Ex Parte Huisman et alDownload PDFPatent Trial and Appeal BoardNov 5, 201310607903 (P.T.A.B. Nov. 5, 2013) Copy Citation 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. 10/607,903 06/27/2003 Gjalt W. Huisman MBX 025 DIV CON 7536 116248 7590 11/06/2013 Pabst Patent Group 1545 Peachtree Street Atlanta, GA 30309-2492 EXAMINER HUTSON, RICHARD G ART UNIT PAPER NUMBER 1652 MAIL DATE DELIVERY MODE 11/06/2013 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 GJALT W. HUISMAN, LAURA Z. LUO, and OLIVER P. PEOPLES __________ Appeal 2012-005719 Application 10/607,903 Technology Center 1600 __________ Before DEMETRA J. MILLS, ERIC GRIMES, and JEFFREY N. FREDMAN, Administrative Patent Judges. MILLS, Administrative Patent Judge. DECISION ON APPEAL This is an appeal under 35 U.S.C. § 134. The Examiner has rejected the claims for obviousness. We have jurisdiction under 35 U.S.C. § 6(b). Appeal 2012-005719 Application 10/607,903 2 STATEMENT OF CASE Claims 1 and 7 are representative and read as follows: 1. A bacterial strain producing polyhydroxyalkanoates wherein the bacterial strain is selected from the group consisting of Ralstonia eutropha, Pseudomonas putida and Escherichia coli and is genetically modified to express a heterologous nuclease gene, wherein the nuclease is secreted into the periplasmic space and released when the bacteria is lysed, wherein the bacteria expresses a nuclease which is secreted into the periplasmic space in an amount effective to degrade at least 95% of all of the nucleic acid released following lysis of the cells in less than 24 hours and reduce the viscosity of a cell lysate in a bacterial cell culture having a density of at least 50 g/l so that recovery of product is enhanced. 7. A bacterial strain producing polyhydroxyalkanoates, wherein the bacterial strain is selected from the group consisting of Ralstonia eutropha, Pseudomonas putida and Escherichia coli and is genetically modified to express a heterologous nuclease gene integrated into the chromosome of the bacterial host, wherein the nuclease is secreted into the periplasmic space and released when the bacteria is lysed, wherein the bacteria expresses a nuclease which is secreted into the periplasmic space in an amount effective to degrade at least 95% of all of the nucleic acid released following lysis of the cells in less than 24 hours. Cited References Greer, WO 94/10289, published May 11, 1994. Miller et al., Secretion and Processing of Staphylococcal Nuclease by Bacillus subtilis, 169 J. BACTERIOLOGY 3508-3514 (1987). Bernard Atkinson & Ferda Mavituna, BIOCHEMICAL ENGINEERING AND BIOTECHNOLOGY HANDBOOK (Stockton Press, 2nd. ed., 1991).1 1 We note that page 7 of the Answer includes a typographical error indicating that, “Atkinson et al. teach that Alcaligenes eutrophus (Ralstonia eutrophus) has been studied in detail due to its ability to accumulate large amounts of P(3HB) (i.e. ability to grow to cell densities of approximately 85 Appeal 2012-005719 Application 10/607,903 3 Liebl et al., Expression, Secretion, and Processing of Staphylococcal Nuclease by Corynebacterium glutamicum, 174 J. BACTERIOLOGY 1854- 1861 (1992). Sang Yup Lee & Ho Nam Chang, Production of Poly(hydroxyalkanoic acid), 52 ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 28-58 (1995). Boynton et al., Reduction of Cell Lysate Viscosity during Processing of Poly(3-Hydroxyalkanoates) by Chromosomal Integration of the Staphylococcal Nuclease Gene in Pseudomonas putida, 65 APPLIED AND ENVIRONMENTAL MICROBIOLOGY 1524-1529 (1999). Grounds of Rejection Claims 1, 3, 4, 6, and 7 are rejected under 35 U.S.C. § 103(a) as being unpatentable over Greer, Atkinson, and Lee in view of Liebl or Miller. FINDINGS OF FACT The Examiner’s findings of fact are set forth in the Answer at pages 4- 8. Discussion ISSUE The Examiner concludes that One of ordinary skill in the art would have been motivated to genetically engineer a Alcaligenes eutrophus (Ralsotnia [sic] eutropha) polyhydroxyalkanoates producing bacterial strain, as taught by Atkinson et al., to express the Staphylococcal aureus nuclease as taught by Liebl et al. or g/l and produce P(3HB) at 61.5 g/l, or 80% wt/wt of dry cell mass, page 30 through 32).” This reference citation, however, is from Lee page 32, section 3.2, not Atkinson pages 30-32. Appeal 2012-005719 Application 10/607,903 4 Miller et al. or a homologous nuclease gene that has been modified to enhance nuclease activity, so that this