Ex Parte Liu et al

Board of Patent Appeals and Interferences

May 13, 2010

11520715 (B.P.A.I. May. 13, 2010)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

Ex parte JINGDONG LIU, YIHUA ZHOU, DAVID K. KOVALIC
STEVEN E. SCREEN, JACK E. TABASKA and YONGWEI CAO
____________

Appeal 2009-009417
Application 11/520,715
Technology Center 1600
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Decided: May 13, 2010
____________

Before ERIC GRIMES, TONI R. SCHEINER, and DONALD E. ADAMS,
Administrative Patent Judges.

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL
This appeal under 35 U.S.C. § 134 involves claims 4-15, the only
claims pending in this application. We have jurisdiction under 35 U.S.C.
§ 6(b).
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STATEMENT OF THE CASE
The claims are directed to a transgenic plant. Claim 4 is illustrative:
4. A transgenic plant having in its genome an exogenous DNA
construct comprising a nucleic acid sequence encoding a polypeptide having
an amino acid sequence characterized as having at least 50% identity to the
amino acid sequence of SEQ ID NO: 52139.

The Examiner relies on the following evidence:

James A. Wells, Additivity of Mutational Effects in Proteins, 29(37)
Biochemistry 8509-8517 (1990).

J. Thomas Ngo et al., Computational Complexity, Protein Structure
Prediction, and the Levinthal Paradox, in The Protein Folding Problem and
Tertiary Structure Prediction (K. Merz et al. eds., Boston) (1994).

Janet M. Thornton et al., From structure to function: Approaches and
limitations, Nature Structural Biology, Structural Genomics Supplement
991-994 (2000).

Sylvain Darnet et al., (Darnet I), Functional identification of sterol 4α-
methyl oxidase cDNAs from Arabidopsis thaliana by complementation of a
yeast erg25 mutant lacking sterol-4α-methyl oxidation, 508 FEBS 39-43
(2001).

Sylvain Darnet et al. (Darnet II), Plant sterol biosynthesis: identification of
two distinct families of sterol 4α-methyl oxidases, 378 Biochem. J. 889-898
(2004).

Ozlem Keskin et al., A new, structurally nonredundant, diverse data set of
protein-protein interfaces and its implications, 13 Protein Science 1043-
1055 (2004).

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The rejections presented by the Examiner follow:
1. Claims 4-15 stand rejected under 35 U.S.C. § 101 and the enablement
provision of 35 U.S.C. §112, first paragraph.
2. Claims 4-9 and 12-15 stand rejected under the written description
provision of 35 U.S.C. § 112, first paragraph.
We reverse the rejection under the written description provision of 35
U.S.C. § 112, first paragraph. We affirm the rejection under 35 U.S.C.
§ 101 and the enablement provision of 35 U.S.C. §112, first paragraph.

Utility:
ISSUE

Has the Examiner erred in finding that Appellants’ claimed invention
lacks a specific and substantial asserted utility, or a well established utility?

FINDINGS OF FACT
FF 1. The Examiner finds that SEQ ID NO: 53139 is the predicted
polypeptide encoded by SEQ ID NO: 25824 and “exhibits 58% homology to
a putative C-4 [S]terol methyl oxidase from rice” (Ans. 5).
FF 2. The “[s]tate of the art related with plant C-4 sterol methyl oxidases
suggests that [the] physiological role of plant C-4 sterol methyl oxidases
remains to be elucidated” (Ans. 6).
FF 3. Darnet I teaches that “while Arabidopsis 4-C methyl oxidase is able
to complement a yeast erg25 mutant lacking 4-C sterol methyl oxidase
activity . . . its role within the plant cell is unclear” (Ans. 10).
FF 4. Darnet II teaches that the “distinct biochemical properties associated
with different members of plant C-4 sterol methyl oxidases, and the
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physiological roles of said distinct biochemical properties remains to be
understood” (Ans. 6).
FF 5. The Examiner finds that “the predicted amino acid sequence of SEQ
ID NO: 52139 does not begin with ‘methionine (M)’ at its N-terminus end,”
but instead “starts with ‘Glutamine (Q)’ which may imply that the predicted
SEQ ID NO: 52139 [sequence] is [a] partial [sequence]” (Ans. 5).
FF 6. “Appellant[s] provided no empirical data to verify that SEQ ID NO:
52139 is a functional protein, and whose expression in a plant can impart
useful characteristics to the plant” (id.).

