DCT

1:19-cv-00614

Bay State Milling Co v. Arcadia Biosciences Inc

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I. Executive Summary and Procedural Information

  • Parties & Counsel:
  • Case Identification: 1:19-cv-00614, D. Del., 04/01/2019
  • Venue Allegations: Venue is alleged to be proper in the District of Delaware as Defendant Arcadia Biosciences, Inc. is a Delaware corporation.
  • Core Dispute: Plaintiffs allege that Defendant’s "GoodWheat™" line of high amylose wheat products infringes six U.S. patents related to the genetic modification of wheat to increase its amylose and resistant starch content.
  • Technical Context: The technology involves genetic engineering of wheat to suppress the activity of starch branching enzymes, thereby altering the starch composition to favor amylose over amylopectin, which is significant for developing food ingredients with enhanced health benefits.
  • Key Procedural History: The complaint alleges that on August 14, 2018, the Patent Trial and Appeal Board (PTAB) issued a decision against Arcadia in an interference proceeding, finding that Arcadia was not entitled to claim an invention related to the patents-in-suit. It also alleges multiple instances of pre-suit notice of the patents, including correspondence dating back to October 2016.

Case Timeline

Date Event
2000-02-21 Patent Priority Date (’114 Patent)
2005-12-30 Patent Priority Date (’139, ’087, ’262 Patents)
2007-01-01 Arcadia scientist allegedly aware of foundational research (approx.)
2010-01-01 Arcadia allegedly began growing high amylose wheat (approx.)
2010-02-23 Issue Date (’114 Patent)
2010-04-20 Issue Date (’139 Patent)
2011-10-04 Arcadia files provisional patent application for high amylose wheat
2011-11-04 Patent Priority Date (’533, ’413 Patents)
2012-02-14 Issue Date (’087 Patent)
2012-05-14 Arcadia employees publish paper on high amylose wheat
2013-08-06 Issue Date (’262 Patent)
2013-12-03 Arcadia allegedly on notice of ’114, ’139, and ’087 Patents via USPTO filing
2015-06-23 Issue Date (’533 Patent)
2016-10-06 Arista allegedly put Arcadia on direct notice of five patents-in-suit
2017-03-07 Issue Date (’413 Patent)
2018-08-14 PTAB issues judgment on priority against Arcadia in interference proceeding
2018-11-07 Arcadia announces test marketing for "GoodWheat™" product
2019-01-21 Arcadia employee publishes paper on high amylose wheat lines
2019-04-01 Complaint Filing Date

II. Technology and Patent(s)-in-Suit Analysis

U.S. Patent No. 7,667,114 - Starch Branching Enzyme (Issued February 23, 2010)

The Invention Explained

  • Problem Addressed: In typical wheat, starch is composed of about 25% amylose and 75% amylopectin (Compl. ¶16). The patent addresses the technical challenge of altering this ratio to produce wheat with novel properties, such as high amylose content, for food and industrial applications (’114 Patent, col. 1:8-14).
  • The Patented Solution: The invention is based on the discovery that amylose content is dependent on starch branching enzyme II (SBEII), which has two types, SBEIIa and SBEIIb (Compl. ¶20). The patent provides the nucleic acid sequence for wheat SBEIIb and methods for identifying "null or altered alleles" of this gene, which can be combined with null alleles of other starch synthesis genes (like SBEIIa) to produce wheat grain containing high levels of amylose (’114 Patent, Abstract; ’114 Patent, col. 4:15-20). The complaint includes a diagram from the patents' development history illustrating the complex genomic architecture of wheat, which provides context for the need to identify and modify multiple gene copies to achieve the desired trait (Compl. ¶22, Figure 1).
  • Technical Importance: This approach provided a genetic pathway to create wheat with high levels of resistant starch, a dietary fiber known to have significant health benefits such as helping to control blood sugar (Compl. ¶¶18-19).

