PATENT BATTLES ON AND OFF THE COURT
Phill Jones

Pioneer agbiotech companies have sprouted, bloomed, and merged with larger firms. During the industry's growth, patent rights sometimes get tangled. In October, the Court of Appeals for the Federal Circuit pruned one patent dispute that has roots dating back over a dozen years.

The court case began on May 12, 2004, when Syngenta announced that it had acquired a type of corn glyphosate tolerance technology from Bayer CropScience. The technology, GA21, enables farmers to control weeds in corn with post emergence applications of glyphosate herbicide. Syngenta said that it will offer the technology through the Garst brand and licenses with other seed companies.

On the same day, Monsanto made its own announcement: the company filed a lawsuit in the Delaware district court, alleging that Syngenta infringed a Monsanto patent by attempting to make and use glyphosate resistant genes and crops. Two months later, Monsanto sued Syngenta in an Illinois federal district court. This time, the company alleged that Syngenta infringed patents held by Monsanto's DeKalb Genetics Corporation. Eventually, both lawsuits merged into one Delaware court suit.

The combined lawsuit has three patents allegedly infringed by Syngenta: U.S. Patents Nos. 5,538,880, 6,013,863 and 4,940,835. The '880 and '863 patents, owned by Monsanto subsidiary Dekalb, claim methods of producing herbicide resistant transgenic corn plants and seeds. Monsanto contended that Syngenta had performed steps with the GA21 corn product, such as growing glyphosate tolerant corn plants from GA21 seed, which infringe claims 5 and 6 of the '863 patent and claims 4 to 9 of the '880 patent.

Syngenta argued that they could not have infringed the claims. Using particle bombardment, DeKalb had transformed corn cells with a gene construct provided by its collaborator, Rhone-Poulenc Argo, S.A. The result was GA21. DeKalb claimed the basic technique in the first claim of the '880 and '863 patents. Syngenta had neither performed the technique nor infringed claim 1 of either patent. The company could not have infringed the asserted claims, Syngenta argued, because these claims are dependent claims. They are dependent upon the two first claims of the '880 and '863 patents.

Delaware district court's Judge Sue L. Robinson agreed with Syngenta. A dependent claim incorporates all the limitations of the claim to which it refers. Syngenta must have carried out all steps described in the first claims of the two patents, steps that DeKalb had performed.

The third patent, Monsanto's '835 patent, contains claims to chimeric plant genes that confer glyphosate tolerance and function in "plant cells." Judge Robinson interpreted the term "plant cells" as embracing both monocot and dicot cells. The patent application of the '835 patent had been filed in 1986. At that time, according to several court cases, no method existed to transform monocot plant cells. The judge concluded that the asserted claims of the '835 patent are invalid due to a lack of enablement.

On May 10, 2006, Judge Robinson granted Syngenta's motion for summary judgment. Monsanto appealed to the Court of Appeals for the Federal Circuit. The appellate court affirmed Judge Robinson's decision on October 4, 2007. Monsanto has the option of appealing to the US Supreme Court.

Inventors Tackle a Brave New World of Obviousness
On April 30, the US Supreme Court reversed the Federal Circuit's decision in KSR International Co. v. Teleflex Inc. In doing so, the Court made it easier for a defendant to defeat patent infringement liability, while making it tougher for an inventor to get a patent.

In its KSR opinion, the Federal Circuit had applied the "teaching, suggestion, or motivation" test. Courts have used the TSM test to determine whether a patented invention would have been obvious, and therefore, not worthy of patent protection. The TSM test goes like this. Suppose that the prior art taught elements of a claimed invention. A patent claim is only proved obvious if the prior art, the nature of the problem solved by the invention, or the knowledge of a person having ordinary skill in the art revealed some motivation or suggestion to combine prior art teachings.

The Supreme Court decided, however, that prior art need not contain an explicit motivation or suggestion to combine elements of an invention. The motivation or suggestion, the Court says, may be found in the demands of the relevant technical field or in the marketplace.

On October 10, the US Patent and Trademark Office (USPTO) published its examination guidelines for determining obviousness in light of the Supreme Court KSR decision, including a list of rationales that patent examiners can use to support a finding of obviousness. According to one of these rationales, the formerly discredited "obvious to try" argument, the inventor had merely selected from a finite number of identified, predictable solutions with a reasonable expectation of success. The PTO's Board of Patent Appeals and Interferences has already applied the obvious-to-try rationale in at least one biotech case.

