Ex Parte Xi et al

Patent Trial and Appeal Board

Oct 15, 2018

13213427 (P.T.A.B. Oct. 15, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/213,427 08/19/2011
52059 7590 10/17/2018
LIFE TECHNOLOGIES CORPORATION
Attn: IP Department
5823 Newton Drive
Carlsbad, CA 92008
FIRST NAMED INVENTOR
Lei Xi
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
ATTORNEY DOCKET NO. CONFIRMATION NO.
LT00287 8249
EXAMINER
BERTAGNA, ANGELA MARIE
ART UNIT PAPER NUMBER
1637
NOTIFICATION DATE DELIVERY MODE
10/17/2018 ELECTRONIC
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.
Notice of the Office communication was sent electronically on above-indicated "Notification Date" to the
following e-mail address(es):
LSGDocketing@thermofisher.com
pair_thermofisher@firsttofile.com
LifetechDocket@system.foundationip.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte LEI XI, KEITH P. BJORNSON, and STEPHEN P. HENDRICKS
Appeal2017-000907
Application 13/213,427 1
Technology Center 1600
Before ROBERT A. POLLOCK, RICHARD J. SMITH, and
RACHEL H. TOWNSEND, Administrative Patent Judges.
TOWNSEND, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal under 35 U.S.C. § 134 involving claims to a method
of detecting nucleic acid polymerase activity, which have been rejected as
obvious. We have jurisdiction under 35 U.S.C. § 6(b).
We affirm-in-part.
STATEMENT OF THE CASE
Methods for measuring polymerase activity are known. Traditionally,
such assays involve providing a mixture of primers with a template nucleic
acid and radio-isotope labeled deoxynucleotide triphosphates (dNTP) and
1 Appellants identify the real party in interest as Life Tech. Corp. of
Carlsbad, CA, a wholly owned subsidiary of Thermo Fisher Scientific Corp.
of Waltham, MA. (Appeal Br. 3.)
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Application 13/213,427
measuring the quantity of incorporated radio-isotope labeled dNTP. (Spec.
1.) Using radioactive methods, however, "requires skilled experts,
specialized facilities for radioisotopes and produces radioisotope-
contaminated waste." (Id.) Non-radioactive methods are also known, such
as the "M13/SYBR Green assay, and a real-time assay using a DNA binding
dye, DAPI", but those assays "have the disadvantage of being complicated,
[and of] involving expensive instruments for monitoring the reactions,
lengthy preparation time and a large quantity of reagents." (Id.)
Appellants' invention is directed to a non-radioactive method using
fluorescence resonance energy transfer (FRET), "a process by which energy
is passed non-radioactively between a donor molecule [fluorophore] and an
acceptor molecule [fluorophore or quencher]." (Id. at 1-2.) "In order for
energy transfer to occur, the donor and acceptor molecules must typically be
in close proximity (e.g., up to 70 to 100 Angstroms)." (Id. at 2.)
"Pairs of molecules that can engage in ... FRET are termed FRET
pairs." (Id.) The invention involves a FRET substrate that is a primer-
template duplex where the template has a 5' single-stranded tail that is
labeled with one member of the FRET pair, and the second member of the
FRET pair is located in the duplex, either on the primer or the template, but
not at the 3' end of the primer. (Id. at 8.) This arrangement "ensures that
extension of the primer into the single-stranded region of the FRET substrate
can occur if a polymerase is present." (Id.) "The quencher and fluorophore
are separated at a distance such that when the duplex is not polymerized the
fluorophore is quenched by the quencher and when the duplex is
polymerized, the fluorophore is not quenched by the quencher." (Id.) Thus,
for example, "[ w ]hen unpolymerized, the single-stranded tail with the
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quencher attached may loop back and quench the fluorophore. When
polymerized, the tail becomes a part of the duplex and the distance between
the fluorophore and quencher is increased to a point at which the quencher
can no longer quench the fluorophore." (Id. at 14.)
