NUtech Ventures v. Syngenta Seeds, Inc. et al

Filing 115

MEMORANDUM AND ORDER - IT IS ORDERED: The Court construes the term "hyperthermophilic glycosyl hydrolase," appearing in Claim 1 of the '592 Patent, to mean "glycosyl hydrolase derived from organisms capable of growth above 70 C ." The Court construes the term "said substrate comprises extract of plant transformed with said recombinant hyperthermophilic glycosyl hydrolase," appearing in Claim 1 of the '592 Patent, to mean "the plant substrate include s extract of plant that has been transformed with the recombinant hyperthermophilic glycosyl hydrolase." The Court construes the term "wherein the glycosyl hydrolase is localized with the substrate in tissue of the plant," appearing in Claim 1 of the '592 Patent, to mean "wherein the glycosyl hydrolase and substrate of the transformed plant are located inside the same cell." Ordered by Chief Judge Laurie Smith Camp. (TCL )

IN THE UNITED STATES DISTRICT COURT
FOR THE DISTRICT OF NEBRASKA
NUTECH VENTURES,
Plaintiff,

CASE NO. 8:12CV289

vs.
SYNGENTA SEEDS, INC., and
TRENTON AGRI PRODUCTS LLC,

MEMORANDUM
AND ORDER

Defendants.

This matter is before the Court on the parties’ Joint Claim Construction
Statement (Filing No. 75).

Plaintiff and Counterclaim Defendant NuTech Ventures

(“NUTech”) has sued Defendants and Counterclaim Plaintiffs Syngenta Seeds, Inc.
(“Syngenta”) and Trenton Agri Products LLC (“Trenton”) (collectively “Defendants”)
alleging that the Defendants have infringed U.S. Patent No. 6,506,592 B1 (the “‘592
Patent”). The parties collectively have requested that the Court construe certain terms
in the ‘592 Patent.
BACKGROUND
I.

General Patent Overview
The ‘592 Patent is titled “Hyperthermophilic Alpha-Glucosidase Gene and Its

Use,” and generally relates to plant matter that has been genetically transformed so that
it produces an enzyme not naturally produced in the plant. (Filing No. 1-1, summary;
Filing No. 85 at 2.) The patent application was filed on August 18, 1999, and claims
priority to a provisional application that was filed a year earlier. The ‘592 Patent issued
on January 14, 2003, and includes nine claims directed to a “method of converting plant
substrate.” Dr. Paul Blum (“Dr. Blum”), a professor and researcher at the University of
Nebraska in Lincoln, Nebraska, developed the technology used in the ‘592 Patent, and

NUTech owns the ‘592 Patent.

NUTech claims that the Defendants’ use of a bio-

engineered corn called Enogen relies on technology from the ‘592 Patent to convert the
starch in corn into smaller sugars during ethanol production.
II.

General Scientific Overview
The ‘592 Patent relates to reactions that occur during a chemical process called

hydrolysis. Carbohydrates can be considered a group of sugar molecules joined by
chemical bonds. Carbohydrates, such as starch, store energy. When the chemical
bonds in a group of sugar molecules are broken, the starch can be processed for use in
different industries, such as the production of ethanol. The chemical bonds between
sugar molecules in starch are called “glycosidic bonds.” To convert starch into sugars,
the chemical bonds between the sugar molecules are broken by water through
hydrolysis.
The natural hydrolysis reaction can be very slow, so ethanol producers add
proteins to the process called “enzymes” to act as catalysts to speed up the reactions.
Enzymes are proteins that function as catalysts in biochemical reactions by acting on
one or more starting plant materials called “substrates.” Environmental conditions, such
as temperature and pH, can greatly affect the activity of an enzyme. In general, the
activity of an enzyme increases with temperature because molecules move and interact
more quickly at higher temperatures. Temperature also affects the integrity and stability
of enzymes. Increased temperature can cause the protein structure of an enzyme to
weaken, which can hinder its ability to catalyze reactions. Depending on their structure
and other characteristics, some enzymes are only active at moderate temperatures,
whereas other related enzymes catalyzing the same reactions are capable of activity at
2

relatively high temperatures. The thermophilicity of an enzyme relates to the ability of
the enzyme to catalyze reactions at relatively high temperatures.
While active enzymes can convert plant material to products such as ethanol,
continued activity at times may not be desirable.

For this reason, cells of living

organisms have evolved to regulate enzyme activity. For example, cells can regulate
when and where an enzyme is produced. Those skilled in the art can take advantage of
natural regulatory mechanisms in living cells to design recombinant enzymes to
catalyze desired activity. For example, those skilled in the art can engineer the cellular
location and activity of enzymes to control when certain processes occur.
III.

Invention Background
The claims in the ‘592 Patent involves a specific type of enzymes called “glycosyl

hydrolases” that aid in breaking glycosidic bonds during hydrolysis. NUTech claims
that, prior to the invention, companies typically added enzymes at some point during the
hydrolysis process to speed up production.

This is because industrial hydrolysis

involved not only adding water and enzymes to a mixture of plant material, but also
heating the mixture to a very high temperature. Thus, the enzymes had to be heat
resistant to perform their function at high temperatures. Enzymes that can resist heat
and perform their function at high temperatures are called “thermostable” enzymes.
Purchasing and storing thermostable enzyme additives is expensive and represents a
significant cost in the starch hydrolysis process.
In the ‘592 Patent, Dr. Blum claims to have identified and cloned a glycosyl
hydrolase derived from an organism that grows in locations that experience high
temperatures.

Dr. Blum also developed a bioengineered plant containing glycosyl
3

hydrolases from these organisms.

Because the organisms could survive in high

temperatures, the glycosyl hydrolases derived from the organisms were thermostable,
and could survive at high temperatures. Further, the enzymes were already located in
the bioengineered plants, so companies would not have to purchase, store, and then
add the enzyme additives to convert the starch in the plant material. Because of their
hyperthermophilic origin, the enzymes would not significantly interfere with the plants’
normal metabolism, and were not toxic to the plants even when the enzymes were
found inside the same cells as the plant substrate.
IV.

