Ex Parte Tsuji et al

Patent Trial and Appeal BoardFeb 23, 2016

11427482 (P.T.A.B. Feb. 23, 2016)

UNITED STA TES p A TENT AND TRADEMARK OFFICE APPLICATION NO. FILING DATE 111427,482 0612912006 38108 7590 02/25/2016 CERMAK NAKAJIMA MCGOWAN LLP 127 S. Peyton Street Suite 210 ALEXANDRIA, VA 22314 FIRST NAMED INVENTOR Yuichiro Tsuji 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-236 2511 EXAMINER RAMIREZ, DELIA M ART UNIT PAPER NUMBER 1652 NOTIFICATION DATE DELIVERY MODE 02/25/2016 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 YUICHIRO TSUJI, NA OTO KA TO, NAOTO KOY AMA, and YUJI JOE Appeal2013-007048 Application 11/427,482 Technology Center 1600 Before JEFFREY N. FREDMAN, JOHN G. NEW, and ULRIKE W. JENKS, Administrative Patent Judges. FREDMAN, Administrative Patent Judge. DECISION ON APPEAL This is an appeal 1 under 35 U.S.C. Â§ 134 involving claims to a method for producing L-threonine. The Examiner rejected the claims as obvious. We have jurisdiction under 35 U.S.C. Â§ 6(b). We affirm. 1 Appellants identify the Real Party in Interest as Ajinomoto Co., Inc. (see App. Br. 3). Appeal2013-007048 Application 11/427,482 Statement of the Case Background "Sulfur is an essential factor for bacterial cell growth and is usually included in the medium for L-threonine fermentation in the form of ammonium sulfate. With regard to L-threonine production by fermentation; however, regulation of the sulfur concentration in the fermentation medium and the effect of lowering the sulfur concentration are unknown" (Spec. i-f 9). The Claims Claims 1, 4, 6-10, 13, 15-18, 20, and 21 are on appeal. 2 Independent claims 1 and 10 are representative and reads as follows: 1. A method for producing L-threonine comprising: A) culturing an Escherichia coli that has an ability to produce 50g/[L] or higher of L-threonine, in a fermentation medium containing a carbon source, a nitrogen source, and a sulfur source, B) regulating the sulfur concentration in the medium so that it is 0.35 g/L or lower during said culturing of step A); and C) collecting L-threonine from the medium. 10. A method for producing a composition comprising a dried crude fermentation broth, comprising: A) culturing an Escherichia coli that has an ability to produce 50g/[L] or higher of L-threonine, in a fermentation medium containing a carbon source, a nitrogen source, and a sulfur source, B) maintaining the sulfur concentration in the medium during fermentation so that it is 0.35 g/L or lower, C) drying the crude fermentation broth so that the water content is 10% or less by weight. 2 Claims 2, 3, 5, 11, 12, 14, and 19 were cancelled (see Response to Non-final Action 10/27/2008). 2 Appeal2013-007048 Application 11/427,482 The Issues A. The Examiner rejected claims 1, 4 and 6-9 under 35 U.S.C. Â§ 103(a) as obvious over Kruse3, De Hollander4, and Debabov5 (Ans. 3--4). B. TheExaminerrejectedclaims 10, 13, 15-18,20,and21 under35 U.S.C. Â§ 103(a) as obvious over Kruse, De Hollander, Debabov, and Binder6 (Ans. 4--5). A. 35 U.S.C. Â§ 103(a) over Kruse, De Hollander, and Debabov The Examiner finds that Kruse teaches "a method for the production of L-threonine" comprising "culturing E. coli BKIIM B-3996 ... in a fed- batch culture" medium that includes a carbon source and a nitrogen/sulfur source (ammonium sulfate), and collecting the produced L-threonine (Ans. 2). The Examiner finds that the specification of the instant application teaches E. coli BKIIM B-3996 (also called E. coli VKPM B-3996), the same L-threonine producing strain taught by Kruse (ii .. ns. 2). The Examiner finds that, as evidenced by Debabov, the E. coli strain of Kruse (E. coli BKIIM B- 3996) has been shown to produce 85 g/L in a batch culture (Ans. 3). The Examiner acknowledges that neither Kruse nor Debabov "teach a fed-batch culture where sulfur concentration is regulated" (Ans. 3). The Examiner finds that De Hollander teaches that "in fed-batch cultures one could achieve sustained [microbial] growth by providing essential nutrients which are limiting and that the limiting nutrient will be present in the culture 3 Kruse et al., WO 2005/014840 Al, published Feb. 17, 2005. 4 De Hollander et al., US 5,763,230, issued June 9, 1998. 5 Debabov et al., US 5,538,873, issued July 23, 1996. 6 Binder et al., US 5,431,933, issued July 11, 1995. 