Ex Parte Cheikh et al

Board of Patent Appeals and Interferences

May 28, 2009

09300482 (B.P.A.I. May. 28, 2009)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE BOARD OF PATENT APPEALS
AND INTERFERENCES
____________

Ex parte NORDINE CHEIKH, JINGDONG LIU, and VIRGINIA M.
PESCHKE
____________

Appeal 2008-005234
Application 09/300,482
Technology Center 1600
____________

Decided:1 May 29, 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 2008-005234
Application 09/300,482

This appeal under 35 U.S.C. § 134 involves claims 1, 11-13, 15-22,
24, 28, 30, and 31, 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 11 is
illustrative:
11. An isolated nucleic acid molecule, wherein said isolated nucleic acid
molecule comprises a nucleic acid sequence selected from the group
consisting of SEQ ID NOs: 1, 4, 14, 27, 225, 298, 311, 356, 569, and
619 or complements thereof.

The Examiner relies on the following prior art references to show
unpatentability:
Robert B. Russell and Geoffrey J. Barton, Structural Features can be
Unconserved in Proteins with Similar Folds, 244 J. MOL. BIOL. 332-350
(1994).

David Gerhold and C. Thomas Caskey, It’s the genes! EST access to human
genome content, 18 BIOESSAYS 973-981 (1996).

Timothy N. C. Wells and Manuel C. Peitsch, The chemokine information
source: identification and characterization of novel chemokines using the
WorldWideWeb and Expressed Sequence Tag Databases, 61 J. LEUKOC.
BIOL. 545-550 (1997).

Teresa K. Attwood, The Babel of Bioinformatics, 290 SCIENCE 471-473
(2000).

2
Appeal 2008-005234
Application 09/300,482

The rejections presented by the Examiner are as follows:
1. Claims 1, 11-13, 15-22, 24, 28, 30, and 31 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.
2. Claims 1, 22, 24, and 28 stand rejected under the enablement provision of
35 U.S.C. § 112, first paragraph.
3. Claims 1, 22, 24, and 28 stand rejected under the written description
provision of 35 U.S.C. § 112, first paragraph.
We reverse.

Utility:
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 phosphogluconate pathway in plants”
(Spec. 1: 7-9).
FF 2. The phosphogluconate pathway “is one of the two major pathways in
plants by which carbohydrates may be ultimately degraded into CO2, the
other being glycolysis followed by the TCA cycle” (Spec. 1: 18-21).
FF 3. Appellants disclose maize or soybean phosphogluconate pathway
enzymes or fragments thereof encoded by a first nucleic acid molecule
which specifically hybridizes with a second nucleic acid molecule selected
3
Appeal 2008-005234
Application 09/300,482

from the group consisting of a complement of SEQ ID NO: 1 through SEQ
ID NO: 699 or a complement thereof (Spec. 15: 13-17; see generally Spec.
15: 18 - 23:11).
FF 4. According to Appellants’ Specification, the disclosed sequences or
ESTs “can represent copies of up to the full length [mRNA] transcript”
(Spec. 8: 8).
FF 5. Appellants’ Table A illustrates that SEQ ID NOs: 1-699 share some
percent identity with maize or soybean nucleic acids that encode various
enzymes in the phosphogluconate pathway (Spec. 224: 1 - 240: 9).
FF 6. Appellants disclose that SEQ ID NOs: 1-11 encode “a maize or
soybean glucose-6-phosphate-1-dehydrogenase enzyme,” “fragment
thereof,” or homologue thereof (Spec. 51: 3-7 and 52: 4-5).
FF 7. Appellants disclose that SEQ ID NO: 4 has 44 percent identity with
a nucleic acid molecule that encodes a soybean glucose-6-phosphate 1
dehydrogenase (Spec. 224: 10; App. Br. 7).
FF 8. Appellants disclose that SEQ ID NOs: 12-103 encode “a maize or
soybean 6-phosphogluconate dehydrogenase enzyme,” “fragment thereof,”
or homologue thereof (Spec. 50: 11-12; 52: 4-5).
FF 9. Appellants disclose that SEQ ID NO: 14 has 72 percent identity with
a nucleic acid molecule that encodes a maize 6-phosphogluconate
dehydrogenase (Spec. 224: 24; App. Br. 7).
FF 10. 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
4
Appeal 2008-005234
Application 09/300,482

whole by one or more of the nucleic acid molecule[s] of the
present invention.