Key Claims at a Glance

  • The complaint asserts infringement of independent claim 1 (Compl. ¶114).
  • Claim 1 of the ’114 Patent recites:
    • A wheat plant comprising
    • a null allele of a gene on a long arm of chromosome 2 encoding wheat starch branching enzyme IIb (BEIIb),
    • in combination with one or more null alleles of genes which encode starch branching enzyme IIa (BEIIa), granule bound starch synthase (GBSS), starch synthase II (SSII) or starch branching enzyme I (BEI).
  • The complaint asserts infringement of dependent claims 2-9 (Compl. ¶117).

U.S. Patent No. 7,700,139 - Method and Means for Improving Bowel Health (Issued April 20, 2010)

The Invention Explained

  • Problem Addressed: The complaint notes the patent describes methods for improving indicators of bowel health in mammals, which can be achieved through diet (Compl. ¶36).
  • The Patented Solution: The patent claims a method of improving bowel health by feeding a mammal an "altered wheat starch" characterized by specific biochemical properties: an amylose proportion of at least 40% w/w, a reduced level of SBEIIa enzyme activity, and a specific amylopectin chain length distribution (Compl. ¶¶36-37, 118). This altered starch is derived from genetically modified wheat plants.
  • Technical Importance: This patent links specific, genetically-driven changes in wheat starch composition directly to physiological health outcomes in mammals, providing a basis for developing functional foods with scientifically supported health claims (Compl. ¶36).

Key Claims at a Glance

  • The complaint asserts infringement of independent claim 1 (Compl. ¶118).
  • Claim 1 of the ’139 Patent recites:
    • A method for decreasing pH of bowel contents, increasing total short chain fatty acid (SCFA) concentration..., or increasing the amount of one SCFA... in a mammalian animal,
    • comprising the step of feeding the animal an effective amount of an altered wheat starch...
    • wherein the proportion of amylose in the starch... is at least 40%, and
    • wherein said grain comprises (i) a reduced level of SBEIIa enzyme activity... and (ii) amylopectin with a proportion of 4-12 dp chain length fraction of 49.99% or less...
  • The complaint asserts infringement of dependent claims 2-5, 7-21, and 23-34 (Compl. ¶120).

Multi-Patent Capsule: U.S. Patent No. 8,115,087

  • Patent Identification: U.S. Patent No. 8,115,087, "Wheat With Altered Branching Enzyme Activity and Starch and Starch Containing Products Derived Therefrom," issued February 14, 2012 (Compl. ¶38).
  • Technology Synopsis: The patent describes wheat grain with reduced SBEIIa activity and optionally reduced SBEIIb activity, leading to increased levels of amylose (Compl. ¶41). It claims wheat grain with null mutations in two or three SBEIIa genes and an amylose content of at least 30% (Compl. ¶¶42, 124).
  • Asserted Claims: Independent claim 1 is asserted (Compl. ¶124).
  • Accused Features: Arcadia's RS100 and RS140 wheat lines are accused of infringing because they allegedly have stop or splice junction mutations in two or three SBEIIa genes and amylose proportions of 93.3% and 85.0%, respectively (Compl. ¶125).

Multi-Patent Capsule: U.S. Patent No. 8,501,262

  • Patent Identification: U.S. Patent No. 8,501,262, "Method and Means for Improving Bowel Health," issued August 6, 2013 (Compl. ¶43).
  • Technology Synopsis: The patent claims a process for producing a food or beverage by obtaining wheat grain with at least 40% amylose, at least 1% resistant starch, and a reduced level of SBEIIa activity relative to wild-type grain (Compl. ¶¶46, 128).
  • Asserted Claims: Independent claim 1 is asserted (Compl. ¶128).
  • Accused Features: Arcadia is accused of infringing by producing food, such as bread and pasta, from its RS100 high amylose wheat line, which allegedly meets the claimed amylose, resistant starch, and reduced SBEIIa levels (Compl. ¶129).

