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 .
Election/Restrictions
Applicant’s election without traverse of the species SEQ ID NO:2 in the reply filed on March 12, 2026 is acknowledged.
Improper Markush Grouping
Claims 1-3, and all claims dependent thereon, are rejected on the judicially-created basis that it contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984). The improper Markush grouping includes species of the claimed invention that do not share both a substantial structural feature and a common use that flows from the substantial structural feature. The members of the improper Markush grouping do not share a substantial feature and/or a common use that flows from the substantial structural feature for the following reasons: Claims 1-3 are drawn to a recombinant DNA molecule comprising a DNA sequence having at least 85%, 90%, or 95% sequence identity to a sequence selected from the group consisting of SEQ ID NOs:2-8, 12-14, and 16-19. The species SEQ ID NOs:2-8, 12-14, and 16-19 do not share a substantial structural feature as well as a common use that flows from the substantial structural feature because SEQ ID NOs:2-8, 12-14, and 16-19 are different types of regulatory sequences obtained from different genes in different plant species, as evidenced by the description of the sequences at pages 4-6 of the specification. In response to this rejection, Applicant should either amend the claim(s) to recite only individual species or grouping of species that share a substantial structural feature as well as a common use that flows from the substantial structural feature, or present a sufficient showing that the species recited in the alternative of the claims(s) in fact share a substantial structural feature as well as a common use that flows from the substantial structural feature. This is a rejection on the merits and may be appealed to the Board of Patent Appeals and Interferences in accordance with 35 U.S.C. §134 and 37 CFR 41.31(a)(1) (emphasis provided).
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.
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.
Claim 4 is drawn to the recombinant DNA molecule of claim 1, wherein the DNA sequence comprises gene regulatory activity.
Claim 1 as it reads on the elected species is drawn to a recombinant DNA molecule comprising a DNA sequence selected from the group consisting of:
a) a sequence with at least 85 percent sequence identity to SEQ ID NO:2;
b) a sequence comprising SEQ ID NO: 2; and
c) a fragment of SEQ ID NO:2, wherein the fragment has gene-regulatory activity; wherein said sequence is operably linked to a heterologous transcribable DNA molecule.
The specification at page 9 in paragraph [0037] defines “gene regulatory activity” as referring to “the ability to affect the expression of an operably linked transcribable DNA molecule, for instance by affecting the transcription and/or translation of the operably linked transcribable DNA molecule”.
The specification at page 4 in paragraph [0012] describes SEQ ID NO:2 as a DNA sequence of the 3’ UTR, T-Cl.Hsp16.9_2:1, derived from the Hsp16.9 (heat shock protein 16.9) protein gene from Coix lacryma-jobi (Job’s tears).
The specification at pages 29-32 (Example 2) discloses transgenic corn plants transformed with plant expression vectors containing 3’ UTR regulatory elements, including SEQ ID NO:2, operably linked to a GUS transgene. The specification also discloses that the 3’ UTR, T-Cl.Hsp16.9_2:1 has been experimentally determined to enhance gene expression preferentially in roots and leaves, as well as cob, silk and embryo (paragraph [100]).
The specification does not describe the gene regulatory activity of other DNA molecules comprising other DNA sequences with at least 85% sequence identity to SEQ ID NO: 2.
With respect to the effect of altering the structure of UTR regulatory element polynucleotides, it was known at the time of filing that altering their structure can also alter their function. Regulatory polynucleotide sequences such as promoters and untranslated regions require the presence of different types of regulatory regions to effect function. Consequently, a change in the sequence of a promoter or an untranslated region may alter its function.
See, for example, Sullivan et al. (Mutational analysis of the DST element in tobacco cells and transgenic plants: identification of residues critical for mRNA instability. RNA. 1996 Apr;2(4):308-15), who made substitution mutations in conserved regions of the DST (downstream element) from the 3' untranslated region (UTR) of SAUR (small auxin up RNA) genes. Five- and six-base substitutions in the ATAGAT and GTA regions of DST, respectively, resulted in inactivation of the element as an instability determinant. Smaller, two-base substitution mutations within the ATAGAT and GTA regions had varying effects on DST function in BY-2 cells, ranging from little or no effect to significant increases in reporter mRNA half-life and accumulation. In contrast, all two-base substitution mutations tested resulted in inactivation of DST in intact tobacco leaves.
