Ex Parte Haselbeck et al

Patent Trial and Appeal Board

Sep 20, 2012

09815242 (P.T.A.B. Sep. 20, 2012)

UNITED STATES PATENT AND TRADEMARK OFFICE
UNITED STATES DEPARTMENT OF COMMERCE
United States Patent and Trademark Office
Address: COMMISSIONER FOR PATENTS
P.O. Box 1450
Alexandria, Virginia 22313-1450
www.uspto.gov
APPLICATION NO. FILING DATE FIRST NAMED INVENTOR ATTORNEY DOCKET NO. CONFIRMATION NO.
09/815,242 03/21/2001 Robert Haselbeck ELITRA.011A 7191
210 7590 09/21/2012
MERCK
P O BOX 2000
RAHWAY, NJ 07065-0907
EXAMINER
SCHNIZER, RICHARD A
ART UNIT PAPER NUMBER
1635
MAIL DATE DELIVERY MODE
09/21/2012 PAPER
Please find below and/or attached an Office communication concerning this application or proceeding.
The time period for reply, if any, is set in the attached communication.
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
__________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
__________

Ex parte ROBERT HASELBECK, KARI L. OHLSEN,
JUDITH W. ZYSKIND, DANIEL WALL, JOHN D. TRAWICK,
GRANT J. CARR, ROBERT T. YAMAMOTO, and H. HOWARD XU
__________

Appeal 2012-002535
Application 09/815,242
Technology Center 1600
__________

Before LORA M. GREEN, FRANCISCO C. PRATS, and
JACQUELINE WRIGHT BONILLA, Administrative Patent Judges.

GREEN, Administrative Patent Judge.

DECISION ON APPEAL
This is a decision on appeal under 35 U.S.C. § 134 from the
Examiner‟s rejection of claims 12, 31, 45-69, 77-86, 89-96, 100, and 101.
1

We have jurisdiction under 35 U.S.C. § 6(b).

1
Claims 87 and 104 stand as objected to as depending from rejected claims
(App. Br. 5). In addition, the Examiner has not included claim 103 in the
statement of the rejection (App. Br. 5, see Ans. 5).
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STATEMENT OF THE CASE
Claims 12, 31, and 100 are the independent claims on appeal, and read
as follows:
12. A method for screening a candidate compound for the ability to
reduce cellular proliferation comprising the steps of:
(a) providing a sublethal level of an antisense nucleic acid comprising
SEQ ID NO: 1463, thereby producing a sensitized cell, provided that cell is
a prokaryotic organism;
(b) contacting said sensitized cell with a compound; and
(c) determining the degree to which said compound inhibits
proliferation of said sensitized cell relative to a nonsensitized cell.

31. A method for screening a candidate compound for the ability to
reduce cellular proliferation comprising:
(a) providing a sublethal level of an antisense nucleic acid
complementary to at least a portion of a nucleic acid encoding a gene
product in a cell to reduce the activity or amount of said gene product in said
cell, thereby producing a sensitized cell, provided that said cell is a
prokaryotic organism and wherein said gene product is either:
i) encoded by a nucleic acid which hybridizes to SEQ ID NO:
1463 under stringent conditions, wherein the stringent conditions are
hybridization in 6x SSC at about 45°C followed by one or more
washes in 0.lx SSC/O.2% SDS at about 68°C; or
ii) encoded by a nucleic acid which hybridizes SEQ ID NO:
1463 under moderate conditions, wherein the moderate conditions are
hybridization in 6x SSC at about 45°C followed by one or more
washes in O.2x SSC/O.1 % SDS at about 42-65°C;
(b) contacting said sensitized cell with a compound; and
(c) measuring the growth of said sensitized cell, wherein a decrease in
growth of said sensitized cell relative to a nonsensitized cell indicates that
the compound reduces cellular proliferation.

100. A method for screening a candidate compound for the ability to reduce
cellular proliferation comprising the steps of:
(a) providing a sublethal level of an antisense nucleic acid, wherein
said antisense nucleic acid reduces the activity or amount of SEQ ID NO:
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12600, thereby producing a sensitized cell, provided that said sensitized cell
is a prokaryotic organism and whereby the antisense nucleic acid binds to a
nucleic acid that encodes SEQ ID NO: 12600;
(b) contacting said sensitized cell with a compound; and
(c) measuring proliferation of said sensitized cell,
wherein a decrease in proliferation of said sensitized cell relative to a
nonsensitized cell indicates that the compound reduces cellular proliferation.