3 Appeal2013-007048 Application 11/427,482 fluid at a very low concentration" (Ans. 3). The Examiner finds that De Hollander teaches that "there are different types of nutrient limitation strategies that can be used, such as limitation by carbon, by sulfur, or by phosphorous" (Ans. 3). The Examiner finds that De Hollander teaches "a working example which shows that a phosphorous limiting nutrient strategy using an L-lysine producing C. glutamicum strain resulted in improved production of L-lysine" (Ans. 3). The Examiner finds that it would have been obvious to one of ordinary skill in the art at the time the invention was made to "use a sulfur limiting nutrient strategy by supplying sulfur at a rate which avoids accumulation, thus maintaining sulfur at negligible levels, in view of the teachings of De Hollander ... regarding the increase in L-amino acid production when a phosphorous limiting nutrient strategy or a phosphorous/carbon source limiting nutrient strategy was used in a microbial culture" (Ans. 4). The issues with respect to this rejection are: (i) Does the evidence of record support the Examiner's conclusion that Kruse, De Hollander, and Debabov render claims 1, 4, and 6-9 obvious? (ii) If so, have Appellants presented evidence of secondary considerations, that when weighed with the evidence of obviousness, is sufficient to support a conclusion of non-obviousness? Findings of Fact 1. The Specification teaches that " [ s ]ulfur is an essential factor for bacterial cell growth and is usually included in the medium for L-threonine fermentation in the form of ammonium sulfate" (Spec. i-f 9). 4 Appeal2013-007048 Application 11/427,482 2. Table 1 of the Specification is reproduced below: 1.H 0.54 3{:.f.â€¢ ~ .i) 0. ?.9 3~ .-6 {LS: {f125 ~>9"9 o.,; O . .l5 40.S 0,1: t\10 -t3 .6 (Spec. i-f 119). Table 1 provides results of effect of regulation of initially added sulfur on L-threonine fermentation yield in fed-batch culture (Spec. i-fi-1 110, 118). 3. Table 2 of the Specification is reproduced below: (LO (Spec. i-f 125). Table 2 provides results of effect of regulation of sulfur in the feed medium on L-threonine fermentation yield in fed-batch culture (Spec. ,-r,-r 120, 124). 4. Kruse teaches a fermentation process, characterized in that: a bacterium of the Enterobacteriaceae family (e.g., E. coli BKIIM B-3996) is cultured in a first nutrient medium, and a further nutrient medium comprising at least one carbon source, at least one nitrogen source (such as ammonium sulfate), at least one phosphorous source; and removing the formed L-threonine, wherein the concentration of the carbon source during 5 Appeal2013-007048 Application 11/427,482 culturing is adjusted to not more than 30 g/L (Kruse 4, 1. 14 to 5, 1. 14; 20, 1. 25; 13, 11. 5---6). 5. Kruse teaches that the "first nutrient medium comprises as the source of carbon one or more of the compounds ... in concentrations of 1 to 50 g/kg"; that the "sources of nitrogen can be used individually or as a mixture in concentrations of 1 to 40 g/kg"; that the "source of phosphorus in the first nutrient medium [is] in concentrations of 0 .1 to 5 g/kg" and that "magnesium sulfate or iron sulfate ... are present in concentrations of 0.003 to 3 g/kg" (Kruse 11, 1. 29 to 12, 1. 28). 6. Debabov teaches a process for producing L-threonine using E. coli BKIIM B-3996, capable in producing 85 g/L L-threonine for a 36-hour fermentation period, in a fermentation medium, which contains a source of carbon and nitrogen (Debabov col. 4, 11. 9-15; col. 1, 11. 12-15; col. 2, 11. 9- 10). 7. Example 1 ofDebabov, which teaches a nutrient medium for E. coli BKIIM B-3996, wherein saccharose is a carbon source, and ammonium sulfate is a nitrogen/sulfur source, is reproduced below: ~aci;;b;p;~-s~ {1\;"H.:;b,S04 KHJl04 MgSO.o..7H20 FeS04.~0 Mg$04.5~0 yewit autolyz;ate water Â· 4_Q o.~ 0,2 0.,04 0.002 0~002 0~2 to ma..\e 100 percent (Debabov, col. 4, 11. 49---65; col. 3, 11. 57---62). 8. De Hollander teaches that In a batch fermentation an organism grows until one of the essential nutrients in the medium becomes exhausted .. .In 6 Appeal2013-007048 Application 11/427,482 fed-batch fermentations ... The microorganism will continue to grow, at a growth rate dictated by the rate of nutrient feed. Generally a single nutrient, very often the carbon source, will become limiting for growth .... Different types of nutrient limitation can be employed. Carbon source limitation is most often used. Other examples are limitation by the nitrogen source ... limitation by sulphur and limitation by phosphorous. The latter two types of limitation are less common employed, because most organisms require only small amounts of these compounds for growth, and it can be difficult to achieve such a limitation during an industrial scale fermentation, especially when raw materials of a complex or partly unknown composition are used. (col. 1, 1. 