Ex Parte Stewart et al

Patent Trial and Appeal Board

Apr 2, 2018

13950545 (P.T.A.B. Apr. 2, 2018)

UNITED STA TES p A TENT AND TRADEMARK OFFICE
APPLICATION NO. FILING DATE
13/950,545 07/25/2013
23557 7590 04/04/2018
SALIW ANCHIK, LLOYD & EISENSCHENK
A PROFESSIONAL ASSOCIATION
PO Box 142950
GAINESVILLE, FL 32614
FIRST NAMED INVENTOR
C. NEAL STEWART
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.
UTR.129XCD1 1067
EXAMINER
BURAN, ASHLEY KATE
ART UNIT PAPER NUMBER
1662
NOTIFICATION DATE DELIVERY MODE
04/04/2018 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):
euspto@slepatents.com
PTOL-90A (Rev. 04/07)
UNITED ST ATES PATENT AND TRADEMARK OFFICE
BEFORE THE PATENT TRIAL AND APPEAL BOARD
ExparteC. NEAL STEWART and DAVID GEORGEJAMESMANN 1
Appeal 2017-002951
Application 13/950,545
Technology Center 1600
Before JEFFREYN. FREDMAN, RICHARD J. SMITH, and
RY ANH. FLAX, Administrative Patent Judges.
FLAX, Administrative Patent Judge.
DECISION ON APPEAL
This is a decision on appeal under 35 U.S.C. § 134(a) involving
claims to a DNA construct (and methods of using) comprising a promoter
operably linked to a heterologous nucleotide sequence of interest. 2 The
Examiner's rejection of claims 1-22 under 35 U.S.C. § 103(a) is appealed.
We have jurisdiction under 3 5 U.S. C. § 6(b ).
We affrrm.
1 Appellants identify the Real Party in Interest as "University of Tennessee
Research Foundation." Br. 1.
2 We herein refer to the Specification filed on July 25, 2013 ("Spec."); Final
Office Action mailed May 18, 2015 ("Final Action"); Appeal Brief filed
Feb. 16, 2016 ("Br."); Examiner's Answer mailed July 5, 2016 ("Answer").
Appeal 2017-002951
Application 13/950,545
STATEMENT OF THE CASE
The Specification states:
Recent advances in plant genetic engineering have enabled the
engineering of plants having improved characteristics or traits,
such as disease resistance, insect resistance, herbicide resistance,
enhanced stability or shelf-life of the ultimate consumer product
obtained from the plants and improvement of the nutritional
quality of the edible portions of the plant. Thus, one or more
desired genes from a source different than the plant, but
engineered to impart different or improved characteristics or
qualities, can be incorporated into the plant's genome. One or
more new genes can then be expressed in the plant cell to exhibit
the desired phenotype such as a new trait or characteristic.
Spec. 1:15-22.
Independent claim 1, reproduced below, is representative:
1. A DNA construct comprising a promoter operably
linked to a heterologous nucleotide sequence of interest, wherein
said promoter:
a) consists of SEQ ID NO:l;
b) consists of a fragment of SEQ ID NO: 1, wherein said
fragment initiates/drives transcription of said operably linked
heterologous polynucleotide sequence in a plant cell and consists
of nucleotides 1-607 of SEQ IDNO:l; or
c) consists of a fragment of the sequence set forth in SEQ
ID NO:l, wherein said fragment initiates/drives transcription of
said operably linked heterologous polynucleotide sequence in a
plant cell and consists of nucleotides 1-1991 of SEQ ID NO: 1.
Br. 10 (Claims App'x).
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Application 13/950,545
The following rejections are appealed:
Claims 1-5, 7-10, 13-17, and 19-22 stand rejected under 35 U.S.C.
§ 103( a) over Albert, 3 Christensen, 4 and McLaughlin. 5 Final Action 2-3.
Claims 6, 11, 12, and 18 standrejectedunder35U.S.C.§103(a)over
Albert, Christensen, McLaughlin, and Cherian. 6 Id. at 6.
FINDINGS OFF ACT
We adoptthe Examiner's findings of fact as set forth in the Final
Action and Answer. Final Action 2-1 O; Answer 2-17. We note the
following to highlight certain evidence.