PRINCIPLES OF LAW
“Enablement, or utility, is determined as of the application filing
date.” In re Brana, 51 F.3d 1560, 1567 n.19 (Fed. Cir. 1995). The Court in
Brenner specifically addressed the possibility that an invention might later
be shown to be useful, but concluded that utility must be shown before a
patent could be granted. See Brenner v. Manson, 383 U.S. 519, 535-36
(1966) (The court was not “blind to the prospect that what now seems
without ‘use’ may tomorrow command the grateful attention of the public.
But a patent is not a hunting license. It is not a reward for the search, but
compensation for its successful conclusion.”).
“[A] claimed invention [must] have a specific and substantial utility to
satisfy § 101.” In re Fisher, 421 F.3d 1365, 1371 (Fed. Cir. 2005)
(emphasis added). “[T]o satisfy the ‘substantial’ utility requirement, an
asserted use must show that that claimed invention has a significant and
presently available benefit to the public.” Id.
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Regarding the “specific” utility requirement, “an application must
disclose a use which is not so vague as to be meaningless.” Id. Thus, “an
asserted use must . . . show that that claimed invention can be used to
provide a well-defined and particular benefit to the public.” Id.
The how to use prong of section 112 incorporates as a matter of
law the requirement of 35 U.S.C. § 101 that the specification
disclose as a matter of fact a practical utility for the invention.
If the application fails as a matter of fact to satisfy 35 U.S.C. §
101, then the application also fails as a matter of law to enable
one of ordinary skill in the art to use the invention under 35
U.S.C. § 112.

In re Fisher, 421 F.3d at 1378 (quoting In re Ziegler, 992 F.2d 1197, 1200-
01 (citations omitted)).

ANALYSIS
The claims have not been argued separately and therefore stand or fall
together. 37 C.F.R. § 41.37(c)(1)(vii). Claim 4 is representative.
Based on the foregoing factual findings (FF 1-6), the Examiner
concludes that “identifying and studying the properties of the protein itself
or the mechanisms in which the protein is involved requires further basic
research and does not define a ‘real world’ context of use” (Ans. 6).
Therefore, the Examiner concludes that “[t]he claimed invention is not
refined and developed to the point where specific benefit exists, as no
guidance is provided as to how a plant transformed with a nucleotide
sequence encoding SEQ ID NO: 52139 should be used in a manner to
achieve a useful outcome” (Ans. 7).
Appellants contend that “[s]terol methyl oxidase has a physiological
function, namely oxidative removal of methyl groups at the start of sterol
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biosynthesis. Therefore, one of ordinary skill in the art would recognize that
the claimed nucleic acid molecules have utility” (App. Br. 6). In this regard,
Appellants contend that “the question of utility is not the question of ‘which’
effect occurs. Rather, the question of utility is the question ‘if’ an effect is
engendered, i.e., if at least a single utility is present” (App. Br. 7). We are
not persuaded.
Appellants’ contention begs the question – what single utility is
present? The art of record establishes that the role of C-4 methyl oxidase is
not understood in plants (FF 3-4; Ans. 20). The Examiner has provided
persuasive reasoning that the polypeptide having SEQ ID NO: 52139 may be
a fragment of the actual C-4 methyl oxidase protein and therefore not exhibit
C-4 methyl oxidase activity (FF 5). Appellants have failed to establish a
factual basis on this record to support their assertion that the polypeptide
with the amino acid sequence of SEQ ID NO: 52139 is a functional C-4
methyl oxidase which will exhibit a useful effect in a transgenic plant (FF 6;
Ans. 20). Accordingly, we agree with the Examiner’s conclusion that
further research would be required to (1) understand how “the polypeptide of
SEQ ID NO: 52139 would affect a plant” and (2) “determine how to use the
claimed transgenic plant” (Ans. 21).
Appellants contend that their Specification provides a number of
utilities for the claimed transgenic plant (Reply Br. 11-12). In this regard,
Appellants contend that the Specification “provides that expression of the
disclosed polynucleotides in plants, including expression of SEQ ID NO:
25824, may be analyzed by those of skill in the art to identify improved
properties of the claimed transgenic plants” (Reply Br. 11). Appellants also
contend that:
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[T]he claimed transgenic plants may be monitored for changes
in expression resulting from transformation with the claimed
polynucleotides, allowing one of skill in the art to ascertain
what regions of the polynucleotides and translated polypeptides
are important in gene expression or suppression, or how such
expression or suppression affects desired characteristics of a
transgenic plant.

(Reply Br. 12). Notwithstanding Appellants’ contentions to the contrary,
these asserted utilities support the Examiner’s conclusion that further
research would be required to provide a well-defined and particular benefit
to the public: the asserted utilities amount to further experimentation on the
claimed transgenic plant itself.
We are not persuaded by Appellants’ contention that the Examiner
“acknowledg[es] Appellants’ use of transgenic plants to alter C-4 sterol
methyl oxidase activity. See e.g., Office Action at page 4” (App. Br. 7).
Page 4 of the Final Rejection states:
The Specification as filed does not show that expression of the
SEQ ID NO: 25824 encoding SEQ ID NO: 52139 resulted in
any useful trait in the transgenic plant. One skilled in the art
would not know how to use the claimed transgenic plant
comprising a polynucleotide encoding SEQ ID NO: 52139 for
any useful purpose.

