Ex Parte Blau et al

Board of Patent Appeals and Interferences

Mar 18, 2011

10508264 (B.P.A.I. Mar. 18, 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.
10/508,264 09/20/2004 Astrid Blau 13111-00016-US 5914
23416 7590 03/18/2011
CONNOLLY BOVE LODGE & HUTZ, LLP
P O BOX 2207
WILMINGTON, DE 19899
EXAMINER
WORLEY, CATHY KINGDON
ART UNIT PAPER NUMBER
1638
MAIL DATE DELIVERY MODE
03/18/2011 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 ASTRID BLAU, MATHIEU KLEIN, and
BIRGIT WENDEL
__________

Appeal 2010-009081
Application 10/508,264
Technology Center 1600
__________

Before DEMETRA J. MILLS, MELANIE L. McCOLLUM, and STEPHEN
WALSH, Administrative Patent Judges.

WALSH, Administrative Patent Judge.

DECISION ON APPEAL1
This is an appeal under 35 U.S.C. § 134(a) involving claims to a
collection of transgenic plants comprising genes from a donor organism.
The Patent Examiner rejected the claims on grounds of indefiniteness and

1 The two-month time period for filing an appeal or commencing a civil
action, as recited in 37 C.F.R. § 1.304, or for filing a request for rehearing,
as recited in 37 C.F.R. § 41.52, begins to run from the “MAIL DATE”
(paper delivery mode) or the “NOTIFICATION DATE” (electronic delivery
mode) shown on the PTOL-90A cover letter attached to this decision.
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obviousness. We have jurisdiction under 35 U.S.C. § 6(b). We affirm.

STATEMENT OF THE CASE
Claims 1-4, 6, 12, 38 and 53-55 are on appeal. Claim 1 is
representative and reads as follows:
1. A population of transgenic plants that comprises a plurality of
transgenic plants of which each plant has integrated into its genome one or
more than one copy of one codogenic gene segment of a cellular donor
organism that encodes one protein of the cellular donor organism, but has
integrated no other codogenic gene segment encoding another protein of the
cellular donor organism, wherein the integrated codogenic gene segment
comprises a start codon and a stop codon that define an open reading frame
encoding the protein;
[w]herein the integrated codogenic gene segment is operably linked to a
regulatory sequence so that the open reading frame is transcribed and
translated;
wherein said plurality of transgenic plants as a whole comprises at least 50%
of all codogenic gene segments that encode a protein of the cellular donor
organism; and
wherein the plurality of transgenic plants is obtained by
a) providing a known codogenic gene segment that encodes one
protein of a cellular donor organism and integrating one or more than one
copy of the codogenic gene segment into the genome of a plant;
b) providing another known codogenic gene segment that encodes
another protein of the cellular donor organism and integrating one or more
than one copy of the other codogenic gene segment into the genome of
another plant;
c) repeating step b) so that the resulting plurality of transgenic
plants as a whole comprises at least 50% of all codogenic gene segments of
the cellular donor organism. (App. Br. A-1.)

The Examiner rejected the claims as follows:
• claims 1-4, 6, 12, 38 and 53-55 under 35 U.S.C. § 112, second
paragraph, as indefinite;
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Application 10/508,264

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• claims 1-4, 6, 12, 38, and 53-55 under 35 U.S.C. § 103(a) as
unpatentable over Pineda2 and Lazo;3 and
• claims 1-4, 6, 12, 38, and 53-55 under 35 U.S.C. § 103(a) as
unpatentable over Reuber4 and Lazo.