Patent Prosecution History
Dr. Blum originally filed a provisional patent application in 1998, and a formal

patent application in 1999. The United States Patent and Trademark Office (“USPTO”)
spent over three years reviewing the application before a patent was issued in 2003.
Both parties’ arguments reference the prosecution history to aid their respective claim
constructions.

By reviewing the prosecution history, the Court does not prejudge

infringement or validity of the ‘592 Patent. However, this information is useful for
background, and can be considered in interpreting terms.1
The parties agree that, generally in the 1990s, the method in the industry was to
add separately produced enzymes to plant material for use in hydrolysis. The ‘592
1

The Court cannot prejudge infringement or validity in the Markman ruling. See PPG Indus. v.
Guardian Indus. Corp., 156 F.3d 1351, 1355 (Fed. Cir. 1998) (“Claims are often drafted using terminology
that is not as precise or specific as it might be. As long as the result complies with the statutory
requirement to ‘particularly point[ ] out and distinctly claim[ ] the subject matter which the applicant
regards as his invention,’ . . .that practice is permissible. That does not mean, however, that a court,
under the rubric of claim construction, may give a claim whatever additional precision or specificity is
necessary to facilitate a comparison between the claim and the accused product. Rather, after the court
has defined the claim with whatever specificity and precision is warranted by the language of the claim
and the evidence bearing on the proper construction, the task of determining whether the construed claim
reads on the accused product is for the finder of fact.”).

4

Patent states that “[a] variety of industries, such as food and chemical, employ
hydrolases for the production of glucose, sucrose and other sugars,” and that “[h]igh
value is placed on thermostability and thermoactivity of enzymes for use in the
bioprocessing of starch . . . .” (Filing No. 1-1 at 1:25–30.) The ‘592 Patent also notes
that “the current method used in the industry” in the 1990s was “to add separately
produced commodity enzymes to plant material.” (Id. at 3:1–2.)
The USPTO Examiner originally rejected Dr. Blum’s pending claims as obvious.
The USPTO explained that the original application lacked reference to previously
published papers on related subjects, and thus failed to disclose the prior art. Much of
the prosecution history concerned a 1992 article entitled “Production of Active Bacillus
Licheniformis Alpha-Amylase in Tobacco and Its Application in Starch Liquiefaction”
written by Jan Pen and others (the “Pen Article”). 1 The USPTO noted that the Pen
Article concerned a tobacco plant with enzymes that had the characteristic of being less
active at lower temperatures and highly active at high temperatures. Accordingly, the
USPTO rejected the application as obvious considering the prior art.
Dr. Blum responded to the USPTO by differentiating the enzymes described in
the Pen Article from the enzymes in his application. Br. Blum explained that in the Pen
Article, the plant substrate was located inside the plant cells, and the enzyme was
outside the plant cells. Thus, the enzyme and the plant substrate were separated into
different cellular compartments, and were brought together for the processing through
homogenization.

In contrast, the Dr. Blum argued that his invention used a

“hyperthermophilic” glycosyl hydrolase.

According to Dr. Blum’s application, his

1

The Pen Article appears in multiple filings. References to the Pen Article in this Memorandum
and Order will be to its first appearance at Filing No. 83-6.

5

invention did not require separation of the plant substrate from the enzymes, because
the activity of the enzyme was not detectable at normal plant growth temperatures. The
USPTO Examiner initially rejected this argument because the patent itself did not
specifically state that the enzyme and the plant material could coexist in the cells.
Specifically, the USPTO noted that the claims in the application “did not specifically
require nonsequestered localization of the transgenic enzyme in the plant.” (Filing No.
86-5 at ECF 82.)
Dr. Blum responded by amending the ‘592 Patent’s claims to include the phrase
“wherein the glycosyl hydrolase is located with the substrate in tissue of the plant.”
(See Filing No. 1-1 at ECF 40.) Dr. Blum distinguished his invention from the prior art
mentioned in the Pen Article by explaining that “[s]ince enzyme and substrate are
present in different cellular compartments [in the method of the Pen Article], no
degradation of the substrate occurs during growth. The enzymatic reaction is initiated . .
. when by homogenation the enzyme and the substrate are brought together.” (Filing
No. 86-5 at ECF 101.) In contrast, Dr. Blum stated that “[s]uch separate localization is
not required in the method of the present invention.” (Id.) Based on this amendment,
the USPTO withdrew its rejection, and allowed the patent to issue.
The claim issued as independent Claim 12 in the ‘592 Patent. Claims 2-9 of the
‘592 Patent all depend on Claim 1. The parties’ claim construction dispute relates to
Claim 1 and dependent Claim 9 in the ‘592 Patent. Claim 1 states:

2

Prior to the final amendment, the text of what is now Claim 1 was referred to as “claim 25.”

6

A method for converting plant substrate, comprising heating said substrate
in the presence of recombinant hyperthermophilic glycosyl hydrolase,
wherein said substrate comprises extract of plant transformed with said
recombinant hyperthermophilic glycosyl hydrolase, and wherein the
glycosyl hydrolase is localized with the substrate in tissue of the plant.
(Filing No. 1-1 at 41:53-59.) Claim 9 states:
The method of claim 1, wherein said substrate is heated at a temperature
of between about 65° C. and about 85° C.
(Id. at 42:62-63.)
V.

Procedural Background
NUTech filed its Complaint on August 15, 2012, alleging that the Defendants

infringed the ‘592 Patent through use of a bio-engineered corn called Enogen in the
ethanol production process. It is alleged that Enogen is a transgenic corn that has been
bioengineered to express an “alpha-amylase,” which allows it to be thermostable and
active during the high temperatures required for starch hydrolysis in ethanol production
(specifically during the dry-grind that occurs during ethanol production).