(Fin. Rej. 4.) We are also not persuaded by Appellants’ contention that “the
Examiner has admitted that ‘the specification teaches that SEQ ID NO:
25824 encodes for a polypeptide (SEQ ID NO: 52139) belonging to a
putative C-4 sterol methyl oxidase family of proteins which are involved in
lipid metabolism.’ Office Action mailed June 25, 2007 at page 5” (Reply
Br. 14). Appellants have taken the Examiner’s statement out of context.
The June 25, 2007 Office Action stated that:
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Table 1 of [Appellants’] Specification indicates that SEQ ID
NO: 25824 encodes for a polypeptide (SEQ ID NO: 52139)
belonging to a putative C-4 sterol methyl oxidase family of
proteins which are involved in lipid metabolism. The claimed
invention lacks specific and substantial utility because basic
research is required to determine how this protein affects plant
cells.

(June 25, 2007 Office Action 5, emphasis added.)
Lastly, we recognize Appellants’ contentions regarding Bensen1
(Reply Br. 2-9). Appellants have not, however, established a relationship
between their disclosure and the disclosure in Bensen. While Bensen may
have satisfied the utility requirement for the invention claimed therein, for
the reasons set forth above, Appellants have not done so on this record.

CONCLUSION OF LAW
The Examiner did not err in finding that Appellants’ claimed
invention lacks a specific and substantial asserted utility, or a well
established utility.
The rejection of claim 4 under 35 U.S.C. § 101 is affirmed. The
rejection of claim 4 under the enablement provision of 35 U.S.C. §112, first
paragraph, is a corollary to the rejection under 35 U.S.C. § 101 (see Ans. 8).
Accordingly, the rejection of claim 4 under the enablement provision of 35
U.S.C. §112, first paragraph is affirmed. Claims 5-19 fall together with
claim 4.

1 Bensen et al. US 7,410,800 B2 Aug. 12, 2008.
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Written Description:
ISSUE

Has the Examiner erred in finding Appellants’ Specification fails to
describe the common attributes that identify members of the claimed genus?

FINDINGS OF FACT
FF 7. The Examiner finds that Appellants’ “specification does not describe
structure of sequences which have 50%, 60%, 70%, 80%, 90% or 95%
sequence identity to SEQ ID NO: 52139” or “the function of said sequences
upon their expression in a transgenic plant” (Ans. 16-17).
FF 8. The Examiner finds that Appellants’ “specification does not describe
the structures comprising at least 20 contiguous nucleotides of SEQ ID NO:
25824, and encoding a polypeptide which may have the biological function
of SEQ ID NO: 52139 (Ans. 17).
FF 9. The Examiner finds that Appellants’ Specification fails to describe
the common attributes that identify members of the claimed highly variant
genus (id.).

PRINCIPLES OF LAW
The written description must define the genus to enable one skilled in
the art to “visualize or recognize the identity of the members of the genus,”
e.g., by providing a description of “structural features commonly possessed
by members of the genus that distinguish them from others.” University of
California v. Eli Lilly & Co., 119 F.3d 1559, 1568 (Fed. Cir. 1997).

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ANALYSIS
The Examiner concludes that because Appellants’ “disclosure fails to
describe the common attributes that identify members of the recited [highly
variant] genus . . . SEQ ID NOs: 25824 and 52139 are insufficient to
describe the claimed genus” (Ans. 17; FF 9). We disagree.
Appellants’ claimed invention requires, inter alia, a polynucleotide
comprising at least about 50% identity to a nucleic acid sequence of SEQ ID
NO: 52139 or a fragment of at least 20 contiguous nucleotides of the coding
sequence of SEQ ID NO: 25824 (see Claims 4 and 14). Claims 5-9 and 12-
13 depend directly or indirectly from claim 4. Claim 15 depends from claim
14. Accordingly, each claim specifies a specific structural starting point -
the sequence set forth in SEQ ID NOs: 52139 or 25824. Each claim then
limits the genus of sequences to those that are derived from SEQ ID NOs:
52139 or 25824. These structural features enable persons of ordinary skill in
this art to recognize the identity of members of the genus of sequences set
forth in Appellants’ claimed invention as required under Lilly.

CONCLUSION OF LAW
The Examiner erred in finding Appellants’ Specification fails to
describe the common attributes that identify members of the claimed highly
variant genus.
The rejection of claims 4-9 and 12-15 under the written description
provision of 35 U.S.C. § 112, first paragraph, is reversed.

Appeal 2009-009417
Application 11/520,715

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TIME PERIOD FOR RESPONSE
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

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