DEFINITENESS
The Issue
The rejection focuses on the meaning of “codogenic gene segment.”
Claim 1 at part c) requires that the claimed plant population comprise “at
least 50% of all codogenic gene segments of the cellular donor organism.”
The Examiner’s position is that “it is unclear how one can define all of the
codogenic gene segments in a donor organism given the definition and
example in the specification.” (Ans. 5.)
Appellants contend that “[t]he term ‘codogenic gene segment’ in
claim 1 is recited as 1) encoding one protein of a cellular donor organism
and 2) comprising a start codon and a stop codon that define an open reading
frame encoding the protein.” (App. Br. 5.) That is, although the
Specification lists alternative meanings, the “Examiner’s concern has
focused on an embodiment which is not claimed.” (Id. at 6.) As Appellants
read claim 1 part c), “the recitation of codogenic gene segment at line 19

2 Omaira Pineda et al., Environmental Stress Tolerance Genes,
WO 01/36598 A1, published May 25, 2001.
3 Gerard R. Lazo et al., A DNA Transformation-Competent Arabidopsis
Genomic Library in Agrobacterium, 9 BIO/TECHNOLOGY 963-967 (1991).
4 T. Lynne Reuber et al., Transcription Factors For Increasing Yield,
US 2007/0022495 A1, published Jan. 25, 2007.
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also requires that the codogenic gene segment encode a protein.” (Reply Br.
5, referencing line numbers assigned at Reply Br. 3.)
The issue is whether claim 1, part c) requires that the codogenic gene
segment encode a protein.
Findings of Fact
1. The Specification states:
The term “codogenic gene segment” refers to a nucleic acid.
Nucleic acids . . . include DNA and RNA sequences which can
be single- or double-stranded . . . . In particular, the term
“codogenic gene segment” refers to the coding sequence, i.e.
the part of a gene which encodes a protein, polypeptide or part
thereof.

(Spec. 2, ll. 10-17.)
Principles of Law
During patent examination the pending claims must be
interpreted as broadly as their terms reasonably allow. When
the applicant states the meaning that the claim terms are
intended to have, the claims are examined with that meaning . .
. . The reason is simply that during patent prosecution when
claims can be amended, ambiguities should be recognized,
scope and breadth of language explored, and clarification
imposed.

In re Zletz, 893 F.2d 319, 321 (Fed. Cir. 1989) (citations omitted).
Analysis
Part c of claim 1 reads:
(c) repeating step b) so that the resulting plurality of
transgenic plants as a whole comprises at least 50% of all
codogenic gene segments of the cellular donor organism.
(Claim 1, emphasis added.)

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We agree with the Examiner that “codogenic gene segment” in line
195 of claim 1 includes the full scope of the Specification’s definition of the
term. The Specification states that the term “refers to a nucleic acid.”
(FF1.) Giving weight to “codogenic,” the definition includes gene segments
coding for tRNAs, which are not proteins, as the Examiner found. We also
agree with the Examiner that the Specification’s phrasing “[i]n particular,
the term . . . refers to” is reasonably understood as particularly referring not
only to a protein, but also to a polypeptide, and to parts thereof. (Ans. 5.)
On its face, line 19 does not explicitly or impliedly limit “codogenic gene
segment” to a segment that encodes a protein. Reading line 19 in light of the
Specification’s guidance does not alter that conclusion.
We agree with Appellants that the first nine occurrences of
“codogenic gene segment” in claim 1 are further defined and explicitly
limited by additional words or phrases: “. . . that encodes one protein” (lines
3 and 12); or “encoding another protein” (lines 4-5 and 15); or “comprises a
start codon and a stop codon that define an open reading frame” (line 6); or
“is operably linked to a regulatory sequence so that the open reading frame
is transcribed and translated” (lines 7-8); or “that encode a protein” (lines 9-
10); or “the” referencing a defined antecedent (line 13); or “the other”
referencing a defined antecedent (line 16). We do not agree with the
Examiner that those usages or occurrences are unclear. (Ans. 6, discussing
claim lines 5 and 6 and claim part b.) However, the tenth occurrence of

