Ex Parte Mueller et al

Patent Trial and Appeal Board

May 15, 2017

13914234 (P.T.A.B. May. 15, 2017)

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.
13/914,234 06/10/2013 Alexander Paul Mueller LT81US 2733
19135 7590 05/17/2017
LanzaTech New Zealand Limited
8045 Lamon Ave, Suite 400
Skokie, IL 60077
EXAMINER
EKSTROM, RICHARD C
ART UNIT PAPER NUMBER
1652
NOTIFICATION DATE DELIVERY MODE
05/17/2017 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):
ip @ lanzatech. com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte ALEXANDER PAUL MUELLER,
MICHAEL KOEPKE, and SHILPA NAGARAJU
Appeal 2016-002855
Application 13/914,234
Technology Center 1600
Before JEFFREY N. FREDMAN, TAWEN CHANG, and
TIMOTHY G. MAJORS, Administrative Patent Judges.
FREDMAN, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal1 under 35U.S.C. § 134 involving genetically
engineered, carboxydotrophic, acetogenic bacteria. The Examiner rejected
the claims as obvious and on the grounds of obviousness-type double
patenting. We have jurisdiction under 35 U.S.C. § 6(b). We affirm-in-part.
Statement of the Case
Background
“2-butanol is an organic compound that is produced on a large scale,
primarily as a precursor to the industrial solvent methyl ethyl ketone (MEK
or butanone)” (Spec. 13). “MEK is an important ingredient in paints and
1 Appellants identify the Real Party in Interest as the LanzaTech New
Zealand Limited (see App. Br. 2).
Appeal 2016-002855
Application 13/914,234
inks, with a global market of US$2 billion that is growing at 1.9% per
annum” (Spec. 14).
“The invention generally provides, inter alia, methods for the
production of MEK and/or 2-butanol by microbial fermentation of a
substrate comprising CO and/or CO2, and recombinant microorganisms of
use in such methods” (Spec. 1 6).
The Claims2
Claims 1—3, 13, 14, 16, and 19-25 are on appeal. Claim 1 is
representative and reads as follows:
1. Genetically engineered, carboxydotrophic, acetogenic
bacteria comprising an exogenous nucleic acid encoding a
meso-2,3-butanediol dehydrogenase enzyme and an exogenous
nucleic acid encoding a diol/glycerol dehydratase enzyme,
wherein the bacteria are Clostridium autoethanogenum or
Clostridium ljungdahlii.
The Issues
A. The Examiner rejected claims 1—3, 13, 14, 16, and 19-25 under
35 U.S.C. § 103(a) as obvious over Donaldson3 and Abrini4 (Ans. 2-4).
B. The Examiner rejected claims 1—3, 13, 14, 16, 19—22, and 25 on the
ground of nonstatutory double patenting as being unpatentable over claims
1—15 of copending Application No. 14/011,872 (now US 9,284,564) in view
of Donaldson and Abrini (Ans. 4—5).
2 Claims 11 and 12 stand allowed (see Final Act. 9).
3 Donaldson et al., US 2007/0292927 Al, published Dec. 20, 2007.
4 Abrini et al., Clostridium autoethanogenum, sp. nov., an anaerobic
bacterium that produces ethanol from carbon monoxide, 161 Arch.
Microbiol. 345-351 (1994).
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Application 13/914,234
A. 35 U.S.C. § 103(a) over Donaldson andAbrini
The Examiner finds Donaldson teaches
recombinant bacteria for producing 2-butanone or 2-butanol
(abstract; paragraphs [0058] and [0061]). Suitable host cells
include Clostridum bacteria, of which many species are
carboxydotrophic and acetogenic (paragraph 0196]). The
bacteria are engineered to include appropriate enzymes for
producing 2-butanone or 2-butanol, including acetolactate
synthase, acetolactate decarboxylase, butanediol dehydrogenase
and butanediol dehydratase, and optionally including butanol
dehydrogenase when synthesis of 2-butanol is desired
(paragraph [0197]).
(Ans. 2).
