to generate the 5’ UTR variants.
Fifth, Applicant argues that the results of Kedde do not demonstrate unpredictability. Instead, Kedde corroborates Applicant’s structural narrowing and underscores that the genus is not “highly variant” (page 10, paragraph 5-page 13, paragraph 4).
Applicant's arguments and the cited prior art have been fully considered but they are not persuasive.
As an initial matter, claims 11 and 49 are directed to mutations in the 5’ or 3’ UTR of nanos3. Although Applicant has cited mutations in other genes as also showing that they disrupt the maternal-effect of a primordial germ cell (PGC) development gene without impairing the somatic/zygotic function of the gene, these do not suggest possession of nanos3 mutations that have this function outside of the mutations to motif 1 in the 3’ UTR of nanos3 as cited by the Applicant as there are distinct structural components in the other genes that may cause those mutations to have the recited function that are not necessarily found in nanos3
Regarding Applicant’s first and second argument, they recite two mutations in the same motif 1 region as being capable of causing the recited function. They also identify two other genes that have conserved motifs but do not recite any mutation in those genes that generate the required function. As stated in the rejection above, the two recited mutations in motif 1 of the nanos3 3’ UTR are not sufficient to show possession of the entire genera (any mutation within the nanos3 3’ UTR). The limited number of recited mutations specifically disclosed that lead to a fertile homozygous mutated female fish for producing a sterile fish are not representative of the genera because the genera are highly variant. Furthermore, Applicant’s arguments suggest that the only region in the 3’ UTR that would have a similar function is mutations in motif 1 as Applicant considers motif 1 as the sole functional hotspot (page 13, paragraph 3 of Remarks). Therefore, this would suggest that only mutations in Motif 1 would have this function and not any 3’ UTR mutation as presently claimed.
Regarding Applicant’s third argument, none of the identified frameshift mutations are in nanos3. Therefore, Applicant has not shown any frameshift mutation in nanos3 that has the recited function and is not in possession of the recited mutated fish.
Regarding Applicant’s fourth argument, paragraph 0086 does not recite any mutations in the 5’ UTR region of nanos3. Furthermore, although Applicant cites that one can use motif mapping as recited in Example 17, Applicant doesn’t recite any motifs in the 5’ UTR of nanos3 that would be of interest nor provide any examples of mutations of the 5’ UTR in nanos3 that have the required function in the specification. Therefore, Applicant has not shown any 5’ UTR mutation in nanos3 that has the recited function and is not in possession of the recited mutated fish.
Regarding Applicant’s fifth argument, Applicant’s interpretation of the data of Kedde is incorrect. First, seed-site mutations of the miR-430 binding site as shown in Figure 5B increases nos1 expression levels as the inhibitory miR can no longer bind and degrade nanos3 transcripts, increasing expression. Therefore, seed-site mutations do not suppress translation as claimed. Second, Applicant is incorrect in stating that Motif 1 is the sole functional hot spot as mutations in the putative Dnd interaction sequence 2 (outside of motif 1, as shown in Figure 33) suppressed nanos3 expression levels while mutations in putative Dnd interaction sequence 1 did not. Therefore, there are at least two regions that can be mutated to reduce nanos3 expression through post-translational regulation as both mutations are hypothesized to reduce the binding of an RNA binding protein that blocks the miR 430 seed region, opening up the seed site and allowing degradation of the nanos3 mRNA (Figure 6 of Kedde and paragraphs 0164-0165 of the specification). Furthermore, as stated above, Kedde teaches that 4 of 5 mutations of the 3’ UTR of nanos1 (also known as nanos3) did not cause a reduction in expression of nanos1.
As such, the site of the mutations within the nanos3 3’ UTR region is important for producing fertile homozygous mutated female fish for producing a sterile fish. As these results show, only certain mutation sites can lead to fertile homozygous mutated female fish for producing a sterile fish.
Therefore, Applicant’s arguments are unpersuasive and the 112a rejection is maintained.
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.
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.
Claims 11, 42, 49, and 51 are rejected under 35 U.S.C. 103 as being unpatentable over Draper et al. (Developmental Biology 305: 589-598. 2007), Kedde et al. (Cell 131: 1273-1286. 2007), NCBI (nanos homolog 3 [ Danio rerio (zebrafish) ]; Gene ID: 140631), and Skugor et al. (Mar Biotechnol 16: 256-264. 2014; referenced in IDS).
