MONSANTO TECHNOLOGY LLC

Patent Trials and Appeals Board

Mar 30, 2022

2021005330 (P.T.A.B. Mar. 30, 2022)

UNITED STATES PATENT AND TRADEMARK OFFICE 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 APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO. 15/015,968 02/04/2016 BRIAN J. MARTINELL MONS:371US 8654 73905 7590 03/30/2022 DENTONS US LLP P.O. BOX 1302 Chicago, IL 60604 EXAMINER KUBELIK, ANNE R ART UNIT PAPER NUMBER 1662 NOTIFICATION DATE DELIVERY MODE 03/30/2022 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): patents.us@dentons.com PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE ____________ BEFORE THE PATENT TRIAL AND APPEAL BOARD ____________ Ex parte BRIAN J MARTINELL, ANNA MARY O’KEEFE, DAVID ALAN SOMERS, EDWARD JAMES WILLIAMS, and XUDONG YE ____________ Appeal 2021-005330 Application 15/015,968 Technology Center 1600 ____________ Before JOHN G. NEW, MICHAEL A. VALEK, and JAMIE T. WISZ, Administrative Patent Judges. VALEK, Administrative Patent Judge. DECISION ON APPEAL Appellant1 submits this appeal under 35 U.S.C. § 134(a) involving claims to a method of transforming a plant plastid that were rejected for obviousness under 35 U.S.C. § 103. We have jurisdiction under 35 U.S.C. § 6(b). We AFFIRM. 1 We use the word “Appellant” to refer to “applicant” as defined in 37 C.F.R. § 1.42(a). Appellant identifies Bayer US LLC as the real party in interest. Appeal Br. 1. Herein, we refer to the Final Office Action mailed Sept. 9, 2020 (“Final Act.”); Appellant’s Appeal Brief filed April 7, 2021 (“Appeal Br.”); Appellant’s Response to Notice of Defective Appeal Brief filed April 15, 2021 (“Claims App.”); Examiner’s Answer mailed July 14, 2021 (“Ans.”); and Appellant’s Reply Brief filed Sept. 13, 2021 (“Reply Br.”). Appeal 2021-005330 Application 15/015,968 2 STATEMENT OF THE CASE Claims 1, 3-6, 8-11, 13-30, 34, and 36-38 are on appeal and can be found in the Claims Appendix of the Appeal Brief. Claim 1 reads as follows: 1. A method of transforming a plant plastid, comprising the steps of: (a) preparing an explant from a seed of a plant, wherein the seed is a dry seed comprising a mature embryo, the explant comprising meristematic tissue of the mature embryo of the seed; (b) transforming at least one plastid of a plant cell of the explant with an exogenous DNA molecule, the exogenous DNA molecule comprising: (i) a first arm region homologous to a first plastid genome sequence; (ii) a second arm region homologous to a second plastid genome sequence; and (iii) an insertion sequence positioned between the first arm region and the second arm region of the exogenous DNA molecule, (c) developing a plastid transformed shoot from the explant on a selection medium; and (d) regenerating a rooted plant from the transformed shoot on a regeneration medium; wherein the cells of the explant do not form a callus tissue prior to or after the transforming step (b), wherein a plant growth regulator is not present in the selection medium, wherein the transformed plastid is comprised within a meristematic cell of the explant; and wherein the insertion sequence is incorporated into a plastid genome of the cell between the first plastid genome sequence and the second plastid genome sequence. Claims App. 2. Appeal 2021-005330 Application 15/015,968 3 Appellant seeks review of Examiner’s rejection of claims 1, 3-6, 8- 11, 13-30, 34, and 36-38 under 35 U.S.C. § 103 as obvious over Tissot,2 Martinell,3 Calabotta,4 Kumar,5 and Ruhlman.6 See Appeal Br. 3-13. The issue for this rejection is whether the preponderance of the evidence supports Examiner’s conclusion that Appellant’s claims are obvious over the cited prior art. Findings of Fact FF1. Tissot teaches a method for transforming plastids from plants such as soybean. Tissot, Abstr. Tissot teaches a transformation vector containing a heterologous expression cassette “bordered by two soybean plastid DNA fragments, RHRR (Right Homologous Recombination Region) and LHRR (Left Homologous Recombination Region), which allow targeted integration into the region of the ribosomal RNA operon of the soybean plastid.” Id. ¶ 50. The expression cassette positioned between the RHRR and LHRR contains a chimeric gene made up of DNA sequences that confer resistance to spectinomycin and streptomycin. Id. ¶ 51. FF2. Tissot teaches transformation of soybean plastids using particle bombardment of soybean somatic embryos to introduce the transformation vector. Tissot ¶¶ 55-60. The transformed lines are selected on media 2 US 2007/0039075 A1, published Feb. 15, 2007 (“Tissot”). 3 US 8,030,076 B2, issued Oct. 4, 2011 (“Martinell”). 4 US 8,362,317 B2, issued Jan. 29, 2013 (“Calabotta”). 5 Shashi Kumar et al., “Plastid-Expressed Betaine Aldehyde Dehyrogenase Gene in Carrot Cultured Cells, Roots, and Leaves Confers Enhanced Salt Tolerance,” 136 Plant Phys. 2843-2854 (2004) (“Kumar”). 