FF 1. The Specification describes that disclosed and claimed
"SEQ ID NO:l" is a "nucleotide sequence[] of the 5' upstream
region[] of PvUbil,"whichis shown at the Specification's Figure 3A
such that "[t]he first 45 nucleotides of ubiquitin coding region are also
shown and indicated by double underlining." Spec. 3:11-14. The
Specification further describes that PvUbil (Figure 3A) is an ubiquitin
gene from the Panicum virgatum, switchgrass plant. Id. at 26:1-20.
3 US 6,638, 766 B2 (issued Oct. 28, 2003) ("Albert").
4 Alan H. Christensen et al., Maize polyubiquitingenes: structure, thermal
perturbation of expression and transcript splicing, and promoter activity
following transfer to protoplasts by electroporation, 18 PLANT MOL. BIO.
675-89 (1992) ("Christensen").
5 Samuel B. McLaughlin & Lynn Adams Kszos, Development of
switchgrass (Panicum virgatum) as a bioenergy feedstock in the United
States, 28 BIOMASS & BIOENERGY 515-35 (2005) ("McLaughlin").
6 Sam Cherian & M. Margarida Oliveria, Transgenic Plants in
Phytoremediation: Recent Advances and New Possibilities, 39(24)
ENVIRONMENT AL SCI. & TECH. 93 77-90 (2005) ("Cherian").
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Application 13/950,545
FF2. McLaughlin discloses that the switchgrass plant,
Panicum virgatum, is a valuable agricultural product, "as an
agricultural crop and as fuel for industry." McLaughlin 515
(Abstract); see also Final Action 2-3, 5-8 and Answer 2, 4--10, 12,
15-17 (discussing McLaughlin).
FF3. McLaughlin discloses "explor[ing] potential applications
of genetic transformation as a tool for enhancing switchgrass
productivity and/or the content of biochemical that could be used in
bioproduct production" and "transformations involving both
resistance to the herbicide Basta and transmission of green fluorescent
protein have been documented at the molecular level and through
demonstration of heritable traits in offspring of transformed
switchgrass. McLaughlin 527; see also Final Action 2-3, 5-8 and
Answer 2, 4--10, 12, 15-17 (discussing McLaughlin).
FF4. Albert discloses:
nucleic acid sequences isolated from sugarcane and to methods
of using them. In particular, the invention[] relates to nucleotide
sequences which are derived from sugarcane polyubiquitin genes
and which are capable of directing constitutive expression of a
nucleic acid sequence of interest that is operably linked to the
sugarcane polyubiquitin nucleotide sequences. The sugarcane
polyubiquitin nucleotide sequences are useful in regulating
expression of a nucleic acid sequence of interest in mono-
cotyledonous and dicotyledonous plants.
Albert Abstract; see also Final Action 2-9 and Answer 2-3, 5-12, 15-
17 (discussing Albert).
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FF5. Albert discloses:
Ubiquitin involvement has been shown in protein
turnover, heat shock response, and many other important cellular
processes. Consistent with its essential biological roles, the
structure of the protein is very highly conserved in all eukaryotes.
Many genes encoding ubiquitin contain various numbers of
tandem repeats of the entire protein coding region and hence are
called polyubiquitin genes. The primary translation product is a
polyprotein, which is processed to form ubiquitin monomers
post-translationally.
Ubiquitin protein is abundant throughout the plant body,
and several polyubiquitin genes have been shown to be expressed
in most or all cell types under most or all environmental
conditions.
Albert 13 :46---62 (citations omitted); see also Final Action 2-9 and
Answer 2-3, 5-12, 15-17 (discussing Albert).
FF6. Albert discloses "[ s ]everal polyubiquitin promoters have
been isolated and used to drive transgene expression [Christensen et
al., PlantMol Biol 18, 675-89 (1992)." Albert 14:8-10; see also Final
Action 2-9 and Answer 2-3, 5-12, 15-17 (discussing Albert).