50 to col. 2, 1. 1). 9. Example 2 of De Hollander teaches testing of different ratios of phosphorous and carbon and of a phosphorus limitation for a lysine over- producing Corynebacterium glutamicum strain, determining the conditions of optimum phosphorous/ carbon ratio, and further determining as a result that relative concentration of lysine and biomass in the culture are strongly dependent on the degree of phosphorous limitation (col. 6, 11. 25-5 6). 10. Table 1 of the Ishikawa Declaration7 discloses production of lysine by E. coli WC196LC/pCABD2 under sulfur-limited condition. 7 Declaration of Kohei Ishikawa, dated Mar. 24, 2010. 7 Appeal2013-007048 Application 11/427,482 Table 1. Experimenbl condition and results MgS04â€¢7H20 (g/l) MgCl2Â·6II;~O (gil) ----"------"--"----"""---Â· Â·~Â·Â·----------------- LOOO 0.000 0.750 0.206 0.500 0.412 0.250 0.619 0.100 0.742 0.075 0.763 0.050 0.784 0.025 0.804 0.010 0.816 0 0.825 (Ishikawa Declaration 2). lysine production (gll) 5.440 5.955 6.615 6.580 5.670 4.690 5.625 4.345 4.445 3.900 11. Table 1 of the Iida Declaration8 discloses production of L- threonine by E. coli VKPM B-5318 under phosphorous-limited condition. (Iida Declaration 2). Principles of Law l''--Â·~!s~~~~~;~;:;;i::~Â·Â·Â·Â·-Â·Â·f Â·-~~~~~~~1 ~ t~ .... ,....,.1:,.~-=--~""-L.~ \Â·Z-" J ... ,.!,,~ ~ f :.~;~.-~ ~ ~-.......... ,.....-.................... ........, ......................... ,... ....... ...,_,,_._,_._..,~ .. -.. ..._ .... ;,..::::~2..- .... { ~ {"!: ~ _.Â·~-c {'!- ; ~--......... _Â· ........ ...:.,Â·.Â· .... ~ _.\'? ...... .:.Â· .. Â· ....... ; .. ,,.~-- ... ~>) ... :~--- ~ l -~ l ~:iÂ·Â·< ' i i::: :::: :1: :::~ ::: =il!ti] Although the record may establish evidence of secondary considerations which are indicia of nonobviousness, the record may also establish such a strong case of obviousness that the objective evidence of nonobviousness is not sufficient to outweigh the evidence of obviousness. 8 Declaration of Yohei Iida, dated Feb. 17, 2011. 8 Appeal2013-007048 Application 11/427,482 Newell Cos. v. Kenney Mfg. Co., 864 F.2d 757, 769 (Fed. Cir. 1988), cert. denied, 493 U.S. 814 (1989). See also Pfizer Inc. v. Apotex Inc., 480 F.3d 1348, 1372 (Fed. Cir. 2007) (unexpected results not sufficient to outweigh a strong showing of obviousness). Analysis We adopt the Examiner's findings of fact and reasoning regarding the scope and content of the prior art (Ans. 2-5; FF 4--9) and agree that the claims are rendered obvious by Kruse, De Hollander, and Debabov. We address Appellants' arguments below. Prima F acie Obviousness Appellants argue that "in Kruse and DeHollander, there is absolutely no description of limiting the sulfur concentration to 0.35 g/L or lower in the fermentation process to produce L-threonine" (App. Br. 6). We are not persuaded. Kruse teaches that the amounts of medium components may vary over a wide range (FF 5) while De Hollander teaches optimizing the amounts of medium components (FF 9). "When the general conditions of a claim are disclosed in the prior art, it is not inventive to discover the optimal or workable ranges by routine experimentation." In re Aller, 220 F.2d 454, 456 (CCPA 1955). De Hollander expressly suggests, as a part of this routine experimentation, to assess limitation conditions of carbon, nitrogen, sulfur and phosphorous in the nutrient bacterial feed (FF 7-9). De Hollander discloses the general principle of limitation by these ingredients, as well as teaches a specific example of optimizing the ratio of phosphorous to carbon in a lysine producing bacterium strand, and of determining as a result that 9 Appeal2013-007048 Application 11/427,482 relative concentration of lysine and biomass in the culture are strongly dependent on the degree of phosphorous limitation (FF 9). Appellants argue that De Hollander teaches away from limiting sulfur in the fermentation because it discloses that "limiting sulfur is far less common than