Ex Parte 8241878 et alDownload PDFPatent Trial and Appeal BoardSep 29, 201595002167 (P.T.A.B. Sep. 29, 2015) Copy Citation UNITED STATES PATENT AND TRADEMARK OFFICE ____________ BEFORE THE PATENT TRIAL AND APPEAL BOARD ____________ BUTAMAX™ ADVANCED BIOFUELS LLC Requester and Respondent v. GEVO, INC. Patent Owner and Appellant ____________ Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 Technology Center 3900 ____________ Before TONI R. SCHEINER, RICHARD M. LEBOVITZ, and RAE LYNN P. GUEST, Administrative Patent Judges. LEBOVITZ, Administrative Patent Judge. DECISION ON APPEAL This is a decision on the appeal by the Third Party Requester from the Patent Examiner’s confirmation of the patentability of claims 1–15 in the above-identified inter partes reexamination of United States Patent 8,241,878 B2. The Board’s jurisdiction for this appeal is under 35 U.S.C. §§ 6(b), 134, and 315 (pre-AIA). We reverse and designate the reversal a new grounds of rejection under 37 C.F.R. § 41.77(b). Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 2 STATEMENT OF THE CASE The patent in dispute in this appeal is United States Patent 8,241,878 B2 (“the ’878 patent”) which issued Aug. 14, 2012. The Patent Owner and real party in interest is Butamax™ Advanced BioFuels LLC (“Patent Owner”). Patent Owner Respondent Brief (“Resp’t Br”) 1. Patent Owner is the Respondent in this Appeal. The Third Party Requester and real party in interest in this Appeal is Gevo, Inc. (“Requester”). Requester Appeal Brief (“Appeal Br.”) 1. Requester is the Appellant in this Appeal. Requester requested inter partes reexamination of the ’878 patent under 35 U.S.C. §§ 311–318 and 37 C.F.R. §§ 1.902–1.997. Request for Inter Partes Reexamination (Sept. 10, 2012). Reexamination was ordered by the Examiner and culminated in confirming the patentability of the claims. Action Closing Prosecution (“ACP”) (Dec. 18, 2013). Requester appeals from this determination. The ’878 patent is currently involved in the following litigation: Butamax Advanced Biofuels, Inc. v. Gevo, Inc., Civ. No. 12-1036 in the U.S. District Court for the District of Delaware. Patent Owner disclosed another litigation involving Requester Gevo, which is also in the District Court of Delaware. Notice of Concurrent Proceedings (Aug. 21, 2015). A Memorandum Opinion by the District Court Judge in the Civ. No. 12-1036 was issued on Aug. 3, 2015. In the Memorandum Opinion, the District Court Judge found that claims 1 and 3 were invalid as indefinite under 35 U.S.C. § 112, second paragraph. Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 3 CLAIMS Claims 1–15 are pending. Claim 1, reproduced below, is the only independent claim on appeal. 1. A method of converting 2,3-dihydroxyisovalerate to α- ketoisovalerate, comprising providing a recombinant yeast host cell expressing a heterologous dihydroxy-acid dehydratase (DHAD) protein that comprises (i) an amino acid sequence having at least 95% identity to SEQ ID NO: 179 or 187; and (ii) three conserved cysteine residues that correspond to positions 56, 129, and 201 of SEQ ID NO:179; wherein the substrate 2,3-dihydroxyisovalerate is present in the yeast host cell and wherein the expressed heterologous DHAD protein catalyzes the conversion of 2,3-dihydroxyisovalerate to α-ketoisovalerate. ISSUE Initially, the Examiner had rejected all the pending claims over disclosures in eight different publications, each said to anticipate the claimed subject matter under 35 U.S.C. § 102. RAN 6–7; Non-Final Office Action (Oct. 24, 2012). Patent Owner argued that the claims are entitled to the benefit of provisional applications 61/100,801 (“the ’801 provisional”) and 61/100,806 (“the ’806 provisional) (collectively, “the provisionals”), both filed on Sept. 29, 2008, which is before the publication of each anticipatory reference cited by the Examiner. Patent Owner Response 2, 4 (Jan. 24, 2013); ’878 patent, “Related U.S. Application Data.” The Examiner reconsidered the priority issue and accorded the ’878 patent the priority dates of the ’801 and ’806 provisional applications, withdrawing all the anticipation rejections because the cited publications did not qualify as prior Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 4 art. RAN 