Ex Parte SHEN et al

Patent Trial and Appeal Board

Jun 3, 2013

12179406 (P.T.A.B. Jun. 3, 2013)

UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte BEN SHEN and MICHAEL J. SMANSKI
__________

Appeal 2011-011254
Application 12/179,406
Technology Center 1600
__________

Before JEFFREY N. FREDMAN, JOHN A. EVANS, and
ANNETTE R. REIMERS, Administrative Patent Judges.

FREDMAN, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal1 under 35 U.S.C. § 134 involving claims to nucleic
acids encoding a platencin/platensimycin biosynthetic gene cluster. The
Examiner rejected the claims as failing to comply with the written
description requirement and as indefinite. We have jurisdiction under 35
U.S.C. § 6(b). We affirm-in-part.

1 Appellants identify the Real Party in Interest as the Wisconsin
Alumni Research Foundation (App. Br. 2).
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Statement of the Case
Background
The Specification teaches “the cloning, via a novel PCR strategy, of
the entire platensimycin/platencin biosynthetic gene cluster, the sequencing
of this roughly 50 kD segment, and the development of an efficient genetic
system for the engineering of organisms for the biosynthesis of
platensimycin and platencin” (Spec. 15, ll. 11-14).
The Claims
Claims 1-8, 10, 14-18, 20, 22, and23 are on appeal. Claims
1 and 14 are representative and are reproduced below:
1. An isolated polynucleotide encoding a plurality of
genes from the Streptomyces platensis
platencin/platensimycin biosynthetic gene cluster.

14. A host cell comprising a polynucleotide encoding a
plurality of genes from the Streptomyces platensis
platencin/platensimycin biosynthetic gene cluster, said
plurality of genes being located in one or more non-natural
vectors.

The Issues

A. The Examiner rejected claims 1-8, 10, 14-18, 20, 22, and 23 under 35
U.S.C. § 112, second paragraph as indefinite (Ans. 9-10).
B. The Examiner rejected claims 1-8, 10, 14-18, 20, 22, and 23 under 35
U.S.C. § 112, first paragraph, as failing to comply with the written
description requirement (Ans. 5-9).

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A. 35 U.S.C. § 112, second paragraph
The Examiner finds that “the specification does not teach the metes
and bounds of the genes of the platencin/platensimycin biosynthetic gene
cluster, including orf14. The protein sequences are not described by primary
sequence. Therefore, the metes and bounds of the ‘genes’ of the biosynthetic
gene cluster cannot be readily ascertained” (Ans. 9-10). The Examiner finds
that “the size of the polynucleotide encoding a plurality of genes can not be
ascertained when the specification does not describe the metes and bounds
of the elected specie orf14 or any of the other alleged Orfs” (id. at 10). The
Examiner also finds that “[a]s to claim 7, there are no nucleic acid segments
A, B, C or D described by Figure 7” (id.).
The issue with respect to this rejection is: Does the evidence of record
support the Examiner’s conclusion that the claims are indefinite?
Findings of Fact
1. Figures 3A and 3B of the Specification are reproduced below:

“A 70-kb DNA region from S. platensis MA7327 harboring the PTM/PTN
biosynthetic locus represented by four overlapping cosmids and (FIG. 3B)
genetic organization of the PTM/PTN cluster with boundaries predicted on
the basis of bioinformatics analysis” (Spec. 8, ll. 1-4).
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2. The Specification teaches that “the inventors localized a 70-kb
DNA region, covered by four overlapping cosmids, from S. platensis
MA7327 that harbors the PTM/PTN biosynthetic gene cluster (FIG. 3A)
(Manallack et al., 2008). They have sequenced 40-kb of this locus, revealing
36 open reading frames (ORFs) (FIG. 3B)” (Spec. 44, ll. 23-26).
3. The Specification teaches that “[p]ending experimental
confirmation, the boundaries of the PTM/PTN gene cluster have been
assigned to be at ORF7 (upstream) and ORF35 (downstream), respectively,
on the basis of bioinformatics analysis” (Spec. 44, ll. 26-28).
4. The Specification teaches “four additional ORFs (orf8, orf10,
orf12, orf13) encoding other enzyme functions whose role in PTM and PTN
biosynthesis cannot be assigned on the basis of bioinformatics” (Spec. 45, ll.
7-8).
5. Figure 7 is reproduced below:

“FIGS. 7A-B: Production of PMN and PCN by S. platensis MA7237,
SB12001, and SB12002” (Spec. 9, ll. 3-4).

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6. Table 1 of the Specification is reproduced below:

(Spec. 46, ll. 1-35).
7. The Specification teaches that in “certain embodiments of this
invention, the platensimycin biosynthetic gene cluster (FIG. 3 and SEQ ID
NO:l) will be introduced into a vector or vectors” (Spec. 17, ll. 17-18).
Principles of Law
During prosecution of an application before the USPTO, the
threshold standard of ambiguity for indefiniteness is lower than it might
be during litigation of an issued patent. Ex parte Miyazaki, 89 USPQ2d
1207, 1212 (BPAI 2008) (precedential). “[I]f a claim is amenable to two
or more plausible claim constructions, the USPTO is justified in
requiring the applicant to more precisely define the metes and bounds of
the claimed invention by holding the claim . . . indefinite.” Id. at 1211.
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Analysis
Claim 1
Claim 1 does not recite any specific boundaries, structure, or
requirements for the polynucleotide which encodes “a plurality of genes
from the Streptomyces platensis platencin/platensimycin biosynthetic gene
cluster” (Claim 1). Thus, in order to interpret the metes and bounds of this
claim, we look to the Specification. The Specification states that “[p]ending
experimental confirmation, the boundaries of the PTM/PTN gene cluster
have been assigned to be at ORF7 (upstream) and ORF35 (downstream),
respectively, on the basis of bioinformatics analysis” (Spec. 44, ll. 26-28; FF
3). However, Table 1 of the Specification states that orf1-orf5 are “ORFs
beyond the upstream boundary” and that orf35-orf36 are “ORFs beyond the
downstream boundary.”
Thus, even within the Specification itself there are several possible
interpretations of the components of the phrase “platencin/platensimycin
biosynthetic gene cluster.” A first interpretation would place the boundaries
of the cluster at the ends of ORF7 and ORF35, including both of these ORFs
in the cluster, consistent with the teaching that these are the upstream and
downstream boundaries (FF 3). A second interpretation, consistent with
Table 1, would place the cluster boundaries between ORF6 and ORF 34,
including both of these ORFs in the cluster, since Table I states that ORFs 1-
5 and ORFs 35-36 are beyond the upstream and downstream boundaries,
respectively (FF 6).
Even these two alternatives do not exhaust the possible alternative
interpretations. The Specification teaches that in “certain embodiments of
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this invention, the platensimycin biosynthetic gene cluster (FIG. 3 and SEQ
ID NO:l) will be introduced into a vector or vectors” (Spec. 17, ll. 17-18; FF
7). This suggests that the gene cluster is composed of SEQ ID NO: 1.
However, the Specification also teaches that “the inventors localized a 70-kb
DNA region . . . that harbors the PTM/PTN biosynthetic gene cluster . . .
They have sequenced 40-kb of this locus, revealing 36 open reading frames”
(Spec. 44, ll. 23-26; FF 2). In the absence of experimental confirmation (FF
3), the Specification here implies that the cluster may include additional
sequences in the 30 kb not sequenced and not part of SEQ ID NO: 1, since
no information is available regarding this 30 kb portion of the 70-kb region.
Thus, two further interpretations are that the “platencin/platensimycin
biosynthetic gene cluster” comprises either the ~40 kb of SEQ ID NO: 1 or
the entire 70-kb cloned region.
We therefore conclude that claim 1 is subject to multiple, inconsistent
interpretations and that the metes and bounds of claim 1 would have been
indefinite when interpreted by the skilled artisan in light of the Specification.
Claim 7
Claim 7 states that the “polynucleotide comprises 500 or more bases
of segment A, B, C or D of FIG. 7” (Claim 7). However, as the Examiner
notes, figure 7 does not teach any segments whatsoever, much less segment
A, B, C or D (FF 5). We conclude that claim 7 is indefinite.
Claims 3, 6, 8, 16, and 18
Each of claims 3, 6, 8, 16, and 18 are drawn to genes either “encoded
by SEQ ID NO: 1” or which comprise portions of SEQ ID NO: 1. We
separately address these claims because the indefiniteness issue in claim 1
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does not impact these claims which are limited to sequences found in SEQ
ID NO: 1. The artisan would have recognized the metes and bounds of SEQ
ID NO: 1, including subportions including 5000 or more bases of SEQ ID
NO: 1.
We therefore conclude that claims 3, 6, 8, 16, and 18 are definite.
Conclusion of Law2
The evidence of record supports the Examiner’s conclusion that
claims 1, 2, 4, 5, 7, 10, 14, 15, 17, 20, 22, and 23 are indefinite.
The evidence of record does not support the Examiner’s conclusion
that claims 3, 6, 8, 16, and 18 are indefinite.
A. 35 U.S.C. § 112, first paragraph, written description
The Examiner finds that “specification does not place any structure,
chemical or functional limitations on the variants of proteins or genes. The
recitation of ‘platencin/platensimycin biosynthetic gene cluster’ does not
convey a common structure” (Ans. 8). The Examiner finds that “[n]o
common structural attributes identify the members of the genus. The general
knowledge and level of skill in the art do not supplement the omitted
description, because specific, not general guidance is needed” (id. at 9). The
Examiner finds that the “genus of polypeptides with the claimed function is
substantial and highly variant because the polypeptides do not have a
common structure and function” (id.).
The Examiner, focusing on ORF14 in the gene cluster, finds that the
“specification does not provide an identification of the open reading frame

