Ex Parte Takumi et al

Patent Trial and Appeal BoardApr 25, 2016

12706032 (P.T.A.B. Apr. 25, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE APPLICATION NO. FILING DATE 121706,032 02/16/2010 38108 7590 04/27/2016 CERMAK NAKAJIMA MCGOWAN LLP 127 S. Peyton Street Suite 210 ALEXANDRIA, VA 22314 FIRST NAMED INVENTOR Kazuhiro Takumi UNITED STATES DEPARTMENT OF COMMERCE United States Patent and Trademark Office Address: COMMISSIONER FOR PATENTS P.O. Box 1450 Alexandria, Virginia 22313-1450 www .uspto.gov ATTORNEY DOCKET NO. CONFIRMATION NO. US-424 9888 EXAMINER SAIDHA, TEKCHAND ART UNIT PAPER NUMBER 1652 NOTIFICATION DATE DELIVERY MODE 04/27/2016 ELECTRONIC Please find below and/or attached an Office communication concerning this application or proceeding. The time period for reply, if any, is set in the attached communication. Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the following e-mail address( es): cgoode@cnmiplaw.com ip@cnmiplaw.com scermak@cnmiplaw.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte KAZUHIRO TAKUMI and GEN NONAKA Appeal2013-003632 Application 12/706,032 Technology Center 1600 Before ERIC B. GRIMES, ULRIKE W. JENKS, and ROBERT A. POLLOCK, Administrative Patent Judges. PERCURIAM. DECISION ON APPEAL This is a decision on appeal 1 under 35 U.S.C. Â§ 134 from the Examiner's rejection of claims 1-15. We have jurisdiction under 35 U.S.C. Â§ 6(b ). We affirm. STATEMENT OF THE CASE The Specification discloses "techniques for improving the ability of bacteria to produce L-amino acids, and thereby provide a[] bacterium which is able to produce one or more L-amino acids" (Spec. 3--4 i-f 11 ). The 1 Appellants identify the Real Party in Interest as Ajinomoto Co., Inc. (App. Br. 3). Appeal2013-003632 Application 12/706,032 Specification discloses that higher yields "were achieved by finding that the ability of a bacterium to produce an L-amino acid can be improved by introducing a specific mutation into the yeaS gene" (Spec. 4 ,-r 12). Independent claim 1 is representative of the claims on appeal and reads as follows (emphasis added): 1. A method for producing an L-amino acid comprising: a) culturing in a medium a bacterium belonging to the family Enterobacteriaceae, which is able to produce an L-amino acid, and has been modified to have a mutation in a yeaS gene selected from the group consisting of: (I) replacing the amino acid residue at position 28 with an amino acid residue other than threonine in the protein encoded by the yeaS gene, (II) replacing the amino acid residue at position 137 with an amino acid residue other than phenylalanine residue in the protein encoded by the yeaS gene, (III) replacing the amino acid residue at position 188 with an amino acid residue other than leucine in the protein encoded by the yeaS gene, and, (IV) combinations thereof; and b) collecting the L-amino acid from the medium; wherein the yeaS gene without said mutation encodes a protein selected from the group consisting of: (A) a protein comprising the amino acid sequence of SEQ ID NO: 2, and (B) a protein comprising the amino acid sequence of SEQ ID NO: 2, but wherein 1 to 10 amino acid residues are substituted, deleted, inserted or added, and the protein has an activity of improving an L-cysteine-producing ability in the bacterium belonging to the family Enterobacteriaceae as compared to a non-modified bacterium when expression of the protein is increased in the bacterium. The other independent claims, claims 13 and 15, similarly recite the limitation of "a protein comprising the amino acid sequence of SEQ ID 2 Appeal2013-003632 Application 12/706,032 NO: 2, but wherein 1 to 10 amino acid residues are substituted, deleted, inserted or added." Issue The Examiner has rejected claims 1-15 under 35 U.S.C. Â§ 112, second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which applicant regards as the invention (Ans. 4). The issue presented is whether the scope of independent claims 1, 13, and 15 would be unclear to one ordinary skill in the art due to the recitation in these claims of the requirement for a replacement amino acid residue at position 28, 137, or 188 in "a protein comprising the amino acid sequence of SEQ ID NO: 2, "wherein 1 to 10 amino acid residues are ... deleted, inserted or added." Principles of Law "[\V]e readÂ§ 112, ~ 2 to require that a patent's claims, viewed in light of the specification and prosecution history, inform those skilled in the art about the scope of the invention with reasonable certainty." Nautilus, Inc. v. Biosig Instruments, Inc., 134 S. Ct. 2120, 2129 (2014). Analysis The Examiner finds that independent claims 1, 13, and 15 each recite specific mutations at positions 28, 13 7, and 188 in a protein sequence, i.e., "a protein comprising the amino acid sequence of SEQ ID NO: 2 ... wherein 1 to 10 amino acid residues are ... deleted, inserted or added," but that the claims do not "clearly point to the specific mutations" because the 3 Appeal2013-003632 Application 12/706,032 language pertaining to deletions, insertions, and additions would result in an altered numbering system for the amino acid residues of the protein, wherein positions 28, 137 and 188 would not correspond to the intended positions (Ans. 4). The Examiner reasons that "if 1-10 amino acid(s) are inserted/deleted/added at the non-specific positions between 1-27, 29-136 or 138-187 of SEQ ID NO: 2; there will be mutational shift or change in the specific mutations sought and corresponding to positions 28, 137 & 188 of SEQ ID NO: 2" (Ans. 4). The Examiner reasons that, "if the mutation is merely a substitution of 1-10 amino