6 Tracey Ruhlman et al., “The Role of Heterologous Chloroplast Sequence Elements in Transgene Integration and Expression,” 152 Plant Phys. 2088- 2104 (2010) (“Ruhlman”). Appeal 2021-005330 Application 15/015,968 4 containing spectinomycin to obtain homoplastomic callus. Id. ¶¶ 63-65; 69. Rooted transplastomic plants may then be regenerated from embryos obtained from the transformed tissue. Id. ¶¶ 70-71. FF3. Martinell teaches nuclear transformation of meristematic cells of soybean explants using particle bombardment and Agrobacterium-mediated gene delivery “to form shoots that give rise to transgenic plants.” Martinell, Abstr., 3:62-64 (describing “penetration with fine particles” as one method of wounding to facilitate transformation). Explants are prepared for transformation by removing the seed coat and removing primary leaf tissue to expose the meristematic region. Id. at 6:1-5. Martinell teaches the explants are wounded, then inoculated with the Agrobacterium plasmid, then transferred to a medium containing a selection agent, and later placed in a medium conducive to shoot development. Id. at 4:29-42; 6:11-39. FF4. Martinell teaches that this method allows transformed cells to “be induced directly to form shoots that give rise to transgenic plants” without “callus-phase tissue culture.” Martinell, Abstr. Martinell teaches that this methodology is advantageous because it “does not involve a phase of callus culture, and hence the time period of the entire process from seed to transgenic seed is remarkably concise.” Id. at 2:48-50; see id. at 2:61-3:19 (explaining that by delivering the transgene “into cells in the living meristem of a soybean embryo” the method “does not utilize a callus or proliferative phase” and therefore “[t]he time period required for this method is greatly reduced compared to other Agrobacterium-mediated transformation protocols”). FF5. Calabotta teaches the preparation “of explant material comprising meristematic tissue from seeds,” such as soybean seed, for subsequent Appeal 2021-005330 Application 15/015,968 5 genetic transformation and regeneration of transgenic plants. Calabotta, Abstr., 2:46-64. Calabotta further teaches that “[t]he method may be performed . . . without producing a callus tissue culture, by organogenesis or by direct meristem transformation and subsequent shoot growth.” Id. at 4:1- 4. Calabotta also teaches that the transformed meristematic tissue can be used to regenerate a plant “without the use of one or more plant growth regulators such as to alter the development of the explant.” Id. at 3:1-2. FF6. Calabotta teaches that an advantage of its explants is that the excised meristematic material can have an internal moisture content from about 3% to about 20%, resulting in a stable explant that may be stored for long periods of time before use. Calabotta, 2:38-46; 4:5-9 (describing storing the explant for as long as two years prior to transformation and regeneration); 5:28-30 (explaining that “an internal moisture content such as 3% to 7% may be advantageous” for yielding “stable storage conditions (and transformable explants) prior to use”); 17:29-18:24 (describing drying and storing of explants for multiple days prior to transformation). FF7. Kumar describes the transformation of plastids, i.e., chloroplasts, in non-green carrot explants. Kumar 2846. Kumar teaches that the plants regenerated after transformation and selection exhibited almost complete homoplasmy and demonstrate “successful, stable plastid transformation using non-green explants via somatic embryogenesis.” Id. at 2851. FF8. Ruhlman reports “a rapid and reproducible method of chloroplast transformation in lettuce” involving bombardment with particles coated with a plastid transformation vector and subsequent selection and regeneration. Ruhlman 2096, 2101 (“Bombardment and Selection of Transplastomic Lettuce”). Appeal 2021-005330 Application 15/015,968 6 FF9. Ruhlman teaches “[d]irect shoots emerged from leaf explants 21 d after culture in optimized regeneration medium” and that “the shoot regeneration response was variable with different combinations of auxin (NAA) and cytokine (BAP).” Ruhlman 2089. According to Ruhlman, “[m]aximal direct shoot initiation was observed from the leaf explants cultured in medium supplemented with 0.1 μg mL-1 NAA and 0.2 μg mL-1 BAP,” while “[o]ther combinations of PGRs [i.e., plant growth regulators] induced callus formation and decreased shoot regeneration in all cultivars.” Id. Ruhlman 2010 teaches that with the optimized regeneration medium “shoots were formed from the leaf explants without the formation of callus.” Id. at 2091. Analysis We begin with the rejection of independent claim 1. To the extent Appellant presents separate arguments regarding the rejection of dependent claims 3, 10, 14, 28, 29, and 38 (see Appeal Br. 8, 10), we address those