Ex Parte Baum et al

Patent Trial and Appeal Board

Jun 26, 2013

12109122 (P.T.A.B. Jun. 26, 2013)

UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte JAMES A. BAUM, STANISLAW FLASINSKI,
GREGORY R. HECK, STEPHEN R. PENN,
UMA RAO SUKURU, and XIAOHONG SHI
____________

Appeal 2012-002236
Application 12/109,122
Technology Center 1600
____________

Before TONI R. SCHEINER, DEMETRA J. MILLS, and ULRIKE W.
JENKS, Administrative Patent Judges.

ULRIKE W. JENKS, Administrative Patent Judge

DECISION ON APPEAL
This is an appeal1 under 35 U.S.C. § 134 involving claims directed to
recombinant DNA comprising an inhibitory insect protein. The Patent
Examiner has rejected the claims as lacking adequate written description.
We have jurisdiction under 35 U.S.C. § 6(b). We affirm.

1 Appellants state that the Real Party-In-Interest is MONSANTO
TECHNOLOGY LLC (App. Br. 2).
Appeal 2012-002236
Application 12/109,122

2
STATEMENT OF THE CASE
The Specification disclosed a polynucleotide sequence encoding
“Bacillus thuringiensis crystal protein exhibiting insect inhibitory
activity . . . transgenic plants and microorganisms that contain the
polynucleotides, isolated peptides derived from the crystal protein, and
antibodies directed against the crystal protein are also provided.” (Spec.
Abstract, 112 ¶ 00319.) The invention described in the Specification further
“provides for isolated proteins, wherein the isolated protein comprises a
polypeptide sequence of at least 9 amino acids in length that is contained
within SEQ ID NO:5. The isolated protein can have a polypeptide sequence
at least 12, 16, 32 or 250 amino acids in length.” (Spec. ¶ 0032.)
Claims 1, 5-12, and 14-20 are on appeal,2 and can be found in the
Claims Appendix of the Appeal Brief (App. Br. 24-26). Claims 1, 15, and
16 are independent claims. Claims 1 and 12 are illustrative of the claims on
appeal, and read as follows (emphasis added):
1. A recombinant DNA comprising a promoter that functions in a
plant cell, a polynucleotide which encodes an insect inhibitory
protein, wherein said insect inhibitory protein comprises a polypeptide
sequence that has at least about 95% sequence identity to the
corresponding insect inhibitory polypeptide sequence contained
within SEQ ID NO:5, and a 3’ non-translated region containing a
polyadenylation signal, wherein said promoter, said polynucleotide,
and said 3’ nontranslated region are operably linked.
12. The recombinant DNA of claim 1, wherein said corresponding
insect inhibitory polypeptide sequence comprises a peptide sequence
of at least 250 amino acid residues.

2 Claims 2-4 and 13 are allowed. (Ans. 3.)
Appeal 2012-002236
Application 12/109,122

3
The following ground of rejection is before us for review:
The Examiner has rejected claims 1, 5-12, and 14-20 under 35 U.S.C.
§ 112, first paragraph as failing to comply with the written description
requirement.

I. The Issue
The Examiner takes the position that:
Applicant has not described the necessary and sufficient
structural features of an insect inhibitory protein with 95%
identity to SEQ ID NO:5 and has thus not described nucleic
acids that encode them. Further, Applicant has not described
the necessary and sufficient structural features for inhibitory
activity toward Hemipterans, Heteropterans, Leptinotarsans, or
Homopterans.
(Ans. 6.) “[T]he QQSQT and QPVLVPP motifs may provide some small
portion of the necessary description, [however] there are not enough of them
to describe the full scope of claimed sequences.” (Ans. 6.) “[T]he claims
are not drawn to nucleic acids encoding proteins having no claimed function
and 95% identity to SEQ ID NO:5. They are drawn to nucleic acids
encoding proteins with an insect inhibitory function; dependent claims
specify the order to which these insect belong.” (Ans. 8.)
According to the Examiner, determining:
[P]ore formation [alone] is not sufficient for toxicity; the toxin
must first bind to receptors on gut cells before pores can be
formed. The specification does not teach the amino acids
responsible for binding to gut cell receptors in Hemipterans,
Heteropterans, Leptinotarsans, and/or Homopterans. . . .
a Dipteran toxin does not describe a Hemipteran, Heteropteran,
Leptinotarsan, and/or Homopteran inhibitor.
(Ans. 8.)
Appeal 2012-002236
Application 12/109,122

4
The issue before us is: Does the evidence of record support the
Examiner’s conclusion that the disclosure of the Specification fails to
provide descriptive support for the claims?

Findings of Fact
FF 1. The Specification disclosed that SEQ ID NO: 5 is a protein
sequence comprising 309 amino acids. (Spec., see Sequence Listing 2-3.)
“[T]he isolated protein comprises a polypeptide sequence of at least 9 amino
acids in length that is contained within SEQ ID NO:5. The isolated protein
can have a polypeptide sequence at least 12, 16, 32 or 250 amino acids in
length.” (Spec. ¶ 0032.)
FF 2. The Specification disclosed that “[a]lthough the TIC807 protein
shares significant sequence identity to the Cry51Aal protein, the TIC807
protein surprisingly displayed no significant level of activity when fed to
certain lepidopteran insects.” (Spec. 107, ¶ 00315.)

