Ex Parte Gaddy et al

Patent Trials and Appeals BoardJun 21, 2019

13331182 - (D) (P.T.A.B. Jun. 21, 2019)

UNITED STA TES p A TENT AND TRADEMARK OFFICE APPLICATION NO. 13/331, 182 7590 J upeng Bio FILING DATE 12/20/2011 06/21/2019 1650 Pump Station Road Fayetteville, AR 72701 FIRST NAMED INVENTOR James L. Gaddy 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. CEL 28-10 3296 EXAMINER CLAYTOR, DEIRDRE RENEE ART UNIT PAPER NUMBER 1651 MAIL DATE DELIVERY MODE 06/21/2019 PAPER 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. PTOL-90A (Rev. 04/07) UNITED STATES PATENT AND TRADEMARK OFFICE BEFORE THE PATENT TRIAL AND APPEAL BOARD Ex parte JAMES L. GADDY, DINESH K. ARORA, CHING-WHAN KO, JOHN RANDALL PHILLIPS, RAHUL BASU, CARL V. WILKSTROM, and EDGAR C. CLAUSEN Appeal2018-009078 Application 13/331,182 Technology Center 1600 Before JEFFREY N. FREDMAN, ULRIKE W. JENKS, and JOHN G. NEW, Administrative Patent Judges. JENKS, Administrative Patent Judge. DECISION ON APPEAL Pursuant to 35 U.S.C. Â§ 134(a), Appellants 1 appeal from Examiner's decision to reject claims for failure to satisfy the written description requirement and for obviousness. We have jurisdiction under 35 U.S.C. Â§ 6(b). We AFFIRM. 1 The Appeal Brief lists Jupeng Bio as the real party in interest. Appeal Br. 3. We have considered, and herein refer to, the Specification of Dec. 20, 2011 ("Spec."); Final Office Action of March 2, 2017 ("Final Act."); Appeal Brief of Dec. 11, 2017 ("Appeal Br."); Examiner's Answer of Jan. 23, 2018 ("Answer"); and Reply Brief of March 22, 2018 ("Reply Br."). Appeal2018-009078 Application 13/331,182 STATEMENT OF THE CASE The Specification describes "methods for the production of ethanol from a gaseous substrate containing at least one reducing gas using anaerobic (or facultative) acetogenic bacteria.'' Spec. 1 :14-16. The Specification explains that '"[t]he bacteria can be removed from the aqueous phase and recycled to the bioreactor to rnair1tair1 high cefl concentrations, thus maximizing productivity." id. at 1 :26----28. The Specification notes that "[e]thanol concentrations are typically only 1-2 g/L" in ,vild strain bacteria. Id. at 2:24. Claims 12-32 and 35-57 are on appeal, and can be found in the Claims Appendix of the Appeal Brief. Appeal Br. 16-23. Claim 36 is representative of the claims on appeal, and reads as follows: 36. A continuous method for producing ethanol from the anaerobic bacterial fermentation of a gaseous substrate comprising carbon monoxide, the method comprising: culturing in a fermentation bioreactor anaerobic, acetogenic bacteria in a continuously fed liquid nutrient medium to provide a fermentation broth and supplying to said fermentation bioreactor said gaseous substrate comprising carbon monoxide (CO); maintaining a specific rate of CO uptake in said fermentation bioreactor at an amount of 0.3 to 2 mmol CO/ gram dry cells weight of bacteria/ minute in the fermentation broth after said bacteria achieve a stable cell concentration in said fermentation bioreactor, wherein a free acetic acid concentration in said fermentation bioreactor is less than 5 g/L free acetic acid, producing ethanol in a fermentation broth at a productivity greater than 10 g/L per day; and producing both ethanol and acetate in said fermentation broth in a ratio of ethanol to acetate ranging from 1: 1 to 20: 1. Appeal Br. 19-20 (Claims Appendix). 2 Appeal2018-009078 Application 13/331,182 Appellants request review of the following rejections made by Examiner: I. Claims 12-32 and 35-57 under 35 U.S.C. Â§ 112, first paragraph, as failing to comply with the written description requirement. Final Act. 2-5. II. Claims 12-32 and 35-57 under 35 U.S.C. Â§ 103 (a) as being obvious over Report I2, Holtzapple3, Phillips4, and Report II. 5 Final Act. 7-8. I. FVritten Description The issue with respect to this rejection is whether the preponderance of the evidence of record supports Examiner's conclusion that Appellants' Specification fails to provide written descriptive support for the claimed genus of acetogenic bacteria. Findings of Fact FF 1. The Specification discloses that useful bacteria include: "Acetogenium kivui, Acetobacterium woodii, Acetoanaerobium noterae, Clostridium aceticum, Butyribacterium methylotrophicum, C. acetobutylicum, C. thermoaceticum, Eubacterium limosum, C. ijungdahlii PETC, C. ijungdahlii ERI-2, C. ijungdahlii C-01, C. ijungdahlii 0-52, and 2 DE93 008947, Biological Production of Ethanol from Coal, TASK 4 REPORT: CONTINUOUS REACTOR STUDIES (1992) ("Report I"). 3 Holtzapple et al., US 6,043,392, issued Mar. 28, 2000 ("Holtzapple"). 4 Phillips et al., Biological Production of Ethanol from Coal Synthesis Gas, 37 APPL. BIOCHEM. AND BIOTECH. 559-571 (1993) ("Phillips"). 5 DE9 l O 14808, Biological Production of Ethanol from Coal, TASK 3 REPORT: ENHANCING ETHANOL CONCENTRATION/ETHANOL RECOVERY STUDIES (1991) ("Report II"). 