Novozymes A/S et al. v. Danisco A/S et al.

Filing 698

ORDER construing term "isolated variant" in Patent No. 7,717,723. Signed by District Judge Barbara B. Crabb on 10/17/2011. (llj)

IN THE UNITED STATES DISTRICT COURT
FOR THE WESTERN DISTRICT OF WISCONSIN
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - NOVOZYMES A/S and
NOVOZYMES NORTH AMERICA, INC.,
ORDER
Plaintiffs,
10-cv-251-bbc
v.
DANISCO A/S,
GENECOR INTERNATIONAL WISCONSIN, INC.,
DANISCO US INC. and DANISCO USA INC.,
Defendants.
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - The parties have responded to the court’s October 7, 2011 order requesting
supplemental briefing on the proper construction of the term “isolated variant” in U.S.
Patent No. 7,713,723. The parties’ proposed constructions address two issues: (1) the
degree to which the variant must be separated from other materials; and (2) whether the
variant must be separated from cellular material. Plaintiffs say that a variant is isolated if it
“has undergone a detectable amount of separation from cellular and/or non-cellular material.”
Dkt. #681, at 5. Defendants say that the variant must be “separated from cellular materials
such that it is substantially free from cells and cell debris.” Dkt. #682, at 1.

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With respect to the cellular/non-cellular issue, plaintiffs point to a passage in the
specification that discusses “recovering the variant from the cells and/or culture medium.”
‘723 pat., col. 20, lns. 45-46. Because “the culture medium includes non-cellular material,”
plaintiffs suggest that it is sufficient to separate the variant from cellular or non-cellular
material. Plts.’ Br., dkt. #681, at 3. Second, plaintiffs note that the specification lists
several ways of recovering the variant, including centrifugation and filtration. ‘723 pat., col.
20, lns. 54-61. According to plaintiffs, these methods “are capable of separating out cellular
or non-cellular material or both.” Plts.’ Br., dkt. #681, at 3.
Defendants cite several passages of the specification that use the modifier “isolated”
in different contexts:
In the present context, “derived from” is intended not only to indicate an
alpha-amylase produced or producible by a strain of the organism in question,
but also an alpha-amylase encoded by a DNA sequence isolated from such
strain and produced in a host organism transformed with said DNA sequence.
‘723 pat., col. 5, lns. 4-9.
The DNA sequence encoding a parent alpha-amylase may be isolated from any
cell or microorganism producing the alpha-amylase in question, using various
methods well known in the art.
Id. at col. 17, lns. 39-42.
Once an alpha-amylase-encoding DNA sequence has been isolated, and
desirable sites for mutation identified, mutations may be introduced using
synthetic oligonucleotides.

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Id. at col. 18, lns. 15-17.
Another method for introducing mutations into alpha-amylase-encoding DNA
sequences is described in Nelson and Long (1989). It involves the 3-step
generation of a PCR fragment containing the desired mutation introduced by
using a chemically synthesized DNA strand as one of the primers in the PCR
reactions. From the PCR-generated fragment, a DNA fragment carrying the
mutation may be isolated by cleavage with restriction endonucleases and
reinserted into an expression plasmid.
Id. at lns. 35-43. Defendants say that “[i]n each of these instance the term ‘isolated’ refers
to DNA that has been separated from the cells in which it was made.” Dfts.’ Br., dkt. #682,
at 4.
Also, defendants cite a passage discussing how a variant is “recovered”
The alpha-amylase variant secreted from the host cells may conveniently be
recovered from the culture medium by well-known procedures, including
separating the cells from the medium by centrifugation or filtration, and
precipitating proteinaceous components of the medium by means of a salt
such as ammonium sulphate, followed by the use of chromatographic
procedures such as ion exchange chromatography, affinity chromatography, or
the like.
‘723 pat., col. 20, lns. 54-61.
I am not persuaded that isolation under the ‘723 patent requires separation from
cellular material. Although the examples defendants cite may involve separation from a cell,
these are simply examples of ways that DNA can be separated. Defendants cite no evidence
that “isolation” inherently means separation from cellular material or that the specification
defines the term that way. Further, the passage defendants cite on “recovery” refers to

