Ex Parte Lubys

Patent Trial and Appeal Board

Nov 16, 2017

12167527 (P.T.A.B. Nov. 16, 2017)

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.
12/167,527 07/03/2008 Arvydas Lubys 104055.60524US 5659
23911 7590
CROWELL & MORING LLP
INTELLECTUAL PROPERTY GROUP
P.O. BOX 14300
WASHINGTON, DC 20044-4300
EXAMINER
AULT, ADDISON D
ART UNIT PAPER NUMBER
1636
NOTIFICATION DATE DELIVERY MODE
11/20/2017 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):
edocket @ crowell. com
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PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
Ex parte ARVYDAS LUBYS
Appeal 2017-001258
Application 12/167,527
Technology Center 1600
Before ERIC B. GRIMES, JEFFREY N. FREDMAN, and
JOHN E. SCHNEIDER, Administrative Patent Judges.
FREDMAN, Administrative Patent Judge.
DECISION ON APPEAL
This is an appeal1 under 35 U.S.C. § 134 involving claims to a
positive selection vector. The Examiner rejected the claims as obvious. We
have jurisdiction under 35 U.S.C. § 6(b). We reverse.
Statement of the Case
Background
“Cloning describes insertion of a DNA sequence of interest into a
cloning vector which is capable of replication . . . There are many types of
cloning vectors including plasmids” (Spec. 1). “Two major strategies,
namely insertional inactivation and positive selection, have been developed
1 Appellant identifies Thermo Fisher Scientific Baltics UAB as the Real
Party in Interest (see App. Br. 1).
Appeal 2017-001258
Application 12/167,527
and implemented in order to deal with the problem of identifying
transformants containing recombinant plasmids” (Spec. 2).
The approach of positive selection is [] based on insertional
inactivation of a gene located within the cloning vector.
However . . . [the] gene is toxic to the host. Therefore, host
cells with uncut or self-ligated (empty) molecules of positive
selection cloning vector cannot grow. As a result, only those
cells that contain recombinant plasmids with the foreign DNA
fragment inserted within the toxic gene will grow and form
colonies.
(Spec. 3). “However, the structure of cloning vectors based on insertional
inactivation . . . may lead to false-negative results” (Spec. 5). “Thus, a need
exists for an improved cloning vector which is based on a configuration
which minimizes the generation of false-negative clones . . . such a vector
should retain the feature of a positive selection cloning vector” (Spec. 6).
The Claims
Claims 1 and 3-13 are on appeal. Independent claim 1 is
representative and reads as follows:
1. A positive selection vector for transformation into a host
cell comprising a toxic gene encoding a product that is lethal to
the host cell, wherein the toxic gene comprises:
an essential sequence region whose integrity is necessary
in order for the encoded toxic gene product to be lethal to the
host cell;
an inessential sequence region which encodes a section
of the toxic product and whose integrity is not essential in order
for the encoded toxic gene product to be lethal to the host cell;
a regulatory sequence inserted in-frame into the
inessential sequence region and encoding amino acids
additional to the encoded toxic gene product; and
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Appeal 2017-001258
Application 12/167,527
a cloning site within the essential sequence region for
insertion of a nucleic acid sequence,
wherein the regulatory sequence and the cloning site are
positioned so as to allow the regulatory sequence to be operably
linked to a nucleic acid sequence when the nucleic acid
sequence is inserted into the cloning site and wherein the toxic
gene encodes a nuclease.
The Issue
The Examiner rejected claims 1 and 3-13 under 35 U.S.C. § 103(a) as
obvious over Fermentas Catalog2 and Mead3 (Ans. 2 4).
The Examiner finds the Fermentas Catalog teaches:
the pJETI [sic, pJETl] vector, which comprises a nucleic acid
sequence encoding an eco471 R endonuclease, a multiple
cloning site, a promoter operably linked to the sequence
encoding an eco471 R endonuclease, an origin of replication,
an[] Eco321 site, and an ApR conferring sequence. The
reference also teaches how to construct the vector.