additional arguments after our analysis of claim 1. Examiner’s rejection is premised on using “Martinell’s and Calabotta’s soybean seed explants as the starting material in Tissot’s plastid transformation method.” Ans. 13.; Final Act. 6. Examiner explains that, unlike the somatic embryos transformed in Tissot, “Martinell’s and Calabotta’s starting material does not form[] callus prior to or after transformation and thus meets that limitation of the claims.” Ans. 35. Examiner finds that one of ordinary skill would have been motivated to make this combination because Martinell and Calabotta teach that their explants are advantageous for a variety of reasons “including speed, storability, reduced contamination, and increased transformation frequency.” Appeal 2021-005330 Application 15/015,968 7 Id. at 18; see also Final Act. 8-9. Examiner further determines there would have been a reasonable expectation that the meristematic tissue explants taught in Martinell and Calabotta could be successfully used as the starting material in Tissot’s plastid transformation method because Ruhlman teaches “that callus formation is not required for plastid transformation” and Kumar teaches “that plastid transformation of non-green explants is possible.” Final Act. 11. Regarding the limitation excluding the use of a PGR in the selection medium, Examiner finds that whether or not to use a PGR is an obvious “design choice.” Final Act. 6. More specifically, Examiner explains that while some of the references teach the use of PGRs: Calabotta teaches that plant growth regulators are not necessary during the selection step when their transformation target, which has pre-formed meristem tissue, is used. When using Calabotta's starting material one of ordinary skill in the art could choose to not use PGRs during selection; its use or not is a design choice. Thus, the combination of references makes obvious not using PGRs during selection. Ans. 12 (internal citations omitted). Examiner also points out that to the extent Appellant is arguing that certain references teach the use of PGRs “for formation and regeneration of shoots,” Appellant is “arguing a limitation not in the claims,” which “only require that the selection medium not have PGRs.” Id. at 18. After considering the record and the arguments in the Appeal Brief, we adopt Examiner’s findings and reasoning regarding the scope and content of the prior art (Final Act. 3-15; Ans. 3-10; FF1-FF9) and agree that Appellant’s claims would have been obvious over the cited references. We address Appellant’s arguments below. Appeal 2021-005330 Application 15/015,968 8 Appellant argues Examiner’s prima facie case relies on improper hindsight because Examiner concedes that the various references contain differing teachings when comparing specific aspects of plant transformation and plant tissue culture. For instance, the Final Action . . . concedes that there are a number of differences in methods and starting materials between Martinell, Calabotta, and Tissot. This also applies to other cited references Ruhlman and Kumar, for instance with respect to use of, or effects of, plant growth regulators ("PGR's") . . . Ruhlman and Kumar are recognized as having different teachings for use of PGR's (auxins and cytokinins), whether to form callus or to regenerate plants. Further, this is relevant because, as the Declaration of Dr. Xudong Ye (Exhibit G) at ¶ 15 points out, use of cytokinin on pre-formed meristem tissue present in the recited explants would interfere with shoot growth and would instead result in formation of non-regenerable callus tissue. Appeal Br. 5; see also id. 11-13 (repeating Appellant’s improper hindsight arguments). Appellant’s arguments are unavailing. That the various references individually differ from the recited method does not distinguish claim 1 because the rejection is based on the combination of references articulated by Examiner. Soft Gel Techs., Inc. v. Jarrow Formulas, Inc., 864 F.3d 1334, 1341 (Fed. Cir. 2017) (quoting In re Merck & Co., 800 F.2d 1091, 1097 (Fed. Cir. 1986)) (“Non-obviousness cannot be established by attacking references individually where the rejection is based upon the teachings of a combination of references.”). As noted above, Examiner has articulated a rationale both for combining Martinell and Calabotta’s meristem tissue explants, which those references teach do not form callus prior to or after transformation, with Tissot’s plastid transformation method (Final Act. 8-9; Ans. 18) and for not using a PGR in the selection medium as taught in Appeal 2021-005330 Application 15/015,968 9 Calabotta (Final Act. 6; Ans. 12). Those rationales are supported by the record and sufficient to establish a prima facie case of obviousness. See FF4-FF6. Thus, we do not agree that Examiner has impermissibly used Appellant’s claims as a “roadmap” to piece