Multi-Patent Capsule: U.S. Patent No. 9,060,533

  • Patent Identification: U.S. Patent No. 9,060,533, "High Amylose Wheat," issued June 23, 2015 (Compl. ¶47).
  • Technology Synopsis: The patent claims a specific type of bread wheat (Triticum aestivum) grain having a combination of null alleles for both SBEIIa (5 or 6 alleles) and SBEIIb (2, 4, or 6 alleles), a high germination rate, and an amylose content of at least 50% (Compl. ¶51).
  • Asserted Claims: Independent claim 1 is asserted (Compl. ¶132).
  • Accused Features: Arcadia is accused of infringing with its RS140 line, which is alleged to be Triticum aestivum having the claimed combination of genetic mutations and phenotypic traits, including an amylose content of about 85.0% (Compl. ¶133).

Multi-Patent Capsule: U.S. Patent No. 9,585,413

  • Patent Identification: U.S. Patent No. 9,585,413, "Food Ingredients Produced from High Amylose Wheat," issued March 7, 2017 (Compl. ¶52).
  • Technology Synopsis: The patent claims a process for producing food or drink ingredients by processing wheat grain that has loss-of-function mutations in its SBEIIa genes, resulting in a total SBEII protein level of 2% to 30% of wild-type and an amylose content of at least 60% (Compl. ¶¶55, 136).
  • Asserted Claims: Independent claim 1 is asserted (Compl. ¶136).
  • Accused Features: Arcadia is accused of infringing by producing food ingredients from its RS101 and RS140 lines, which allegedly have the claimed genetic mutations and resulting protein and amylose levels (Compl. ¶137).

III. The Accused Instrumentality

Product Identification

  • The accused instrumentalities are Arcadia's "GoodWheat™" high amylose wheat products, including but not limited to its RS100, RS101, and RS140 lines of wheat, as well as flour, food ingredients, and food products derived therefrom (Compl. ¶¶3, 104, 109).

Functionality and Market Context

  • The complaint alleges, based on Arcadia's own scientific papers and patent applications, that the accused wheat lines were developed to contain high levels of amylose (up to 94%) by creating "stop mutations and/or splice junction mutations" in the genes encoding starch branching enzymes SBEIIa and SBEIIb (Compl. ¶¶71-76, 94, 115, 125). These products are marketed to food companies and consumers as high-fiber, resistant starch ingredients for healthier foods like bread and pasta, with commercial sales anticipated in 2019 (Compl. ¶¶100, 102-103).

IV. Analysis of Infringement Allegations

’114 Patent Infringement Allegations

Claim Element (from Independent Claim 1) Alleged Infringing Functionality Complaint Citation Patent Citation
A wheat plant comprising a null allele of a gene on a long arm of chromosome 2 encoding wheat starch branching enzyme IIb (BEIIb), Arcadia's RS100 and RS140 lines are alleged to be wheat plants that have a "null allele stop mutation and/or splice junction mutation on a long arm of chromosome 2" for the SBEIIb enzyme. ¶115 col. 4:15-20
in combination with one or more null alleles of genes which encode starch branching enzyme IIa (BEIIa)... The accused wheat lines are alleged to have "stop or splice junction null mutations" in the genes encoding the SBEIIa enzyme. ¶115 col. 4:15-20

Identified Points of Contention (’114 Patent):

  • Scope Questions: A primary question may be the definition of a "null allele." The complaint alleges that "stop mutation and/or splice junction mutation" meets this requirement (Compl. ¶115). The court may need to construe whether this term requires a complete loss of function and whether the specific mutations in Arcadia's products achieve that standard.
  • Technical Questions: The infringement theory relies on technical disclosures in Arcadia's own publications, such as the "2019 Paper" (Compl. ¶115). A key evidentiary question will be whether Plaintiffs can prove that the commercially sold "GoodWheat™" products possess the same genetic mutations and characteristics described in those publications.