Furthermore, the vector can be used by inserting a nucleic acid
sequence into the sequence encoding an eco471 R endonuclease
to inactivate it, and thus the Fermentas catalog teaches insertion
of a cloning site in a position that meets the limitation of being
an “essential sequence region”.
(Ans. 2-3).
The Examiner acknowledges the Fermentas Catalog “does not teach
use of a T7 promoter or an in-frame insertion of the promoter” and finds that
2 Fermentas catalog, http://www.fermentas.com/en/support/technical-
reference/phage-plasmid-dna/pjetl2 (accessed Feb. 14, 2012).
3 Mead et al., Single-stranded DNA ‘blue’ T7 promoter plasmids: a versatile
tandem promoter system for cloning and protein engineering, 1 Protein
Engineering 6774 (1986).
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Application 12/167,527
“[ijnstead, the Fermentas catalog teaches a PlacUV5 promoter upstream of
the eco471 R gene without addressing whether or not the promoter is fused
‘in frame’ or whether the amino acids/sequence in and around the promoter
is ‘inessential’” (Ans. 3). The Examiner finds Mead teaches “a vector with a
T7 promoter inserted in-frame into an inessential region of a gene (a 3-
galactosidase [sic, P-galactosidase] gene)” {Id.).
The Examiner finds it obvious “to modify the pJETI vector of
Ferm[e]ntas with an in-frame T7 promoter fused to the toxic gene” because
“it is useful to have the T7 promoter inserted into the toxic gene for selection
and expression purposes” (Ans. 3). The Examiner also finds “the T7
promoter system is commonly used and has been developed extensively.
Systems that are well-characterized and predictable have art-recognized
advantages of saving time and money in comparison to poorly characterized
or underdeveloped systems” (Ans. 4).
The issue with respect to this rejection is: Does the evidence of record
support the Examiner’s conclusion that Fermentas Catalog and Mead render
the vector of claim 1 obvious?
Findings of Fact
1. Fermentas Catalog teaches the “positive selection vector pJETI
. . . was derived from pUC19 by replacing the 5’-terminal part of the lacZ
gene encoding the N-terminal fragment of beta-galactosidase with the gene
coding for the Eco47I restriction endonuclease. In the absence of cognate
methylation, the endonuclease is lethal to E.coli host cells” (Fermentas
Catalog 4).
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Application 12/167,527
2. Fermentas Catalog teaches “[ijnsertional inactivation of the
eco47IR gene is the mechanism to obtain a positive selection using the
plasmid pJETl” {Id.).
3. The Fermentas Catalog plasmid map is reproduced below:
“The map . . . shows enzymes which have unique targets within pJETl” {Id.
at 4 (image from page 5)).
4. Fermentas Catalog teaches “the multiple cloning site (MCS)
used for positive selection was incorporated into eco47IR by silent
mutagenesis” {Id. at 4).
5. Fermentas Catalog teaches “[a]fter the cloning of DNA into
eco47IR the integrity of this gene is disrupted. Therefore, only those cells
survive after the transformation and are able to form a colony in presence of
ampicillin which have the recombinant plasmid. This feature ensures
positive selection of recombinant clones” {Id. at 4).
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Application 12/167,527
6. Mead teaches: “Chimeric phage-plasmid expression vectors
were constructed from pUC18/19 plasmids by cloning a single-stranded
DNA (ssDNA) origin of replication from bacteriophage fl and inserting a
bacteriophage T7 promoter within the P-galactosidase gene” (Mead 67,
abstract).
7. Mead teaches a “T7 promoter permits in vivo or in vitro
expression of single proteins by the translation of T7 RNA polymerase
transcripts. Insertional inactivation of the T7 promoter-containing P-
galactosidase gene permits a simple blue-to-white color cloning assay” {Id.).
8. Mead teaches:
The choice of a T7 promoter in the constructs described here,
instead of a bacteriophage SP6 promoter, was made on the basis
of more extensive developments with the T7 system[.] The T7
RNA polymerase gene has been cloned and over-produced . . .
which simplifies the purification of this enzyme as well as
making it more economical to use.
(Mead 73, col. 1).
9. Mead teaches the T7 promoter sequence “consists of the two
complementary oligonucleotides,
5 ’-TAATACGACTCACTATAGGG-3 ’
3 ’ -ATTATGCTGAGTGATATCCC-5 ’ ”
(Mead 67, col. 2).