bacterial strain would express a nuclease which is secreted into the periplasmic space in an amount effective to degrade at least 95% of all the nucleic acid released following lysis of the cells in less than 24 hours and reduce the viscosity of a cell lysate in a bacterial cell culture having a density of at least 50 g/l so that recovery of product is enhanced. The expression of such a nuclease could be from a plasmid DNA or from genetic material integrated into host chromosome. A nuclease excreted into the medium as a result of such a genetically engineered bacterial strain would inherently result in the degradation of at least 95% of all the nucleic acid released following lysis of the cells in less than 24 hours. The motivation for producing a nuclease by a genetically engineered bacterial strain used in the fermentation process is to reduce the amount of nucleic acids in the medium which result in an increase in the viscosity of the medium, causing problems in the downstream processing steps, as taught by Greer et al. Greer et al. give further motivation for genetically engineering a bacterial strain to express a nuclease, because they teach that purified preparations of nucleases are expensive and a bacterial strain that was genetically engineered to express a nuclease activity would not require an external nuclease or hydrogen peroxide to be added to the fermentation. One would have had a reasonable expectation of success because both Liebl et al. and Miller et al. were able to express functional Staphylococcal aureus nuclease in different bacterial species, specifically Corynebacterium glutamicum and Bacillus subtilis and Liebl et al. teach that the Staphylococcal aureus nuclease is a heat-stable biochemically well characterized enzyme. One would have been further motivated to engineer the bacterial strain to excrete/secrete the nuclease into the growth medium following cell lysis, in an effective amount to enhance the recovery of product from the growth medium. (Ans. 6-7.) Appeal 2012-005719 Application 10/607,903 5 Appellants argue that In this case, there could be no predictable outcome since the evidence in the application clearly shows that success would have been possible in such a small number of cases, that absent screening for organisms with (1) secrete nuclease into the periplasmic space, (2) make very large amount of nuclease, and (3) which is not released until the organisms are lyzed, there was no possibility of success. One cannot ignore the importance of the amount of nuclease expressed. The Board’s attention is drawn to the examples. Even if one selected a Gram negative bacteria that made PHA, and engineered it to express nuclease, one would not know to select one expressing high amounts sufficient to degrade the nucleic acid in the culture medium. (App. Br. 23.) Appellants argue that, “Holmes steers one away from nucleases. Greer provides no disclosure that would steer one back to using nucleases, let alone recombinantly producing the nuclease as claimed.” (Id. at 21.) Appellants further argue that, “[n]one of Liebl or Miller discloses engineering nuclease secretion into the periplasmic space. Liebl and Miller disclose engineering the bacteria in those references to secrete nuclease into the cell culture medium.” (Id. at 24.) Appellants cite to the Declaration of Dr. Wolfgang Liebl, submitted October 13, 2009 as evidence that the nuclease of Liebl is secreted into the culture medium. (Decl. 2.) In summary, Appellants argue that, “[t]he prior art in combination does not even vaguely guide one to recombinantly expressing nuclease in a Gram negative bacteria which is secreted into and stored in a high amount until the cells is lysed, to solve downstream processing problems.” (App. Br. 29.) Appeal 2012-005719 Application 10/607,903 6 The issue is: Does the cited prior art support the Examiner’s obviousness rejection? PRINCIPLES OF LAW “In rejecting claims under 35 U.S.C. § 103, the examiner bears the initial burden of presenting a prima facie case of obviousness. Only if that burden is met, does the burden of coming forward with evidence or argument shift to the applicant.” In re Rijckaert, 9 F.3d 1531, 1532 (Fed. Cir. 1993) (citations omitted). In order to determine whether a prima facie case of obviousness has been established, we consider the factors set forth in Graham v. John Deere Co., 383 U.S. 1, 17 (1966): (1) the scope and content of the prior art; (2) the differences between the prior art and the claims at issue; (3) the level of ordinary skill in the relevant art; and (4) objective evidence of nonobviousness, if present. “The combination of familiar elements according to known methods is likely to be obvious when it does no more than yield predictable results.