limiting other ingredients, and is actually difficult to achieve", and that "limiting sulfur and phosphorous is less commonly employed because most organisms require only small amounts of sulfur and phosphorous, and it is difficult to achieve such limitation during industrial scale fermentation" (App. Br. 6). Appellants admit that De Hollander has shown the effect of limiting phosphorous, or limiting both phosphorous and carbon in combination, on lysine production by Corynebacterium glutamicum, but contend that "there are no statements or indications about limiting sulfur, nor the effect of such, other than those as mentioned above" (Id.). We find the teaching away arguments unpersuasive. A teaching away requires a reference to actually criticize, discredit, or otherwise discourage the claimed solution. See In re Fulton, 391F.3d1195, 1201 (Fed. Cir. 2004) ("The prior art's mere disclosure of more than one alternative does not constitute a teaching away from any of these alternatives because such disclosure does not criticize, discredit, or otherwise discourage the solution claimed"). De Hollander's teaching that limiting sulfur may be difficult in industrial fermentation using unknown medium sources (FF 8) represents a nonpreferred embodiment, but does not rise to the level of discrediting such sulfur limitation. De Hollander merely discloses an alternative in an example (limiting phosphorous and/or carbon) and a successful one in favor 10 Appeal2013-007048 Application 11/427,482 of establishing the principle of using nutrient limitation, which is not, by itself, sufficient to demonstrate a teaching away. Disclosed examples and preferred embodiments do not constitute a teaching away from a broader disclosure or non-preferred embodiments. In re Susi, 440 F .2d 442, 446 n.3 (CCPA 1971). Secondary Considerations Applicants contend that the Ishikawa Declaration presents proof that "the sulfur-limiting conditions in the fermentation of threonine-producing bacteria is novel, unobvious, and completely unexpected from the prior art teachings" (App. Br. 7). "More specifically, the data shows that less and less lysine was produced as the sulfur concentration in the medium was decreased" (Id.). We are not persuaded. The Ishikawa Declaration does not conclusively establish that "less and less lysine was produced as the sulfur concentration in the medium was decreased" (id.), and in fact, for most of the data points, the data points to the contrary conclusion (FF9). Thus, at the highest MgSQ4.7H20 concentration of 1.000 g/l, the data shows lysine production of 5 .440 g/l, which on dropping the MgSQ4. 7H20 concentration to 0.750 g/l and 0.500 g/l, in fact increases, not decreases the lysine production- to 5.955 g/l, and 6.615 g/l, respectively (FF9). The production is further higher than 5.440 g/l, respectively- 6.580 g/l, 5.670 g/l and 5.625 g/l, for three MgSQ4.7H20 concentrations lower than 1.000 g/l, specifically- 0.250 g/l, 0.100 g/l and 0.050 g/l. While for three concentrations on the very low end (0.075 g/l, 0.025 g/l and 0.010 g/l) Appellants show a higher lysine production as compared to 11 Appeal2013-007048 Application 11/427,482 zero MgSQ4. 7H20 g/l, it is unclear, given the rest of the data, whether this shows an effect, as asserted by Appellants, of decreasing lysine production with decreasing MgS04. 7H20 concentration, or simply some other effect, i.e. too critically low MgSQ4. 7H20 concentrations for bacterial growth (Id.). In this regard, we also note a comparison between the data Appellants presented in the specification as to their own invention (FF 2, 3), and the three lower concentrations in the Ishikawa Declaration for which Appellants purport an effect of sulfur limiting condition giving a positive effect on lysine fermentation (0.075 g/l, 0.025 g/l and 0.010 g/l) (FF9). Thus, in comparison the lowest sulfur concentration, which Appellants tested and reported in their own specification is 0.2 g/l of (NH4)2S04 in Table 1, and 1.0 g/l of (NH4)2S04 in Table 2. Appellants provide no explanation of the discrepancies of the higher tested concentrations in Appellants' specification, as compared to the lower tested concentrations in Appellants' data in the Ishikawa Declaration. The burden of showing unexpected results rests on "he who asserts them." See In re Klosak, 455 F.2d 1077, 1080 (CCPA 1972). Given the above discussed