Claims 1-3, 5, 6, 8, 9, 11-17, 32-37, 39, 40, 42, 43, 45-51, 54, 55,
and 57----62 are on appeal. Claim 1 is representative and reads as follows:
1. A method of detecting nucleic acid polymerase activity, the
method comprising:
a) providing a primer-template duplex comprising a nucleic
acid template and a nucleic acid primer, wherein the template
comprises a single-stranded tail having a 5' end having a first
FRET label attached and the template further comprises a
second FRET label within the duplex region of the primer-
template duplex, wherein one FRET label is a quencher and the
other FRET label is a fluorophore;
b) contacting the duplex with a nucleic acid polymerase;
c) contacting the duplex with at least one nucleotide
triphosphate or analog thereof;
d) incorporating the at least one nucleotide triphosphate or
analog thereby extending the duplex; and
e) detecting a signal from the fluorophore, wherein a change in
the signal compared to a control is indicative of nucleic acid
polymerase activity.
(Br. 25.)
The following grounds of rejection by the Examiner are before us on
review:
Claims 1-3, 5, 6, 8, 9, 12, 13, 16, 17, 57, and 60 under 35 U.S.C.
§ 103(a) (pre-AIA) as unpatentable over Gold2 and Shapiro. 3
2 Gold et al, US 6,020,130, issued Feb. 1, 2000.
3 Shapiro, WO 2005/003388 A2, published Jan 13, 2005.
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Claims 11, 14, 15, 32-37, 39, 40, 42, 43, 45-50, 54, 58, 59, 61, and 62
under 35 U.S.C. § I03(a) (pre-AIA) as unpatentable over Gold, Shapiro, and
N azarenko. 4
Claim 51 under 35 U.S.C. § I03(a) (pre-AIA) as unpatentable over
Gold, Shapiro, and Biroccio5.
Claim 55 under 35 U.S.C. § I03(a) (pre-AIA) as unpatentable over
Gold, Shapiro, Nazarenko, and Biroccio.
DISCUSSION
Obviousness of claims 1-3, 5, 6, 8, 9, 12, 13, 16, 17, 57, and 60
The Examiner finds that Gold teaches a method for monitoring the
activity of polymerase, where the method employs a primer-template duplex
that has a stem-loop structure with a 5' single-stranded tail. (Final Action 6
( citing, e.g., Gold Examples 2 ("Polymerase Inhibition Assays") and 4
("Polymerase Inhibition Assays").) The Examiner explains that in the
method of Gold, the duplex is contacted with a polymerase and at least one
nucleotide, at least one nucleotide is incorporated into the primer, and
polymerase activity is detected through gel-based detection of radiolabels.
(Id. at 6, 7 .)
The Examiner notes that Gold's detection does not employ FRET.
(Id. at 6.) However, the Examiner concludes that it would have been
obvious to employ FRET in the Gold method of monitoring polymerase
activity instead of the gel-based detection of radio labels in light of the
4 Nazarenko, US 7,537,886 Bl, issued May 26, 2009.
5 Biroccio et al., Selection of RNA Aptamers That Are Specific and High-
Affinity Ligands of the Hepatitis C Virus RNA-Dependent RNA Polymerase,
46(8) J. of Virology, 3688-96, 2002
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Application 13/213,427
teachings of Shapiro. (Id.) The Examiner explains that Shapiro teaches a
method for monitoring the activity of a polymerase using two labels of a
FRET pair. (Id. 6-7.) According to the Examiner, Shapiro's method
involves providing a primer-template duplex that includes a fluorophore and
quencher, contacting that duplex with a polymerase and at least one
nucleotide triphopshpate, incorporating at least one nucleotide into the
primer, and determining polymerase activity based on the detection of a
signal from the fluorophore and comparing that signal to a control. (Id. at 6-
7 ( citing, e.g., Shapiro 2, 4---6).) The Examiner points out that Shapiro
teaches that the fluorophore and quencher may be contained in the template
or in the primer and template and that "the two labels in a FRET pair can be
positioned in any desired location relative to each other provided that a
signal indicative of the polymerase activity is produced." (Id. at 7 (citing
page 2).)