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“separating the cells from the medium,” not separating the cells from the variant. Because it
is undisputed that the medium includes non-cellular material, this passage seems to support
plaintiffs’ position more than defendants.
With respect to the degree of separation required, plaintiffs note that the invention
is intended to be used in “industrial” settings, such as starch conversion and the production
of ethanol and detergent. ‘723 pat., col. 20, ln. 65 - col. 21, ln. 20. Because these processes
“do not require the alpha-amylase to be highly processed or purified . . . one of ordinary skill
in the art would understand that alpha-amylase variants described in the ‘723 patent only
need to be separated . . . to the extent necessary to perform [their] intended function in
industrial applications.” Plts.’ Br., dkt. #681, at 4-5. In addition, plaintiffs cite a passage
in which the inventor “contemplated that a variant of the invention may be incorporated in
an amount corresponding to 0.00001-10 mg (calculated as pure, active enzyme protein) of
alpha-amylase per liter of wash/dishwash liquor using conventional dosing levels of
detergent.” ‘723 pat., col. 21, lns. 40-44. Plaintiffs say this low concentration shows that
“very minimal separation . . . is all that is required by the ‘723 patent.” Plts.’ Br., dkt. #681,
at 6. For their part, defendants cite no evidence for a “substantially free” limitation.
I do not find either side’s proposed construction persuasive on this issue. Defendants
seem to pull their “substantially free” limitation out of thin air and they simply substitute
one ambiguity for another. They say that “[t]he jury will be able to determine whether the

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accused whole broth products are substantially free of cells and cell debris using the plain and
ordinary meaning of the term substantially,” Dfts.’ Br., dkt. #682, at 6, but that assumes
that “substantially” has an “ordinary meaning” in this context. What guideposts would the
jury have to determine whether the variant had been “substantially” separated from cellular
material? Defendants do not say. This is not an issue the jury can decide from its own
experience and common sense.
Defendants cite Cohesive Technologies, Inc. v. Waters Corp., 543 F.3d 1351, 1362
(Fed. Cir. 2008), for the proposition that the term “substantially” does not need
construction, but that case is not instructive because neither side was challenging the
meaning of the term. Generally, the court of appeals has stated that “substantially” must be
construed. E.g., Anchor Wall Systems, Inc. v. Rockwood Retaining Walls, Inc., 340 F.3d
1298, 1310-11 (Fed. Cir. 2003) (remanding because court failed to construe “substantially”);
Medrad, Inc. v. MRI Devices Corp., 401 F.3d 1313, 1318-19 (Fed. Cir. 2005) (construing
“substantially”).
Plaintiffs’ proposed construction is not much better. Although it might be true that
the industrial setting of the invention does not require a high degree of separation, it does
not follow that “isolated” means a “detectable” amount of separation.

Further, this

construction suffers from the same problem as defendants’ because “detectable” would likely
require further construction. Detectable by what? And why does it matter whether the

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separation is “detectable”? What function would that serve? Plaintiffs’ proposal runs the
risk of reading the limitation out of the claim.
In the absence of a requirement in the patent for a particular degree of separation, I
adhere to my view in the summary judgment opinion that an “isolated” variant must be
sufficiently separated so that it is easier to recover. It was undisputed n the parties’ summary
judgment submissions that the general purpose of isolating a variant is to assist in identifying
and recovering that variant. A construction reflecting that purpose is thus consistent with
the way a person of ordinary skill in the art would interpret the meaning of “isolated” and
insures that the term has independent meaning in the claim.

ORDER
IT IS ORDERED that the term “isolated variant” in United States Patent No.
7,717,723 means “a variant that is sufficiently separated from other material to make the

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variant easier to recover.”
Entered this 17th day of October, 2011.
BY THE COURT:
/s/
BARBARA B. CRABB
District Judge

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