NUTech

alleges that Syngenta modified Enogen corn so it produces a specific type of enzyme
derived from an organism that grows at very high temperatures, which is then used in
the process of converting starch into smaller sugars during the production of ethanol.
When using Syngenta’s Enogen corn, ethanol plants no longer need to purchase and
separately add a commodity enzyme that breaks down starch during ethanol
production. Enogen corn can also reduce the amount of water and energy required to
make ethanol. NUTech argues that the ‘592 Patent discloses and claims the use of a
genetically modified plant that produces an enzyme such as the one found in Enogen.

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VI.

Disputed Terms and Phrases:
The parties have identified four terms that appear in the ‘592 Patent’s nine claims

to be construed by the Court. Three of the terms come from Claim 1, and the fourth
comes from Claim 9. The disputed terms and the parties’ proposed construction are
reproduced below from Ex. A to the parties’ Joint Claim Construction Statement (Filing
No. 75-1):
Term/Phrase

NUTech

Defendants

“hyperthermophilic”

“an organism capable of
growth above 70° C, or
proteins derived from such
an organism”

Term encompassed by the
phrase “hyperthermophilic
glycosyl hydrolase”

“hyperthermophilic
glycosyl hydrolase”3

“‘glycosyl hydrolase’ derived
from organisms capable of
growth above 70° C”

“glycosyl hydrolase that is
capable of activity at
temperatures above 70° C
and has undetectable activity
at temperatures supporting
plant growth”

“said substrate
comprises extract of plant
transformed with said
recombinant
hyperthermophilic
glycosyl hydrolase”

“the ‘plant substrate’[4]
includes extract of plant that
has been transformed with
the recombinant
‘hyperthermophilic glycosyl
hydrolase’”

“said substrate is endogenous
to the plant transformed with
said recombinant
hyperthermophilic hydrolase
and is not separately added or
mixed”

“wherein the glycosyl
hydrolase is localized with
the substrate in tissue of
the plant”

“wherein the glycosyl
hydrolase and substrate of
the transformed plant are
located inside the same cell
tissue of the transformed

“wherein the glycosyl
hydrolase is located having
access to, and thus is capable
of acting on, the substrate”

3

The parties have agreed to the following construction of “glycosyl hydrolase”:

“enzyme, which hydrolyzes substances linked by glycosyl bonds, for example,
polysaccharides”
4

The only times the term “plant substrate” appears in the parties Joint Claim Construction
Statement is in their agreed upon construction of the term and in NUTech’s proposed construction of
Term #2. The parties’ agreed upon construction of “plant substrate” is:
“plant material that can be acted upon by an enzyme”

8

plant”

Defs. do not believe “in tissue
of the plant” needs to be
construed.

“heated at a temperature
between approximately 65° C
and approximately 85° C”

“heated at a temperature
above about 65° C and not
exceeding about 85° C”

Claim 9 “heated at a temperature
between about 65° C and
about 85° C”

CLAIM CONSTRUCTION STANDARD
To determine whether a patent has been infringed, the Court must undertake a
two-step analysis. “‘First, the [C]ourt determines the scope and meaning of the patent
claims asserted.’” Cordis Corp. v. Boston Scientific Corp., 658 F.3d 1347, 1354 (Fed.
Cir. 2011) (quoting Cybor Corp. v. FAS Techs., Inc., 138 F.3d 1448, 1454 (Fed. Cir.
1998) (en banc)).

Second, “‘the properly construed claims are compared to the

allegedly infringing device.’”

Id.

Claim construction is a way “‘of elaborating the

normally terse claim language in order to understand and explain, but not change, the
scope of the claims.’” Terlep v. Brinkmann Corp., 418 F.3d 1379, 1382 (Fed. Cir. 2005)
(quoting Embrex, Inc. v. Serv. Eng’g Corp., 216 F.3d 1343, 1347 (Fed. Cir. 2000)). It is
also “a matter of resolution of disputed meanings and technical scope, to clarify and
when necessary to explain what the patentee covered by the claims, for use in the
determination of infringement. It is not an obligatory exercise in redundancy.” U.S.
Surgical Corp. v. Ethicon, Inc., 103 F.3d 1554, 1568 (Fed. Cir. 1997). “[A] sound claim
construction need not always purge every shred of ambiguity. The resolution of some
line-drawing problems . . . is properly left to the trier of fact.” Acumed LLC v. Stryker
Corp., 483 F.3d 800, 806 (Fed. Cir. 2007) (citing Abbott Labs. v. Baxter Pharm. Prods.,
Inc., 471 F.3d 1363, 1368 (Fed. Cir. 2006); PPG Indus. v. Guardian Indus. Corp., 156
9

F.3d 1351, 1355 (Fed. Cir.1998); Modine Mfg. Co. v. U.S. Int'l Trade Comm'n, 75 F.3d
1545, 1554 (Fed. Cir. 1996)).
“The words of a claim are generally given their ordinary and customary meaning,
which is ‘the meaning that the term would have to a person of ordinary skill in the art in
question at the time of the invention.’” NTP, Inc. v. Research In Motion, Ltd., 418 F.3d
1282, 1293 (Fed. Cir. 2005) (quoting Phillips v. AWH Corp., 415 F.3d 1303, 1312 (Fed.
Cir. 2005) (en banc)). An inventor may, however, “choose to be his own lexicographer
and use terms in a manner other than their ordinary meaning, as long as the special
definition of the term is clearly stated in the patent specification or file history.” Vitronics
Corp. v. Conceptronic, Inc., 90 F.3d 1576, 1583 (Fed. Cir. 1996) (citing Hoechst
Celanese Corp. v. BP Chems. Ltd., 78 F.3d 1575, 1578 (Fed. Cir. 1996)).
To determine the meaning of a claim term, “the court looks to those sources
available to the public that show what a person of ordinary skill in the art would have
understood disputed claim language to mean.’” Phillips, 415 F.3d at 1314 (quoting
Innova/Pure Water, Inc. v. Safari Water Filtration Sys., 381 F.3d, 1111, 1116 (Fed. Cir.
2004)). Such “sources include ‘the words of the claims themselves, the remainder of
the specification, the prosecution history, and extrinsic evidence concerning relevant
scientific principles, the meaning of technical terms, and the state of the art.’” Id. When
interpreting any asserted claim, “court[s] should look first to the intrinsic evidence of
record,” which encompasses “the patent itself, including the claims, the specification
and, if in evidence, the prosecution history.” Vitronics, 90 F.3d at 1583 (citing Markman,
52 F.3d at 979). Following this analysis of the intrinsic evidence, extrinsic evidence may
be considered only if necessary to determine the “‘meaning or scope of technical terms
10

in the claims.’” See id. (quoting Hormone Research Found., Inc. v. Genentech, Inc.,
904 F.2d 1558,1562 (Fed. Cir. 1990)).