together disparate pieces of the cited references. See Appeal Br. 4-6. Appellant’s reliance on paragraph 15 of the declaration of Dr. Xudong Ye dated December 16, 2019 (“Ye Decl.”) is also unpersuasive. Dr. Ye testifies that Ruhlman and other references teach that PGRs are “necessary to allow for regeneration of their transformed lettuce leaf tissue” and that this is “because no shoot meristem was present in the leaf tissue . . . such meristem needs to form before regeneration can occur.” Ye Decl. ¶ 13. In contrast, “[u]se of a transformation target already containing meristematic tissue allows for more rapid regeneration without callus or meristem formation during selection” and “[t]hus PGRs are not required during selection” and “use of cytokinin [a PGR] on pre-formed meristematic tissue would interfere with shoot growth.” Id. ¶ 15. While this testimony may distinguish Ruhlman individually, it does not distinguish the combination of references, which relies on Calabotta’s teaching that a soybean meristem explant can be used as the transformation target without the presence of a PGR in the selection medium. Moreover, the advantages of using a transformation target containing meristematic tissue that Dr. Ye identifies to distinguish Ruhlman, i.e., that it allows for more rapid regeneration without callus formation, are the same advantages that Calabotta and Martinell teach for their soybean explants. See FF4, FF5. Thus, if anything, the testimony in paragraph 15 of the Ye Declaration supports Examiner’s finding that a Appeal 2021-005330 Application 15/015,968 10 skilled artisan would have been motivated to use Calabotta and Martinell’s starting materials in Tissot’s plastid transformation method. Appellant’s argument that “Tissot and Kumar only describe plastid transformation of callus cultures with actively dividing cells” is unavailing for the same reasons. See Appeal Br. 6-7 (quoting Ye Decl. ¶ 8). The rejection is premised on the substitution of Calabotta and Martinell’s starting materials, which contain meristematic tissue and can be selected and regenerated without forming callus before or after transformation, for the starting material in Tissot’s plastid transformation method. That other references such as Tissot and Kumar teach different starting materials only serves to distinguish those references individually and not the combination of references on which the rejection is based. See Soft Gel, 864 F.3d at 1341. Appellant also contends that the cited references do not provide a reasonable expectation of success. Appeal Br. 8-11. More specifically, Appellant argues that Ruhlman and Kumar teach that PGRs are required for selection and shoot growth and “combining Ruhlman with Kumar means disregarding the different effects (callus formation versus regeneration) described by Ruhlmann and Kumar for added PGR’s.” Id. at 9. We disagree. As explained above, Calabotta teaches that it is not necessary to use a PGR in the selection medium when using its transformation target. FF5. That Ruhlman and Kumar teach the use of PGRs in certain aspects of their processes does not undermine Calabotta’s teaching, which is itself sufficient to demonstrate a reasonable expectation of success in omitting PGRs from the selection medium. Appeal 2021-005330 Application 15/015,968 11 To the extent Appellant contends that a skilled artisan would have expected that callus formulation from Calabotta’s and Martinell’s meristematic tissue explants would be required when they were used in Tissot’s method, we again disagree. See Appeal Br. 9-11; Reply Br. 4-6. Both Calabotta and Martinell teach that, at least with respect to nuclear transformation, shoots can be generated from their transformed explants without callus formation. FF4, FF5. And Ruhlman teaches “shoots were formed from the leaf explants” in its plastid transformation experiments “without the formation of callus.” FF9. Appellant’s arguments largely focus on this teaching from Ruhlman, which Appellant argues were shown to be inaccurate “in Appellants’ response of December 27, 2019” and in the Ye Declaration. See Appeal Br. 9-11; Reply Br. 10-13. There are multiple problems with these arguments. First, as Examiner points out, both the Ye Declaration and Appellant’s response address a prior rejection that relied on a different Ruhlman reference, Ruhlman 2007.7 See Ans. 20-22. There appears to be material differences between the processes described in Ruhlman and Ruhlman 2007. Compare Ruhlman 2089 (describing optimal regeneration conditions as a medium containing 0.1 μg mL-1 NAA and 0.2 μg mL-1 BAP and contrasting that with “[o]ther combinations of PGRs that induced callus formation”) with Ye Decl. ¶¶ 11-12 (stating that Ruhlman 2007 uses a medium containing 0.1 μg mL-1 NAA and 0.1 μg mL-1 BAP, which other references 7 Tracey Ruhlman et al., “Expression of cholera toxin