FF7. Albert discloses that "[t]he term 'promoter,' 'promoter
element,' or 'promoter sequence' as used herein, refers to a DNA
sequence which when ligated to a nucleotide sequence of interest is
capable of controlling the transcription of the nucleotide sequence of
interest into mRN A," and "[p ]romoters may be constitutive or
regulatable. The term 'constitutive' when made in reference to a
promoter means that the promoter is capable of directing transcription
of an operably linked nucleic acid sequence in the absence of a
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Application 13/950,545
stimulus." Albert 11 :45--49, 12:25-30; see also Final Action 2-9 and
Answer 2-3, 5-12, 15-17 (discussing Albert).
FF8. Albert discloses "the nucleotide sequence of the
sugarcane polyubiquitin ubi4 gene" and "the nucleotide sequence of
the sugarcane polyubiquitin ubi9 gene." Albert 6:33-34, 6:64---65,
Figure 3, Figure 7; see also Final Action 2-9 and Answer2-3, 5-12,
15-17 (discussing Albert).
FF9. Albert discloses the "GUS activity [gene encoding P-
glucuronidase] following transient expression of GUS under the
control of the sugarcane ubi4 promoter (ubi4), sugarcane ubi9
promoter (ubi9), and maize ubil promoter (mzubil) in sugarcane
suspension cells[] and tobacco leaves." Albert 7:10-18, 7:30-34,
Figure 9, Figure 12; see also Final Action 2-9 and Answer 2-3, 5-12,
15-17 (discussing Albert). Albert Figures 9 and 12 teach that scubi4
and scubi9 promoters control expression of a respective associated
gene/nucleotide sequence of interest similarly to a maize mzubil (or
ZmUbil) promoter and that such gene expression is elevated with
respect to a control not including such promoters. Albert Figures 9
and 12; see also Final Action 2-9 and Answer 2-3, 5-12, 15-17
(discussing Albert).
FFlO. Further to the preceding fmding of fact, Albert discloses:
The term "nucleotide sequence of interest" refers to any
nucleotide sequence, the manipulation of which may be deemed
desirable for any reason (e.g., confer improved qualities), by one
of ordinary skill in the art. Such nucleotide sequences include,
but are not limited to, coding sequences of structural genes ( e. g,
reporter genes, selection marker genes, oncogenes, drug
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resistance genes, growth factors, etc.), and non-codingregulatmy
sequences which do not encode an mRNA or protein product,
(e.g., promoter sequence, polyadenylation sequence, termination
sequence, enhancer sequence, etc.).
Albert 8:62-9:5; see also Final Action 2-9 and Answer 2-3, 5-12,
15-17 (discussing Albert).
FFl 1. Albert discloses "[t]he probes provided herein are useful
in the detection, identification and isolation of, for example,
sequences such as those listed as SEQ ID NOs:7 [portion of scubi4
gene] and 10 [portion of scubi9 gene] as well as of homo logs thereof'
and"[ o ]ne of skill in the art knows that the antisense DNA segment to
be introduced into the plant may include the full length coding region
of the targeted gene or a portion thereof." Albert 19 :5 0-5 3, 24 :5-8;
see also Albert 35:40-36:20 (Example 2, describing the process for
constructing ubiquitin gene plasmids and promoters and their pairing
with a nucleotide sequence of interest); see also Final Action 2-9 and
Answer 2-3, 5-12, 15-17 (discussing Albert).
FF 12. Christensen is directed to and discloses maize
polyubiquitin genes, e.g., ZmUbil, and their promoter activity and
"[an] ubiquitin promoter-CAT fusion gene was constructed by
subcloning the Bam HI-Hind III restriction fragment containing the
CAT gene and the nopaline synthase 3' untranslated region and
polyadenylation signals ofpNOS-CAT into theBam HI andHindIII
sites ofpUC18." Christensen675-76, 678, Fig. 2 (maize Ubi-1
nucleotide sequence); see also Final Action 2--4, 6-9 and Answer 2,
4--12, 14--17 (discussing Christensen).
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FF13. Christensen discloses:
A chimeric gene was constructed from the Ubi-1 promoter and
5' untranslated sequence (including intron) by fusion to the
coding region of a gene encoding CAT and the 3' untranslated
and polyadenylation signals of a nopaline synthase gene.