Principle of Law
The test for determining whether a Specification is sufficient to
support a particular claim “is whether the disclosure of the application relied
upon ‘reasonably conveys to the artisan that the inventor had possession at
that time of the later claimed subject matter.’” Ralston Purina Co. v. Far-
Mar-Co, Inc., 772 F.2d 1570, 1575 (Fed. Cir. 1985) (quoting In re Kaslow,
707 F.2d 1366, 1375 (Fed. Cir. 1983)).
When an Applicant claims a class, the Applicant “must describe that
class in order to meet the description requirement of the statute.” In re
Lukach, 442 F.2d 967, 968 (CCPA 1971).
Appeal 2012-002236
Application 12/109,122

5
Moreover, as our reviewing court has more recently pointed out, the
written description requirement “ensures that when a patent claims a genus
by its function or result, the specification recites sufficient materials to
accomplish that function - a problem that is particularly acute in the
biological arts.” Ariad Pharms., Inc. v. Eli Lilly and Co., 598 F.3d 1336,
1352-53 (Fed. Cir. 2010) (en banc).
In Ariad, the court found that the written description “doctrine never
created a heightened requirement to provide a nucleotide-by-nucleotide
recitation of the entire genus of claimed genetic material; it has always
expressly permitted the disclosure of structural features common to the
members of the genus.” Id. at 1352.
However, “merely drawing a fence around the outer limits of a
purported genus is not an adequate substitute for describing a variety of
materials constituting the genus and showing that one has invented a genus
and not just a species.” Id. at 1350. “[W]hile 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.” Id.
at 1352 (citations omitted).

Analysis
Appellants Specification does not specifically define the term
“contained within SEQ ID NO: 5” as recited in claims 1, 15, and 16.
However, the invention described in the Specification further provides for
isolated proteins, wherein the isolated protein comprises a polypeptide
sequence of at least 9 amino acids in length that is contained within SEQ ID
Appeal 2012-002236
Application 12/109,122

6
NO:5. The isolated protein can have a polypeptide sequence at least 12, 16,
32 or 250 amino acids in length. (Spec. ¶ 0032.) SEQ ID NO:5 contains 309
amino acids (FF 1).
In addition, Appellants’ dependent claim 12, limits the polypeptide
sequence of claim 1 to at least 250 amino acid residues. Thus, under the
doctrine of claim differentiation, we find that the scope of the term
“contained within SEQ ID NO: 5” as it appears within claim 1 reads on a
range of polypeptide structures that is broader than merely changing 5% of
the amino acids found in SEQ ID NO: 5. Specifically, claim 1 encompasses
structures ranging from 250 to 309 amino acids, and when read in view of
the Specification claim 1 can potentially also include polypeptides of at least
9, 12, 16, or 32 amino acids in length.
The doctrine of claim differentiation creates a presumption that each
claim in a patent has a different scope. See Comark Communications, Inc. v.
Harris Corp., 156 F.3d 1182, 1187 (Fed. Cir. 1998). “There is presumed to
be a difference in meaning and scope when different words and phrases are
used on separate claims. To the extent that the absence of such difference in
meaning and scope would make a claim superfluous, the doctrine of claim
differentiation states that the difference between claims is significant.” Id. at
1187. With respect to dependent claims, 35 U.S.C. § 112, fourth paragraph,
should be followed. This paragraph states that “a claim in a dependent form
shall be construed to incorporate by reference all the limitations of the claim
to which it refers” and requires the dependent claim to further limit the
subject matter claimed.
Claim 12 encompasses polypeptide sequences that contain only 250
amino acids out of a total of 309 amino acids found in SEQ ID NO: 5. In
Appeal 2012-002236
Application 12/109,122

7
order to comply with 35 U.S.C. § 112, fourth paragraph, the limitation of
“corresponding insect inhibitory polypeptide sequenced contained within
SEQ ID NO: 5” means that the insect inhibitory polypeptide comprises at
least 250 amino acids. Claim 1, however, is much broader because it
includes structures that have up to 309 amino acids. In addition, the
sequences in these structures can also have up to 5% variation in the amino
acids as compared to SEQ ID NO: 5.
The question before us is does the Specification provide descriptive
support for insect inhibitory polypeptide sequences that range from at least
9-309 amino acids, and that contain 95% sequence identity to SEQ ID
NO: 5?
Appellants contend that the Specification as originally filed disclosed
that “[t]he TIC807 gene insert on plasmid pIC17042 was sequenced. The
deduced coding region (presented as SEQ ID NO:4) encodes a protein of
309 amino acids and is presented as SEQ ID NO:5.” (App. Br. 12.)
The written description requirement can be met by disclosing
“complete or partial structure, other physical and/or chemical properties,
functional characteristics when coupled with a known or disclosed
correlation between function and structure, or some combination of such
characteristics.” Enzo Biochem, Inc. v. Gen-Probe Inc., 323 F.3d 956, 964,
(Fed. Cir. 2002).
In this case, the Specification references a complete sequence SEQ ID
NO: 4 encoding the protein of SEQ ID NO: 5 as the sole species in the very
large genus claimed. However, the Specification does not describe any of
the structural features of SEQ ID NO: 5 which give rise to the insect
inhibitory function. In fact, the Specification fails to identify which region,
Appeal 2012-002236
Application 12/109,122