5 We reference the line numbers assigned in Appellants’ Reply Brief at 3.
Although the numbers 5 and 10 are assigned to duplicate lines (in the format
shown the line labeled 19 should be labeled 21), it is simpler to use the
numbers Appellants assigned.
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“codogenic gene segments” in line 19 is unencumbered by explicit, implicit,
or referential limiting words. (Ans. 5.)
We cannot agree with Appellants that the segments recited in line 19
are necessarily limited by process limitations. Although step c) recites
“repeating step b) so that the resulting plurality of transgenic plants as a
whole comprises at least 50% of all codogenic gene segments,” the
population may still include an unknown number of segments coding for
tRNAs, or parts of proteins, which are balanced out by adding some number
of protein encoding segments to make up 50% of the donor’s coding
segments. Thus, we do not agree that reading the claim as a whole requires
reading Appellants’ preferred limited embodiment into line 19. While the
claim includes Appellants’ preferred embodiment, the claim is not properly
interpreted as limited to that embodiment.
The differences between the Examiner’s Specification-based
interpretation and Appellants’ implied-process interpretation confirm there is
an ambiguity in what claim part c) defines. The problem is in knowing what
should be counted. (Ans. 5-6.) The Examiner wrote “the Examiner does not
know how that can be quantitated,” but we are affirming on the ground that
the person of ordinary skill in the art would find the claim ambiguous as to
what should be counted, not because the person of ordinary skill would have
difficulty counting if they knew what to count. We agree with the Examiner
that the ambiguity about which segments to count should be removed. See
Zletz, 893 F.2d at 322 (“[a]n 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”). Even if we accept Appellants’ implied-
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process limitation of line 19 as another plausible construction, we still
affirm. See Ex parte Miyazaki, 89 USPQ2d 1207, 1211 (BPAI 2008) (“if a
claim is amenable to two or more plausible claim constructions, the USPTO
is justified in requiring the applicant to more precisely define the metes and
bounds of the claimed invention by holding the claim unpatentable under
35 U.S.C. § 112, second paragraph, as indefinite”).
Claims 4-6, 12, 38, and 53-55 have not been argued separately and
therefore fall with claim 1. 37 C.F.R. § 41.37(c)(1)(vii).

OBVIOUSNESS
The Issues
According to Appellants, the Reuber reference is a continuation-in-
part application of the US counterpart of the Pineda PCT Application. We
will consider the issues together, referring to Pineda and Lazo.
The Examiner’s position is that Pineda described a population of
transgenic plants in which each plant had integrated into its genome a gene
encoding one transcription factor from the donor organism Arabidopsis.
(Ans. 8.) The transcription factor genes that Pineda integrated into plants
did not total more than 50% of all codogenic gene segments from
Arabidopsis, and thus Pineda’s plant population as whole did not comprise
at least 50% of all codogenic gene segments from the donor organism,
Arabidopsis. (Id. at 9.) According to the Examiner, Lazo described a
genomic library comprising more than 50% of the codogenic gene segments
from Arabidopsis. (Id.) The Examiner concluded: “it would have been
obvious and within the scope of one of ordinary skill in the art to extend the
population taught by Pineda et al to cover at least 50% of the genome of the
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donor organism.” (Id.) The Examiner reasoned that (1) the necessary DNA
was publically available in Lazo’s library, (2) Pineda had taught that one
could make cDNA libraries from different tissues, and (3) “it would have
been obvious . . . to extend the teachings of Pineda et al to go beyond a set of
transcription factors to cover more of the available coding sequences from
Arabidopsis.” (Id.) The Answer refers to Kumagai,6 Tomes,7 and Reuber
for further evidence of the state of the art, each of which is said to teach
“populations of plants expressing multiple nucleic acids, often referred to as
a ‘library.’” (Id. at 10.) According to the rejection, the additional references
disclosed “variations on the theme that it would have been useful to express
nucleic acids in plants to determine the function or effect of the protein
encoded by the nucleic acid.” (Id. at 11.)
Appellants first contend that (1) the references do not provide any
suggestion to modify Pineda’s population or teach the desirability of
modification (App. Br. 10-13), (2) Pineda and Lazo are incompatible rather
than combinable, and direct one in a different direction than the population
claimed with its particular features (id. at 14-16), and (3) Pineda and Lazo
do not teach or suggest all the claim limitations (id. at 16-18). Appellants
contend that Tomes described delivering a plurality of vectors en bloc into
plant cells, but that because Tomes used the donor’s transcriptome, it would
have had an incomplete donor genome sample that could not be scaled up
beyond 100 sequences. (Reply Br. 6-7.) Appellants contend that Kumagai
did not provide a library covering 50% or more of any organism’s genome,