The Court’s “primary focus in determining the

ordinary and customary meaning of a claim limitation is . . . the intrinsic evidence of
record.” Atofina v. Great Lakes Chem. Corp., 441 F.3d 991, 996 (Fed. Cir. 2006) (citing
Phillips, 415 F.3d at 1312-17). The analysis of the intrinsic record begins “with the
language of the claims” themselves. Rexnord Corp. v. Laitram Corp., 274 F.3d 1336,
1341-42 (Fed. Cir. 2001); see also Phillips, 415 F.3d at 1314 (“Quite apart from the
written description and the prosecution history, the claims themselves provide
substantial guidance as to the meaning of particular claim terms.”). However, “[t]he
claims . . . do not stand alone.” Phillips, 415 F.3d at 1315. Instead, “they are part of ‘a
fully integrated written instrument,’” and must be read in view of that fully integrated
written instrument. Id. (quoting Markman, 52 F.3d at 979).
After looking to the language of the claim itself, “[t]he most relevant source [for
ascertaining the meaning of a claim] is the patent's specification, which is ‘the single
best guide to the meaning of a disputed term.’” MBO Labs. Inc. v. Becton, Dickinson &
Co., 474 F.3d 1323, 1329 (Fed. Cir. 2007) (quoting Phillips, 415 F.3d at 1315).
“‘Usually, it is dispositive[.]’” Terlep, 418 F.3d at 1382 (quoting Phillips, 415 F.3d at
1314). The specification may indicate “that certain embodiments are preferred.” Electro
Med. Sys., S.A. v. Cooper Life Scis., Inc., 34 F.3d 1048, 1054 (Fed. Cir. 1994).
Nevertheless, “particular embodiments appearing in a specification will not be read into
the claims when the claim language is broader than such embodiments.” Id. The next
most relevant source of intrinsic evidence “is the prosecution history, which . . . directly
reflects how the patentee has characterized the invention.” Id. (citing Phillips, 415 F.3d
11

at 1317).

“‘[T]he prosecution history can often inform the meaning of the claim

language by demonstrating how the inventor understood the invention and whether the
inventor limited the invention in the course of prosecution, making the claim scope
narrower than it would otherwise be.’” Terlep, 418 F.3d at 1382 (quoting Phillips, 415
F.3d at 1317); see also Computer Docking Station Corp. v. Dell, Inc., 519 F.3d 1366,
1374-75 (Fed. Cir. 2008) (citing Rexnord, 274 F.3d at 1343) (“Statements made during
prosecution may . . . affect the scope of the claims.”).
“In most situations, an analysis of the intrinsic evidence[, including the claims
themselves, the remainder of the specification, and the prosecution history,] [ ] will
resolve any ambiguity in a disputed claim term.” Vitronics, 90 F.3d at 1583. However,
there may be “instances in which intrinsic evidence is insufficient to enable the court to
determine the meaning of the asserted claims, and in those instances, extrinsic
evidence . . . may also properly be relied on to understand the technology and to
construe the claims.” Id. at 1584 (citing Markman, 52 F.3d at 979). “Extrinsic evidence
. . . may be helpful [to ascertain the meaning of a claim term] but is ‘less significant than
the intrinsic record in determining the legally operative meaning of claim language.’”
MBO Labs, 474 F.3d at 1329 (quoting Phillips, 415 F.3d at 1317). Extrinsic evidence is
very broad, and includes basically all evidence but intrinsic evidence. Common forms of
extrinsic evidence include dictionaries, reference books on the topic of the art, expert
testimony, and “other material not part of the public record associated with the patent.”
Id. Although a court may rely on extrinsic evidence, extrinsic evidence “cannot be used
to alter a claim construction dictated by a proper analysis of the intrinsic evidence.” OnLine Tech. v. Bodenseewerk Perkin-Elmer, 386 F.3d 1133, 1139 (Fed. Cir. 2004); see
12

also Intel Corp. v. VIA Techs., Inc., 319 F.3d 1357, 1367 (Fed. Cir. 2003) (emphasis in
original) (“When an analysis of intrinsic evidence resolves any ambiguity in a disputed
claim term, it is improper to rely on extrinsic evidence to contradict the meaning so
ascertained.”).
When the Supreme Court decided claim construction is matter of law for the
courts rather than an issue of fact for the jury, it noted “the importance of uniformity in
the treatment of a given patent[.]” Markman v. Westview Instruments, Inc., 517 U.S.
370, 390 (1996). It also noted:
But whereas issue preclusion could not be asserted against new and
independent infringement defendants even within a given jurisdiction,
treating interpretive issues as purely legal will promote (though it will not
guarantee) intrajurisdictional certainty through the application of stare
decisis on those questions not yet subject to interjurisdictional uniformity
under the authority of the single appeals court.
Id. at 391. Therefore, although prior claim construction rulings with respect to the same
patent-in-suit may not be binding on the Court, they will generally be “entitled to
reasoned deference under the broad principals of stare decisis and the goals articulated
by the Supreme Court in Markman, even though stare decisis may not be applicable per
se.”