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007). Where . . . the claimed and prior art products are identical or substantially identical, or are produced by identical or substantially identical processes, the PTO can require an applicant to prove that the prior art products do not necessarily or inherently possess the characteristics of his claimed product…. Whether the rejection is based on “inherency” under 35 U.S.C. § 102, on “prima facie obviousness” under 35 U.S.C. § 103, jointly or alternatively, the burden of proof is the same, and its fairness is evidenced by the PTO’s inability to manufacture products or to obtain and compare prior art products. In re Best, 562 F.2d 1252, 1255 (CCPA 1977) (emphasis added.) Appeal 2012-005719 Application 10/607,903 7 ANALYSIS We have decided this case in conjunction with Appeal No. 2012- 004554, Application No. 11/924350. In addition, we have reviewed our Decisions in related Appeal Nos. 2002-001357, Application No. 09/281,363, and 2003-001996, Application No. 09/456,940. We further acknowledge that the claims before us include modifications not present in our earlier Decisions. However, in the present case, for the most part, we agree with the Examiner’s fact finding, statement of the rejection and responses to Appellants’ arguments as set forth in the Answer. We find that the Examiner has provided evidence to support a prima facie case of obviousness, except for the subject matter of claim 7. We provide the following additional comment to reasoning set forth in the Answer. Appellants argue that, “Holmes steers one away from nucleases” citing the expense of nucleases, and that “Greer provides no disclosure that would steer one back to using nucleases, let alone recombinantly producing the nuclease as claimed.” (App. Br. 21.) We agree with the Examiner’s indicated motivation to combine Greer with Liebl, Miller, Atkinson and Lee, which is substantially the same issue addressed and decided in our earlier Decision Appeal No. 2003-001996, pages 11-12. The fact that both Greer and Holmes found that the use of nucleases is expensive does not mean that the prior art was not aware of the viscosity problem associated with nucleic acids and fermentation product recover, or unaware that nucleases could be used in place of peroxide to address the viscosity problem. The process made obvious by the cited references involves expressing a nuclease gene in recombinant cells, not Appeal 2012-005719 Application 10/607,903 8 buying purified nucleases to add to the medium. Appellants have not explained why the expense of commercially available nucleases would discourage a skilled artisan from practicing the method suggested by the prior art. We are further unconvinced by Dr. Oliver P. Peoples Declaration, submitted February 8, 2011, which argues that the expense and use of nucleases is prohibitive (Decl. 2) for the reasons discussed above. Appellants further argue that, “[n]one of Liebl or Miller discloses engineering nuclease secretion into the periplasmic space. Liebl and Miller disclose engineering the bacteria in those references to secrete nuclease into the cell culture medium.” (App. Br. 24.) Appellants cite to the Declaration of Dr. Liebl as evidence that the nuclease of Liebl is secreted into the culture medium. (Decl. 2.) We agree with the Examiner’s response to this argument set forth on pages 12-14 of the Answer, and find acceptable the Examiner’s use of Boynton to show that the R. eutropha cells taught by Lee inherently secrete nuclease into the periplasmic space. The Declaration of Dr. Liebl does not address or rebut this finding. Appellants argue that In this case, there could be no predictable outcome since the evidence in the application clearly shows that success would have been possible in such a small number of cases, that absent screening for organisms with (1) secrete nuclease into the periplasmic space, (2) make very large amount of nuclease, and (3) which is not released until the organisms are lyzed, there was no possibility of success. One cannot ignore the importance of the amount of nuclease expressed. (App. Br. 23.) Appeal 2012-005719 Application 