The following ground of rejection is before us for review:
Claims 12, 31, 45-69, 77-86, 89-96, 100, and 101 stand rejected under
35 U.S.C. § 103(a) as being rendered obvious by the combination of Zhang,
2

Zalacain,
3
Fritz,
4
and Ji.
5

We affirm-in-part.

ISSUE (Effective Filing Date)
Are the claims on appeal entitled to an effective filing date that
predates the publication date of the Zhang reference?

Findings of Fact
FF1. The Examiner finds that the “effective filing date of the rejected
claims is considered to be after the publication date” of Zhang, relied upon
by the Examiner in the obviousness rejection (Ans. 5).

2
Zhang et al., Regulated gene expression in Staphylococcus aureus for
identifying conditional lethal phenotypes and antibiotic mode of action, 255
GENE 297-305 (2000).
3
Zalacain et al., WO 01/23418 A1, published Apr. 5, 2001.
4
Fritz et al., US 6,627,747 B1, issued Sep. 30, 2003.
5
Ji et al., Regulated Antisense RNA Eliminates Alpha-Toxin Virulence in
Staphylococcus aureus Infection, 181 J. BACTERIOLOGY 6585-6590 (1999).
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FF2. According to the Examiner, the priority applications filed before the
publication date of the Zhang reference, such as 60/191,078, filed March 21,
2000, do not provide “adequate support in the manner provided by the first
paragraph of 35 U.S.C. 112 for the subject matter of the rejected claims” (id.
at 5-6).
FF3. The Examiner states:
[T]he rejected claims are drawn to antisense sequences that:
- comprise SEQ ID NO: 1463;
- are capable of hybridizing to the complement of SEQ
ID NO: 1463; or
- reduce the activity or amount of SEQ ID NO: 12600,
but the disclosures of the priority documents do not provide an
adequate written description for these genuses.

(Id. at 6.)
FF4. SEQ ID NO: 1463 is a 387 residue polynucleotide that is identical to a
portion of the antisense strand of the Staphylococcus aureus gene yphC (id.).
FF5. SEQ ID NO: 12600 is the amino acid sequence of the full length yphC
protein (id.). The entire yphC open reading frame comprises 1311
nucleotides and encodes a polypeptide of 436 amino acids (id.).
FF6. SEQ ID NO: 77 of US Provisional Application No. 60/191,078
corresponds to SEQ ID NO. 1463 of US Serial No. 09/815,242 (App. Br.
12).
FF7. “SEQ ID NO:1463 of US Serial No. 09/815,242 is the reverse
compliment of nucleotides 122-508 of SEQ ID NO:4228 of US Serial No.
09/815,242” (id. at 13).

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FF8. According to the Examiner:
Because it was known that instant SEQ ID NO: 1463 was
a fragment of the full length yphC gene, one of skill in the art at
the time of the invention, when reading the instant claims,
would have considered the instant claim limitation “an
antisense nucleic acid comprising SEQ ID NO: 1463” to
embrace antisense molecules complementary to the entire
length of the yphC gene and RNA. However, there is no
evidence of record that any of the priority documents disclosed
any molecule that comprises both SEQ ID NO: 1463 and any
other sequence known to flank SEQ ID NO: 1463 on the
antisense strand of the yphC gene. To the best knowledge of
the Examiner, the only sequence disclosed in the priority
documents that comprises SEQ ID NO: 1463 is SEQ ID NO:
1463 itself. There is no evidence of record that Appellant was
in possession, at the time the priority documents were filed, of
any of the naturally occurring flanking sequences of instant
SEQ ID NO: 1463 that the instant claims fairly read on, e.g. the
full length sequence of yphC.

(Ans. 6-7.)

Principles of Law
“In order to gain the benefit of the filing date of an earlier application
under 35 U.S.C. § 120, each application in the chain leading back to the
earlier application must comply with the written description requirement of
35 U.S.C. § 112.” Lockwood v. American Airlines, Inc., 107 F.3d 1565, 1571
(Fed. Cir. 1997). “One shows that one is „in possession‟ of the invention by
describing the invention, with all its claimed limitations, not that which
makes it obvious. Id. at 1572.