2 We also note that the “kD” in claim 2 may be a typo, and that kB
may be intended.
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within SEQ ID NO:1 corresponding to orf14, much less the structural
elements that define a functional bacterial ‘gene’ comprising such” (Ans. 7).
The Examiner finds that “the specification teaches that Orf14 cannot be a
prenyltransferase because it lacks the characteristic active site residues,
despite homology thereto” (id.). The Examiner finds that “Appellants
propose that Orf14 could potentially provide PTM and PTN self-resistance
by drug sequestration. However, Appellants provide no experimental
evidence of any biological activity of the alleged undefined orf14 and
indicate that such needs to be experimentally confirmed” (id.).
The issue with respect to this rejection is: Does the evidence of record
support the Examiner’s conclusion that the claims fail to comply with the
written description requirement?
Principles of Law
“An adequate written description of a DNA . . . ‘requires a precise
definition, such as by structure, formula, chemical name, or physical
properties,’ not a mere wish or plan for obtaining the claimed chemical
invention.” Regents of the University of California v. Eli Lilly & Co., 119
F.3d 1559, 1566 (Fed. Cir. 1997).
“[I]t is the specification itself that must demonstrate possession. And
while the description requirement does not demand any particular form of
disclosure, ... or that the specification recite the claimed invention in haec
verba, a description that merely renders the invention obvious does not
satisfy the requirement” Ariad Pharmaceuticals, Inc. v. Eli Lilly and Co.,
598 F.3d 1336, 1352 (Fed. Cir. 2010).