13–14; ACP. Consequently, the Examiner confirmed the patentability of the claims. Id. Requester appeals from the Examiner’s decision confirming the patentability of the claims. Appeal Br. 1. Requester contends that the Examiner erred in determining that the provisional applications provide written description support for claims 1–15. Id. at 3. The issue in this appeal is whether the Examiner erred in granting the ’878 patent the benefit of the priority dates of the ’801 and ’806 provisional applications. DISCUSSION It is not disputed by Patent Owner that claim 1 reciting “an amino acid sequence having at least 95% identity to SEQ ID NO: 179 or 187” was not present in the applications leading to the ’878 patent until after the publication dates of the eight references initially found by the Examiner to be anticipatory to the claimed subject matter. SEQ ID NOS. 179 and 187 correspond to bacterial of S. mutans and L. lactis dihydroxy-acid dehydratase (DHAD) proteins. Patent Owner contends that the cited publications are not prior art because the publications were not published until after the filing date of the provisional applications. Resp’t Br. 2. The Examiner agreed and withdrew the rejections. Entitlement to the provisional filing dates requires that the later-filed claims of the ’878 patent be described in the provisional applications in such a way that the written description requirements of 35 U.S.C. § 112 are met. See 35 U.S.C. §§ 119(e); 37 C.F.R. § 1.78(a). See Tronzo v. Biomet, Inc., 156 F.3d 1154, 1158 (Fed. Cir. 1998) (discussing requirements of claiming Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 5 benefit of priority date of earlier application under 35 U.S.C. § 120). The disclosure in the earlier provisional applications must reasonably convey to one of ordinary skill in the art that the inventors possessed the later-claimed subject matter when they filed the earlier applications. Id. “[A] prior application itself must describe an invention, and do so in sufficient detail that one skilled in the art can clearly conclude that the inventor invented the claimed invention as of the filing date sought.” Lockwood v. American Airlines, Inc., 107 F.3d 1565, 1572 (Fed. Cir. 1997). To support the priority benefit claim, Patent Owner provided a declaration by Dennis H. Flint, Ph.D. (“Flint Decl.”). Dr. Flint is also an inventor of the ’878 patent. Based on Dr. Flint’s education and experience, we find that there is sufficient evidence that he is qualified to testify about whether the provisional applications described the invention which is now claimed. Flint Decl. ¶¶ 5–10. We summarize Dr. Flint’s testimony in the following findings of fact (“FF”). FF1. Dr. Flint acknowledged that [w]hile the priority applications disclose the use of S. mutans and L. lactis DHADs to create a computer model, i.e., a Profile HMM by which to identify, e.g., fungal and plant DHAD- related proteins, a POSA [person of ordinary skill in the art] would not view the applications to be limited to use of heterologous DHAD proteins sourced solely from fungus and plants. Flint Decl. ¶ 21. FF2. Dr. Flint further testified: Rather, because the priority applications generally conveyed expressing heterologous DHAD proteins, a POSA would have looked to those functionally verified S. mutans and L. lactis DHADs as well. This is particularly so because the priority Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 6 applications state that these bacterial DHAD proteins were functionally verified, making them excellent candidates for use in the claimed methods and the conversion of 2,3- dihydroxyisovalerate to α-ketoisovalerate. Thus, a POSA would have understood that these disclosed and functionally verified DHADs are among the heterologous DHADs for expression in yeast and are within the full scope of claimed methods. Id. FF3. Dr. Flint also testified that the priority applications generally describe the use of heterologous DHADs, and that the use of plant and fungal DHADs are merely preferred options. Id. at ¶¶ 24, 27. FF4. Dr. Flint stated that the skilled worker would have understood that the applications describe the use of “both plant and fungal DHADs, as well as functionally verified S. mutans and L. lactis