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Analysis
Appellants argue that US Provision Application No. 60/191,078
discloses “an assay to identify compounds that decrease cellular proliferation
using sensitized cells (see page 6, line 22 to page 8, line 4 and Example 8B
of US Provisional Application No. 60/191,078)” (App. Br. 12). Appellants
also assert that SEQ ID NO: 77 of that provisional application is identical to
instant SEQ ID NO: 1463 (id.).
Appellants further assert that “[a]lthough the sequences of the yphC
gene or its encoded gene product are not specifically recited in the Sequence
Listing of US Provisional Application No. 60/191,078, their identity could
have been discovered by one of skill in the art using techniques known in the
art” (id.). Appellants argue that the methods for doing so were in fact
disclosed in US Provision Application No. 60/191,078 (id. at 12-13 (citing
US Provision Application No. 60/191,078, p. 21, ll. 9-21 and Example 3)).
Appellants also argue that “SEQ ID NO:1463 of US Serial No.
09/815,242 is the reverse compliment of nucleotides 122-508 of SEQ ID
NO:4228 of US Serial No. 09/815,242” (Reply Br. 3). According to
Appellants:
the antisense nucleic acid would hybridize to the yphC gene
and be able to be used to identify the yphC gene - a technique
used at the time of filing the earliest provisional application
(i.e., March 21,2000). Once the gene sequence was known, one
skilled in the art could easily determine the amino acid
sequence of the encoded gene product using techniques known
in the art. In fact, Zalacain et al. discloses the use of routine
cloning methods known at the time to clone yphC (see Example
1).

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(Id. at 3.)
We initially note that the Examiner only appears to be addressing
independent claim 12. As to that claim, both the Examiner and Appellants
agree that SEQ ID NO: 1463 was disclosed in 60/191,078, filed March 21,
2000, as SEQ ID NO: 77 (see, e.g. FF6). The Examiner‟s position appears
to be that because claim 12 recites “an antisense nucleic acid comprising
SEQ ID NO: 1463,” the ordinary artisan would understand the phrase to
include an antisense molecules complementary to the entire length of the
yphC gene. The Examiner, however, points to no authority that supports
that an applicant must describe all material that is encompassed by the use of
the commonly used transitional phrase “comprising” in a claim.
6
We thus
find that independent claim 12 is entitled to the March 21, 2000 filing date
of 60/191,078, and thus Zhang cannot be applied as a reference as to that
claim, nor the claims dependent thereon.
7

We now turn to the other independent claims. Claim 31 also recites
“SEQ ID NO. 1463.” While claim 31 also recites specific hybridization
conditions, the Examiner‟s findings that Appellants‟ claims are not entitled
to an earlier effective date are all based on the use of the transitional phrase
“comprising,” as discussed above. Thus, for the same reasons set forth with
respect to claim 12, we find that independent claim 31 is entitled to the

6
In that regard, we direct the Examiner‟s attention to Example 4 of the
“Written Description Guidelines training Materials” (2008), which may be
found at http://www.uspto.gov/web/menu/written.pdf.
7
As the Examiner did not address the dependent claims in determining the
effective filing date, we decline to address the dependent claims for the first
time on appeal.
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March 21, 2000 filing date of provisional application 60/191,078, and thus
Zhang cannot be applied as a reference as to that claim, nor the claims
dependent thereon.
Independent claim 100 stands on different footing. Claim 100 recites
“providing a sublethal level of an antisense nucleic acid, wherein said
antisense nucleic acid reduces the activity or amount of SEQ ID NO:
12600.” As found by the Examiner, “SEQ ID NO: 12600 is the amino acid
sequence of the full length yphC protein” (FF5), and is not found in the
60/191,078 provisional application. Appellants argue instead that the
60/191,078 provisional application enables methods of determining the full
length sequence. That is, in essence, Appellants are arguing that SEQ ID
NO: 12600 is rendered obvious by provisional application 60/191,078. In
order to receive benefit, however, the provisional application must also
describe the claimed subject matter as required by the written description
requirement of 35 U.S.C. § 112, first paragraph. Here, Appellants have not
provided scientific reasoning or evidence that the description of the partial
sequence of SEQ ID NO: 1463 (SEQ ID NO: 77 of the 60/191,078
provisional application) also provides written description of the full
sequence of the full length yphC protein, that is SEQ ID NO: 12600. Thus,
as to claim 100, we agree with the Examiner that claim 100 is not entitled to
an effective filing date of the 60/191,078 provisional application, and thus
Zhang is available as a reference as to that claim.