Given that claim 4 as it reads on the elected species broadly encompasses variants of SEQ ID NO: 2 that have at least 85% sequence identity to SEQ ID NO: 2 and that exhibit any type of gene regulatory activity, given the extremely limited disclosure that a polynucleotide having the nucleotide sequence of SEQ ID NO: 2 enhances gene expression preferentially in roots and leaves, as well as cob, silk and embryo, given that at the time of filing it was known in the art that altering the structure of a UTR regulatory element can also alter its function, and given the absence of any description of the effect of varying the sequence of SEQ ID NO: 2 on its ability to exhibit UTR regulatory element or other types of gene regulatory activity, one skilled in the art would not recognize that the applicant was in possession of the claimed invention as a whole at the time of filing. Further, Applicant has not described a representative number of species falling within the scope of the required genus of gene regulatory elements, or the structural features unique to the genus that are correlated with a specific gene regulatory function.
Claims 1-17 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for a recombinant DNA molecule comprising a DNA sequence comprising the nucleotide sequence of SEQ ID NO: 2, does not reasonably provide enablement for a recombinant DNA molecule comprising a DNA sequence comprising a nucleotide sequence that is a fragment of SEQ ID NO: 2, or that is a nucleotide sequence variant of SEQ ID NO: 2. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to use the invention commensurate in scope with these claims.
Claim 1 as it reads on the elected species is drawn to a recombinant DNA molecule comprising a DNA sequence selected from the group consisting of:
a) a sequence with at least 85 percent sequence identity to SEQ ID NO:2;
b) a sequence comprising SEQ ID NO: 2; and
c) a fragment of SEQ ID NO:2, wherein the fragment has gene-regulatory activity; wherein said sequence is operably linked to a heterologous transcribable DNA molecule.
Claim 2 as it reads on the elected species is drawn to the recombinant DNA molecule of claim 1, wherein said sequence has at least 90 percent sequence identity to the DNA sequence of SEQ ID NO: 2..
Claim 3 as it reads on the elected species is drawn to the recombinant DNA molecule of claim 1, wherein said sequence has at least 95 percent sequence identity to the DNA sequence of SEQ ID NO: 2..
Claim 4 is drawn to the recombinant DNA molecule of claim 1, wherein the DNA sequence comprises gene regulatory activity.
Claim 5 is drawn to the recombinant DNA molecule of claim 1, wherein the heterologous transcribable DNA molecule comprises a gene of agronomic interest.
Claim 6 is drawn to the recombinant DNA molecule of claim 5, wherein the gene of agronomic interest confers herbicide tolerance in plants.
Claim 7 is drawn to the recombinant DNA molecule of claim 5, wherein the gene of agronomic interest confers pest resistance in plants.
Claim 8 is drawn to the recombinant DNA molecule of claim 1, wherein the heterologous transcribable DNA molecule encodes an dsRNA, an miRNA, or a siRNA.
Claim 9 is drawn to a transgenic plant cell comprising the recombinant DNA molecule of claim 1.
Claim 10 is drawn to the transgenic plant cell of claim 9, wherein said transgenic plant cell is a monocotyledonous plant cell.
Claim 11 is drawn to the transgenic plant cell of claim 9, wherein said transgenic plant cell is a dicotyledonous plant cell.
Claim 12 is drawn to a transgenic plant, or part thereof, comprising the recombinant DNA molecule of claim 1.
Claim 13 is drawn to a progeny plant of the transgenic plant of claim 12, or a part thereof, wherein the progeny plant or part thereof comprises said recombinant DNA molecule.
Claim 14 is drawn to a transgenic seed, wherein the seed comprises the recombinant DNA molecule of claim 1.
Claim 15 is drawn to a method of producing a commodity product comprising obtaining a transgenic plant or part thereof according to claim 12 and producing the commodity product therefrom.
