Ex Parte Bhat et al

Board of Patent Appeals and Interferences

Jun 16, 2009

11329160 (B.P.A.I. Jun. 16, 2009)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

Ex parte BARKUR G. BHAT, SEKHAR S. BODDUPALLI, GANESH M.
KISHORE, JINGDONG LIU, SHAUKAT H. RANGWALA, and
MYLAVARAPU VENKATRAMESH
____________

Appeal 2008-003946
Application 11/329,160
Technology Center 1600
____________

Decided:1 June 16, 2009
____________

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

ADAMS, Administrative Patent Judge.

DECISION ON APPEAL

1 The two-month time period for filing an appeal or commencing a civil
action, as recited in 37 C.F.R. § 1.304, begins to run from the decided date
shown on this page of the decision. The time period does not run from the
Mail Date (paper delivery) or Notification Date (electronic delivery).

Appeal 2008-003946
Application 11/329,160

This appeal under 35 U.S.C. § 134 involves claims 1, 2 and 10-13, the
only claims pending in this application. We have jurisdiction under
35 U.S.C. § 6(b).

STATEMENT OF THE CASE
The claims are directed to a nucleic acid molecule. Claim 10 is
illustrative:
10. A substantially purified nucleic acid molecule comprising a nucleic
acid sequence having 90% identity to the nucleic acid sequence of SEQ ID
NO: 598 or the complement thereof.

The Examiner relies on the following evidence:
Lorraine A. Everett et al., Pendred syndrome is caused by mutations in a
putative sulphate transporter gene (PDS), 17 NATURE GENETICS 411-422
(1997).

Daryl A. Scott et al., The Pendred syndrome gene encodes a chloride-iodide
transport protein, 21 NATURE GENETICS 440-443 (1999).

NCBI Sequence Accession No. AJ000693 (GI: 2695709),
http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?2695709:OLD02:162684
(Accessed November 15, 2006).

The rejections presented by the Examiner are as follows:
Claims 1, 2 and 10-13 stand rejected under 35 U.S.C. § 101 as lacking
a patentable utility and under the enablement provision of 35 U.S.C. § 112,
first paragraph based on the finding of lack of utility.
We reverse.

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Application 11/329,160

ISSUE

Did the Examiner meet his initial burden of challenging Appellants’
presumptively correct assertion of utility?

FINDINGS OF FACT
FF 1. Appellants disclose that their “invention relates to nucleic acid
sequences from plant cells, in particular, nucleic acid sequences from maize
and soybean plants associated with the tocopherol synthesis pathway in
plants” (Spec. 19: 9-10).
FF 2. “The chloroplast of higher plants exhibit[s] interconnected
biochemical pathways that lead to secondary metabolites, including
tocopherols, that not only perform functions in plants but can also be
important for mammalian nutrition” (Spec. 19: 19-21).
FF 3. Appellants disclose that 4-hydroxyphenylpyruvate dioxygenase (EC
1.13.11.27) is a member of the tocopherol synthesis pathway in plants (Spec.
23: 28 - 24: 14 and 34: 10-18).
FF 4. Appellants disclose SEQ ID NO: 598, a maize sequence that shares
83% identity with a known sequence designated “g2695709” (Spec. 212:
23), which encodes barley 4-hydroxyphenylpyruvate dioxygenase
(attachment to the Examiner’s Answer, page 1). In addition, Appellants
disclose that
The present invention . . . provides a substantially
purified maize . . . 4-hydroxyphenylpyruvate dioxygenase
enzyme or fragment thereof encoded by a first nucleic acid
molecule which specifically hybridizes to a second nucleic acid
molecule, the second nucleic acid molecule having a nucleic
acid sequence selected from the group consisting of a
complement of SEQ ID NO: 598.
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Application 11/329,160

(Spec. 40: 4-8.)
FF 5. Appellants’ Specification discloses
In an aspect of the present invention, one or more of the
nucleic molecules of the present invention are used to
determine the level (i.e., the concentration of mRNA in a
sample, etc.) in a plant (preferably maize or soybean) or pattern
(i.e., the kinetics of expression, rate of decomposition, stability
profile, etc) of the expression of a protein encoded in part or
whole by one or more of the nucleic acid molecule[s] of the
present invention.