Maurice Mitchell Innovations, L.P. v. Intel Corp., No. 2:04-CV-450, 2006 WL

1751779, at *4 (E.D. Tex. June 21, 2006), aff'd, 249 F. App'x 184 (Fed. Cir. 2007).

DISCUSSION
I.

Claim 1: “hyperthermophilic” and “hyperthermophilic glycosyl hydrolase”
Term/Phrase

“hyperthermophilic”

NUTech
“an organism capable of
growth above 70° C, or
proteins derived from such
an organism”

13

Defendants
Term encompassed by the
phrase “hyperthermophilic
glycosyl hydrolase”

“hyperthermophilic
glycosyl hydrolase”

“‘glycosyl hydrolase’ derived
from organisms capable of
growth above 70° C”

“glycosyl hydrolase that is
capable of activity at
temperatures above 70° C
and has undetectable activity
at temperatures supporting
plant growth”

The parties first disagree on whether the term “hyperthermophilic” needs to be
construed.

Defendants argue the term “hyperthermophilic” is merely an adjective

modifying the general subject “glycosyl hydrolase.” NUTech argues that the ‘592 Patent
expressly defined both terms.

NUTech thus claims that its proposed construction

follows the express definition Dr. Blum gave to the term in the ‘592 Patent. Under
NUTech’s proposed construction, the phrase “hyperthermophilic glycosyl hydrolase” is
understood simply by combining the definitions given in the ‘592 Patent for the terms
“hyperthermophilic” and “glycosyl hydrolase.”

According to NUTech, the express

definition of hyperthermophilic refers to two things: (1) an organism capable of growth
above 70° C; and (2) proteins derived from such an organism. A glycosyl hydrolase
enzyme is a protein. Thus, “hyperthermophilic glycosyl hydrolase” refers to “glycosyl
hydrolase derived from organisms capable of growth above 70° C.”
Defendants argue that statements in the specifications and prosecution history
demonstrate that the construction of the term “hyperthermophilic glycosyl hydrolase”
requires that enzymes have “undetectable activity at temperatures supporting plant
growth.”

For example, Defendants point out that the ‘592 Patent refers to activity

several times.

See, e.g., Filing No. 1-1 at 2:54-62 (“The recombinant glycosyl

hydrolases expressed in the transgenic plants are nontoxic in plant tissues because the

14

enzymes are inactive at temperatures supporting plant growth and therefore do not
significantly interfere with normal metabolism in the living plant.”); 2:64–65 (“When
desired, the transgenic plant tissue can be heated to activate the enzymes”); 17:63–64
(“processing milled tissue, at high temperatures to activate the recombinant protein”).
Defendants also argue that NUTech repeatedly referenced undetectable activity at plant
growth temperatures during the patent prosecution process. (Filing No. 85-6 at ECF 76,
101.) Defendants claim that NUTech’s proposed construction does not distinguish
whether the enzyme itself is thermostable or active at high temperatures, and thus
impermissibly broadens the scope of the claim.
The Court concludes that the appropriate construction should rely on the
definitions within the ‘592 Patent. As stated above, when construing a claim term, the
Court looks at the “ordinary meaning in the context of the written description and the
prosecution history.” Phillips, 415 F.3d at 1313. “There are only two exceptions to this
general rule: 1) when a patentee sets out a definition and acts as his own lexicographer,
or 2) when the patentee disavows the full scope of a claim term either in the
specification or during prosecution.” Thorner v. Sony Computer Entm't Am., LLC, 669
F.3d 1362, 1365 (Fed.Cir. 2012); see also SkinMedica, Inc. v. Histogen Inc., 727 F.3d
1187, 1195 (Fed. Cir. 2013) (“If the specification reveals ‘a special definition given to a
claim term by the patentee that differs from the meaning it would otherwise possess[,] ...
the inventor's lexicography governs.’”) (quoting Phillips, 415 F.3d at 1316); Helmsderfer
v. Bobrick Washroom Equip., Inc., 527 F.3d 1379, 1381 (Fed. Cir. 2008) (explaining that
inventors' definition of a claim term controls when they “clearly express an intent” to
redefine a term used in the claims); 3M Innovative Props. Co. v. Avery Dennison Corp.,
15

350 F.3d 1365, 1374 (Fed. Cir. 2003) (“Because 3M expressly acted as its own
lexicographer by providing a definition of embossed in the specification, the definition in
the specification controls the meaning of embossed, regardless of any potential conflict
with the term’s ordinary meaning.”).

For a patentee’s lexicography to control

construction of a claim term, it must be provided “with reasonable clarity,
deliberateness, and precision before it can affect the claim.” Abbott Labs, 334 F.3d at
1355.
In this case, NUTech has acted as its own lexicographer and has expressly
defined the terms “hyperthermophilic” and “glycosyl hydrolase.”

The parties have

agreed that “glycosyl hydrolase” means “enzymes which hydrolyze substances linked
by glycosyl bonds, for example, polysaccharides.” (Filing No. 1-1 at 6:47-49; Filing No.
75-1 at 1.) The ‘592 Patent also defines the term “hyperthermophilic” as referring “to an
organism capable of growth above 70 degrees C., or proteins derived from such an
organism.” (Filing No. 1-1 at 6:50-52.) The definitions provided in the ‘592 Patent are
presented clearly, deliberately, and precisely. The definitions do not create opposing
meanings for the disputed terms. See Abbott Labs, 334 F.3d at 1355 (concluding that
the patent provided two alternative definitions for the disputed terms).

Though the

terms are defined separately, the definition for “hyperthermophilic” is clear that it is an
adjective for organisms capable of growth above 70 degrees Celsius, or proteins
derived from such organisms. The Court’s review of the specification does not suggest
that Dr. Blum operated under a different definition during the prosecution history.
Further, the Defendants do not dispute the meaning of the phrase “glycosyl hydrolase.”
Accordingly, the Court can find no reason to disturb Dr. Blum’s chosen definitions, and
16

concludes that Dr. Blum demonstrated specific intent to define the terms in question in
the Patent. Using the definitions in the ‘592 Patent, the claim term “hyperthermophilic
glycosyl hydrolase” will be construed to mean “glycosyl hydrolase derived from organisms
capable of growth above 70° C.”5

II.

