Ex Parte Gjerde

Board of Patent Appeals and Interferences

Aug 8, 2011

12004726 (B.P.A.I. Aug. 8, 2011)

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.
12/004,726 12/21/2007 Douglas T. Gjerde P027.210 1019
55130 7590 08/08/2011
PHYNEXUS, INC.
3670 CHARTER PARK DRIVE
SAN JOSE, CA 95136
EXAMINER
SHIBUYA, MARK LANCE
ART UNIT PAPER NUMBER
1641
MAIL DATE DELIVERY MODE
08/08/2011 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 BOARD OF PATENT APPEALS
AND INTERFERENCES
__________

Ex parte DOUGLAS T. GJERDE
__________

Appeal 2011-002943
Application 12/004,726
Technology Center 1600
__________

Before DEMETRA J. MILLS, JEFFREY N. FREDMAN, and STEPHEN
WALSH, Administrative Patent Judges.

WALSH, Administrative Patent Judge.

DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134(a) involving claims to a
method for purifying a protein from a sample solution. The Patent Examiner
rejected the claims for obviousness. We have jurisdiction under 35 U.S.C.
§ 6(b). We reverse.
Appeal 2011-002943
Application 12/004,726

2
STATEMENT OF THE CASE
Claims 1, 4-7, 10, 11, 13-16, and 21-24, which are all the pending
claims, are on appeal. Claim 1 is representative and reads as follows:
1. A method for purifying and concentrating a protein from a sample
solution comprising the steps of:
a) introducing the sample solution containing the protein into a first pipette
tip column, wherein said first pipette tip column is comprised of a first
packed bed of extraction medium, wherein the first packed bed of
extraction medium is comprised of a functional group, and whereby at
least some portion of the protein is adsorbed by the first packed bed of
extraction medium;
b) passing a wash solution through the first packed bed of extraction
medium;
c) passing a first desorption solvent through the first packed bed of
extraction medium, whereby at least some fraction of the bound
protein is desorbed from the first packed bed of extraction medium
into the desorption solvent, and wherein, as a result of step (c), the
protein is purified from other components in the sample solution;
d) optionally adjusting the pH of the purified protein in the desorption
solvent;
e) introducing the purified protein into a second pipette tip column, wherein
the second pipette tip column is comprised of a second packed bed of
extraction medium, wherein the second packed bed of extraction
medium is comprised of a functional group, [1] wherein the
functional group of the second packed bed of extraction medium is the
same as the functional group of the first packed bed of extraction
medium, [2] wherein the capacity of the second pipette tip column has
is in the range of 1 % to 95% of the capacity of the first pipette tip
column, and whereby at least some portion of the protein is adsorbed
by the second packed bed of extraction medium;
f) optionally passing a wash solution through the second packed bed of
extraction medium; and
g) passing a second desorption solvent through the second packed bed of
extraction medium, whereby at least some fraction of the bound
protein is desorbed from the second bed of extraction medium into the
second desorption solvent, and [3] wherein the purified protein has a
concentration of at least 5 mg/ml.
Appeal 2011-002943
Application 12/004,726

3
(Bracketed numbers and emphasis added to highlight disputed features.)
The Examiner rejected the claims under 35 U.S.C. § 103(a) as
unpatentable over Gierde1 and Srinivasan.2

OBVIOUSNESS
The Issue
The Examiner’s position is that Gierde taught an extraction method
corresponding to Appellants’ steps a) through g), with differences at three
points:
Gierde [did not teach] [1] that the functional groups in
the first and second packed bed of extraction medium are the
same . . . [2] that the second pipette tip column has a capacity in
the range of 1% or 95% of the capacity of the first pipette tip
column . . . [and] [3] a concentration of at least 5 mg/ml.

(Ans. 5.) The Examiner concluded that the three points of difference would
have been resolved by obvious modifications because (1) changing the
different extraction media used by Gierde in serial extractions to the same
medium would have been obvious “in order to capture the same analyte at
each step while removing other elements using different solutions” (id. at 6);
(2) Srinivasan taught that having a smaller capacity second column “allows
for enhanced detection” (id. at 5-6); and (3) Gierde taught that “the ultimate
analyte concentration is adjustable” (id. at 6-7).

1 Douglas T. Gierde et al., US 2004/0142488 A1, July 22, 2004.
2 Kannan Srinivasan et al., US 2007/0065343 A1, filed Sept. 16, 2005.
Appeal 2011-002943
Application 12/004,726

4
Appellants present these issues:
[1] “[w]ith respect to point 1 . . . this reasoning is improper
because it relies solely on information gleaned from
Appellant’s disclosure” (App. Br. 4);
[2] “[w]ith respect to point 2 . . . Srinivasan uses a smaller
capacity column because only a portion of the effluent obtained
from the first dimension is introduced into the second
dimension column” (id. at 5); and
[3] “[w]ith respect to point 3 . . . Appellants disagree . . .
[because] there are limits to the fold concentration that can be
achieved using a single extraction column as taught by Gierde”
(id.).

Findings of Fact
1. We adopt the Examiner’s findings concerning the explicit teachings in
the prior art.

Principles of Law
“Rejections on obviousness grounds cannot be sustained by mere
conclusory statements; instead, there must be some articulated reasoning
with some rational underpinning to support the legal conclusion of
obviousness.” In re Kahn, 441 F.3d 977, 988 (Fed. Cir. 2006), cited with
approval in KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 417-18 (2007).
“[A]ny need or problem known in the field of endeavor at the time of
invention and addressed by the patent can provide a reason for combining
the elements in the manner claimed.” KSR, 550 U.S. at 420.

Analysis
Concerning issue [2], the evidence supports the Examiner’s findings
that Srinivasan taught that a smaller capacity second column would improve
Appeal 2011-002943
Application 12/004,726

5
analyte detection, and therefore suggested using a smaller capacity second
column. We conclude that although Srinivasan’s reason for using the
smaller capacity second column is not the same as Appellants’ reason, this
portion of the rejection is sound. See KSR, 550 U.S. at 420.
Concerning issue [3], the evidence supports the Examiner’s finding
that Gierde taught that the degree of analyte concentration achieved was
adjustable. Gierde taught that solid phase extraction was used in order to
concentrate analytes, and Srinivasan also described concentrating the
analyte. Appellants’ vague observation that “there are limits” to the prior art
concentrating methods is unpersuasive of error because it does not provide
pertinent evidence or specific reasoning establishing that the Examiner was
wrong as to the degree of concentration achievable with the application of
routine skill.
Concerning issue [1], we agree with Appellants. The rejection
provides no evidence, and articulates no technical explanation, showing that
a person of ordinary skill in the art would have had a good reason to replace
Gierde’s second extraction medium with the first extraction medium, i.e., to
provide for repeated extraction with the same medium. See Kahn, 441 F.3d
at 988.
SUMMARY
We reverse the rejection of claims 1, 4-7, 10, 11, 13-16, and 21-24
under 35 U.S.C. § 103(a) as unpatentable over Gierde and Srinivasan.

REVERSED
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