(Spec. 93: 1-5.) In addition, Appellants’ Specification discloses that “[i]t is
understood that one or more of the nucleic acids of the present invention
may be introduced into a plant cell and transcribed using an appropriate
promoter with such transcription resulting in the cosuppression of an
endogenous tocopherol synthesis pathway enzyme” (Spec. 117: 13-15). In
this regard, Appellants’ Specification discloses that “[t]he objective of the
antisense approach is to use a sequence complementary to the target gene to
block its expression and create a mutant cell line or organism in which the
level of a single chosen protein is selectively reduced or abolished” (Spec.
117: 18-20).
FF 6. Appellants’ Specification further discloses that “[i]t is understood
that the activity of a tocopherol synthesis pathway enzyme in a plant cell
may be reduced or depressed by growing a transformed plant cell containing
a nucleic acid molecule whose non-transcribed strand encodes a tocopherol
synthesis pathway enzyme or fragment thereof” (Spec. 118: 11-14).
FF 7. Based on sequence homology comparisons, Everett determines that
pendrin is a sulfate transporter (Everett 419: col. 2, ll. 32-34; Ans. 7). Scott,
however, reports that they “were unable to detect evidence of [pendrin’s]
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Application 11/329,160

sulfate transport [activity]” (Scott 440: col. 1, ll. 15-16). Scott concludes
that despite pendrin’s 45% homology to “the human sulfate transporter
‘downregulated in adenoma’”; “pendrin does not function as a sulfate
transporter, as suggested by its close homology to other sulfate transporters,
but instead functions as a sodium-independent transporter of chloride and
iodide” (Scott 440: col. 1, ll. 10-11; 441: col. 1, ll. 33-36; Ans. 8).
FF 8. NCBI Sequence Accession No. AJ000693 (GI 2695709) reports the
“cDNA sequence encoding a barley 4-hydroxyphenylpyruvate dioxygenase”
(see generally NCBI Sequence Accession No. AJ000693, attachment to the
Examiner’s Answer).

PRINCIPLES OF LAW
The “utility requirement” originates with the provision of 35 U.S.C.
§ 101 that a patent may be obtained on “any new and useful process,
machine, manufacture, or composition of matter, or any new and useful
improvement thereof.” An inquiry by the PTO into whether a claimed
invention satisfies the utility requirement typically has two distinct prongs.
First, the PTO must determine whether the patent applicant has asserted a
specific and substantial utility for the claimed invention. In re Fisher, 421
F.3d 1365, 1371 (Fed. Cir. 2005). Second, the PTO must ascertain whether
there is any evidence that one of ordinary skill in the art would reasonably
doubt the invention’s asserted utility. In re Brana, 51 F.3d 1560, 1567 n.19
(Fed. Cir. 1995).
[T]he PTO has the initial burden of challenging a presumptively
correct assertion of utility in the disclosure. . . . Only after the
PTO provides evidence showing that one of ordinary skill in the
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art would reasonably doubt the asserted utility does the burden
shift to the applicant to provide rebuttal evidence sufficient to
convince such a person of the invention’s asserted utility. See
In re Bundy, 642 F.2d 430, 433.

In re Brana, 51 F.3d at 1566.