Regarding claims 11 and 49, Draper teaches a fertile homozygous mutated female fish for producing a sterile fish. Draper teaches that they mated Znos1 [nanos1] (nos1-/-) females to wild-type males and found that embryos derived from Znos1 mothers (fertile homozygous mutated female fish) developed into agametic adults that were phenotypically male (n=39/39). In contrast to embryos derived from Znos1 females, embryos derived from Znos1 males mated to wild-type females had normal numbers of PGCs at all stages examined. Thus, nos1(fh49) mutation results in a strict maternal effect-sterile phenotype (sterile offspring) (page 593, column 2, paragraph 1).
Draper does not teach wherein the mutation disrupts the post- transcriptional regulation of a primordial germ cell (PGC) development gene to reduce the maternal-effect of the PGC development gene.
However, Kedde teaches that mutating one URR [U-rich regions] (mut3, downstream of miR-430 site) of nos1 [nanos1] 3’ UTR reduced its expression. mut3 did not reduce gene expression when miR-430 target site was mutated, suggesting that also in this case Dnd1 effect is miRNA dependent (page 1279, column 2, paragraph 3). As can be seen in Figure 6, Dnd1 functions by blocking miR-430 binding sites in the 3’ UTR, preventing degradation of the nanos3 mRNA and Kedde teaches that Dnd1 binds to URRs to mediate miRNA based suppression (page 1279. Column 1, paragraph 2-column 2, paragraph 3). Based on the data of Kedde, the mut3 mutation in the URR region prevents Dnd1 from binding to the nanos3 mRNA to prevent miR-430 binding, thereby opening up the miR-430 binding site for miR-430 to bind and degrade the nanos3 mRNA, reducing nanos3 expression levels.
NCBI teaches that nanos1 and nanos3 are the same gene (See “Also known as” section).
Skugor teaches that the binding of the microRNA (miRNA) gene family miR-430 to target sites within the 3′UTR of zebrafish nanos caused mRNA degradation in somatic cells, but the mRNAs persisted in PGCs despite the presence of miR-430. In zebrafish germ cells, the RNA binding protein DnD was demonstrated to inhibit miRNA access to target 3′UTRs by binding to adjacent U-rich elements. Consistently, loss of DnD functionor its target sequences made zebrafish nanos susceptible to miR-430-mediated degradation and resulted in failure of PGC migration and survival (page 257, column 1, paragraph 1). Skugor teaches that MO [morpholino]-induced DnD reduction on PGCs labeled by the cod gfp-nanos3 3′UTR in cod and zebrafish (Fig. 4d, e). In both species, the fluorescent cells expressing the GFP construct were completely abolished in DnD morphants. The results strongly indicate a DnD-dependent mechanism for stabilization of germ plasm factors, including nanos3 mRNA, required for germ cell survival, a mechanism previously reported in zebrafish (page 259, column 2, paragraph 2-page 260, column 1, paragraph 1).
It would have been obvious to one of ordinary skill in the art before the effective filing date of the claimed invention to have substituted null nanos1 (also known as nanos3) mutation of Draper with a mutation in the 3’ UTR region of nanos3 as identified by Kedde to arrive at the instantly claimed invention. One of ordinary skill in the art would have been motivated to substitute with a reasonable expectation of success because Draper, Kedde, and Skugor all focus on the role of nanos3 in the maintenance of primordial germ cells and fertility. Kedde teaches that mutating the 3’ UTR of nanos3 in the putative DnD interaction sequence 2 region caused DnD to be unable to bind to the 3’ UTR of nanos3, allowing miR-430 to bind to the nanos3 3’UTR. This caused degradation of nanos3 transcripts which lead to a reduction in expression of nanos3. Additionally, Skugor teaches that blocking DnD expression leads to loss of PGC cells. Therefore, it was well understood that one could mutate a region of the 3’ UTR of nanos3 to allow for degradation of nanos3 in primordial germ cells and Draper shows that nanos3 homozygous mutants still produced viable offspring that were sterile. Because the prior art teaches all of the elements of the claimed invention, there is a reasonable expectation of success.
Regarding the limitations “does not impair somatic (claim 11)/zygotic (claim 49) function”, Applicant teaches that discrete mutations in a nos3 3'UTR conserved motif1 did not impair oocytes development. Instead, such mutations only appear to disrupt the post-translational regulation of nos3 mRNA in embryos progeny of mutant females (paragraph 00134). Additionally, Table 3 identifies that the deletion in the 3’ UTR likely corresponds to the motif protecting against miR-430 degradation (page 41). Kedde teaches that mutating one URR [U-rich regions] (mut3, downstream of miR-430 site) of nos1 [nanos1] 3’ UTR reduced its expression. mut3 did not reduce gene expression when miR-430 target site was mutated, suggesting that also in this case Dnd1 effect is miRNA dependent (page 1279, column 2, paragraph 3). Considering that the mutations of the instant application and Kedde affect the miR-430 binding site, the mutation of Kedde is likely to cause a similar effect as the mutation of the Applicant. As such, Kedde should also have the effect of disrupting the maternal activity of the PGC development gene, and not disrupting the function of the PGC development gene during later stages of development.