B-proinsulin fusion protein in lettuce and tobacco chloroplasts - oral administration protects against development of insulitis in non-obese diabetic mice,” 5 Plant Biotech 495-510 (2007) (“Ruhlman 2007”). Appeal 2021-005330 Application 15/015,968 12 suggest resulted in callus formation).8 Thus, neither the Ye Declaration, nor the arguments in Appellant’s response, suggest that Ruhlman’s express teaching that “[m]ost importantly, shoots were formed from the leaf explants without the formation of callus” is inaccurate. Ruhlman 2091 (emphasis added).9 To the extent Appellant argues otherwise in its Reply Brief (see Reply Br. 4-5), those attorney arguments are not supported by evidence and therefore unpersuasive. See In re De Blauwe, 736 F.2d 699, 705 (Fed. Cir. 1984) (explaining that arguments and conclusions unsupported by factual evidence carry no evidentiary weight). Another problem with Appellant’s argument is that even if the Ye Declaration did directly address Ruhlman, it is difficult to reconcile the testimony of Appellant’s inventor that a skilled artisan would understand that callus was formed in Ruhlman’s process with Ruhlman’s express teaching in that reference that no callus was formed. See PharmaStem Therapeutics, Inc. v. ViaCell, Inc., 491 F.3d 1342, 1361 (Fed. Cir. 2007) (holding the jury's determination of non-obviousness was not supported by the testimony of patentee's expert because “[t]he problem with [the expert's] testimony about the prior art references is that it cannot be reconciled with . . 8 The Ye Declaration refers to these concentrations in mg/l. Ye Decl. ¶¶ 11- 12. As Appellant points out, “mg/l . . . is equivalent to μg/ml, which are the units used in Ruhlman.” Reply Br. 8. 9 Appellant argues that Examiner’s response to the Ye Declaration in the Answer “represents a new ground for rejection.” Reply Br. 3-4. We disagree. Examiner specifically addressed the Ye Declaration in the Final Action. See Final Act. 13-15. The response in Examiner’s Answer is consistent with the Final Action and does not change the thrust of the rejection. Moreover, Appellant has elected to continue the appeal and been afforded sufficient opportunity to respond in its Reply Brief. Appeal 2021-005330 Application 15/015,968 13 . the prior art references themselves”). That Appellant seeks to cast this express and facially unambiguous teaching as inaccurate demonstrates the need for clear evidence that is on all fours with the present rejection. Appellant, however, has not identified such. Finally, Appellant’s arguments are unpersuasive because they focus primarily on Ruhlman and Kumar while ignoring the teachings in Calabotta and Martinell that shoots can be generated from their explants without callus formation (FF4, FF5). In this regard, Appellant’s reasonable expectation of success arguments suffer from the same defect as their other arguments-- i.e., they attack the references individually, rather than focusing on the combination articulated by Examiner. See Soft Gel, 864 F.3d at 1341. For these reasons, we determine that Examiner’s rejection of claim 1 is supported by a preponderance of the evidence. Appellant does not argue claims 3-6, 8-11, 13-30, 34, and 36-38 separately from claim 1. Thus, we affirm the rejection of those claims for the same reasons discussed above for claim 1. Appellant contends that “at least one or more of claims 3, 10, 14, 28, 29, and 38, relating to low moisture content and metabolic stasis of the explant, are non-obvious and could be allowable if rewritten in independent form” because “explants derived from dry seeds are not actively growing at the time of transformation and the teachings of Kumar do not lead to an expectation of success when limitations of these claims are present.” Appeal Br. 8; 10. However, as Examiner points out, Calabotta teaches the additional elements of these claims. Ans. 28-29 (citing to Calabotta’s teachings regarding low moisture content, metabolic stasis, and storage/drying of the explants prior to transformation); FF6. Thus, Appeal 2021-005330 Application 15/015,968 14 Appellant’s additional arguments regarding these dependent claims are unpersuasive because they merely address Kumar individually, instead of addressing the combined teachings, specifically those in Calabotta, articulated by Examiner. See Soft Gel, 864 F.3d at 1341. For this reason, as well as those previously explained for claim 1, we determine that Examiner’s rejection of claims 3, 10, 14, 28, 29, and 38 are supported by a preponderance of the evidence. Accordingly, we also affirm the rejection of those claims. CONCLUSION In summary: Claims Rejected 35 U.S.C. § Reference(s)/Basis Affirmed Reversed 1, 3-6, 8-11, 13-30, 34, 36-38 103 Tissot, Martinell, Calabotta, Kumar, Ruhlman 1, 3-6, 8-11, 13-30, 34, 36-38 No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a)(1)(iv). AFFIRMED