ANALYSIS
The claims on appeal are drawn to a substantially purified nucleic acid
that comprises SEQ ID NO: 598 or a complement thereof; or shares 90% or
more identity with SEQ ID NO: 598 or a complement thereof. Claim 10 is
the broadest claim, therefore we focus our discussion on this claim.
Claim 10 is drawn to a substantially purified nucleic acid molecule.
The claimed nucleic acid molecule comprises a nucleic acid sequence
having 90% identity to the nucleic acid sequence of SEQ ID NO: 598 or the
complement thereof. The Examiner finds that the “claimed invention is not
supported by a specific asserted utility because none of the disclosed uses of
the claimed nucleic acids in the specification is [sic] specific” (Ans. 5). We
disagree.
Appellants’ Specification discloses that SEQ ID NO: 598 shares 83%
with a known sequence encoding (barley) 4-hydroxyphenylpyruvate
dioxygenase, and encodes 4-hydroxyphenylpyruvate dioxygenase or a
fragment thereof (FF 4). 4-hydroxyphenylpyruvate dioxygenase is an
enzyme involved in the tocopherol synthesis pathway in plants (FF 3).
Appellants’ Specification further discloses that the inventive nucleic
acid molecules can be used, inter alia, to determine the concentration of
mRNA in a sample, to determine the expression pattern of a protein encoded
in part or whole by one or more of the nucleic acid molecules, and to inhibit
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expression using antisense approaches (FF 5). As Appellants explain,
inhibiting expression using antisense approaches will result in a transformed
plant cell wherein the activity of a tocopherol synthesis pathway enzyme is
reduced or depressed (FF 6).
There is no evidence on this record that Appellants’ claimed nucleic
acid molecules would not be useful in determining the mRNA concentration
of a tocopherol synthesis pathway enzyme, expression pattern of a
tocopherol synthesis pathway enzyme in a sample, or in antisense
approaches to prevent or reduce the function of a tocopherol synthesis
pathway enzyme gene. In addition, there is no evidence on this record that a
full length sequence or further research would be required to perform these
utilities.
The Fisher court held that measuring mRNA concentration or
expression pattern of an uncharacterized EST does not provide a specific and
substantial utility that satisfies § 101. See Fisher, 421 F.3d at 1368 and
1373-74. In this case, however, the EST corresponding to SEQ ID NO: 598
are disclosed to have significant similarity to a sequence encoding a known
enzymes with a known function. In our view, the similarity of the claimed
nucleic acid to a product having known a function is adequate to support the
utility of the claimed nucleic acids as research tools to measure gene
expression or to reduce expression of the encoded product. Accordingly, we
disagree with the Examiner’s assertion that the claimed invention lacks a
patentable utility (Ans. 5-8).
We recognize the Examiner’s assertion that Appellants’ disclosed
83% identity “is only in a small region of gi 2695709” and that there is only
a 61.7% total match between the two sequences (Ans. 7). In response,
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Appellants contend that the Examiner recognizes that their Specification
“discloses that SEQ ID NO: 598 shares 83% identity to a known nucleic acid
sequence encoding a barley 4-hydroxyphenylpyruvate dioxygenase” and
“assuming, arguendo, that the homology between SEQ ID NO: 598 and a
known 4-hydroxyphenylpyruvate dioxygenase is lower than 83%, the
Examiner has provided no support for the proposition that SEQ ID NO: 598
can [sic, cannot] be reasonably used for the utilities asserted in the
specification” (App. Br. 8). In response, the Examiner directs attention to
Everett and Scott, asserting that these references support the conclusion that
the relatively low identity between SEQ ID NO:598 and the
small portion of the ORF of gi 2695709 that encodes the barley
4-hydroxyphenylpyruvate dioxygenase would leave reasonable
doubts to one skilled in the art as to whether or not the sequence
of SEQ ID NO:598 would actually encode the enzymatic
activity of 4-hydroxyphenylpyruvate dioxygenase.

(Ans. 8.) We are not persuaded.
Claims 2 and 10-13 do not require the claimed nucleic acid molecule
to encode a protein having 4-hydroxyphenylpyruvate dioxygenase activity.
The only remaining claim, claim 1, is drawn to a substantially purified
nucleic acid molecule that comprises the nucleic acid sequence of SEQ ID
NO: 598 that encodes a maize tocopherol synthesis pathway enzyme or
fragment thereof, wherein the maize tocopherol synthesis pathway enzyme
is 4-hydroxyphenylpyruvate dioxygenase or fragment thereof. There is no
evidence on this record that SEQ ID NO: 598 does not encode a 4-
hydroxyphenylpyruvate dioxygenase fragment or that the claimed nucleic
acid would not be capable of performing the disclosed utilities.

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CONCLUSION OF LAW
For the foregoing reasons we find that the Examiner has failed to meet
his burden of challenging Appellants’ presumptively correct assertion of
utility. Brana, 51 F.3d at 1566.
Accordingly, the rejection of claims 1, 2 and 10-13 under 35 U.S.C.
§ 101 as lacking a patentable utility and under the enablement provision of
35 U.S.C. § 112, first paragraph based on the finding of lack of utility is
reversed.

REVERSED

cdc

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