3 Appeal2018-009078 Application 13/331,182 Peptostreptococcus productus. Other acetogenic anaerobic bacteria are selected for use in these methods by one of skill in the art." Spec. 9. FF2. The Specification discloses that the term "nutrient medium" encompasses: conventional bacterial growth media which contain vitamins and minerals sufficient to permit growth of a selected subject bacteria. Sugars are not included in these media. Components of a variety of nutrient media suitable to the use of this invention are known and reported in prior publications, including those of the inventors. See, e.g. the nutrient media formulae described in International Patent Publication No. W098/00558; US Patent No. 5,807,722; US Patent No. 5,593,886, and US Patent No. 5,821,111, as well as in the publications identified above. According to the present invention, a typical laboratory nutrient medium for acetate production from CO, CO2, and H2 contains 0.9 mg/L calcium pantothenate. However, a typical laboratory nutrient medium for ethanol production from CO, CO2, and H2 contains 0.02 mg/L calcium pantothenate. Spec. 10. Analysis Examiner found that the claims are drawn to a process of making ethanol from a gaseous substrate comprising CO by anaerobic fermentation with unknown species of Clostridium, unknown anaerobic acetogenic bacteria, and with undisclosed liquid nutrient media, to achieve a specific productivity of greater than 10 g/L day. Final Act. 3. Examiner found that the Specification only provides guidance for the production of ethanol with C. ijungdahlii to obtain the desired results and that no other microorganisms 4 Appeal2018-009078 Application 13/331,182 or nutrient media is shown to be capable of the process as claimed. Id. Examiner found that the disclosed strain of C. ijungdahlii is not representative of the genus of Clostridium or anaerobic acetogenic bacteria capable of fermenting CO to ethanol. Id. at 5. Appellants assert that the Specification as filed describes medium and nutrient requirements, fermentation conditions, and provides 25 examples of fermentations with acetogenic bacteria. Appeal Br. 9-10 ( citing Spec. 10: 1- 11, 16:7, 17:17, 18:21, 19:9, and 20:20). Appellants argue that a number of specific acetogenic Clostridium and other acetogens is expressly disclosed in the Specification. Id. at 11 ( citing Spec. 9: 11-18). Appellants contend that the Senaratne Declaration6 provides evidence that the subject matter conveyed in the application as filed provided one or ordinary skill in the relevant art with the claimed invention. Id. at 12. We find Appellants have the better position. Examiner determined that although other Clostridium and other acetogenic bacteria are listed in the Specification, they were not cultured and shown to be able to produce ethanol at a productivity greater than 10 g/L per day. Ans. 6. In other words, Examiner's position is that the disclosure of a single species, C. ijungdahlii, is not sufficient description of a genus, as claimed. "[T]he written description requirement does not demand either examples or an actual reduction to practice; a constructive reduction to practice that in a definite way identifies the claimed invention can satisfy the written description requirement." Ariad Pharms., Inc. v. Eli Lilly & Co., 598 F.3d 1336, 1352 (Fed. Cir. 2010) (en bane). A "sufficient description of a 6 Declaration by Dr. Senaratne, filed June 23, 2016 ("Senaratne Dec."). 5 Appeal2018-009078 Application 13/331,182 genus ... requires the disclosure of either a representative number of species falling within the scope of the genus or structural features common to the members of the genus so that one of skill in the art can 'visualize or recognize' the members of the genus." Id. at 1350. "The descriptive text needed to meet these requirements varies with the nature and scope of the invention at issue, and with the scientific and technologic knowledge already in existence." Capon v. Eshhar, 418 F.3d 1349, 1357 (Fed. Cir. 2005). Here, the Specification discloses 13 species of acetogenic bacteria and describes various types of nutrient media suitable for use in the claimed methods. FF1-FF2. The Specification exemplifies the claimed method and provides an actual reduction to practice using C. ijungdahlii. The Senaratne Declaration further demonstrates that two species of acetogenic bacteria specifically disclosed by the Specification, namely, Butyribacterium methylotrophicum and Eubacterium limosum, also function to produce greater than 10 g/L/day of ethanol when using the nutrient medium exemplified in Table 1 of the Specification. Senaratne Dec. 2, 4, and 6-7. Furthermore, Examiner has acknowledged that the prior art teaches "the general principles of culturing Clostridium to obtain ethanol continuously with a gaseous substrate" (Ans. 10), and that process parameters for optimizing ethanol production with strains of C. ijungdahlii are known, including "culture media, conditions of agitation, pH and CO feeding." Id. at 8-9. On this record, we find that Examiner has not adequately articulated why the species of acetogenic bacteria and