’139 Patent Infringement Allegations

Claim Element (from Independent Claim 1) Alleged Infringing Functionality Complaint Citation Patent Citation
A method for decreasing pH of bowel contents, increasing total short chain fatty acid (SCFA) concentration... in a mammalian animal, comprising the step of feeding the animal an effective amount of an altered wheat starch... Arcadia allegedly induced infringement by conducting clinical studies and marketing its wheat for its health benefits, which allegedly include decreasing bowel pH and increasing SCFA. ¶119, 121 col. 1:16-20
wherein the proportion of amylose in the starch of the grain, flour or wholemeal is at least 40% Arcadia's RS100 and RS140 wheat lines allegedly have amylose proportions of 93.3% and 85.0%, respectively. ¶119 col. 2:2-4
and wherein said grain comprises (i) a reduced level of SBEIIa enzyme activity relative to wild-type grain... The accused wheat lines allegedly have genes that encode for a reduced level of SBEIIa enzyme activity. ¶119 col. 2:5-8
and (ii) amylopectin with a proportion of 4-12 dp chain length fraction of 49.99% or less... The accused wheat lines allegedly have amylopectin with a chain length fraction of 49.99% or less compared to wild-type wheat. ¶119 col. 2:8-12

Identified Points of Contention (’139 Patent):

  • Scope Questions: A central issue may be whether Arcadia's alleged acts—such as conducting clinical studies for "Improved Metabolic Health" (Compl. ¶92) or marketing products that "promote good health" (Compl. ¶102)—constitute inducement to perform the specific method steps recited in the claim, such as "decreasing pH of bowel contents."
  • Technical Questions: An evidentiary question will be whether the accused wheat products, when ingested, actually result in the specific biochemical outcomes required by the claim, including the claimed amylopectin chain length distribution. The complaint asserts this functionality on "information and belief" (Compl. ¶119).

V. Key Claim Terms for Construction

  • The Term: "null allele" (’114 Patent, Claim 1)
  • Context and Importance: This term is the foundation of the infringement allegation for the ’114 Patent. The complaint equates "stop mutation and/or splice junction mutation" with the term "null allele" (Compl. ¶115). Practitioners may focus on this term because its construction will determine whether Arcadia's specific genetic modifications fall within the claim's scope.
  • Intrinsic Evidence for Interpretation:
    • Evidence for a Broader Interpretation: The ’114 Patent abstract describes screening for "null or altered alleles," which could suggest that a "null" allele is one type of alteration and does not necessarily require a 100% elimination of function to be distinguished from a mere "altered" allele.
    • Evidence for a Narrower Interpretation: The patent does not appear to provide a specific definition of "null allele" that deviates from its generally accepted meaning in the field of genetics, which often implies a complete loss of function. A party might argue that in the absence of a special definition, this plain meaning should control.

VI. Other Allegations

Indirect Infringement

  • The complaint alleges knowing inducement of the ’139 and ’413 Patents. The allegations are based on Arcadia developing, promoting, and encouraging the use of its wheat lines in foods for mammals, including in clinical studies, with the specific intent to achieve the claimed health benefits (Compl. ¶¶121, 123, 139, 141-143).

Willful Infringement

  • Willfulness is alleged for all six patents-in-suit. The complaint alleges pre-suit knowledge based on Arcadia's own USPTO filings citing the asserted patents as early as December 3, 2013 (Compl. ¶65); direct written notice from Arista in October 2016 and June 2018 (Compl. ¶¶61-62); and a 2007 laboratory notebook from an Arcadia scientist allegedly showing awareness of the foundational research underlying the patents (Compl. ¶59).

VII. Analyst’s Conclusion: Key Questions for the Case

  • A core issue will be one of definitional scope: can the term "null allele," as used in the '114 Patent, be construed to cover the "stop or splice junction mutations" allegedly present in Arcadia's wheat lines, or will a stricter, loss-of-function definition place the accused products outside the claim?
  • A second central question will be one of induced infringement: does Arcadia's marketing of its "GoodWheat™" products for their general health benefits, and its alleged use of the products in clinical studies, constitute active inducement of the specific method steps recited in the ’139 and ’413 patents?
  • A key evidentiary question will be one of product identity: can Plaintiffs demonstrate that the commercial "GoodWheat™" products possess the same specific genetic and biochemical characteristics that are described in Arcadia's non-commercial research papers and patent applications, upon which the complaint's infringement allegations heavily rely?