Claim 1: “said substrate comprises extract of plant transformed with said
recombinant hypothermophilic glycosyl hydrolase”
NUTech

Defendants

“the ‘plant substrate’ includes extract of
plant that has been transformed with the
recombinant ‘hyperthermophilic glycosyl
hydrolase’”

“said substrate is endogenous to the plant
transformed
with
said
recombinant
hyperthermophilic hydrolase and is not
separately added or mixed”

The parties next dispute the portion of Claim 1 stating “said substrate comprises
extract of plant transformed with said recombinant hypothermophilic glycosyl
hydrolase.” The parties agree that “plant substrate” is “plant material that can be acted
upon by an enzyme.” However, Defendants argue that the invention is limited to plant
substrate that is converted by the method of Claim 1, and therefore must be
endogenous to the plant. This is because the claim language does not require separate
adding or mixing of enzymes as part of the claim method. Further, Defendants argue
that the ‘592 Patent specifies that the process obviates the need to add commodity
enzymes separately to plan material.

NUTech argues that Defendants’ proposed

construction is contrary to the plain language of the Claim. Specifically, NUTech argues
that the Claim’s use of the word “comprises” demonstrates that the plant substrate must
5

As stated above, the parties agree on the following construction of the term glycosyl hydrolase:
“enzyme, which hydrolyzes substances linked by glycosyl bonds, for example, polysaccharides.”
Accordingly, the Court will not construe that term further, and when used herein, glycosyl hydrolase shall
be construed in the manner agreed to by the parties.

17

include at least extract of plant that has been transformed with the recombinant
hyperthermophilic glycosyl hydrolase.
The parties’ dispute principally turns on the breadth of the word “comprises”
within Claim 1. NUTech argues that its proposed construction relies on the established
meaning of the term “comprises” within patent law.

This Court has previously

recognized that “‘[c]omprising’ is a term of art used in claim language meaning that the
named elements are essential, but that other elements may be added and still form a
construct within the scope of the claim.” GP Indus., LLC v. Bachman, 8:06CV50, 2008
WL 2037415, at *3 (D. Neb. May 9, 2008) (citing Genetech, Inc. v. Chiron Corp., 112
F.3d 495, 501 (Fed.Cir.1997). “A drafter uses the term ‘comprising’ to mean ‘I claim at
least what follows and potentially more.’” CollegeNet, Inc. v. ApplyYourself, Inc., 418
F.3d 1225, 1235 (Fed.Cir.2005) (quoting Vehicular Techs. Corp. v. Titan Wheel Int'l,
Inc., 212 F.3d 1377, 1383–84 (Fed.Cir.2000)). For example, in CollegeNet, the Federal
Circuit construed a patent for online college admission application services. The district
court was asked to construe the term “automatically” within Claim 1 of the patent at
issue.

The district court rejected the defendant’s more limited definition that

automatically meant a process that occurred without human intervention.

Id. The

Federal Circuit upheld the district court and concluded that “[w]hile claim 1 does not
expressly provide for human intervention, the use of ‘comprising’ suggests that
additional, unrecited elements are not excluded. Such elements could include human
actions to expressly initiate the automatic [querying, generating, transmitting, or
receiving], or to interrupt such functions.” Id.

18

Defendants argue that the term “[c]omprising is not a weasel word with which to
abrogate claim limitations . . . [or] restore [ ] excluded subject matter.” Spectrum Int'l,
Inc. v. Sterilite Corp., 164 F.3d 1372, 1380 (Fed. Cir. 1998). In other words, the term
“comprising” is not “a talismanic incantation that counteracts a clear disclaimer.” BASF
Agro B.V. v. Makhteshim Agan of N. Am., Inc., 519 F. App'x 1008, 1017 (Fed. Cir.
2013). Defendants argue that the Claim language requires that the substrate must
naturally be part of the plant containing the recombinant hyperthermophilic glycosyl
hydrolase. Defendants argue that the ‘592 Patent provided only examples of converting
plant extracts that were the source of both the enzyme and the plant substrate. Further,
during the prosecution history, Dr. Blum stated that the invention eliminated the need for
separate enzyme and substrate preparation, and focused on the use of plants as
production hosts. (See Filing No. 86-5 at ECF 51-52.)
The Court concludes that NUTech has not provided a clear disclaimer to negate
Claim 1’s use of the inclusive term “comprising.” It is true that one of the supposed
distinguishing factors of the ‘592 Patent is that the method “obviates the need to add
separately produced commodity enzymes to plant material, as is the current method
used in the industry.” (Filing No. 1-1 at 2:54-3:2, ECF 20-21.) While Claim 1 does not
specifically identify any adding or mixing steps within the method, neither the Claim, the
specification, nor the prosecution history preclude using the recombinant enzyme in
plants transformed through authohydrolysis from being used to convert substrate from
other plants. In other words, while the invention obviates the need for storing or adding
separately prepared commodity enzymes, it does not preclude adding or mixing plant
substrate for transformed plants. The specification explicitly explains that “[e]nzyme
19

substrates included exogenous polysaccharides of defined composition and plant
extracts enriched for endogenous polysaccharides.” (Filing No. 1-1, ’592 Patent at
18:16-18, ECF 28 (emphasis added).) Further, the prosecution history demonstrates
Dr. Blum used the term “comprise” in an inclusive manner. See, e.g. Filing No. 83-4 at
ECF 210 (“In summary, the substrates which are converted by the method of the
present invention comprise plant extract of plants transformed with recombinant
thermostable hydrolase.”) (emphasis added); id. at ECF 211 (“However, as made
explicit by amendment herein to, claim 25, the plant substrate of claims 25-27, 29-31,
33-34 comprises extract of plant transformed with said recombinant thermostable
enzyme.”) (emphasis added). During the prosecution history, Dr. Blum amended what
is now Claim 1 to remove the word “endogenous” and add the language that includes
the term “comprises.”6

