Cory Christensen et al.

Patent Trials and Appeals Board

Oct 24, 2019

14273492 - (D) (P.T.A.B. Oct. 24, 2019)

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.
14/273,492 05/08/2014 Cory CHRISTENSEN CRES:006USC1 9322
125771 7590 10/24/2019
DENTONS US LLP
P.O. Box 061080
Chicago, IL 60606
EXAMINER
BURAN, ASHLEY KATE
ART UNIT PAPER NUMBER
1662
NOTIFICATION DATE DELIVERY MODE
10/24/2019 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):
patents.us@dentons.com
PTOL-90A (Rev. 04/07)
UNITED STATES PATENT AND TRADEMARK OFFICE
____________

BEFORE THE PATENT TRIAL AND APPEAL BOARD
____________

Ex parte CORY CHRISTENSEN and BONNIE HUND
____________

Appeal 2019-002834
Application 14/273,492
Technology Center 1600
____________

Before ULRIKE W. JENKS, TIMOTHY G. MAJORS, and
MICHAEL A. VALEK, Administrative Patent Judges.

VALEK, Administrative Patent Judge.

DECISION ON APPEAL
Appellant1 submits this appeal under 35 U.S.C. § 134(a) involving
claims to a transgenic plant cell having an increased level of cold tolerance.
We have jurisdiction under 35 U.S.C. § 6(b).
We REVERSE.

1 We use the word “Appellant” to refer to “applicant” as defined in
37 C.F.R. § 1.42. Appellant identifies Ceres, Inc. as the real party in
interest. App. Br. 2. Herein, we refer to the Final Action mailed January 25,
2018 (“Final Act.”); Appellant’s Appeal Brief filed September 25, 2018
(“App. Br.”); Appellant’s Response to Notification of Non-Compliant
Appeal Brief filed October 15, 2018 (“Response”); Examiner’s Answer
mailed December 28, 2018 (“Ans.”); and Appellant’s Reply Brief filed
February 27, 2019 (“Reply Br.”).
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STATEMENT OF THE CASE
Claims 15–22 are on appeal and can be found in the Claims Appendix
of the Appeal Brief. Claim 15 is independent and representative of the
claims on appeal. It reads as follows:
15. A plant cell comprising an exogenous nucleic acid said
exogenous nucleic acid comprising a regulatory region operably
linked to a nucleotide sequence encoding a polypeptide,
wherein said polypeptide has 90% or greater sequence identity
to the amino acid sequence of SEQ ID NO:2 and wherein a
plant produced from said plant cell has an increased level of
cold tolerance as compared to the corresponding level of cold
tolerance of a control plant that does not comprise said nucleic
acid.
Response 2.
Appellant seeks review of the following rejections:
I. Claims 15–17, 19, and 22 under 35 U.S.C. § 102 as anticipated by
Churchman,2 and
II. Claims 15–22 under 35 U.S.C. § 103 as unpatentable over
Churchman in view of Alexandrov3 and Peres4.
App. Br. 3–9.
The issue for each rejection is: Does the preponderance of evidence
of record support Examiner’s conclusion that the cited prior art anticipates or
renders obvious Appellant’s claims?