(Spec. 80: 6-10.) 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 phosphogluconate pathway enzyme” (Spec. 111: 19-21). 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.
112: 1-3).
FF 11. Appellants disclose that “[i]t is understood that the activity of a
phosphogluconate 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 phosphogluconate
pathway enzyme or fragment thereof” (Spec. 113: 1-4).
FF 12. Wells teaches that the chemokines family of proteins has been
divided into the CXC, CC, and C subfamilies “depending on the spacings of
highly characteristic cysteine residues within their amino-terminal regions”
(Wells, 545: col. 2, ll. 20-22). Wells teaches that
In addition to the conserved cysteine motif described above, the
CC chemokines share other clear sequence similarities such as a
C-terminal helix and conserved hydrophobic sequences in the
first and third beta sheet. These features make the identification
of novel chemokines in sequence databases relatively easy
because even though the overall sequence identity levels
between chemokines may be as low as 20%, the cysteine
5
Appeal 2008-005234
Application 09/300,482

spacings and hydrophobicity may still be used to detect novel
chemokine sequences.

(Wells, 545: col. 2, l. 28 - 546: col. 1, l. 6.) Therefore, Wells teaches that
despite an overall sequence identity level as low as 20%, the features of the
sequences may still be used to detect novel chemokine sequences.
FF 13. Gerhold discusses ESTs and teaches that “one can best find proteins
related to ras, for example, using a protein or DNA sequence query”
(Gerhold 975: col. 2, ll. 17-19).

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
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.
6
Appeal 2008-005234
Application 09/300,482

In re Brana, 51 F.3d at 1566.
ANALYSIS
Claim 11 is drawn to an isolated nucleic acid molecule. The isolated
nucleic acid molecule of claim 11 comprises a nucleic acid sequence
selected from the group consisting of SEQ ID NOS: 1, 4, 14, 27, 225, 298,
311, 356, 569, and 619 or complements thereof.
The Examiner finds that the claimed nucleic acids are not supported
by a specific asserted utility because none of the disclosed uses of the
nucleic acids are specific (Ans. 4). We disagree.
Appellants’ Specification discloses that the nucleic acids of each of
the SEQ ID NOs recited in claim 11 encodes a protein having a significant
sequence similarity to an enzyme in the phosphogluconate pathway (FF 5).
For example, the Specification discloses that SEQ ID NOs: 4 and 14 have 44
and 72 percent identity with a soybean glucose-6-phosphate and maize 6-
phosphogluconate dehydrogenase respectively (FF 1-3, 7, and 9). Soybean
glucose-6-phosphate and maize 6-phosphogluconate dehydrogenase are
enzymes involved in the phosphogluconate pathway.
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
expression using antisense approaches (FF 10). As Appellants explain,
inhibiting expression using antisense approaches will result in a transformed
plant cell wherein the activity of a phosphogluconate pathway enzyme is
reduced or depressed (FF 11).
7
Appeal 2008-005234
Application 09/300,482

There is no evidence on this record that Appellants’ claimed nucleic
acid molecules would not be useful in determining the mRNA concentration
of a phosphogluconate pathway enzyme, expression pattern of a
phosphogluconate pathway enzyme in a sample, or in antisense approaches
to prevent or reduce the function of a phosphogluconate pathway enzyme
gene. In addition, there is no evidence on this record that a full length
sequence or that 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 ESTs corresponding to the SEQ ID NOs
recited in claim 11 are disclosed to have significant similarity to known
enzymes with known functions. In our view, the similarity of the claimed
nucleic acids to products having known functions 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. 4-6).
Further, while Appellants assert that their Specification provides a
statistically relevant correlation between the claimed nucleic acid sequences
and the respective enzymes (App. Br. 7-8), the Examiner asserts that
Appellants’ reliance on “percentage sequence similarity of less than 100%
does not provide sufficient guidance or support to one skilled in the art so as
to determine what biochemical activity or properties the instantly claimed
subject matter would have” (Ans. 5). In support of this finding, the
8
Appeal 2008-005234
Application 09/300,482

Examiner asserts that Attwood, Gerhold, Wells, and Russell document the
“unpredictability of the relationship between sequence and function” (Ans.
6). The Examiner does not, however, direct our attention to any portion of
the cited references that support this position.
Our review of the cited references leads us to conclude that they do
not support the Examiner’s position. For example, Wells teaches that the
chemokines family of proteins has been divided into the CXC, CC, and C
subfamilies “depending on the spacings of highly characteristic cysteine
residues within their amino-terminal regions” (FF 12). Wells teaches that
In addition to the conserved cysteine motif described above, the
CC chemokines share other clear sequence similarities such as a
C-terminal helix and conserved hydrophobic sequences in the
first and third beta sheet. These features make the identification
of novel chemokines in sequence databases relatively easy
because even though the overall sequence identity levels
between chemokines may be as low as 20%, the cysteine
spacings and hydrophobicity may still be used to detect novel
chemokine sequences.