data, Appellants have not met this burden with the Ishikawa Declaration. Therefore, we do not address any further arguments between the Examiner and Appellants as to additional differences between the Ishikawa Declaration and the prior art, such as Appellants' having used in the Ishikawa Declaration a batch culture, as opposed to a batch-fed culture as in De Hollander (App. Br. 7-9; Ans. 10-11). We do note, however, that Appellants did not compare their data to the closest prior art of Example 1 of Debabov, where an E.coli within the 12 Appeal2013-007048 Application 11/427,482 scope of claim 1 is cultured in a medium containing carbon, nitrogen and 0.544 mass percent sulfur containing compounds to obtain 85 g/L of L- threonine (see FF 7). See In re Baxter Travenol Labs., 952 F.2d 388, 392 (Fed. Cir. 1991) ("when unexpected results are used as evidence of nonobviousness, the results must be shown to be unexpected compared with the closest prior art."). Appellants further present data from the Iida Declaration. In the experiment shown in the Iida Declaration, fed- batch cultures were performed by adding the feed medium containing various concentrations of KH2P04. As shown in the data, when adding the feed medium containing 0, 1, or 2 g/F of KH2P04, the phosphorous concentration in the fermentation medium decreased to approximately 0 in 13 hours after the start of cultivation, and did not increase until the end of the cultivation (Figure. 1 ). That is, phosphorous was limited and the production of L-threonine was unimproved. By contrast, when adding the feed medium containing 3, 4, or 5 g/F ofKH2P04, the phosphorous concentration in the fermentation medium gradually increased at a latter half of the cultivation (Figured). That is, phosphorous was not limited. (App. Br. 10; FFlO; see also Reply Br. 1). We agree with Appellants that the data in the Iida Declaration establishes that when phosphorous was limited the production of L-threonine was unimproved. However, as noted above, the data was not compared with the closest prior art of Debabov at the particular concentration of sulfur in Debabov (FF 7). We conclude that even if the evidence provides a weak indication of a secondary consideration, the showing is insufficient to overcome the strong 13 Appeal2013-007048 Application 11/427,482 showing of obviousness in this case. See Pfizer, Inc. v. Apotex, Inc., 480 F.3d 1348, 1372 (Fed. Cir. 2007) ("[W]e hold that even if Pfizer showed that amlodipine besylate exhibits unexpectedly superior results, this secondary consideration does not overcome the strong showing of obviousness in this case. Although secondary considerations must be taken into account, they do not necessarily control the obviousness conclusion.) This conclusion is reasonable because Iida does not directly demonstrate that the claimed level of sulfur is unobvious over the prior art, only that limiting a different nutrient in a different particular situation with a different particular strain reduced yield of L-threonine. Conclusion of Law (i) The evidence of record supports the Examiner's conclusion that Kruse, De Hollander, and Debabov render claims 1, 4, and 6-9 obvious. (ii) Appellants have not presented evidence of secondary considerations, that when weighed with the evidence of obviousness, is sufficient to support a conclusion of non-obviousness. B. 35 U.S.C. Â§ 103(a) over Kruse, De Hollander, Debabov, and Binder Appellants do not argue separately this obviousness rejection, instead relying upon their arguments to overcome the combination of Kruse, Debabov, and De Hollander. The Examiner provides sound fact-based reasoning for combining Kruse, De Hollander, Debabov, and Binder (see Ans. 5---6). Having affirmed the obviousness rejection of claims 1, 4, and 6- 9 over Kruse, De Hollander, and Debabov for the reasons given above, we 14 Appeal2013-007048 Application 11/427,482 also find that the further obvious combination with Binder renders the rejected claims obvious for the reasons given by the Examiner. SUMMARY In summary, we affirm the rejection of claims 1, 4, and 6-9 under 35 U.S.C. Â§ 103(a) as obvious over Kruse, De Hollander, and Debabov. We affirm the rejection of claims 10, 13, 15-18, 20, and 21under35 U.S.C. Â§ 103(a) as obvious over Kruse, De Hollander, Debabov, and Binder. 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)(l). AFFIRMED 15