According to the Examiner, one of ordinary skill in the art would have
found it obvious to substitute FRET-based detection for the gel-based
detection of radiolabels in the Gold method "to obtain [a] less-labor
intensive assay and also eliminate the need to use radioactivity." (Id. at 7.)
The Examiner explains that the substitution would have included replacing
the radioactive label in the hairpin of Gold, which is located in the 5' single
stranded tail. (Id.) The Examiner further explains that, in light of the
teaching of Shapiro that the relative placement of the labels is only
dependent on the condition-dependent signal being produced, one of
ordinary skill in the art would have found it obvious to position the second
label of the FRET pair internally. (Id. at 8.) The Examiner indicates that
one or ordinary skill in the art would have had a reasonable expectation of
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success in light of the "guidance provided by Shapiro regarding FRET-based
assays." (Id. at 7.)
We agree with the Examiner's findings and conclusion that claim 1
would have been obvious from the combined teachings of Gold and Shapiro.
Appellants first argue that Gold does not teach a method that uses
FRET labels, and, thus, it does not teach or suggest the claimed method
using the claimed primer-template duplex. (Br. 13) This argument is not
persuasive because the Examiner's rejection was based on the combination
of Shapiro with Gold in which Shapiro was relied upon to teach the use of
FRET labels in detecting polymerase activity. "Non-obviousness cannot be
established by attacking references individually where the rejection is based
upon the teachings of a combination of references .... [The reference] must
be read, not in isolation, but for what it fairly teaches in combination with
the prior art as a whole." In re Merck & Co., 800 F.2d 1091, 1097 (Fed. Cir.
1986).
Appellants next argue that Shapiro fails to teach the claimed primer-
template duplex because it teaches separately labeling the template molecule
at the 3' end and then labeling the primer molecule at the 5' end, which
contrasts with the claimed primer-template duplex that has the second FRET
label located internally in the duplex portion and "does not have any FRET
label on the 3' end." (Br. 13-14.) We do not find this argument persuasive
either, because, as the Examiner correctly noted (Ans. 11-12), a reference is
applicable for all that it teaches. See, e.g., In re Mouttet, 686 F.3d 1322,
1331 (Fed. Cir. 2012); Merck & Co. v. Biocraft Labs., 874 F.2d 804, 807
(Fed. Cir. 1989) ("in a section 103 inquiry, 'the fact that a specific
[embodiment] is taught to be preferred is not controlling, since all
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disclosures of the prior art, including unpreferred embodiments, must be
considered."'). While Shapiro exemplifies placing the FRET labels at the 5'
and 3' end of the primer-template duplex, it teaches label placement more
broadly. In particular, Shapiro explains that the important aspect of the
placement of the two FRET labels for FRET detection methods, which
methods are well described in the prior art (see, e.g., Shapiro 6), is that the
labels be positioned relative to each other so that a signal indicative of
polymerase activity is produced, noting that the labels can be attached to any
portion of the nucleotide in a primer or a template and that "either the
template and/or the primer is labeled." (Shapiro 9-10). We also agree with
the Examiner that Shapiro discloses that label placement can be "near the 5'
end of the primer and the 3' end of the template" (Shapiro 9), "which is an
example of label placement other than at the termini." (Ans. 10).
Shapiro also notes that what is important is that "[ t ]he choice of
fluorescence donor and FRET acceptor/quencher probes ... be made so that
a strong donor fluorescence change occurs when the primer and template are
annealed." (Shapiro 9.) Shapiro explains regarding the use of FRET for
measuring polymerase activity, "elongation of the primer by the polymerase
results in an increase of the acceptor:donor fluorescence or decrease in the
donor:acceptor fluorescence ratio as compared with a control that has not
been elongated." (Shapiro 5.) Shapiro also explains that in a method where
one is identifying compounds that modulate nucleic acid polymerase
activity, "[a] change in the signal compared to a control (i.e., where no
compound is added) is indicative that the compound modulates nucleic acid
polymerase activity." (Shapiro 10.) Consequently, we agree with the
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Examiner that Shapiro more broadly teaches that the FRET labels may be
placed in other positions besides at the 3' end of the primer.