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Analysis
Claim 1
Appellants contend that the “examiner confuses the matter in the final
office action by arguing that the claims ‘encompass’ orf14” (App. Br. 4).
Appellants contend that “the extra three bases of the ORF identified merely
encode the stop codon and would therefore not add a 312th residue to the
sequence. Thus, in fact, the examiner has proven that orf14 can easily be
identified using a simple, publicly available translation tool” (id. at 7).
On this point, we agree with Appellants. While the Examiner may or
may not be correct that Table 1 is in error regarding the number of amino
acids in orf14, given the information in Table 1 identifying orf14 as the
homolog of Neut_1128(YP_747348), the ordinary artisan, using the ordinary
tools available, would have been reasonably able to identify the associated
open reading frame (FF 6).
However, this does not address the Examiner’s larger concern
regarding claim 1 that the “recitation of ‘platencin/platensimycin
biosynthetic gene cluster’ does not convey a common structure” (Ans. 8).
While the Specification teaches the 39,194 nucleotides disclosed by
the formula of SEQ ID NO: 1, the Specification does not teach the
remaining 30,000 or so nucleotides of the “70-kb DNA region from S.
platensis MA7327 harboring the PTM/PTN biosynthetic locus . . . with
boundaries predicted on the basis of bioinformatics analysis” (Spec. 8, ll. 1-
4; FF 1). As discussed in the indefiniteness rejection above, the
Specification provides several interpretations of “the Streptomyces platensis
platencin/platensimycin biosynthetic gene cluster”.
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Claim 1 does not expressly limit the phrase “Streptomyces platensis
platencin/platensimycin biosynthetic gene cluster” to SEQ ID NO: 1, but
may be composed of either the orfs 7-35, orfs 6-34, all of SEQ ID NO: 1, the
entire 70-kb cloned region, or possibly other iterations (FF 1-7). Therefore,
for the regions of the gene cluster which have not been sequenced, there is
no structure, formula, chemical name, or physical properties to support the
generic claim to the entire cluster. Lilly, 119 F.3d at 1566. In addition,
while it may have been obvious to obtain the remaining sequence or
experimentally demonstrate which genes properly belong in the gene cluster
and which genes do not, the Specification does not clearly delineate the gene
cluster in a way demonstrating possession. Ariad, 598 F.3d at 1352.
Claims 3, 6, 8, 16, and 18
Each of claims 3, 6, 8, 16, and 18 are drawn to genes either “encoded
by SEQ ID NO: 1” or which comprise portions of SEQ ID NO: 1. We
separately address these claims because the description issue in claim 1 does
not impact these claims which are limited to sequences found in SEQ ID
NO: 1. The artisan would have recognized that SEQ ID NO: 1 provided a
formula which provides descriptive support for these claims.
Conclusion of Law
The evidence of record supports the Examiner’s conclusion that
claims 1, 2, 4, 5, 7, 10, 14, 15, 17, 20, 22 and 23 fail to comply with the
written description requirement.
The evidence of record does not support the Examiner’s conclusion
that claims 3, 6, 8, 16, and 18 fail to comply with the written description
requirement.
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SUMMARY
In summary, we affirm the rejection of claims 1 and 14 under 35
U.S.C. § 112, second paragraph as indefinite. Pursuant to 37 C.F.R. §
41.37(c)(l)(vii), we also affirm the rejection of claims 2, 4, 5, 7, 10, 14, 15,
17, 20, 22, and 23 as these claims were not argued separately.
We reverse the rejection of claims 3, 6, 8, 16, and 18 under 35 U.S.C.
§ 112, second paragraph as indefinite.
We affirm the rejection of claims 1 and 14 under 35 U.S.C. § 112,
first paragraph, as failing to comply with the written description
requirement. Pursuant to 37 C.F.R. § 41.37(c)(l)(vii), we also affirm the
rejection of claims 2, 4, 5, 7, 10, 14, 15, 17, 20, 22, and 23 as these claims
were not argued separately.
We reverse the rejection of claims 3, 6, 8, 16, and 18 under 35 U.S.C.
§ 112, first paragraph, as failing to comply with the written description
requirement.
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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