Claim 16 is drawn to the method of claim 15, wherein the commodity product is seeds, processed seeds, protein concentrate, protein isolate, starch, grains, plant parts, seed oil, biomass, flour and meal.
Claim 17 is drawn to a method of expressing a transcribable DNA molecule comprising obtaining a transgenic plant comprising the recombinant DNA molecule of claim 1 and cultivating plant, wherein the transcribable DNA is expressed.
The specification at page 9 in paragraph [0037] defines “gene regulatory activity” as referring to “the ability to affect the expression of an operably linked transcribable DNA molecule, for instance by affecting the transcription and/or translation of the operably linked transcribable DNA molecule”.
The specification at page 4 in paragraph [0012] discloses that SEQ ID NO:2 is a DNA sequence of the 3’ UTR, T-Cl.Hsp16.9_2:1, derived from the Hsp16.9 (heat shock protein 16.9) protein gene from Coix lacryma-jobi (Job’s tears).
The specification at pages 29-32 (Example 2) discloses transgenic corn plants transformed with plant expression vectors containing 3’ UTR regulatory elements, including SEQ ID NO:2, operably linked to a GUS transgene. The specification also discloses that the 3’ UTR, T-Cl.Hsp16.9_2:1 has been experimentally determined to enhance gene expression preferentially in roots and leaves, as well as cob, silk and embryo (paragraph [100]).
The specification does not disclose or characterize the gene regulatory activity of other DNA molecules comprising other DNA sequences with at least 85% sequence identity to SEQ ID NO: 2.
With respect to the effect of altering the structure of UTR regulatory element polynucleotides, it was known at the time of filing that altering their structure can also alter their function. Regulatory polynucleotide sequences such as promoters and untranslated regions require the presence of different types of regulatory regions to effect function. Consequently, a change in the sequence of a promoter or an untranslated region may alter its function.
See, for example, Sullivan et al. (Mutational analysis of the DST element in tobacco cells and transgenic plants: identification of residues critical for mRNA instability. RNA. 1996 Apr;2(4):308-15), who made substitution mutations in conserved regions of the DST (downstream element) from the 3' untranslated region (UTR) of SAUR (small auxin up RNA) genes. Five- and six-base substitutions in the ATAGAT and GTA regions of DST, respectively, resulted in inactivation of the element as an instability determinant. Smaller, two-base substitution mutations within the ATAGAT and GTA regions had varying effects on DST function in BY-2 cells, ranging from little or no effect to significant increases in reporter mRNA half-life and accumulation. In contrast, all two-base substitution mutations tested resulted in inactivation of DST in intact tobacco leaves.
The full scope of the claimed invention is not enabled because the gene regulatory activity, if any, of fragments and variants of SEQ ID NO: 2 is unpredictable, since altering the structure of a polynucleotide that is a UTR regulatory element can also alter its function.
In the instant case the specification provides no guidance with respect to how to alter the length or the sequence of SEQ ID NO: 2 in a manner that a useful gene regulatory activity is retained or is achieved. Absent such guidance one skilled in the art would have to generate each fragment and variant of SEQ ID NO: 2 encompassed by the claims, and then determine which gene regulatory activities, if any, can be performed by each fragment or variant. Such a trial and error approach to practicing the claimed invention would constitute undue experimentation.
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 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.
Claim(s) 1 and 4-17 is/are rejected under 35 U.S.C. 102(a)(1) and 102(a)(2) as being anticipated by Milligan et al. U.S. Patent No. 7,674,893, issued Mar. 9, 2010.
Claim 1 as it reads on the elected species is drawn to a recombinant DNA molecule comprising a DNA sequence selected from the group consisting of:
a) a sequence with at least 85 percent sequence identity to SEQ ID NO:2;
b) a sequence comprising SEQ ID NO: 2; and
c) a fragment of SEQ ID NO:2, wherein the fragment has gene-regulatory activity; wherein said sequence is operably linked to a heterologous transcribable DNA molecule. The specification at page 9 in paragraph [0037] defines “gene regulatory activity” as referring to “the ability to affect the expression of an operably linked transcribable DNA molecule, for instance by affecting the transcription and/or translation of the operably linked transcribable DNA molecule”. Further, the specification provides no limiting definition of a fragment that has gene-regulatory activity. Accordingly claim 1 encompasses a recombinant DNA molecule comprising a DNA sequence that is any fragment of SEQ ID NO:2 wherein the fragment affects the transcription and/or translation of an operably linked transcribable DNA molecule.