Appellants also argue that (1) the combination of Gold and Shapiro
does not teach or suggest the claimed primer-template duplex because "one
would at best have a primer template duplex labeled at both the 5' end and
the 3' end" and (2) Shapiro's method requires use of denaturing conditions
prior to measuring the FRET signal and one of ordinary skill in the art would
have had no reason to exclude those steps. (Br. 15-16.) Further, with
regard to the combination argument (1) above, according to Appellants,
modifying Gold with Shapiro's FRET labelling would result in Gold not
working for "its intended purpose of being a substrate for the detection of
polymerase inhibition since a polymerase could not extend the modified
hairpin" with a 3' end that is blocked by a FRET label." (Br. 16.)
Moreover, Appellants argue that the Examiner is improperly picking and
choosing elements of each reference "with no teaching, suggestion or
motivation to do so by either Gold or Shapiro." (Br. 17.)
We do not find these arguments persuasive for the reasons explained
by the Examiner. (Ans. 9-15.) First, as discussed above, Shapiro's teaching
as to placement of the FRET labels in order to detect polymerase activity is
not limited to placement of one label at the 5' end of the primer and a second
label at the 3' end of a template. Moreover, as noted above, Shapiro
explains regarding the use of FRET for measuring polymerase activity,
"elongation of the primer by the polymerase results in an increase of the
acceptor:donor fluorescence or decrease in the donor:acceptor fluorescence
ratio as compared with a control that has not been elongated." (Shapiro 5.)
Consequently, Shapiro recognizes that the FRET label should not be
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positioned such that it would block elongation of the primer. As the
Examiner explained, one of ordinary skill in the art
would have considered the FRET detection strategy disclosed
by Shapiro to be broadly applicable and, accordingly, would
have been motivated to apply it to the monitoring of other
primer-template duplexes, such as the duplex described by
Gold, using well known FRET principles to place the two
members of the FRET pair at appropriate positions.
(Ans. 11-12.)
Furthermore, given that it was known that detection of polymerase
activity involves a measurement from elongation of the primer ( as even
acknowledged by Shapiro), we agree with the Examiner (Ans. 12) that one
of ordinary skill in the art would not find the combination of the broad
teachings of Shapiro regarding FRET label placement with Gold to render
Gold unsuitable for its intended purpose (Ans. 13). Rather, as the Examiner
notes, in substituting FRET detection for the radiolabeled detection in Gold,
one of ordinary skill in the art would have "immediately recognized that a
FRET label could not be placed at the 3' end of the primer-template duplex
of Gold since it would eliminate the ability of the duplex to [] undergo
polymerase-mediated extension, and instead would have placed the two
labels elsewhere in the primer-template duplex." (Ans. 11.) The Examiner
explains that given the teachings of Shapiro and the knowledge of the FRET
methodology, one of ordinary skill in the art would have had a reasonable
expectation of success in positioning "one FRET label in the 5' single-
stranded tail[, which is where the radiolabel is positioned in Gold] and the
other FRET label at a position internal thereto in the duplex region but not at
the 3' end of the primer portion of the hairpin primer-template duplex[,
which one of ordinary skill in the art would know would block primer
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Application 13/213,427
extension]." (Final Action 8.) Appellants do not contest the Examiner's
assertion in this regard.
Regarding Appellants' second argument concerning Shapiro's use of
denaturing steps, we agree with the Examiner that claim 1 does not require
real-time detection of polymerase activity (Ans. 12), but the method of claim
1 uses the transition term "comprising." "The transition 'comprising' in a
method claim indicates that the claim is open-ended and allows for
additional steps." Invitrogen Corp. v. Biocrest Mfg., L.P., 327 F.3d 1364,
1368 (Fed. Cir. 2003). Consequently, claim 1 does not exclude detection of
polymerase activity after a denaturation step. Furthermore, even if the claim
is interpreted to require real-time detection, Shapiro indicates that the
denaturation step can be a heat denaturation step (Shapiro 5 ("application of
denaturing conditions ( which includes the addition of a denaturant or
chaotropic agent and/or the application of heat)") (emphasis added)),
which the Examiner notes, and Appellants do not dispute, "is perfectly
capable of functioning in a simple and rapid real-time detection assay."