(Id.) Therefore, Wells teaches that despite an overall sequence identity level
as low as 20%, the features of the sequences may still be used to detect
novel chemokine sequences. Further, the Gerhold paper discusses ESTs and
teaches that “one can best find proteins related to ras, for example, using a
protein or DNA sequence query” (FF 13).
Accordingly, we find that the evidence relied upon by the Examiner
fails to support the Examiner’s rejection on this record.

9
Appeal 2008-005234
Application 09/300,482

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, 11-13, 15-22, 24, 28, 30, and
31 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.

Written Description:
ISSUE
Have Appellants provided an adequate written description of their
claimed invention?

FINDINGS OF FACT
FF 14. The Examiner finds that Appellants’ Specification “discloses SEQ
ID NOs: 1, 4, 14, 27, 225, 298, 311, 356, 569, and 619” (Ans. 7).
FF 15. The Examiner finds that Appellants’ “claims 11-13, 15-22, 30, and
31 drawn to a substantially purified nucleic acid molecule consisting of SEQ
ID NOs: 1, 4, 14, 27, 225, 298, 311, 356, 569 and 619 or complement
thereof meet the written description provision of 35 USC [sic] 112, first
paragraph” (id.).

10
Appeal 2008-005234
Application 09/300,482

PRINCIPLES OF LAW
“The burden of showing that the claimed invention is not described in
the application rests on the PTO in the first instance.” In re Edwards, 568
F.2d 1349, 1354 (CCPA 1978).
The “written description” requirement . . . serves both to satisfy the
inventor’s obligation to disclose the technologic knowledge upon which
the patent is based, and to demonstrate that the patentee was in
possession of the invention that is claimed. . . .
The descriptive text needed to meet these requirements varies with the
nature and scope of the invention at issue, and with the scientific and
technologic knowledge already in existence.
Capon v. Eshhar, 418 F.3d 1349, 1357 (Fed. Cir. 2005). See Falko-Gunter
Falkner v. Inglis, 448 F.3d 1357, 1366 (Fed. Cir. 2006) (“[E]xamples are not
necessary to support the adequacy of a written description[;] . . . the written
description standard may be met . . . even where actual reduction to practice
of an invention is absent.”).
ANALYSIS
The Examiner finds that Appellants’ Specification
does not teach or disclose any open reading frames (ORFs) that
are contained within SEQ ID NOs: 1, 4, 14, 27, 225, 298, 311,
356, 569, and 619 such that a maize or soybean
phosphogluconate pathway enzyme or fragment thereof would
be obtained by expression of an isolated nucleic acid molecule
as instantly claimed.

(Ans. 7.) Based on this reasoning the Examiner concludes that “one of skill
in the art would not recognize that applicants were in possession of a
purified nucleic acid molecule that encodes a maize or soybean
phosphogluconate pathway enzyme or fragment thereof as instantly
claimed” (id.). We are not persuaded.
11
Appeal 2008-005234
Application 09/300,482

Each of claims 1, 22, 24, and 28 requires that the claimed nucleic acid
comprise a nucleic acid defined by SEQ ID NO. The Specification describes
the nucleic acid sequence – the chemical structure – of the SEQ ID NOs that
define the claimed nucleic acids. The Specification provides evidence that
the nucleic acid sequences have significant similarity to known genes and,
based on that structural similarity, discloses that the SEQ ID NOs recited in
the claims encode specific protein products. The Examiner has not provided
sufficient evidence to support a conclusion that the Specification’s
disclosure is factually wrong.
Therefore, the Examiner’s finding that Appellants’ Specification fails
to teach an open reading frame within SEQ ID NOs: 1, 4, 14, 27, 225, 298,
311, 356, 569, and 619 is not sufficient in and of itself to conclude that
Appellants’ claimed invention lacks written descriptive support. As
Appellants point out “[t]he fact that the claims at issue are intended to cover
molecules that include the recited sequence joined with additional
sequences, or complements of the recited sequence, does not mean that
Appellants were any less in possession of the claimed nucleic acid
molecules” (App. Br. 14).
Accordingly, the evidence of record fails to establish that Appellants’
claims lack written descriptive support for nucleic acid molecules that
encode a maize or soybean phosphogluconate pathway enzyme or fragment
thereof that comprises a nucleic acid identified by SEQ ID NO.