6 Monto H. Kumagai et al., WO 01/07600 A1, published Feb. 1, 2001.
7 Dwight T. Tomes et al., US 2003/0221212 A1, published Nov. 27, 2003.
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and that because Kumagai taught transient expression, it led away from
creating transgenic organisms. (Id. at 8.) Finally, Appellants contend that
even if the references had a common goal (to determine function or effect of
the protein encoded by a nucleic acid), knowledge of the goal does not
render its achievement obvious. (Id.) According to Appellants, the
references achieved their goals in completely different ways, resulting in
populations of plants different from the population claimed, which “has
practical advantages over the products of the references.” (Id. at 9.)
The issues are:
whether Pineda and Lazo, in view of the state of the art, provided a
reason to use the steps recited in the claims to obtain a population of plants
having the properties defined in the claims; and
whether Reuber and Lazo, in view of the state of the art, provided a
reason to use the steps recited in the claims to obtain a population of plants
having the properties defined in the claims.
Findings of Fact
1. We adopt the Examiner’s specific findings of fact concerning the
Pineda and Lazo disclosures.
Principles of Law
When determining whether a claim is obvious, an Examiner must
make “a searching comparison of the claimed invention – including all its
limitations – with the teachings of the prior art.” In re Ochiai, 71 F.3d 1565,
1572 (Fed. Cir. 1995). An invention
composed of several elements is not proved obvious merely by
demonstrating that each of its elements was, independently, known in
the prior art….[I]t can be important to identify a reason that would
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have prompted a person of ordinary skill in the relevant field to
combine the elements in the way the claimed new invention does.

KSR Int’l Co. v. Teleflex Inc., 550 U.S. 398, 418 (2007). Thus, “[r]ejections
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).
Analysis
Although the Examiner concluded the claims are indefinite, the
Examiner nevertheless examined the claims by comparing the invention to
combinations of references that teach transformation of one clone at a time
into one individual plant at a time, “in order to expedite prosecution.” (Ans.
7-8.) We conclude that the embodiment examined would not have been
obvious on this record.
We agree with the Examiner that those of ordinary skill in the art were
motivated to use transgenic plant populations to learn the functions and
effects of proteins encoded by various genes. However, we also agree with
Appellants that knowing the goal does not necessarily render particular
solutions to the problem obvious. In this case, Appellants have pointed to
particular differences between the claimed plants and those known in the art,
and they argue that the rejection did not explain how each of those different
features would have been obvious. (See App. Br. 16-18; Reply Br. 9-17.)
The evidence shows that the plant population defined in the claims has
features distinct from the plants described in Pineda, Reuber, Lazo, Tomes,
or Kumagai. We are persuaded by Appellants’ arguments that the rejection
did not explain why those distinctive features would have been obvious.
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SUMMARY
We affirm the rejection of claims 1-4, 6, 12, 38 and 53-55 under
35 U.S.C. § 112, second paragraph, as indefinite.
We reverse the rejection of claims 1-4, 6, 12, 38, and 53-55 under
35 U.S.C. § 103(a) as unpatentable over Pineda and Lazo.
We reverse the rejection of claims 1-4, 6, 12, 38, and 53-55 under
35 U.S.C. § 103(a) as unpatentable over Reuber and Lazo.

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

lp

CONNOLLY BOVE LODGE & HUTZ, LLP
P O BOX 2207
WILMINGTON DE 19899