(Ans. 12.)
Moreover, as to the detection, we note that the method of claim 1
simply requires detection of a signal from a fluorophore and that a change in
the signal compared to a control is indicative of polymerase activity. The
invention described in the Specification, as discussed above, explains that
[ w ]hen unpolymerized, the single-stranded tail with the
quencher attached may loop back and quench the fluorophore[,
but] [w]hen polymerized, the tail becomes a part of the duplex
and the distance between the fluorophore and quencher is
increased to a point at which the quencher can no longer quench
the fluorophore.
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(Spec. at 14.) While the language of claim 1 may or may not capture the
invention thus described, the claim language "detecting a signal from the
fluorophore, wherein a change in the signal compared to a control is
indicative of nucleic acid polymerase activity" does not preclude the
polymerase activity measurement described by the combination of Gold and
Shapiro. The detection of compounds modulating nucleic acid polymerase
activity using radiolabeling is described by Gold. (See, e.g., Gold 15:8-36
(describing Example 2)) Regarding FRET-label detection and polymerase
activity measurement, as Shapiro explains, when the duplex is exposed to
denaturing conditions, a signal from the label is detected, and a change in the
signal compared to a control (i.e., where no compound that modulates
nucleic acid polymerase activity is added) is indicative that the compound
modulates nucleic acid polymerase activity. (Shapiro 10.) Thus, employing
FRET-labelling and its use in detecting polymerase activity for the
radiolabeling described by Gold would result in a process where the
detecting step as claimed would have been obvious to carry out. And, for
the reasons the Examiner noted (Final Action 7) ("to obtain less labor-
intensive assay and also to eliminate the need to use radioactivity'), we agree
with the Examiner that it would have been obvious to substitute Shapiro's
teaching of the use of FRET technology in place of the radiolabel detecting
used by Gold.
We also disagree with Appellants that the Examiner has improperly
used hindsight reconstruction. For the reasons discussed above, we
determine that the Examiner has properly considered only the teachings of
the prior art and the knowledge of one of ordinary skill in the art in arriving
at the conclusion that the invention recited in claim 1 is rendered obvious by
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Gold and Shapiro. "The obviousness analysis cannot be confined by ...
overemphasis on the importance of published articles and the explicit
content of issued patents." KSR Int'! Co. v. Teleflex Inc., 550 U.S. 398,419
(2007). "[I]nterrelated teachings of multiple patents ... and the background
knowledge possessed by a person having ordinary skill in the art, ... [ can
provide] an apparent reason to combine the known elements in the fashion
claimed." Id. at 418. As the Examiner explained, "the ordinary artisan
would have been motivated by the disclosure of Shapiro to substitute FRET
detection for the gel-based radioactive label detection method of Gold,
recognizing that doing so would result in a less labor-intensive assay and
also avoid the need to use hazardous radioactive labels." (Final Action 8.)
For all of the foregoing reasons, therefore, we sustain the Examiner's
rejection of claim 1 as being obvious from Gold and Shapiro.
Claims 2, 3, 5, 6, 8, 9, 12, 13, 16, 17, 57, and 60 have not been argued
separately and therefore fall with claim 1. 37 C.F.R. § 4I.37(c)(l)(iv).
Obviousness of claims 11, 14, and 15
Appellants do not present any additional argument concerning the
alleged non-obviousness of claims 11, 14, and 15 beyond what was asserted
for claim 1, except to state that N azarenko does not teach or suggest the
primer-template duplex. (Appeal Br. 18.) The Examiner did not rely on
N azarenko for such a teaching because the Examiner determined that such
was rendered obvious by the combination of Gold and Shapiro. For the
reasons discussed above with respect to claim 1, we do not find Appellants'
arguments persuasive as to claims 11, 14, and 15.