The Examiner finds “[w]hile Donaldson et al. broadly teach the use of
Clostridium bacteria as host cells there is no explicit disclosure of
Clostridium autoethanogenum as a host cell” (Ans. 3). The Examiner finds
that Abrini teaches “Clostridium autoethanogenum is a carboxydotrophic,
acetogenic bacterium” (Id).
The Examiner finds it obvious “to have used the Clostridium
autoethanogenum bacteria described by Abrini et al. as a host cell according
to the disclosure of Donaldson et al. because C. autoethanogenum is merely
one member of the Clostridium bacteria which Donaldson et al. teach may
act as a suitable host cell” (Ans. 3^4).
The issue with respect to this rejection is: Does the evidence of
record support the Examiner’s conclusion that C. autoethanogenum would
have been an obvious species for use in the process of Donaldson?
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Application 13/914,234
Findings of Fact
1. Donaldson teaches the “present invention relates to methods for
the production of 2-butanol using recombinant microorganisms . . . The
present invention also provides recombinant microorganisms and methods
for producing 2-butanone, an intermediate in the 2-butanol biosynthetic
pathways disclosed herein” (Donaldson !! 58, 61).
2. Donaldson teaches:
Microbes that are metabolically active at high titer levels of
2-butanol are not well known in the art. Although butanol-
tolerant mutants have been isolated from solventogenic
Clostridia, little information is available concerning the butanol
tolerance of other potentially useful bacterial strains. Most of
the studies on the comparison of alcohol tolerance in bacteria
suggest that butanol is more toxic than ethanol. . . . the yield of
1 -butanol during fermentation in Clostridium acetobutylicum
may be limited by butanol toxicity. The primary effect of
1 -butanol on Clostridium acetobutylicum is disruption of
membrane functions.
(Donaldson^ 190).
3. Donaldson teaches the “criteria for selection of suitable
microbial hosts include the following: intrinsic tolerance to 2-butanol, high
rate of carbohydrate utilization, availability of genetic tools for gene
manipulation, and the ability to generate stable chromosomal alterations”
(Donaldson! 191).
4. Donaldson teaches “suitable microbial hosts for the production
of 2-butanol and 2-butanone include, but are not limited to, members of the
genera Clostridium’'’ (Donaldson! 196).
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Application 13/914,234
5. Abrini teaches “the isolation of a new species of Clostridium,
facultative chemolithoautotrophic, which produces ethanol besides acetate
and CO2, from CO” (Abrini 345, col. 2).
6. Abrini teaches “strain JA1-1 represents the first fully-described
example of Clostridium, that forms significant amounts of ethanol by
fermentation of carbon monoxide. We therefore propose for this strain the
name of Clostridium autoethanogenum’'' (Abrini 350, col. 1).
Principles of Law
A prima facie case for obviousness requires “a reason that would have
prompted a person of ordinary skill in the relevant field to combine the
elements in the way the claimed new invention does” KSR Int 7 Co. v.
Teleflex Inc., 550 U.S. 398, 418 (2007).
Analysis
Appellants contend
even if some species of Clostridium could be considered
suitable host microorganisms according to Donaldson, this
group does not include C. autoethanogenum or C. ljungdahlii.
A number of species of Clostridium, including C.
autoethanogenum and C. ljungdahlii, fail to meet the host
microorganism selection criteria set forth by Donaldson,
specifically “intrinsic tolerance to 2-butanol, high rate of
carbohydrate utilization, availability of genetic tools for gene
manipulation, and the ability to generate stable chromosomal
alterations” (paragraph 0191).
(App. Br. 8). In particular, Appellants contend “neither C. autoethanogenum
nor C. fjungdahlii produce butanol natively and, thus, do not have intrinsic
tolerance to butanol” (Id. at 9).