Expression of CAT activity from the Ubi-1 promoter as
measured in protoplasts electroporated with this plasmid (pUBI-
CAT). High levels of CAT activity were measured ...
and further,
A more than IO-fold higher level of CAT activity was measured
in the former than in the latter. On the other hand, in extracts of
electroporated tobacco protoplasts, the CAT activity derived
from transcription ofpUBI-CAT was less than one-tenth of that
from p35S-CAT (Fig. 6B, tracks 1, 2). Thus, the maize Ubi-1
promoter drives more than 10-fold higher expression of the CAT
gene in maize protoplasts than the cauliflower mosaic virus 35S
promoter, whereas the converse is true in tobacco protoplasts.
Christensen 685-86; see also Final Action 2--4, 6-9 and Answer 2, 4--
12, 14--17 (discussing Christensen).
FF 14. Christensen discloses "[ s ]imilar polyubiquitin genes [to
ZmUbil] are found in other eukaryotic organisms, although the
number of tandem repeats varies widely" and "the Ubi-1 promoter
system described here should prove useful for facilitating
transformation of maize and other agronomically important cereals.
Christensen 686, 687; see also Final Action 2--4, 6-9 and Answer 2,
4--12, 14--17 (discussing Christensen).
FF15. Cherian discloses that "[c]ertainplants, called
hyperaccumulators, are good candidates in phytoremediation,
particularly for the removal of heavy metals" and "[p ]hytoremediation
efficiency of plants can be substantially improved using genetic
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engineering technologies." Cherian 93 77; see also Final Action 6-8
and Answer 6-8, 15-17 (discussing Cherian).
FF 16. Cherian discloses that " [ c] ontaminants such as mercury
(Hg), arsenate (As), and selenium (Se) are a serious problem in many
parts of the world and plant genetic engineering has been attempted as
a strategy to remove these metals from soil" and that Pt eris vittata is a
hyperaccumulator of the heavy metal arsenic (As) and a suitable plant
for phytoremediation. Cherian 9378 (Table 1 ), 9383; see also Final
Action 6-8 and Answer 6-8, 15-17 (discussing Cherian).
FFl 7. Cherian teaches and suggests genetically engineering
phytoremediating plants to over express certain genes, such as those
for enzymes involved in heavy metal tolerance and herbicide
resistance. Cherian 9385, 9386 (Table 4); see also Final Action 6-8
and Answer 6-8, 15-17 (discussing Cherian).
FFl 8. The Specification describes that "Pteris vittata" is a fem.
Spec. 23:8.
DISCUSSION
"[T]he examiner bears the initial burden, on review of the prior art or
on any other ground, of presenting a primafacie case ofunpatentability. If
that burden is met, the burden of coming forward with evidence or argument
shifts to the applicant." In re Oetiker, 977F.2d1443, 1445 (Fed. Cir. 1992).
"The combination of familiar elements according to known methods
is likely to be obvious when it does no more than yield predictable results."
KSR Int 'l Co. v. Teleflex Inc., 550 U.S. 398, 416 (2007). "[T]he analysis
need not seek out precise teachings directed to the specific subject matter of
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the challenged claim, for a court can take account of the inferences and
creative steps that a person of ordinary skill in the art would employ." Id. at
418. "Indetermining whetherthe subject matter of a patent claim is
obvious, neither the particular motivation nor the avowed purpose of the
patentee controls. What matters is the objective reach of the claim. If the
claim extends to what is obvious, it is invalid under§ 103." KSR, 550 U.S.
at 419. Further,
an implicit motivation to combine exists not only when a
suggestion may be gleaned from the prior art as a whole, but
when the "improvement" is technology-independent and the
combination of references results in a product or process that is
more desirable, for example because it is stronger, cheaper,
cleaner, faster, lighter, smaller, more durable, or more efficient.
Because the desire to enhance commercial opportunities by
improving a product or process is universal--and even common-
sensical-- . . . there exists in these situations a motivation to
combine prior art references even absent any hint of suggestion
in the references themselves. In such situations, the proper
question is whether the ordinary artisan possesses knowledge
and skills rendering him capable of combining the prior art
references.