Regarding claims 42 and 51, Skugor teaches that the main target sequence GCACUU for the highly conserved seed of miR-430 was identified in zebrafish and tilapia (page 259, column 1, paragraph 1). As such, although Draper, Kedde, and Skugor focused on experimenting in Zebrafish and Cod, Skugor clearly identifies Tilapia as another potential experimental fish for disrupting miR-430 binding and it would have been obvious that one could perform the same experiments in tilapia.
Response to Arguments
Applicant's arguments filed May 5, 2025, are acknowledged.
First, Applicant argues that Draper teaches a coding-region knockout and not a 3’ UTR mutation and that nos1-/- females become progressively sterile themselves owing to loss of stage I oocytes. Thus, Draper fails to disclose or suggest a mutation that "reduces the maternal effect of the PGC-gene without impairing its somatic function/zygotic function" as required by each independent claim. Instead, Draper teaches that a skilled person would expect any additional reduction in nos expression to aggravate sterility, not selectively eliminate the maternal effect.
Applicant argues Kedde uses a transient reporter, not a heritable allele, and did not test the impact on the zygotic function or maternal function of the mutation. A person skilled in the art would not expect a nanos3 3'UTR edited female to retain somatic/zygotic function of the gene while abolishing maternal function of the gene since a skilled person in the art would expect that the reduced nanos3 expression would compromise fertility directly in the female.
Applicant argues Skugor does not teach a genomic alteration of nanos3, nor are any adults produced, and no heritable, maternal-effect sterility is shown.
Therefore, Applicant argues the cited prior art does not teach at least the following elements:
* Stable 3'-UTR mutation that selectively abolishes maternal but not somatic/zygotic activity.
* Fertile homozygous females carrying that mutation.
* Progeny sterility without parental somatic defects (page 14, paragraph 2-page 15, paragraph 2).
Furthermore, Applicant argues that the Office Action states that the null allele of Draper is merely a starting point, and that the combined teachings supply the 3' UTR mutation. However, Draper itself underscores that any further reduction of nos activity worsens the phenotype: homozygous females quickly lose all germ-line activity and their ovaries become agametic. The skilled person therefore would avoid new mutations predicted to reduce expression (as Kedde mut 3 does), because Draper shows that loss of zygotic nos expression destroys female fertility, which is directly opposite to the desired outcome.
The Office Action states that the ordinary person would know to focus on mutation 3. Applicant notes that Kedde mut 3 depresses expression everywhere. In HEK-293 cells, mut 3 cuts endogenous p27 RNA 1.5-fold and protein 5-fold, unless the miR-430 site is also destroyed. That is the opposite of the claimed retention of somatic/zygotic activity. Nothing in Kedde enables a skilled person to predict which single nucleotide or short deletion would yield Applicant's selective maternal knock- down yet leave later expression unharmed (page 16, paragraph 7-page 17, paragraph 4).
Applicant's arguments have been fully considered but they are not persuasive.
As an initial matter, it is worth pointing out that the Applicant routinely refers to combining the null mutation of Draper with the 3’ UTR mutation of Skugor. However, this is not the rejection of record. Instead, the rejection considers substituting (as is accurately identified on page 15, paragraph 3 of the Remarks) the null mutation of Draper with the 3’ UTR mutation of Kedde. As such, Applicant’s arguments regarding the lack of motivation to combine the mutation of Draper with the mutation of Kedde are not considered to be relevant to the rejection of record and are not persuasive.
In response to applicant's arguments against the references individually, one cannot show nonobviousness by attacking references individually where the rejections are based on combinations of references. See In re Keller, 642 F.2d 413, 208 USPQ 871 (CCPA 1981); In re Merck & Co., 800 F.2d 1091, 231 USPQ 375 (Fed. Cir. 1986). Although the mutation of Draper may cause somatic or zygotic changes, the mutations of the combined teachings of Draper, Kedde, NCBI, and Skugor is not the null mutation of Draper but a mutation in the 3’ UTR of nanos3 that impacts DnD binding. This allows miR-430 to bind and degrade the mRNA in cells that express miR-430. As such, the combined teachings do not teach a null mutation that impacts somatic and zygotic function. Furthermore, as stated supra, considering that the mutations of the instant application and Kedde are presumed to affect DnD binding and opening the miR-430 binding site to miR-430 in primordial germ cells, it naturally flows that the mutation of Kedde will cause a similar effect as the mutation of the Applicant. As such, Kedde should also have the effect of disrupting the maternal activity of the PGC development gene, and not disrupting the somatic/zygotic function.