DHADs, as suitable heterologous DHADs for expression in yeast” because “the applications disclose that these DHADs are functionally verified.” Id. at ¶¶ 25, 26. FF5. The ’801 provisional incorporates by reference US Patent Application 61/100,792 (“the ’792 application”). The ’801 provisional teaches that the “analysis used to obtain 2Fe-2S DHADs is described in commonly owned and co-pending US Patent Application 61/100,792 [“the ’792 application”], which is herein incorporated by reference.” ’801 provisional 31:4–6. FF6. Dr. Flint states that ’792 application provides “separate, additional support for the claimed invention” because it describes S. mutans and L. lactis [2Fe-2S] DHADs which “confirm[s] a POSA’s understanding that S. mutans and L. lactis bacterial DHADs are among [2Fe-2S] DHADs expressed in yeast.” Flint Decl. ¶¶ 36, 37. Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 7 We have considered Dr. Flint’s testimony, as well as the Examiner’s well-reasoned discussion in the Right of Appeal Notice. However, we are of the opinion that the Examiner erred in according claim 1 the benefit of the ’801 and ’806 provisional applications. 1 First, we agree with Patent Owner and the Examiner that the provisional applications describe the expression of heterologous DHADs in yeast. There is an express description of this broad embodiment in the “Summary of the Invention” and in the claims of the ’801 provisional. The following disclosure in the ’801 provisional is pertinent to this issue. FF7. In the “Summary of the Invention,” it is stated that “[p]referred in the present invention are cells that comprise introduced fungal and plant dihydroxyacid dehydratase Fe-S cluster proteins [DHAD].” ’801 provisional 2:23–25. FF8. The “Summary of the Invention” of the ’801 provisional also contains a broader disclosure describing the use of heterologous DHADs at page 3, lines 8–16 (emphasis added): In another embodiment the invention provides a method for the conversion of 2,3-dihydroxyisovalerate to α-ketoisovalerate comprising a) providing a recombinant yeast host cell 1) at least one heterolog[o]us gene encoding a 2Fe-2S dihydroxy-acid dehydratase [DHAD] wherein the 1 In arguing that the claims are entitled to the benefit of the provisional applications, Patent Owner mainly identified support in the ’801 provisional application. When the ’806 provisional was cited, Patent Owner referred to the same disclosure as in the ’801 provisional. See Flint Decl. ¶¶ 16, 17, 19. Consequently, we have focused the discussion on the disclosure in the ’801 provisional application. Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 8 recombinant yeast host cell has reduced activity of at least one endogenous Fe-S cluster protein; and 2) a source of 2,3-dihydroxyisovalerate; and b) growing the recombinant host cell of (a) under conditions where the 2,3 dihydroxyisovalerate is converted to α- ketoisovalerate. FF9. This same disclosure appears in claim 15 of the ’801 provisional at page 57, lines 12–20. However, the issue of whether to accord claim 1 the benefit of the provisional applications is narrower than the determination of whether a genus of heterologous DHADs are described. The disputed claim limitation is directed to “an amino acid sequence having at least 95% identity to SEQ ID NO: 179 or 187.” A description of a broad genus is not necessarily a description of every species within the genus. The disputed claim limitation is directed to specific species of the broadly claimed and described genus of heterologous DHADs, i.e., “an amino acid sequence having at least 95% identity to SEQ ID NO: 179 or 187.” To determine whether the ’878 patent is entitled to the benefit of the provisional applications, we must determine whether the inventors invented the narrower genus that includes 1) heterologous DHAD which are SEQ ID NO: 179 and 187; and 2) heterologous DHAD having a sequence of at least 95% identity to SEQ ID NO: 179 and 187. In our opinion, it is a close call on whether the inventors invented a method of using SEQ ID NOS. 179 and 187, which are bacterial DHADs, in yeast. As pointed out by the Requester, the bacterial sequences were used by the inventors to produce a Profile Hidden Markov Model (HMM) for Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 9 choosing DHADs from plant and fungal DNA. The following findings of facts are pertinent: FF10. The provisional application explains that “a Profile Hidden Markov Model (HMM) was prepared based on amino acid sequences of eight functionally verified DHADS.” ’801 provisional 31:6–8. FF11. The amino acid sequences used for the HMM include the bacterial sequences Streptococcus mutans (DNA SEQ ID NO:178; Protein SEQ ID NO:179) and Lactococcus lactis (DNA SEQ ID NO:186; protein SEQ ID NO:187), which correspond to the amino acid sequences recited in claim 1 of the ’878 patent. ’801 provisional application 31:11, 15–16. These sequences are also listed in Table 4 containing “Functionally verified DHADs used for Profile HMM.” Id. at 8:15. FF12. As explained in the ’801 provisional, the HMM profile was used to identify other DHADs: Any protein that matches the Profile HMM with an E value of < 10 -5 is a DHAD related protein, which includes 4Fe- 4S DHADs, 2Fe-2S DHADs . . . . Sequences matching the Profile HMM are then analyzed for the presence of the three conserved cysteines, corresponding to positions 56, 129, and 201 in the Streptococcus mutans DHAD. The presence of all three conserved cysteines is characteristic of proteins having a [2Fe-2S] 2+ cluster. Proteins having the three conserved cysteines include . . . 2Fe-2S DHADs. ’801 provisional 31:28 to 32:3. FF13. The conserved cysteines in Streptococcus mutans DHAD protein correspond to those in the claimed SEQ ID NO: 179. ’801 provisional 56:1–5. Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 10 FF14. DHAD amino acid sequences from fungi and plant were identified using the HMM profile. ’801 provisional 30:31 to 32:6. Thus, SEQ ID NOS: 179 and 187 are described in the ’801 provisional, but for the purpose of creating a HMM profile to obtain other DHAD sequences. FF10–FF12. Dr. Flint’s testimony in many places appears to be more directed to the obviousness of using S. mutans and L. lactis as heterologous DHADs for expression in yeast. For example in FF2, Dr. Flint states that the bacterial DHAD proteins would have been “excellent candidates for use in the claimed methods.” Nonetheless, Dr. Flint testifies persuasively that S. mutans (SEQ ID NO: 179) and L. lactis (SEQ ID NO:187) are functionally verified heterologous DHADs (FF4). Because the provisional applications expressly disclose using heterologous DHADs, the evidence of record supports the finding that the ordinary skilled worker would have understood that SEQ ID NOS: 179 and 187 are within the scope of the disclosed genus of heterologous DHADs. FF10–FF14. Dr. Flint also referred to the incorporation by reference of the ’792 application as support for the benefit claim. FF5, FF6. Dr. Flint testified that the ’792 application confirms that the S. mutans and L. lactis are among those DHADs expressed in yeast. FF6. “To incorporate material by reference, the host document must identify with detailed particularity what specific material it incorporates and clearly indicate where that material is found in the various documents.” Advanced Display Sys., Inc. v. Kent State Univ., 212 F.3d 1272, 1282 (Fed. Cir. 2000). The ’792 application is directed to expression of these bacterial DHADs in yeast, but the ’792 application is not incorporated by reference Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 11 for this purpose (FF5) and does not identify the yeast expression portion of the application as the material which is incorporated. The incorporation by reference to the ’792 application in the ’801 provisional application is for the analysis used to obtain 2Fe-2S DHADs. FF5. Consequently, with regard to this one point, we do not find Dr. Flint’s testimony supported by the evidence of record. Even though we have concluded that there is sufficient evidence that the provisional applications describe expression of SEQ ID NOS. 179 and 187 in yeast, the analysis does not end there. In addition to reciting SEQ ID NOS. 179 and 187, the claim also includes DHADs with “an amino acid sequence having at least 95% identity” to these sequences. Dr. Flint did not address this specific limitation in the claim. It does not appear that the Examiner did either. See RAN 13. We have made “an objective inquiry into the four corners of the specification from the perspective of a person of ordinary skill in the art” (Ariad Pharms. Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1351 (Fed. Cir. 2010)) and have been unable to identify support for 95% identity limitation. The following findings of fact from the ’801 provisional are pertinent to this issue: FF15. 2Fe-2S DHADs that may be used in the present disclosure include those from fungi and plants. Representative fungal or plant 2Fe-2S DHADs are listed in Tables 1 and 2. Fungal or plant 2Fe-2S DHADs with amino acid sequence identities of 95% or greater were removed from the analysis providing this list for simplification. However, any sequences with 95% or greater amino acid identities to any of these sequences are useful in the present invention. ’801 provisional 30:31 to 32:4 (emphasis added.) Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 12 FF16. The proteins identified by this process that have a fungal or plant origin, such as SEQ ID NOs:46, 48, 50, 52, 54, 56, 58, 60, 62, 64, 66, 68, 70, 72, 74, 76, 78, 80, 82, 84, 86, 88, 90, 92, 94, 96, 98, 100, 102, 104, 106, 108, 110, 112, 114, 116, 118, 120, 122, 124, 126, 128, 130, 132, 134, 136, 138, 140, 142, 144, 146, 148, 150 and 152 may be used in the present invention, as well as any protein with amino acid identity of at least about 95%, 96%, 97%, 98%, or 99% to any of these sequences. ’801 provisional 32:15–21 (emphasis added.) FF17. Particularly suitable is the DHAD from Kluyveromyces lactis (SEQ ID NO:114) [a yeast species] and DHADs with at least about 90% amino acid sequence identity to SEQ ID NO:114 using the Clustal W method of alignment using 25 the default parameters of GAP PENALTY=10, GAP LENGTH PENALTY=0.1, and Gonnet 250 series of protein weight matrix over the full length of the protein sequence. ’801 provisional 32:22–27 (emphasis added.) FF18. In addition, 2Fe-2S DHADs that may be used may be identified using sequence comparisons with any of the fungal or plant 2Fe-2S DHADs whose sequences are provided herein, where sequence identity may be at least about 80%–85%, 85%–90%, 90%–95% or 95%–99%. ’801 provisional 32:30 to 33:2 (emphasis added). These disclosures in the ’801 provisional application establish that inventors invented a method of using DHADs which have sequence identify to one of the plant or fungal sequences disclosed in the application. FF15– FF18. However, we have not been direct to disclosure in the ’801 application that describes using DHADS which have sequence identity to a Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 13 heterologous DHAD, let alone a heterologous DHAD which has “at least 95% identity” to SEQ ID NO:179 or SEQ ID NO:187. Dr. Flint did not provide persuasive testimony that one of ordinary skill in the art would have recognized that the inventors invented the claimed group of DHADs with at least 95% identity to SEQ ID NO:179 or 187. In our opinion, there is too much mental footwork necessary to discern a description of the full scope of claim 1 in the provisional applications. The ’801 provisional expressly describes three classes of DHADs useful in the claimed methods: 1) heterologous DHADs; 2) DHADs of plant or fungal origin; and 3) DHADs that have a certain amount of amino acid sequence identity to one of the identified plant or fungal sequences. To described the claimed limitation of “an amino acid sequence having at least 95% identity to SEQ ID NO: 179 or 187,” the skilled worker would have had to first recognize, as testified by Dr. Flint, that SEQ ID NOS. 179 and 187 are heterologous DHADs. Second, the skilled worker would have had to recognize a fourth class, 4) heterologous DHADs with a certain amount of amino acid sequence identity to one of the identified heterologous sequences. While such a class might have been obvious to one of ordinary skill in the art, that is not the proper standard to apply. “Entitlement to a filing date does not extend to subject matter which is not disclosed, but would be obvious over what is expressly disclosed . . . [i]t extends only to that which is disclosed.” Lockwood, 107 F.3d at 1571–72. We have not been pointed to disclosure in the provisional applications that persuasively shows that the inventors described this fourth class. Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 14 Consequently, we conclude that the subject matter of claim 1 is not described in the ’801 and ’806 provisional applications. Because claim 1 does not have the benefit of the priority date of the provisional applications, the publications cited in Grounds of Rejection 1–8 are prior art under 35 U.S.C. § 102. RAN 6–7. We hereby set forth new grounds of rejection under 37 C.F.R. § 41.79(b) corresponding to Grounds 1–8 set forth in the RAN and in the Non-Final Office Action dated Oct. 24, 2012 (pp. 10–19). Id. The findings are adopted herein. NEW GROUND OF REJECTION This decision contains a new ground of rejection pursuant to 37 C.F.R. § 41.77(b) which provides that “[a]ny decision which includes a new ground of rejection pursuant to this paragraph shall not be considered final for judicial review.” Correspondingly, no portion of the decision is final for purposes of judicial review. A requester may also request rehearing under 37 C.F.R. § 41.79, if appropriate, however, the Board may elect to defer issuing any decision on such request for rehearing until such time that a final decision on appeal has been issued by the Board. For further guidance on new grounds of rejection, see 37 C.F.R. § 41.77(b)–(g). The decision may become final after it has returned to the Board. 37 C.F.R. § 41.77(f). 37 C.F.R. § 41.77(b) also provides that the Patent Owner, WITHIN ONE MONTH 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. The owner may file a response requesting reopening of prosecution before the examiner. Such a response must be either an amendment of the claims so rejected or new evidence relating to the claims so rejected, or both. (2) Request rehearing. The owner may request that the proceeding be reheard under § 41.79 by the Board upon the same record. . . . Any request to reopen prosecution before the examiner under Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 15 37 C.F.R. § 41.77(b)(1) shall be limited in scope to the :claims so rejected.” Accordingly, a request to reopen prosecution is limited to issues raised by the new ground(s) of rejection entered by the Board. A request to reopen prosecution that includes issues other than those raised by the new ground(s) is unlikely to be granted. Furthermore, should the patent owner seek to substitute claims, there is a presumption that only one substitute claim would be needed to replace a cancelled claim. A requester may file comments in reply to a patent owner response. 37 C.F.R. § 41.77(c). Requester comments under 37 C.F.R. § 41.77(c) shall be limited in scope to the issues raised by the Board's opinion reflecting its decision to reject the claims and the patent owner's response under paragraph 37 C.F.R. § 41.77(b)(1). A newly proposed rejection is not permitted as a matter of right. A newly proposed rejection may be appropriate if it is presented to address an amendment and/or new evidence properly submitted by the patent owner, and is presented with a brief explanation as to why the newly proposed rejection is now necessary and why it could not have been presented earlier. Compliance with the page limits pursuant to 37 C.F.R. § 1.943(b), for all patent owner responses and requester comments, is required. The examiner, after the Board's entry of a patent owner response and requester comments, will issue a determination under 37 C.F.R. § 41.77(d) as to whether the Board's rejection is maintained or has been overcome. The proceeding will then be returned to the Board together with any comments and reply submitted by the owner and/or requester under 37 C.F.R. § 41.77(e) for reconsideration and issuance of a new decision by the Board as provided by 37 C.F.R. § 41.77(f). REVERSED; 37 C.F.R. § 41.77(b) Appeal 2015-005083 Reexamination Control 95/002,167 Patent 8,241,878 B2 16 PATENT OWNER: E I DU PONT DE NEMOURS AND COMPANY LEGAL PATENT RECORDS CENTER Chestnut Run Plaza 721/2340 974 Centre Road, P.O. Box 2915 Wilmington, DE 19805 THIRD PARTY REQUESTOR: Fraser D. Brown COOLEY, LLP 1299 Pennsylvania Avenue, NE Suite 700 Washington, DC 20004 Copy with citationCopy as parenthetical citation