Dystar Textilfarben Gmbh & Co. DeutschlandKGv. C.H. Patrick Co., 464
F.3d 1356, 1368 (Fed. Cir. 2006).
The Examiner determined that, while none of the cited references
expressly discloses the nucleotide sequence SEQ ID NO:l or its sub-parts,
as claimed, the prior art combination of Albert, Christensen, and
McLaughlin would have made obvious using a promoter of such a sequence
or portion thereof, i.e., PvUbil, to control the expression of another
nucleotide sequence of interest. See Answer 2---6. The Examiner
determined:
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It would have been obvious to one of ordinary skill in the
art to utilize the ZmUbil, ScUbi4, or ScUbi9 coding sequence or
the ZmUbil, ScUbi4, or ScUbi9 5' UTRs as a probe in order to
identify other polyubiquitin genes in other plant species and
obtain the corresponding 5 'UTR promoter sequences. One
would have been motivated to do so because (i) Christensen et al
teach that the maize Ubil promoter drives expression at least 10-
fold higher in monocot plant species than the constitutive CaMV
35S promoter, (ii) Albert et al teach that Ubi promoters from
sugarcane drive constitutive expression similar to the Zm Ubil
and thus greater than the CaMV 35S promoter, and (iii) Albert et
al suggest using the Ubi sequences to obtain other polyubiquitin
promoters; and thus, one would have been motivated to probe
genomic sequences for Ubi genes in order obtain other promoters
that drive high-level constitutive expression in high-value
monocot plant species.
Furthermore, it would have been obvious to specifically
target the monocot plant species P ani cum vi rgatum for isolation
of the ubiquitin gene. One would have been motivated to
specifically target the Panicum virgatum Ubil gene given the
high value of the switchgrass plant in both agricultural and
energy industries (as taught by McLaughlin et al) and to obtain
its 5' UTR promoter, which given the extensive teachings of
Albert et al and Christensen et al would have been expected to
drive a high level of expression in monocots. In doing so, one
would naturally isolate a promoter sequence consisting SEQ ID
NO: 1 or a fragment consisting nucleotides 1-607 or 1-1991 of
SEQ ID NO: 1 that drives a high level of constitutive expression
in a plant. One would have had a reasonable expectation of
success of isolating said promoters given that (i) it was known
that ubiquitin protein sequences are highly conserved among
even very diverse organisms (and thus, one would be readily able
to recognize a given sequence as a ubiquitin gene) and further
that this conservation "is the same as for other plant ubiquitins"
and (ii) that methods of probing and isolating DNA for
polyubiquitin genes and their 5' UTRs were well known and
routine in the art (as taught by Christensen et al and Albert et al).
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Furthermore, one would reasonably expect that instant SEQ ID
NO: 1 would drive high-level constitutive expression given that
this expression pattern and level is exhibited by at least 3 other
similar polyubiquitin promoters from other monocot species (i.e.
ZmUbil, ScUbi4, and ScUbi9).
Answer 5---6. We conclude, under the above cited precedent, the Examiner
has established a prima facie case that the claims would have been obvious
over Albert, Christensen, and McLaughlin.
Appellants argue "a person of ordinary skill in the art would not have
been motivated to obtain the specifically claimed promoter sequences"
claimed. Br. 5 (holding and underlining omitted). Appellants summarize
the Examiner's prima facie case for obviousness as follows:
The Examiner argues that because certain ubiquitin promoters
are known and because switchgrass is of high interest as a
bioenergy crop, it would have been obvious to identify and
isolate the claimed promoters from the switchgrass genome.
This rejection is, in essence, tantamount to stating that, since the
switchgrass is of interest as a bioenergy crop and genetic
mapping of switchgrass has been performed to identify
differences between switchgrass populations and generate
genetic links to various traits so as to improve yield and breeding
techniques for switchgrass, it would have been obvious to
identify and isolate the claimed ubiquitin promoters and then
utilize such promoters in a DNA construct comprising a
heterologous gene operably linked to: a) a promoter consisting
ofSEQIDNO: 1.