2 Michelle L. Churchman et al., SIAMESE, a Plant-Specific Cell Cycle
Regulator, Controls Endoreplication Onset in Arabidopsis Thaliana, 18 THE
PLANT CELL 3145–57 (2006) (“Churchman”).
3 US 2006/0057724 A1; published March 16, 2006 (“Alexandrov”).
4 Adrian Peres et al., Novel Plant-specific Cyclin-dependent Kinase
Inhibitors Induced by Biotic and Abiotic Stresses, 282 J. BIO. CHEM. 25588–
96 (2007) (“Peres”).
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Analysis
Rejection I: Anticipation by Churchman
Examiner finds that Churchman discloses leaf cells transformed to
express a polypeptide “that shares 98.4% identity with instant SEQ ID
NO: 2.” Final Act. 3 (emphasis omitted). While Churchman makes no
mention of cold tolerance, Examiner determines that its transformed plant
cells would necessarily exhibit the increased level of cold tolerance recited
in claim 15 and therefore Churchman anticipates that claim. See id. at 8.
Appellant argues that the record does not support Examiner’s finding
that increased cold tolerance is inherent in Churchman’s transformed plant
cells. In particular, Appellant urges the transformation disclosed in
Churchman may or may not result in a plant having increased cold tolerance
as recited in claim 15, but that a limitation must necessarily be present for it
be deemed inherent to the prior art. See App. Br. 6–7. Appellant relies on
the Declaration of Dr. Roger Pennell dated March 7, 2017 (“Pennell Decl.”)
as evidence that “not all transgenic plants [expressing a polypeptide with the
recited sequence identity] necessarily exhibit increased growth under cold-
stress condition as compared to control plants.” App. Br. 7. The Pennell
Declaration points to the results in Example 3 of the Specification showing
that out of six events in which plants were successfully transformed to
express SEQ ID NO:2 only seedlings from two of those events exhibited
increased cold tolerance relative to the control in the inventors’ assay. Id.
(citing Pennell Decl. ¶ 17). According to Dr. Pennell:
This is often observed when creating transgenic plants. . . .
Although plant transformation is often routine, the phenotypes
of individual transformation events harboring identical
transgenes are not uniform. For transgenes that impart a
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phenotype, it is typical to find that more than half of the
successfully transformed plants actually exhibit phenotypes that
are indistinguishable from controls. Interestingly, transformed
plants that do not exhibit a phenotype are nevertheless often
likely to express the transgene because they were marker-
selected for vector integration in transcriptionally active regions
of the chromatin. Some of the causes for this phenomenon are
dosage effects, threshold mechanism, differential tissue
expression, genetic background dependence, transgene
silencing, disruption of endogenous genes by transgene
insertion, and paramutation. Thus, any one or a combination of
multiple mechanisms may explain why expression of a
transgene by a transformation event is not accompanied by the
phenotype, and, even if the transgene is expressed, there is no
guarantee that the transformation event exhibits the phenotype.