CONCLUSION OF LAW
Appellants provided an adequate written description of their claimed
invention.
12
Appeal 2008-005234
Application 09/300,482

The rejection of claims 1, 22, 24, and 28 under the written description
provision of 35 U.S.C. § 112, first paragraph is reversed.

Enablement:
ISSUE
Have Appellants provided an enabling description of their claimed
invention?
FINDINGS OF FACT
FF 16. The Examiner finds that because the nucleic acids identified in the
claims by SEQ ID NO each comprise “several ATG codons, any of which
may be a possible start site for translation into a peptide, but no ORF has
been disclosed as that encoding the claimed protein” it would require “trial
and error experimentation to determine how to make a maize or soybean
phosphogluconate pathway enzyme or fragment using the instantly claimed
purified nucleic acid molecules” (Ans. 8-9).

PRINCIPLES OF LAW
Enablement is a question of law, based on underlying findings of fact.
See, e.g., In re Wands, 858 F.2d 731, 735 (Fed. Cir. 1988).
When rejecting a claim under the enablement
requirement of section 112, the PTO bears an initial burden of
setting forth a reasonable explanation as to why it believes that
the scope of protection provided by that claim is not adequately
enabled by the description of the invention provided in the
specification of the application; this includes, of course,
providing sufficient reasons for doubting any assertions in the
specification as to the scope of enablement.
In re Wright, 999 F.2d 1557, 1561-62 (Fed. Cir. 1993).
13
Appeal 2008-005234
Application 09/300,482

To satisfy the enablement requirement of 35 U.S.C. § 112, first
paragraph, a patent application must adequately disclose the claimed
invention so as to enable a person skilled in the art to practice the invention
at the time the application was filed without undue experimentation. Enzo
Biochem, Inc. v. Calgene, Inc., 188 F.3d 1362, 1371-72 (Fed. Cir. 1999).
However, “nothing more than objective enablement” is required, and
therefore it is irrelevant whether this teaching is provided through broad
terminology or illustrative examples. In re Marzocchi, 439 F.2d 220, 223
(CCPA 1971). “[T]here must be sufficient disclosure, either through
illustrative examples or terminology, to teach those of ordinary skill how to
make and how to use the invention as broadly as it is claimed.” In re Vaeck,
947 F.2d 488, 496 & n. 23 (Fed. Cir. 1991). Therefore, it
is incumbent upon the Patent Office, whenever a rejection on
this basis is made, to explain why it doubts the truth or accuracy
of any statement in a supporting disclosure and to back up
assertions of its own with acceptable evidence or reasoning
which is inconsistent with the contested statement. Otherwise,
there would be no need for the applicant to go to the trouble and
expense of supporting his presumptively accurate disclosure.
In re Marzocchi, 439 F.2d at 224.

ANALYSIS
The Examiner’s reasoning is based on the premise that the nucleic
acids recited by SEQ ID NO have not been shown to encode a maize or
soybean phosphogluconate pathway enzyme or fragment thereof.
Appellants’ Specification, however, states that the nucleic acid sequences of
the SEQ ID NOs recited in the claims have significant similarity to known
genes and, based on that structural similarity, the nucleic acids encode
14
Appeal 2008-005234
Application 09/300,482

specific protein products. The Examiner has not provided sufficient
evidence to support a conclusion that the Specification’s presumptively
accurate disclosure is wrong. The Examiner’s rejection therefore is not
supported by a preponderance of the evidence on this record.
Therefore, the Examiner’s finding that Appellants’ Specification fails
to teach an open reading frame within SEQ ID NOs: 1, 4, 14, 27, 225, 298,
311, 356, 569, and 619 is not sufficient in and of itself to conclude that
Appellants’ Specification lacks an enabling description of the claimed
invention.

CONCLUSION OF LAW
Appellants provided an enabling description of their claimed
invention.
The rejection of claims 1, 22, 24, and 28 under the enablement
provision of 35 U.S.C. § 112, first paragraph is reversed.

REVERSED

cdc
ARNOLD & PORTER LLP
ATTN: IP DOCKETING DEPT.
555 TWELFTH STREET, N.W.
WASHINGTON DC 20004-1206
15