Claim 4 is drawn to the recombinant DNA molecule of claim 1, wherein the DNA sequence comprises gene regulatory activity.
Claim 5 is drawn to the recombinant DNA molecule of claim 1, wherein the heterologous transcribable DNA molecule comprises a gene of agronomic interest.
Claim 6 is drawn to the recombinant DNA molecule of claim 5, wherein the gene of agronomic interest confers herbicide tolerance in plants.
Claim 7 is drawn to the recombinant DNA molecule of claim 5, wherein the gene of agronomic interest confers pest resistance in plants.
Claim 8 is drawn to the recombinant DNA molecule of claim 1, wherein the heterologous transcribable DNA molecule encodes an dsRNA, an miRNA, or a siRNA.
Claim 9 is drawn to a transgenic plant cell comprising the recombinant DNA molecule of claim 1.
Claim 10 is drawn to the transgenic plant cell of claim 9, wherein said transgenic plant cell is a monocotyledonous plant cell.
Claim 11 is drawn to the transgenic plant cell of claim 9, wherein said transgenic plant cell is a dicotyledonous plant cell.
Claim 12 is drawn to a transgenic plant, or part thereof, comprising the recombinant DNA molecule of claim 1.
Claim 13 is drawn to a progeny plant of the transgenic plant of claim 12, or a part thereof, wherein the progeny plant or part thereof comprises said recombinant DNA molecule.
Claim 14 is drawn to a transgenic seed, wherein the seed comprises the recombinant DNA molecule of claim 1.
Claim 15 is drawn to a method of producing a commodity product comprising obtaining a transgenic plant or part thereof according to claim 12 and producing the commodity product therefrom.
Claim 16 is drawn to the method of claim 15, wherein the commodity product is seeds, processed seeds, protein concentrate, protein isolate, starch, grains, plant parts, seed oil, biomass, flour and meal.
Claim 17 is drawn to a method of expressing a transcribable DNA molecule comprising obtaining a transgenic plant comprising the recombinant DNA molecule of claim 1 and cultivating plant, wherein the transcribable DNA is expressed.
Milligan et al. teach a recombinant DNA molecule comprising a DNA sequence (SEQ ID NO:2) that is an MRS2 promoter that comprises a fragment (“TAAAAAA”) of SEQ ID NO: 2 (nucleotides 260 to 266) and that can be operably linked to a heterologous transcribable DNA molecule (column 5; columns 18-19; columns 31-33) – see nucleotides 1230 to 1236 of SEQ ID NO: 2 of Milligan et al., columns 39-40. The fragment has gene-regulatory activity in the context of the regulatory expression element. A transgenic plant comprising the recombinant DNA molecule is cultivated and the transcribable DNA is expressed (columns 33-34). The regulatory expression element can be operably linked to a heterologous transcribable DNA molecule that encodes an dsRNA (column 19). The regulatory expression element can be operably linked to a heterologous transcribable DNA molecule that comprises a gene of agronomic interest, including a gene that confers herbicide tolerance in plants and a gene that confers pest resistance in plants (column 19; column 36). Milligan et al. teach a transgenic plant cell, plant, progeny and seed comprising the recombinant DNA molecule, including a monocotyledonous plant cell and a dicotyledonous plant cell (abstract; column 4; columns 22-24; columns 34-35). Milligan et al. teach a method of producing a commodity product by obtaining a transgenic plant or part thereof and producing the commodity product therefrom, wherein the product is a seeds (column 4). Accordingly Milligan et al. anticipate claims 1 and 4-17.
Remarks
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CYNTHIA E COLLINS whose telephone number is (571)272-0794. The examiner can normally be reached M-F 8:30 am - 5:00 pm.
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/CYNTHIA E COLLINS/Primary Examiner, Art Unit 1662