8
or regions, within the 309 amino acid protein is involved in the inhibitory
activity which requires binding to the receptor before pore formation. There
has been no disclosure of what correlates this structure with the function of
the insect inhibitory activity. The Specification also does not disclose which
polypeptide structures having at least 9-250 amino acids have the insect
inhibitory function.
Appellants contend that the Specification in paragraph 0175 disclosed
that “[i]t is further anticipated that comparisons between TIC807 and other
related proteins may permit extrapolation of protein domains that contribute
to the insecticidal activity of TIC807 proteins.” (App. Br. 13.)
We find that paragraph 0175 of the Specification discloses a laundry
list of experiments that may be carried out to someday determine the
particular structures or potential domains of TIC807 (SEQ ID NO: 5) that
are involved and necessary for the insect inhibitory activity. Presenting a
wish list and instructions on how you may proceed to go about studying the
crystal protein is not the same as describing it in such a way that an ordinary
artisan would be apprised of the structure of the compound by merely
looking at the sequence.
Appellants point out that “SEQ ID NO:5 ‘display[s] complete
sequence conservation over short stretches of contiguous amino acid
sequences of up to seven residues in length’ such as a QQSQT motif and a
QPVLVPP motif.” (App. Br. 15.)
We are not persuaded. What is missing from the Specification is any
indication that QQSQT motif and a QPVLVPP are necessary for
maintaining the insect inhibitory function of protein of SEQ ID NO: 5. All
that is shown is that these two very short amino acid sequence stretches are
Appeal 2012-002236
Application 12/109,122

9
found in another insect inhibitory protein Cry15Aa1 (Spec. Fig. 1).
However, the Specification does not provide a correlation between these
structures and the insect inhibitory activity.
Appellants contend that the present Specification and claims mirror
example 11B of the Written Description Training Guidelines, Revision 1, of
March 25, 2008. We do not find Appellants argument convincing.
Written Description example 11B, claim 2 recites “An isolated nucleic
acid that encodes a polypeptide with at least 85% amino acid sequence
identity to SEQ ID NO: 2; wherein the polypeptide has activity Y.” In
example 11B, “the [example 11B] specification identifies two domains
responsible for activity Y, i.e., a binding domain and catalytic domain. The
example 11B specification also predicts that conservative mutations in these
domains will result in a protein having activity Y.” A correlation was found
to exist between the function of the claimed protein and the structure of the
disclosed binding and catalytic domains in written description guideline
example 11B. No such disclosure is present in the instant Specification
regarding domains of the polypeptide responsible for insect inhibitory
activity, and no structure/function correlation is present in the instant case.
Thus, example 11B does not mirror the facts in the present case.
The Examiner finds that “the instant specification does not describe
the domains responsible for activity. The specification provides no
description of domains responsible for Hemipteran, Heteropteran,
Leptinotarsan, and/or Homopteran inhibitor activity. Thus, Example 11b
Written Description Guidelines supports a finding that the claims are not
described.” (Ans. 10.)
Appeal 2012-002236
Application 12/109,122

10
We agree with the Examiner’s position that the disclosure of a laundry
list of comparisons and extrapolations that may be performed and could
possibly provide information with regard to teasing out which domains are
responsible for activity against for Hemipteran, Heteropteran, Leptinotarsan,
and/or Homopteran does not meet the description requirement. Appellants’
reliance on Fig. 1 of the Specification showing a sequence comparison
between SEQ ID NO: 5 and Cry15Aa1 as providing regions of conservation
by showing what amino acids are conserved between the two proteins
provides no information with regards to which domains are important for the
activity against Hemipteran, Heteropteran, Leptinotarsan, and/or
Homopteran. But for the two short sequences QQSQT and QPVLVPP the
remaining conserved amino acids are randomly distributed along the entire
length of the protein. This does not provide information with regard to
defining domains that are important for insect inhibitory activity, more
structural information is required to describe a genus. See Ariad at 1350.
Because the claims encompass polypeptide sequences “contained in”
SEQ ID NO:5 which may have as few as 9 amino acids, and because the
Specification does not describe the regions of the polypeptide providing for
the claimed function, we find that the preponderance of the evidence of
record support the Examiner’s position that the Specification does not
provide sufficient descriptive support for the claims. We thus, affirm the
rejection of claim 1 under 35 U.S.C. § 112, first paragraph as lacking
descriptive support. As claims 5-12, and 14-20 have not been argued
separately, they fall together with claim 1. 37 C.F.R. § 41.37(c)(1)(vii).

Appeal 2012-002236
Application 12/109,122

11
SUMMARY
We affirm the rejection of claims 1, 5-12, and 14-20 under 35 U.S.C.
§ 112, first paragraph as failing to comply with the written description
requirement.

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

lp