There is no indication that the ‘592 Patent disclaimed the

language proposed by NUTech to nullify the inclusive language encompassed by the
term “comprises.”7 Accordingly, the phrase “said substrate comprises extract of plant
transformed with said recombinant hyperthermophilic glycosyl hydrolase” is construed to

6

The amendment in its entirety appears below:

(AMENDED) A method for converting plant [endogenous] substrate comprising heating
said substrate in the presence of recombinant thermostable enzyme, wherein said
substrate comprises extract of plant transformed with said recombinant thermostable
enzyme, and wherein said thermostable enzyme is a hydrolase selected from the group
consisting of glycosyl hydrolase, protease, lipase and nuclease.
Filing No. 83-4 at ECF 208-9 (brackets and underlining in original to show deleted and added language,
respectively).) Dr. Blum also stated: “Claim 25 has been amended to make explicit that the substrate
comprises extract of plant transformed with recombinant thermostable hydrolase.” (Id. at 208.)
7

In reaching its conclusion, the Court does not intend to define the limits or scope of the ‘592
Patent. See TransAmerica Life Ins. Co. v. Lincoln Nat. Life Ins. Co., 550 F. Supp. 2d 865, 904 (N.D. Iowa
2008) (stating that “the court is not required to determine the ‘overall scope’ of the patent as a first step in
claim term construction.”) The Court’s construction is limited to its conclusion that term “comprises” is
inclusive, and that it has not been limited through disclaimer.

20

mean “the ‘plant substrate’ includes extract of plant that has been transformed with the
recombinant ‘hyperthermophilic glycosyl hydrolase.’”

III.

Claim 1: “wherein the glycosyl hydrolase is localized with the substrate in
tissue of the plant”
NUTech

Defendants

“wherein the glycosyl hydrolase and “wherein the glycosyl hydrolase is located
substrate of the transformed plant are having access to, and thus is capable of
located inside the same cell in tissue of acting on, the substrate”
the transformed plant”

The parties’ next dispute focuses on the “localization” of plant substrate, and the
extent to which plant substrate must be sequestered from the hypothermophilic glycosyl
hydrolase.8 NUTech’s proposed construction requires that the claimed enzyme and
plant substrate be located inside the same cell in tissue of the transformed plant.
NUTech essentially argues that the phrase “localized with the substrate” denotes a
spatial relationship between the enzyme and the plant substrate.

The Defendants

argue that the enzyme must act on the substrate to convert it. Thus, according to
Defendants, “localized with the substrate” means the glycosyl hydrolase is located with
access to the substrate, so that it is capable of acting upon it. Defendants argue that
under NUTech’s proposed construction, an enzyme could be located within the same
cell but in different cell compartments. In such a situation, the enzyme would not have
access to the substrate, and the conversion would not occur. NUTech argues that the
requirements were not so narrow, and distinguishing between the prior art only required
that the enzyme and substrate be located in the same cell.

8

The Court agrees with Defendants that the phrase “in the tissue of the plant” does not need to
be construed.

21

The Court concludes that the Claim language and the specification are at least
ambiguous,9 and the prosecution history informs the proper construction of the phrase
““wherein the glycosyl hydrolase is localized with the substrate.” The parties’ dispute
focuses in large part on Dr. Blum’s attempts to distinguish his invention from the prior
art. According to Dr. Blum, the Pen Article “describes sequestering of [a] recombinant
bacterial enzyme, extracellularly, by introducing a barrier between the transgene
product and the substrate to restrict access of enzyme to plant starch and thereby avoid
starch hydrolysis until the harvested seeds are combined with starch from another
source and the mixture is homogenized.” (Filing No. 86-5 at ECF 75-76.) The Pen
Article explained that “[t]he enzyme was properly secreted into the intercellular space.”
(Filing No. 83-6 at ECF 2.) The Pen Article suggested that “[a]n even more promising
approach may be the sequestered localization of an industrial enzyme in a crop where
the substrate is also present, thus creating a potential bioconversion. This obviates the
need for down-stream processing of the enzymes completely.” (Id. at ECF 5 (internal
marks omitted).) An example of this “promising approach” was “the expression of an
9

Defendants argue that none of the experiments described in the ‘592 Patent indicates whether
the glycosyl hydrolase and substrate were located in the same cell. However, the specification does
indicate that the “hyperthermophilic glycosyl hydrolases” used in the claimed method “are inactive at
temperatures supporting plant growth and therefore do not significantly interfere with the normal
metabolism in the living plant.” (Filing No. 1-1 at 2:60-63, ECF 20.) Thus, according to Defendant, the
specification supports a conclusion that “localization” refers to the enzyme’s ability to act upon the
substrate.
NUTech argues the specification and the preferred embodiment support its construction.
Specifically, NUTech argues that Example 5 references enzymes that were not secreted outside the cell,
nor were they directed to any particular organelle within the cell, and thus had to be located within the
cytoplasm of a plant cell. (See Id. at 23:3-24:9, ECF 31; Filing No. 99 at ECF 30-31.) NUTech further
explains that the substrates contemplated by the ‘592 Patent include starch, and starch is a substrate
located within a membrane-bound organelle inside a cell called an amyloplast. (Id. at ECF 31.) Thus,
NUTech claims, the enzymes in Exhibit 5 and the characteristics of starch demonstrate that they are
located inside the same cell, but that the amyloplast membrane separates the starch from the cytoplasm.

22

extracellular [alpha]-amylase in potatoes or corn used for starch production.”

(Id.)