Regarding Applicant’s argument that Kedde mut 3 depresses expression everywhere and thus, does not retain somatic/zygotic activity, it is worth noting that Skugor, as stated above, directly identifies that the binding of the microRNA (miRNA) gene family miR-430 to target sites within the 3′UTR of zebrafish nanos caused mRNA degradation in somatic cells, but the mRNAs persisted in PGCs despite the presence of miR-430. In zebrafish germ cells, the RNA binding protein DnD was demonstrated to inhibit miRNA access to target 3′UTRs by binding to adjacent U-rich elements. Consistently, loss of DnD function or its target sequences made zebrafish nanos susceptible to miR-430-mediated degradation and resulted in failure of PGC migration and survival (page 257, column 1, paragraph 1). Therefore, miR-430 binding is expected to occur in HEK-293 cells as they express miR-430 and do not express DnD even without the mutation impacting DnD binding. Furthermore, the Applicant’s identified mutation in motif 1 (within the binding region of DnD) is hypothesized to reduce the binding of an RNA binding protein that blocks the miR 430 seed region (i.e. DnD), opening up the seed site and allowing degradation of the nanos3 mRNA (paragraphs 0164-0165 of the specification). This is the same mechanism of action of the mut3 of Kedde. Therefore, it would naturally flow that the mut3 of Kedde would also have the same function of maintaining somatic/zygotic function as the mutations of motif 1 identified by the Applicant.
Second, Applicant argues that under the Graham factors, the Office Action must supply a reasoned rationale for substituting an uncharacterized URR point mutation for Draper's null allele with a reasonable expectation of success. The prior art does not recognize that fine-tuning miR-430 sensitivity in the egg could leave somatic/zygotic Nos3 function untouched, which is a discovery represented in the present application. The unpredictability of post- transcriptional regulation in early embryos acknowledged by Kedde, which notes multiple URRs and context-specific Dnd1 rescue, renders the proposed substitution an impermissible hindsight reconstruction.
Kedde's own conclusion is that deleting a single URR ("mut3") lowers nos1 expression unless the miR-430 site is also removed; a result that would have warned a person skilled in the art that altering the 3' UTR would likely impair somatic/zygotic function, not preserve it, and therefore would defeat the goal of obtaining normally developing (fertile) mutant females. Draper shows that total nos1 loss produces offspring that entirely lack germ cells. A skilled person would thus expect that any manipulation further depressing nos transcripts (as Kedde's mut3 does) would only worsen sterility, not generate the selective "maternal-only" effect required by the claims (page 15, paragraph 3-page 16, paragraph 2).
Applicant's arguments have been fully considered but they are not persuasive.
In response to applicant's argument that the references fail to identify the same rationale as argued by the Applicant (fine-tuning miR-430 sensitivity in the egg could leave somatic/zygotic Nos3 function untouched), the examiner recognizes that obviousness may be established by combining or modifying the teachings of the prior art to produce the claimed invention where there is some teaching, suggestion, or motivation to do so found either in the references themselves or in the knowledge generally available to one of ordinary skill in the art. See In re Fine, 837 F.2d 1071, 5 USPQ2d 1596 (Fed. Cir. 1988), In re Jones, 958 F.2d 347, 21 USPQ2d 1941 (Fed. Cir. 1992), and KSR International Co. v. Teleflex, Inc., 550 U.S. 398, 82 USPQ2d 1385 (2007). In response to Applicant's argument that the examiner's conclusion of obviousness is based upon improper hindsight reasoning, it must be recognized that any judgment on obviousness is in a sense necessarily a reconstruction based upon hindsight reasoning. But so long as it takes into account only knowledge which was within the level of ordinary skill at the time the claimed invention was made, and does not include knowledge gleaned only from the applicant's disclosure, such a reconstruction is proper. See In re McLaughlin, 443 F.2d 1392, 170 USPQ 209 (CCPA 1971).