acid(s) of SEQ ID NO: 2, there will not [be] a question of indefiniteness of the claims as substitution ... [of] one amino acid with another will not alter the numbering of the claimed mutations at positions 28, 137 & 188 of SEQ ID NO: 2" (Ans. 4).2 Appellants argue that the yeaS gene "is known in the art, and the DNA and protein sequences have also been reported" (App. Br. 5). Appellants argue that, in the claims, "the starting material before mutation[] is clearly defined as either the protein described in part (A) or (B)" (App. Br. 5). Appellants argue that the Examiner asserts that the claims are "indefinite for stating that 1-10 amino acids can be variable, and such [variation] will change the numbering sequence, and so positions 28, 137, and 188 will no 2 The Examiner contemplates a direct one to one substitution of the amino acids. This interpretation is reasonable in light of the Specification that explains "a target gene can also be inactivated by introducing a mutation for an amino acid substitution (missense mutation), a stop codon (nonsense mutation), or a frame shift mutation which adds or deletes one or two nucleotides into the coding region of the target gene on a chromosome" (Spec. i-f 124; see also i-f 178). 4 Appeal2013-003632 Application 12/706,032 longer be the same" (App. Br. 5). Appellants argue that although "this assertion could be true when read in a vacuum, the person of ordinary skill in the art would know [how] to identify where the specific claimed mutation( s) are to be made relative to the original sequence of SEQ ID NO: 2, even if the sequence contains between 1-10 changes" (App. Br. 5---6). Appellants argue that the recited changes, i.e., wherein 1 to 10 amino acid residues are varied, "are the result of random, but non-functional mutations, since the activity of the resulting protein is maintained ... and so the randomly mutated sequence could easily be compared to SEQ ID NO: 2" (App. Br. 6). Appellants argue that a "person of ordinary skill in the art would understand where original positions 28, 137, and/or 188 would be in a slightly randomly mutated sequence" (App. Br. 6). Appellants argue that such "determinations are routine and clearly within the skill in the art, especially with readily available and routinely used software alignment programs which can match up sequences and find commonalities, particularly when the variation is only up to 10 amino acids" (App. Br. 6). We are not persuaded by Appellants' arguments. We agree with Appellants that, in many cases, one of ordinary skill in the art would be able to use sequence alignment programs comparing SEQ ID N0:2 and SEQ ID N0:2 with 1-10 insertions or deletions to determine which positions in the mutated sequence now correspond to the original positions of 28, 137, and 188. The independent claims, however, also encompass sequences that allow for 10 amino acid changes including deletions and insertions clustered around any one of the specified original positions, i.e., 28, 137, or 188, such that, even with the use of sequence comparison software, one of skill in the 5 Appeal2013-003632 Application 12/706,032 art would not be able to determine exactly which position in the mutated protein corresponds to the original position 28, 137, and 188 of the non- mutated SEQ ID N0:2. (See Ans. 11, "a person of ordinary skill in the art would not be able to determine the appropriate locations of the mutation sites following addition/ deletion/insertion of 1-10 amino acids irrespective which sequencing alignment program(s) is used".) We agree with the Examiner's position that when there are changes in the sequence that cause a shift in the numbering it may not be possible to determine which amino acid corresponds the original position especially if the amino acids around any one of the positions is changed as well. In view of the above, we agree with the Examiner that one of skill in the art would not be able to determine the scope of the independent claims with a reasonable certainty. Thus, we affirm the rejection of independent claims 1, 13, and 15 as being indefinite under 35 U.S.C. Â§ 112, second paragraph. Claims 2-12 and 14 have not been argued separately from the independent claims and therefore fall with those claims. See 37 C.F.R. Â§ 41.37(c)(l)(iv). To the extent our reasoning differs from that of the Examiner, we designate our affirmance as a new grounds of rejection pursuant to 37 C.F.R. Â§ 41.50(b). SUMMARY We affirm the rejection of claims 1-15 under 35 U.S.C. Â§ 112, second paragraph. This decision contains new ground of rejection pursuant to 37 C.F.R. Â§ 41.50(b) (Sept. 13, 2004; revised, 76 FR 72270, Nov. 22, 2011, effective Jan. 23, 2012). 37 C.F.R. Â§ 41.50(b) provides "[a] new ground of rejection pursuant to this paragraph shall not be considered final for judicial review." 6 Appeal2013-003632 Application 12/706,032 37 C.F.R. Â§ 41.50(b) also provides that Appellant, WITHIN TWO MONTHS FROM THE DATE OF THE DECISION, must exercise one of the following two options with respect to the new grounds of rejection to avoid termination of the appeal as to the rejected claims: ( 1) Reopen prosecution. Submit an appropriate amendment of the claims so rejected or new evidence relating to the claims so rejected, or both, and have the matter reconsidered by the Examiner, in which event the proceeding will be remanded to the Examiner .... (2) Request rehearing. Request that the proceeding be reheard under Â§ 41.52 by the Board upon the same record .... No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. Â§ 1.136(a). AFFIRMED; 37 C.F.R. Â§ 41.50(b) 7