10/607,903 9 We agree with the Examiner’s response to the expectation of success and predictability arguments set forth on pages 10-12 of the Answer. In particular, we agree with the Examiner that Appellants’ disclosure in the Specification that about 10% of their nuclease expressing clones expressed a high level of nuclease is not unpredictable in the screening art. With respect to unpredictability in the screening art, it has been held that some experimentation, even a considerable amount, is not “undue” if, e.g., it is merely routine. (compare, In re Wands, 858 F.2d 731, 737 (Fed. Cir. 1988)(addressing the predictability issue with respect to the enablement requirement)). With respect to the claimed level of nuclease production, secretion and degradation, we agree with the Examiner that, in Boynton, PHA producing R. eutropha cells were generated using the same nuclease encoding gene taught by Leibl [sic] et al. above (See Boynton et al. Materials AND Methods, p 1524 and Figure 3, p 1527 and supporting text p 1526). Boynton et al. teach that the transformant “R. eutropha secreted nuclease into the periplasm but not into the growth medium” (p1526, Construction of nuclease integrants of other PHA producers). Thus the bacterial strain that is obvious over the above references inherently produces the nuclease such that it is secreted into the periplasmic space because they are gram negative bacteria. Boynton et al. further characterize the nuclease activity of the periplasmic nuclease of the transformed R. eutropha cells in the data provided in Figure 3 and the supporting text, in which they show the result of chromosomal DNA treatment with periplasmic fractions of R. eutropha MBX917 (::nuckan) (lane 4) and R. eutropha NCIMB40124HD untransformed parent strain (lane 5) at 37°C for 1 hour. As is evident from the results of Figure 3, after only one hour of incubation with the transformed R. eutropha periplasmic fraction, all of the visible high molecular weight DNA was digested to smaller molecular weight fragments. Based upon this level of digestion of high molecular weight chromosomal DNA for only one hour at 37°C, Appeal 2012-005719 Application 10/607,903 10 clearly the level of nuclease produced in the transformed R. eutropha strain would digest at least 95% of all nucleic acid released following lysis of the bacterial cells in a 24 hour period. (Ans. 13-14.) In other words, we find consistent with our earlier Decision in Appeal No. 2003-001996, page 13, that, “[u]nder these circumstances, it is incumbent upon appellants to establish through objective evidence that such levels of overexpression of nuclease [as in the cited references] do not necessarily provide the function set forth in claim 1 on appeal.” Claim 7 Appellants provide separate argument for claim 7 on page 31 of the Brief. Claim 7 requires a strain “genetically modified to express a heterologous nuclease gene integrated into the chromosome of the bacterial host.” Appellants argue that, “[a]s noted above, Miller and Liebl disclose plasmid expression. No reason is provided for why one would go to the trouble of integrating the nuclease into the chromosome.” (App. Br. 32.) In response, the Examiner argues that It is routine knowledge in the art that nuclear material integrated into the host chromosome is more stable than that nuclear material which remains on an extra-chromosomal plasmid. As all of these methods are routine in the art, it appears that the integration of the nuclease encoding gene into the host chromosome would be so as to increase the stability of the nuclease encoding material in the transformed host cell. (Ans. 17-18.) We are not persuaded by the Examiner’s argument. The Examiner fails to support this rejection with evidence in the prior art to support his position that it is routine knowledge in the art that nuclear material Appeal 2012-005719 Application 10/607,903 11 integrated into the host chromosome is more stable than that nuclear material which remains on an extra-chromosomal plasmid. Therefore, we are constrained to reverse the rejection of claim 7, as unsupported by evidence in the record. CONCLUSION OF LAW The cited references support the Examiner’s obviousness rejection, except the rejection of claim 7 is reversed. No time period for taking any subsequent action in connection with this appeal may be extended under 37 C.F.R. § 1.136(a). AFFIRMED-IN-PART cdc Copy with citationCopy as parenthetical citation