Principles of Law
A prima facie case for obviousness “requires a suggestion of all
limitations in a claim,” CFMT, Inc. v. Yieldup Int’l Corp., 349 F.3d 1333,
1342 (Fed. Cir. 2003) and “a reason that would have prompted a person of
ordinary skill in the relevant field to combine the elements in the way the
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Application 12/167,527
claimed new invention does.” KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398,
418 (2007).
Analysis
Appellant notes that “Fermentas teaches the MCS in the pJETl vector
is in the middle of the eco47IR gene in a region that does not tolerate any
insertions” (App. Br. 8). Appellant contends the skilled artisan “would not
have reasonably expected that the T7 promoter could be inserted in-frame
into the eco47IR gene of pJETl to be in operable linkage with the MCS and
still maintain the activity of the Eco47IR nuclease” (Id. ). Appellant also
contends “one of skill in the art would not have reasonably expected that a
regulatory sequence could be introduced by silent mutagenesis and also be in
a position to be in operable linkage with a DNA sequence inserted in an
essential region of a gene” (Id. at 9).
The Examiner responds “Mead clearly and unambiguously teaches in-
frame fusions between a T7 promoter and a gene of interest, and that
Appellant’s claims, in their current form, do not exclude embodiments in
which an artisan could make a simple substitution between the pJETl
construct and the in-frame T7 promoter of Mead” (Ans. 7). The Examiner
finds the “claim merely stipulates that the regulatory sequence/promoter
sequence is inserted into an ‘inessential’ region of the gene . . . This is
extremely broad language, and should not be construed as limiting the
regulatory sequence to a certain position in the gene product” (Id.). The
Examiner contends that “Claim 13 lacks any suggestion at all that the
promoter be part of, or overlap, the toxic gene ORF” (Id. at 7-8).
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Application 12/167,527
We find that Appellant has the better position. Claims 1 and 13 both
require “an inessential sequence region which encodes a section of the toxic
product” with either “a regulatory sequence inserted in-frame into the
inessential sequence region” (claim 1) or a “promoter sequence inserted in­
frame into the inessential sequence region” (claim 13).
Thus, both independent claims require insertion of the promoter or
regulatory sequence within the toxic gene product sequence. As Appellant
correctly notes, the only regulatory sequence in the original pJETl vector is
the Piacuvs promoter located outside the eco47IR sequence (see App. Br. 6).
Thus, a simple substitution of the T7 promoter for the Piacuvs promoter
would not result in the claimed invention because the T7 promoter would
not be located in an “inessential sequence region” that “encodes a section of
the toxic product” as required by claims 1 and 13. So while a substituted T7
promoter might be in an “inessential sequence region”, that region would not
“encode a section of the toxic product” and would therefore not be within
the scope of claims 1 and 13.
We further agree with Appellant that the teaching in the Fermentas
Catalog that insertions into the toxic gene product result in insertional
inactivation (FF 2, 3, 5) would have been reasonably understood by the
ordinary artisan as evidence that any substantive insertion into the toxic gene
sequence of a T7 promoter would render the gene inactive, and therefore
unusable for the positive selection required for the vector. Thus, the
evidence of record supports Appellant’s position that there would not have
been a reasonable expectation of success in inserting the T7 promoter into
the toxic gene sequence of the eco47IR gene in the pJETl vector.
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Application 12/167,527
To the extent that the Examiner is relying upon the concept of silent
mutagenesis, the Examiner provides no evidence that there is a sequence
within the pJETl plasmid that would be capable of silent mutagenesis to the
twenty nucleotide sequence of 5’-TAATACGACTCACTATAGGG-3’ of
the T7 promoter as disclosed in Mead (FF 9).
Conclusion of Law
The evidence of record does not support the Examiner’s conclusion
that Fermentas Catalog and Mead render the vector of claim 1 obvious.
SUMMARY
In summary, we reverse the rejection of claims 1 and 3-13 under 35
U.S.C. § 103(a) as obvious over Fermentas Catalog and Mead.
REVERSED
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