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Conclusion of Law
We find that Zhang is not available as a reference as to independent
claims 12 and 31, and the claims dependent thereon. As the only rejection
applied as to those claims is the combination of Zhang, Zalacain, Fritz, and
Ji, claims 12, 31, 45-69, 77-86, 89-96, and 101 are free of rejection.
Thus, the only claim that is subject to the obviousness rejection is
claim 100.

ISSUE (Obviousness)
Has the Examiner established by a preponderance of the evidence that
claim 100 is rendered obvious by the combination of Zhang, Zalacain, Fritz,
and Ji?

FINDINGS OF FACT
FF9. We adopt the Examiner‟s findings of fact, conclusions of law, and
response to argument as to the obviousness rejection as our own.

ANALYSIS
Appellants argue that Zalacain and Fritz “disclose identifying
potential anti-bacterials that target yphC,” but the claimed invention is
drawn to the use of sensitized cells to identify compounds that can reduce
cellular proliferation (App. Br. 14).
Zhang, Appellants assert, “discloses a method to discern the
molecular target of a known antibiotic” (id. at 15; see also id. at 16).
Appellants argue that there “is no mention of using the system for targeted
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drug discovery” (id. at 16). Appellants thus assert that the Examiner has
used impermissible hindsight to combine the references to arrive at the
claimed invention (id.).
Appellants‟ arguments have been carefully considered, but are not
found to be convincing.
Our mandate is to give claims their broadest reasonable interpretation
consistent with the Specification. In re American Academy Of Science Tech
Center, 367 F.3d 1359, 1364 (Fed. Cir. 2004). “An essential purpose of
patent examination is to fashion claims that are precise, clear, correct, and
unambiguous. Only in this way can uncertainties of claim scope be removed,
as much as possible, during the administrative process.” In re Zletz, 893
F.2d 319, 322 (Fed. Cir. 1989).
If the claim preamble, when read in the context of the
entire claim, recites limitations of the claim, or, if the preamble
is “necessary to give life, meaning, and vitality” to the claim,
then the claim preamble should be construed as if in the balance
of the claim. . . . If, however, the body of the claim fully and
intrinsically sets forth the complete invention, including all of
its limitations, and the preamble offers no distinct definition of
any of the claimed invention‟s limitations, but rather merely
states, for example, the purpose or intended use of the
invention, then the preamble is of no significance to claim
construction because it cannot be said to constitute or explain a
claim limitation.
Pitney Bowes, Inc. v. Hewlett-Packard Co., 182 F.3d 1298, 1305 (Fed. Cir.
1999).
Claim 100 recites:
A method for screening a candidate compound for the ability to
reduce cellular proliferation comprising the steps of:
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(a) providing a sublethal level of an antisense nucleic
acid, wherein said antisense nucleic acid reduces the activity or
amount of SEQ ID NO: 12600, thereby producing a sensitized
cell, provided that said sensitized cell is a prokaryotic organism
and whereby the antisense nucleic acid binds to a nucleic acid
that encodes SEQ ID NO: 12600;
(b) contacting said sensitized cell with a compound; and
(c) measuring proliferation of said sensitized cell,
wherein a decrease in proliferation of said sensitized cell
relative to a nonsensitized cell indicates that the compound
reduces cellular proliferation.

The recitation of “screening a candidate compound for the ability to
reduce cell proliferation” in the preamble is a statement of intended use, as it
does not change the steps of the claim. Moreover, the recitation of “a
candidate compound” does not preclude testing a known antibiotic to
determine if it targets yphC. Thus, Appellants‟ arguments are not
commensurate in scope with the claimed subject matter.

CONCLUSION OF LAW
We conclude that the Examiner has established by a preponderance of
the evidence that claim 100 is rendered obvious by the combination of
Zhang, Zalacain, Fritz, and Ji.

SUMMARY
The rejection of claims 12, 31, 45-69, 77-86, 89-96, 100, and 101
under 35 U.S.C. § 103(a) as being rendered obvious by the combination of
Zhang, Zalacain, Fritz, and Ji is affirmed as to claim 100.

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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-IN-PART

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