types of nutrient media disclosed in the Specification would not be seen as sufficiently representative, especially in conjunction with the background knowledge possessed by 6 Appeal2018-009078 Application 13/331,182 ordinarily skilled persons in this art. Accordingly, we reverse the Examiner's written description rejection. II. Obviousness over Report L Holtzapple, Phillips, and Report II. Examiner found that Report I teaches a process of producing ethanol by culturing C. ijungdahlii, an acetogenic species of Clostridium, wherein the culturing and manipulating steps result in ethanol production greater than 10 g/L and wherein both ethanol and acetate are produced in the fermentation broth in a ratio of ethanol to acetate ranging from 1: 1 to 20: 1. Final Act. 7. Examiner found that Report I teaches CO uptake of 0.16 to 0.5 mmol/CO per gram of cells. Id. Examiner found that Report I does not teach recovery of ethanol by distillation or the claimed concentration of cobalt or calcium pantothenate in the medium. Id. at 8. Examiner concludes that it would have been obvious to one having ordinary skill in the art to modify the process of producing ethanol by continuous fermentation of Clostridium, as taught by Report I, using distillation to recover the ethanol as taught by Holtzapple, and to adjust the concentration of nutrient factors in the media as taught by Phillips and Report II. Id. Appellants argue that the cited references do not teach the production of ethanol at productivity greater than 10 g/L day where both ethanol and acetate are produced in a ratio of 1: 1 to 20: 1, do not describe a process wherein free acetic acid concentration is less than 5 g/L, and do not mention the importance of maintaining a specific rate of CO uptake in the bioreactor at 0.3 to 2 mmol CO/gram dry cells weight of bacteria/minute, as claimed. Appeal Br. 14. The issue with respect to this rejection is whether the preponderance 7 Appeal2018-009078 Application 13/331,182 of the evidence of record supports Examiner's conclusion that the combination of references renders the claimed method obvious. Findings of Fact FF 1. Report I teaches an approach for converting coal synthesis gas comprising "a mixture of CO, H2, CO2, CH4 and sulfur gases" into "ethanol using a bacterial culture of Clostridium ijungdahlii." Report I 2. FF2. Report I teaches that "[ s Jeveral factors have been identified that cause the culture to produce ethanol in favor of acetate" including "manipulation of the nutrients composition and concentration, the addition of reducing agents or sporulating agents to liquid medium and reduction of the medium pH." Id. FF3. Report I teaches that "[h]ighlights of this work include improving the product ratio from 1 :20 ( ethanol to acetate) to 3: 1, and improving the specific ethanol productivity of the culture by 800 percent." Id. at 4. FF4. Report I teaches "[a] continuous stirred-tank reactor with both continuous liquid and gas feed" to provide a continuous culture of C. ijungdahlii for converting the gas to ethanol. Id. at 41. FF5. Report I teaches experiments to determine the effect of liquid flow rates on specific CO uptake rates (Id. at 41 ), teaching that uptake of CO decreased from 0.04 to 0.02 mmol/mg/h when the liquid flow rate was reduced from 200 to 100 mL/d. Id. at 44. FF6. Report I teaches that "the more flow through the system, the 8 Appeal2018-009078 Application 13/331,182 higher the [ethanol] production of the reactor" and that "[t]he specific [CO] uptake rate similarly increases with increasing liquid flow rate." Id. at 54. FF7. Report I teaches experiments to determine the effect of agitation rate on specific CO uptake (Id. at 55), teaching that the specific CO uptake rate was found to vary from 0.01 to 0.03 mmol/mg/h during the experiment. Id. at 58. Increased agitation rates were associated with increased CO uptake. Id. at 61 (see Figure 5.22). FF8. Report I teaches that "[t]he more CO available to the cells, the higher the productivity" and that the key to continuous operation appears to be a "high productivity system with high ethanol concentrations and high ethanol to acetate product ratios." Id. at 69. FF9. Report I teaches using a minimal medium to increase ethanol concentration and that a pH level of 4.0 to 5.0 must be used in conjunction with this medium. Id. at 21. FF 10. Report I teaches a designed medium, which contains calcium pantothenate and C0Cb-6H20, i.e. cobalt. Id. at 24. FF 11. Report I teaches increased ethanol product concentration with the designed medium, wherein a "maximum [ ethanol] concentration in the designed medium was about 22 g/L" and wherein "[t]he product ratio was also dramatically shifted toward ethanol, showing much more ethanol than acetate." Id. at 81. FF12. Report I teaches acetic acid concentrations below 5 g/L (id. at 9 Appeal 2018-009078 Application 13/331,182 79) as shown in figure 5.36, reproduced below. ,11.let Gas Flow Rate (mmol/minl f'igrn g-i:-<>1"lh of C. 1/tmÂµ.;,.b!if i!:I. il~sttned lte