In this case, it would have been obvious to have substituted null nanos1 (also known as nanos3) mutation of Draper with a mutation in the 3’ UTR region of nanos3 as identified by Kedde with a reasonable expectation of success because Draper, Kedde, and Skugor all focus on the role of nanos3 in the maintenance of primordial germ cells and fertility. Kedde teaches that mutating the 3’ UTR of nanos3 in the putative DnD interaction sequence 2 region caused DnD to be unable to bind to the 3’ UTR of nanos3, allowing miR-430 to bind to the nanos3 3’UTR. This caused degradation of nanos3 transcripts which lead to a reduction in expression of nanos3. Therefore, it was well understood that one could mutate a region of the 3’ UTR of nanos3 to allow for degradation of nanos3 in primordial germ cells. As such, there is a reasonable motivation for substituting the mutations to generate the claimed invention even if it is not the same motivation as identified by the Applicant.
Third, Applicant argues unexpected results as Applicant's data show that deleting Motif 1 of the nos3 3' UTR abolishes the maternal contribution but leaves somatic/zygotic transcription robust, yielding fertile FO females whose progeny lack PGCs. Nothing in Draper, Kedde or Skugor suggested this dichotomous outcome (page 16, paragraph 4).
As an initial matter, it is not clear what data Applicant is referring to. The Examiner cannot find in figures that look at nanos3 RNA expression in different tissues to show robust somatic/zygotic transcript levels.
Furthermore, although Applicant argues unexpected results, the claims are not commensurate in scope with the experimental results cited by the Applicant. MPEP 716.02(d) discloses that whether the unexpected results are the result of unexpectedly improved results or a property not taught by the prior art, the "objective evidence of nonobviousness must be commensurate in scope with the claims which the evidence is offered to support." In other words, the showing of unexpected results must be reviewed to see if the results occur over the entire claimed range. In re Clemens, 622 F.2d 1029, 1036, 206 USPQ 289, 296 (CCPA 1980) (Claims were directed to a process for removing corrosion at "elevated temperatures" using a certain ion exchange resin (with the exception of claim 8 which recited a temperature in excess of 100°C). Appellant demonstrated unexpected results via comparative tests with the prior art ion exchange resin at 110°C and 130°C. The court affirmed the rejection of claims 1-7 and 9-10 because the term "elevated temperatures" encompassed temperatures as low as 60°C where the prior art ion exchange resin was known to perform well. The rejection of claim 8, directed to a temperature in excess of 100°C, was reversed.). See also In re Peterson, 315 F.3d 1325, 1329-31, 65 USPQ2d 1379, 1382-85 (Fed. Cir. 2003) (data showing improved alloy strength with the addition of 2% rhenium did not evidence unexpected results for the entire claimed range of about 1-3% rhenium); In re Grasselli, 713 F.2d 731, 741, 218 USPQ 769, 777 (Fed. Cir. 1983) (Claims were directed to certain catalysts containing an alkali metal. Evidence presented to rebut an obviousness rejection compared catalysts containing sodium with the prior art. The court held this evidence insufficient to rebut the prima facie case because experiments limited to sodium were not commensurate in scope with the claims.).
Regarding the claims at issue in the instant application, claim 11 refers to any 3’ UTR mutation while Applicant’s unexpected results refer to mutations in motif 1.
As such, the claims as written are not commensurate in scope with alleged unexpected results.
Fourth, Applicant argues that the prior art teaches away from the claimed invention because the prior art mutations either depressed or abolished expression, while Applicant achieved selective retention (page 16, paragraph 5).
Regarding Applicant’s argument that Kedde mut 3 depresses expression which is the opposite of what the Applicant found and would represent a teaching away, it is worth noting that the Applicant’s identified mutation in motif 1 (within the binding region of DnD) is hypothesized to reduce the binding of an RNA binding protein that blocks the miR 430 seed region (i.e. DnD), opening up the seed site and allowing degradation of the nanos3 mRNA (paragraphs 0164-0165 of the specification). This is the same mechanism of action of the mut3 of Kedde. Therefore, it would naturally flow that the mut3 of Kedde would also have the same function of maintaining somatic/zygotic function as the mutations of motif 1 identified by the Applicant.
Furthermore, the rejection of record recites that it would be obvious that one could substitute the null mutation of Draper with the 3’ UTR mutation of Kedde with a reasonable expectation of success, in part, because of the fact that both mutations impacted nanos3 expression. Therefore, the fact that both mutations reduced expression of nanos3 is not considered to teach away.
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KEENAN A BATES whose telephone number is (571)270-0727. The examiner can normally be reached M-F 7:30-5:00.
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/KEENAN A BATES/Examiner, Art Unit 1631
/JAMES D SCHULTZ/Supervisory Patent Examiner, Art Unit 1631
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