Thus, “[s]ince enzyme and substrate are present in different cellular compartments, no
degradation of the substrate occurs during growth. The enzymatic reaction is initiated
during processing of the crop, when by homogenization the enzyme and the substrate
are brought together.” (Id.)
The USPTO twice rejected Dr. Blum’s patent application because it was not
satisfied that Dr. Blum had distinguished the prior art as described in the Pen Article. In
Dr. Blum’s first attempt to distinguish the prior art, he explained that “[t]he method of the
present invention . . . bypasses the need to sequester the enzyme outside the cell (the
method described by Penn et al.) or otherwise use regulated plant promoters in order to
avoid toxicity.” (Filing No. 83-5 at ECF 19.) On May 14, 2001, the USPTO Examiner
responded that:
While it is agreed that Pen et al. refers to a sequestered localization of a
glycosyl hydrolase, such as amylase in the plant, instant claims do not
specifically require nonsequestered localization of the transgenic enzyme
in the plant. The above claims are directed to a method irrespective of the
localization of the transgenic enzyme in the plant. The above claims are
directed to a method of converting endogenous plant substrate wherein
said plant is transformed with a recombinant thermophilic enzyme. Thus
the transformed plant may or may not have a sequestered localization of
the enzyme. Absent any specific indication in the claims regarding
nonsequestration of the enzyme in the plant, Pen et al. reference makes
the above invention obvious. Hence the above rejection is maintained.
(Filing No. 83-5 at ECF 34-35.)
In other words, the USPTO Examiner did not disapprove of Dr. Blum’s
interpretation of the prior art, but neither was the Examiner satisfied that the claims
specified nonsequestration.

Dr. Blum acquiesced to the Examiner by explicitly

amending the claim to specify localization of the enzyme with the plant substrate. Dr.
23

Blum’s amendment included the phrase “wherein the glycosyl hydrolase is localized
with the substrate in tissue of the plant.” (Filing No. 83-5 at ECF 41.) The USPTO
accepted Dr. Blum’s amendment and allowed the Claim. (Id. at ECF 50.)
Dr. Blum’s negotiation with the USPTO Examiner is telling in construing the
disputed phrase. See Phillips, 415 F.3d at 1317 (stating that “the prosecution history
can often inform the meaning of the claim language by demonstrating how the inventor
understood the invention and whether the inventor limited the invention in the course of
prosecution, making the claim scope narrower than it would otherwise be.”) The Court
understands the Pen Article’s reference to “extracellular” and “intercellular” space to
mean outside a cell or between cells.

This conclusion is supported by Dr. Blum’s

explanation to the USPTO Examiner of his understanding of the Pen Article. The Pen
Article described a “promising approach” of placing the alpha-amylase extracellularly.
(Filing No. 83-6 at ECF 5.) In contrast, Dr. Blum explained that his invention bypassed
the need to sequester the enzyme outside the cell. The USPTO did not take issue with
Dr. Blum’s understanding of the prior art and specifically stated that it was agreed that
the approach from the Pen Article “refers to a sequestered localization of a glycosyl
hydrolase.” (Filing No. 83-5 at ECF 34-35.) Thus, the USPTO implicitly agreed that the
sequestration referred to was sequestration outside the cell, and required that Dr. Blum
specify nonsequestration in the claims.

Accordingly, it is reasonable that the

sequestration refers to cellular location, and there is no indication that the term must be
limited further. Based on the specification as instructed by the prosecution history, the
Court construes the term “wherein the glycosyl hydrolase is localized with the substrate

24

in tissue of the plant” to mean “wherein the glycosyl hydrolase and substrate of the
transformed plant are located inside the same cell.”
IV.

Claim 9: “heated at a temperature between about 65° C and about 85° C”
Plaintiff NUTech

Defs

“heated at a temperature between “heated at a temperature above about 65°
approximately 65° C and approximately C and not exceeding about 85° C”
85° C”

The Court concludes that the final term in dispute need not be construed. As
stated above, claim construction is “a matter of resolution of disputed meanings and
technical scope, to clarify and when necessary to explain what the patentee covered by
the claims, for use in the determination of infringement. It is not an obligatory exercise
in redundancy.” U.S. Surgical Corp., 103 F.3d at 1568. “[A] sound claim construction
need not always purge every shred of ambiguity. The resolution of some line-drawing
problems . . . is properly left to the trier of fact.” Acumed, 483 F.3d at 806. The
disputed temperature range is not terse or technical claim language essential to assist a
trier of fact in understanding the technical scope of the claims. See Terlep, 418 F.3d at
1382.

Accordingly, the Court will not construe the term ““heated at a temperature

between about 65° C and about 85° C.”
CONCLUSION
The Court has construed the terms “hyperthermophilic glycosyl hydrolase,” “said
substrate comprises extract of plant transformed with said recombinant hyperthermophilic
glycosyl hydrolase,” and “wherein the glycosyl hydrolase is localized with the substrate,”
appearing in Claim 1 of the ‘592 Patent.

For the reasons discussed, the Court has

generally adopted the construction proposed by NUTech for each of these terms. the Court

25

will not construe the term ““heated at a temperature between about 65° C and about 85°
C.” Accordingly,
IT IS ORDERED:
1.

The Court construes the term “hyperthermophilic glycosyl hydrolase,”
appearing in Claim 1 of the ‘592 Patent, to mean “glycosyl hydrolase
derived from organisms capable of growth above 70° C.”

2.

The Court construes the term “said substrate comprises extract of plant
transformed with said recombinant hyperthermophilic glycosyl hydrolase,”
appearing in Claim 1 of the ‘592 Patent, to mean “the plant substrate includes
extract of

plant that has been transformed with the recombinant

hyperthermophilic glycosyl hydrolase.”

3.

The Court construes the term “wherein the glycosyl hydrolase is localized
with the substrate in tissue of the plant,” appearing in Claim 1 of the ‘592
Patent, to mean “wherein the glycosyl hydrolase and substrate of the

transformed plant are located inside the same cell.”

Dated this 22nd day of November, 2013.
BY THE COURT:

s/Laurie Smith Camp
Chief United States District Judge

26