Pannell Decl. ¶ 18.
Upon considering the record as a whole, we are persuaded by
Appellant’s argument. Claim 15 recites both a structural requirement (i.e.,
that the cell has exogenous nucleic acid comprising a regulatory region
operably linked to a nucleotide sequence encoding a polypeptide with 90%
or greater sequence identity to SEQ ID NO:2) and a functional requirement
(i.e., that a plant produced from the cell has increased cold tolerance relative
to a control). Examiner has presented sufficient evidence of structural
similarity between the cells in Churchman that have been transformed to
express SMR3 to demonstrate that this functional requirement may be
inherent to that reference. See In re Spada, 911 F.2d 705, 708 (Fed. Cir.
1990) (“[W]hen the PTO shows sound basis for believing that the products
of the applicant and the prior art are the same, the applicant has the burden
of showing they are not.”). However, the evidence in the Pennell
Declaration is sufficient to meet Appellant’s burden to demonstrate that the
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claimed increase in cold tolerance is not necessarily present in Churchman’s
transformed cells. That declaration explains that both generally, and in the
specific instance of claimed transformation, only around 50% of successful
transformation events result in the claimed phenotype.
Examiner states that the “only connection to the cold tolerance
phenotype that the Appellant has provided is the overexpression of the
polypeptide (as further supported by their own data which only distinguishes
the plants based on successful transform[ation] and overexpression of SEQ
ID NO:2).” Ans. 17–18. We disagree. Examples 2 and 3 in the
Specification describe functional assays used to distinguish between
successfully transformed cells that produce plants with increased cold
tolerance and successfully transformed cells that do not. See Spec. ¶¶ 183–
200. And the results in Example 3 support that most of the time a successful
transformation did not result in progeny with increased cold tolerance. Id.
¶¶ 198–200. Thus, based on the record before us, Appellant has shown that
increased cold tolerance is not an inherent feature of cells that have been
successfully transformed to overexpress a peptide with 90% or greater
identity to SEQ ID NO:2. For this reason, Examiner’s rejection is not
supported by the preponderance of the evidence.
Rejection II: Obviousness Over Churchman, Alexandrov, and Peres
Examiner relies on the same inherency finding concerning Churchman
for the obviousness rejection. See Final Act. 10. In addition, Examiner
finds that Alexandrov teaches that transformation of plant cells with a
sequence that “shares 100% identity” with SEQ ID NO:2 “is useful ‘for
making plants with increased biomass and foliage.’” Id. at 11 (quoting
Alexandrov, Sequence Listing for SEQ ID NO:1751). Examiner further
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finds that Peres teaches that SMR3 “expression is upregulated during abiotic
stress conditions – including in response to heat stress, hypoxia, osmotic
stress, salt stress, and UV-B.” Id. (citing Peres 25594 (Fig. 7)). Examiner
determines these teachings would motivate a skilled artisan “to produce
transgenic plants and plant cell expressing” SEQ ID NO:2 and “assay the
transformed plants under abiotic stress conditions” to identify those with
increased cold tolerance. Id. at 12.
Appellant argues that the obviousness rejection should be reversed
because none of the cited references “are asserted to teach increased level of
cold tolerance.” App. Br. 9. As before, Appellant urges that increased cold
tolerance is not an inherent feature of plant cells that have been transformed
to overexpress the claimed peptide. See id. at 9–12. Regarding Peres,
Appellant contends it “merely suggests upregulation of SMR3 . . . during
abiotic stress conditions” not that “SMR3 is upregulated during cold stress”
specifically or that “expressing of SMR3 increases the level of cold
tolerance.” Reply Br. 11; see also App. Br. 15. Therefore, asserts
Appellant, Peres does not evidence a motivation to assay plants produced
from cells transformed according to the teachings in the other references for
increased cold tolerance, nor does it provide a reasonable expectation of
success in doing so. Id.
Upon considering the record as a whole, we are persuaded by
Appellant’s arguments. Like Churchman, neither Alexandrov, nor Peres,
suggests any correlation between the sequences the rejection is based upon
and cold tolerance. Alexandrov teaches that SEQ ID NO:1751 is useful for
making: (1) “lethal plants for genetic confinement systems,” (2) “plants
with increased biomass and foliage,” and (3) “smaller plants.” Alexandrov,
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Sequence Listing for SEQ ID NO: 1751. Peres teaches that a structurally
similar protein, SMR3, is upregulated in response to some types of stress
and not in response to others. See Peres 25594 (Fig. 7). But Peres does not
report whether SMR3 is upregulated in response to cold stress. Even if it
did, Examiner has not sufficiently articulated why that teaching would
motivate a skilled artisan to assay plants transformed to overexpress SMR3
for increased cold tolerance.
As explained above, the Pennell Declaration evidences that cells
successfully transformed to overexpress SEQ ID NO: 2 must be assayed to
identify those giving rise to progeny with increased cold tolerance. Thus,
while the evidence of record supports Examiner’s finding that one would be
motivated to make the claimed transformation (e.g., to increase biomass or
foliage as taught in Alexandrov), it does not demonstrate that one of
ordinary skill in the art would reasonably expect that transformation to
successfully produce progeny with increased cold tolerance as claimed.
Accordingly, we reverse.
DECISION SUMMARY

Claims
Rejected
35 U.S.C. § Reference(s)/Basis Affirmed Reversed
15–17, 19,
22
102 Churchman 15–17, 19,
22
15–22 103 Churchman,
Alexandrov, Peres
15–22

REVERSED