Id. (holding and underlining omitted). We agree with Appellants' summary
of the Examiner's position as accurate; but, ratherthan supportingnon-
obviousness as Appellants contend, we find the Examiner's rationale to be
reasonable as it establishes that there would have been motivation to
genetically engineer switchgrass using an ubiquitin promoter to enhance
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some desired phonotype, e.g., herbicide tolerance, in the plant. Furthermore,
per the Examiner's rationale, in genetically modifying switchgrass it would
make sense to use the plant's own ubiquitin promoterPvUbil, which is SEQ
ID NO: 1, and there would have been a reasonable likelihood of successfully
doing so.
McLaughlin teaches thatthe species Panicum virgatum, switchgrass,
is a valuable agricultural product and one that has been studied for ways to
genetically engineer it to enhance its commercial value. FF2-FF3. Once the
skilled artisan had set out on the known course of genetically engineering
switchgrass, for example, to provide enhanced resistance to herbicide (see
FF3), that artisan would also have obviously referenced teachings of
effective genetic engineering techniques to do so, which would have
included the teachings Christensen and Albert. Albert teaches that ubiquitin
promoters (from, e.g., sugarcane-ScUbi4, andmaize-ZmUbil) are useful
in genetically engineering plants ("polyubiquitin nucleotide sequences are
useful in regulating expression of a nucleic acid sequence of interest in
monocotyledonous and dicotyledonous plants") [Albert, Abstract]; for
example, to exhibit herbicide tolerance or insect tolerance, and teaches
methods of doing so. FF 4--FF 11. Albert also indicates that the sugarcane
ubiquitin promoter is similar to the maize ubiquitin promoter (ZmUbil ).
FF6, FF8, FF9. Albert also expressly invokes the teachings of Christensen,
citing Christensen as teaching that"[ s ]everal polyubiquitin promoters have
been isolated and used to drive trans gene expression." (Albert 14:8-10)
FF6. Christensen teaches using the maize ubiquitin promoter to control
phenotypic responses in other plants. FF12-FF13. Christensen also teaches
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that ubiquitin is a highly conserved protein across species and the gene
comprises predictably repeating sequences, which is the same for other plant
ubiquitins. FF14.
All of the above suggests that using an ubiquitin promoter nucleotide
sequence would be an effective way of controlling the expression of an
associated gene/nucleotide sequence of interest in a plant, for example to
increase herbicide tolerance, and that the switchgrass plant would be an
obvious choice for such genetic engineering. The cited prior art suggests
that a variety of specific ubiquitin promoters would be effective for such a
use, for example, ZmUbil or ScUbi4. The cited prior art also teaches and
suggests that isolating such ubiquitin promoters is well known and routine.
Finally, using an ubiquitin promoter derived from the very plant species of
commercial interest would also have been an obvious choice for genetically
engineering that plant, i.e., using the claimed PvUbil, or SEQ ID NO:l, to
genetically engineer switchgrass. Therefore, for the reasons set forth above
we affrrm this rejection. The dependent claims are not argued separately and
fall with claim 1.
The Examiner also rejected as obvious claims 6, 11, 12, and 18
directed to genetically engineering a fem species with the claimed ubiquitin
promoter, adding the teachings of Cherian to the prior art combination
discussed above. Final Action 6. Cherian teaches that the fem species
Pteris vittata is a valuable plant for accumulating Arsenic from soil to
decontaminate the soil and that the species has been genetically engineered
to enhance its ability to do so, which would make it obvious to use ubiquitin
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promoter engineering as disclosed by Albert and Christensen. FF 15-FFl 7.
Pteris vittata is a type of fem. FFl 8.
Appellants argue "[t]he additional teachings of Cherian et al. fail to
remedy the defects noted above for the combined teachings of Albert et al.
Christensen et al. and McLaughlin et al. as the teachings of Cherian et al.
solely relate to the use of fem species for phytoremediation." Br. 8-9.
Because we find the weight of the evidence supports the Examiner's
case for the obviousness of the claims and are not persuaded by Appellants'
arguments we affrrm this rejection for the reasons set forth above.
SUMMARY
The obviousness rejections are each affrrmed.
No time period for taking any subsequent action in connection with
this appeal may be extended under 37 C.F.R. § 1.136(a)(l )(iv).
AFFIRMED
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