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Application 13/914,234
The Examiner responds
the factors of intrinsic tolerance to 2-butanol, high rate of
carbohydrate utilization, availability of genetic tools for gene
manipulation, and the ability to generate stable chromosomal
alterations are criteria for selecting appropriate host cells, and
not requirements. Thus, if a particular bacterial species is
missing one or more of the suggested criteria this should not be
regarded as necessarily disqualifying
(Ans. 8). In particular, the Examiner finds “(1) there is no objective
evidence showing unexpected or unpredictable properties relating to butanol
tolerance for Clostridium autoethanogenum, and (2) as discussed above,
intrinsic tolerance to 2-butanol is a criterion for selecting appropriate host
cells, and not a requirement” (Id. at 9).
We find that Appellants have the better position. While the Examiner
is correct that 2-butanol tolerance is only one of several criteria for species
selection in Donaldson (FF 3), the failure of Clostridium autoethanogenum
to satisfy the criteria in Donaldson undercuts the Examiner’s known
equivalence rationale that “C. autoethanogenum is merely one member of
the Clostridium bacteria” (Ans. 4).
That is, the prior art at the time of invention was unaware that C.
autoethanogenum was sufficiently tolerant of butanol to function in the
butanol production process of Donaldson (FF 1—2). Therefore, while C.
autoethanogenum is clearly a species of Clostridium, this situation is not the
mere substitution of one element for another known in the field nor a
predictable variation because C. autoethanogenum was not known to
function in Donaldson’s process and Abrini does not evidence that C.
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Application 13/914,234
autoethanogenum would have been butanol tolerant (FF 2, 5, 6; cf KSR, 550
U.S.at416).
Moreover, Appellants positively state that unlike a number of other
Clostridium species “neither C. autoethanogenum nor C. jjungdahlii produce
butanol natively and, thus, do not have intrinsic tolerance to butanol” (App.
Br. 9). The Examiner has provided no evidence showing that C.
autoethanogenum would be tolerant of butanol to satisfy the prima facie case
of equivalence or predictable variation.
Conclusion of Law
The evidence of record does not support the Examiner’s conclusion
that C. autoethanogenum would have been an obvious species for use in the
process of Donaldson.
B. Double Patenting
The Examiner finds: “Since the present application is earlier filed than
Application No. 14/011,872, if the provisional double patenting rejection is
the only rejection remaining in the present application, then the provisional
double patenting rejection will be withdrawn” (Ans. 12). Appellants agree
that: “Since the present application was filed before U.S. 14/011,872, the
Examiner has agreed that the provisional nonstatutory double patenting
rejection should be withdrawn and the application allowed to issue without a
terminal disclaimer upon withdrawal of the outstanding obviousness
rejection” (App. Br. 11; cf. Reply Br. 5).
In this case, US 14/011,872 has matured in US patent 9,284,564,
issued on March 15, 2016. Claim 2 requires a recombinant C.
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Application 13/914,234
autoethanogenum genetically engineered to encode a diol dehydratase, while
dependent claim 10 further requires an alcohol dehydrogenase (see
US 9,284,564, claim 2, 10). The Examiner relied upon Donaldson for the
obvious selection of a butanediol dehydrogenase as the alcohol
dehydrogenase enzyme for preparation of butanol (see Donaldson 1131) to
establish the obviousness-type double patenting.
We note that MPEP § 804(II)(B)(2)(b) states “only a one-way
determination of distinctness is needed to support a double patenting
rejection in the absence of a finding: (A) that ‘the PTO is solely responsible
for any delays’ in prosecution of the earlier-filed application . . . and (B) that
the applicant could not have filed the conflicting claims in a single (i.e., the
earlier-filed) application.” In this case, there is no indication that the
USPTO was responsible for any delays in prosecution of US 13/914,234 and
Appellants do not state that the claims of US 9,284,564 could not have been
filed in the same application with those of the instant application.
We therefore affirm the obviousness-type double patenting rejection.
SUMMARY
In summary, we reverse the rejection of claims 1—3, 13, 14, 16, and
19-25 under 35 U.S.C. § 103(a) as obvious over Donaldson and Abrini.
We affirm the rejection of claims 1—3, 13, 14, 16, 19-22, and 25 on
the ground of nonstatutory double patenting as being unpatentable over
claims 1—15 of copending Application No. 14/011,872 (now US 9,284,564)
in view of Donaldson and Abrini.
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Application 13/914,234
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
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