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Non-Obviousness of claim 32-37, 39-40, 42, 43, 45-50, 54, 58, 59, 61, and
62
With respect to claims 32 and 35, Appellants point out that these
claims require a particular standard. Appellants contend that N azarenko
fails to teach or suggest the required standard.
We agree with Appellants. According to the Examiner, Nazarenko
"teaches that a standard, prepared at different concentrations, may be used to
quantify the extent of polymerase activity (see for example column 9, lines
33-44)." (Final Action 9.) We disagree with the Examiner's assessment of
Nazarenko. Nazarenko teaches that a control sample can be used to quantify
the amount of nucleic acid molecules in a sample. (Nazarenko 9:33--44,
28:27-38; 33:51-59.) While Nazarenko teaches providing a series of
standards having a number of controls with differing known concentrations
of nucleic acid molecules that can be used to determine the amount of a
target nucleic acid molecule in an unknown sample, it does not teach the
control formulations include any "substrate," much less the standard
described in claim 35. Thus, while Nazarenko may have suggested to one of
ordinary skill in the art that standards can be a useful tool in quantitative
analysis, we do not agree with the Examiner that Nazarenko in combination
with Gold and Shapiro would have taught or suggested the claimed standard
used in the claimed method.
Consequently, the Examiner has failed to establish a prima facie case
that the subject matter of claims 32 and 35 and their dependent claims would
have been obvious at the time of Appellants' invention. We reverse the
Examiner's rejection of claims 32-37, 39, 40, 42, 43, 45-50, 54, 58, 59, 61,
and 62 as unpatentable over Gold, Shapiro, and Nazarenko.
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Obviousness of claim 51
Appellants do not present any additional argument concerning the
alleged non-obviousness of claim 51 beyond what was asserted for claim 1.
(Appeal Br. 19--20.) For the reasons discussed above with respect to claim
1, we do not find Appellants' arguments persuasive as to claim 51.
Non-obviousness of claim 55
Appellants do not present any additional argument concerning the
alleged non-obviousness of claim 55 beyond what was asserted for claim 1
and 35. (Appeal Br. 20.) We do not find Appellants' arguments regarding
the combination of Gold and Shapiro persuasive for the reasons discussed
above with respect to claim 1. However, we agree with Appellants'
argument that Nazarenko would not have taught or suggested the claimed
substrate required by claim 3 5 as discussed above. The Examiner does not
rely on Biroccio to cure this defect. Thus, we reverse the Examiner's
rejection of claim 55 as unpatentable over Gold, Shapiro, Nazarenko, and
Biroccio.
SUMMARY
We affirm the rejection of claims 1-3, 5, 6, 8, 9, 12, 13, 16, 17, 57,
and 60 under 35 U.S.C. § 103(a) (pre-AIA) as unpatentable over Gold and
Shapiro.
We affirm the rejection of claims 11, 14, and 15 under 35 U.S.C.
§ 103(a) (pre-AIA) as unpatentable over Gold, Shapiro, and Nazarenko.
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We reverse the rejection of claims 32-37, 39, 40, 42, 43, 45-50, 54,
58, 59, 61, and 62 under 35 U.S.C. § 103(a) (pre-AIA) as unpatentable over
Gold, Shapiro, and Nazarenko.
We affirm the rejection of claim 51 under 35 U.S.C. § 103(a) (pre-
AIA) as unpatentable over Gold, Shapiro, and Biroccio.
We reverse the rejection of claim 55 under 35 U.S.C. § 103(a) (pre-
AIA) as unpatentable over Gold, Shapiro, Nazarenko, and Biroccio.
TIME PERIOD FOR RESPONSE
No time period for taking any subsequent action in connection with
claims for which the rejections were affirmed in this appeal may be extended
under 37 C.F.R. § 1.136(a).
AFFIRMED-IN-PART
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