Inventors should peruse the Patent Office's guidelines before filing a patent application. The document helps to map out potential pitfalls.

PTO Rules! – Or, Does It?
In August, the USPTO published its new rules for filing patent applications, which would become effective on November 1. "These rules better focus examination and will bring closure to the examination process more quickly," said USPTO Director Jon Dudas, "while ensuring quality and maintaining the right balance between flexibility for applicants and the rights of the public." In other words, the new rules would help the Patent Office to clear its backlog of 750,000 patent applications. Who could argue with that? Many have.

The rules limit the ability to file continuing patent applications and the number of claims per application. According to the new rules, patent applicants may file only two new continuing applications and one request for continued examination. Each application may contain up to 25 claims, with no more than 5 of these independent claims. A patent applicant must convince a patent examiner of the necessity for filing additional continuing patent applications or claims.

The published rules with comments run about 130 pages. Here's a very small taste.
If a patent application exceeds the 5 independent/25 total claim threshold, then the patent applicant must file an examination support document (ESD). In counting the claims, an examiner will add claims found in any of the patent applicant's co-pending patent applications that the examiner decides have "patentably indistinct claims" (i.e., claim pretty much the same thing). If the newly filed patent application exceeds the threshold, because it contains claims to more than one invention, then the applicant can submit a suggested restriction requirement (SRR) and choose an invention to which there are no more than 5 independent claims or 25 total claims. If an application exceeds the 5/25 claim threshold and does not contain a SRR or ESD, a patent examiner will require the applicant to file an ESD or amend the application to meet the 5/25 claim requirement.

Does the ESD sound like a simple formality? It isn't. In its 16-page guidelines for drafting an ESD, the USPTO describes an ESD's basic components: a statement that the applicant performed a pre-examination prior art search with data on search logic used, files or database service used, and date of search; a listing of references deemed most closely related to the subject matter of each of the claims; for each cited reference, an identification of all the limitations of each of the claims disclosed by the reference; a detailed explanation pointing out how each of the independent claims is patentable over the cited references; and a showing of where each limitation of each of the claims finds support in the patent application.

Critics charged that the rules will drive up the costs of patent prosecution, while severely limiting the ability of inventors, particularly those in the life sciences, to obtain patent protection. GlaxoSmithKline PLC did more than level criticisms against the USPTO; the company filed for a preliminary injunction to stop implementation of rules that it characterized as vague, arbitrary and capricious. Even if the rules did not have these defects, GSK argued, Congress, not the USPTO, holds the authority to promulgate such restrictive rules. The company had to overcome a difficult hurdle: convince a judge that the new rules will cause the company to suffer irreparable injury.

On October 31, Judge James C. Cacheris heard arguments from GSK and the USPTO in the US District Court for the Eastern District of Virginia. A few hours later, patent bloggers announced GSK's victory. For now, the USPTO has been prohibited from activating the new rules.

GSK reportedly plans to file a request for a permanent injunction. Early indications are that the USPTO will fight.

TOWARDS PLASTID TRANSFORMATION IN MAIZE
Ralph Bock

Transgene expression from the plastid (chloroplast) genome offers unique attractions to plant biotechnologists, including high-level foreign protein expression (presumably due to the high copy number of the plastid genome per cell), absence of epigenetic effects, and the convenient possibility of expressing multiple transgenes by linking them in operons¹. In addition, transplastomic technology greatly improves gene containment due to the maternal inheritance of plastids and their genomes in most crop species, which drastically reduces transgene transmission through pollen. However, broad application of plastid genome (plastome) engineering in agricultural biotechnology has been hampered by the lack of plastid transformation protocols for major crops. Unfortunately, cereals, the world's major food crops, are a particularly recalcitrant species; thus, in spite of enormous efforts, progress has been very limited^2,3 and there are still no protocols available for the production of stable transplastomic plants in any cereal species.

The availability of efficient methods for plant tissue culture and regeneration as well as the development of stringent selection protocols for transplastomic lines represent the main bottlenecks in plastid transformation. Leaf material is the preferred source material for plastid transformation, because it is rapidly produced in large amounts and allows multiple successive rounds of selection and regeneration. The latter is of utmost importance to the development of workable plastid transformation protocols, because primary plastid transformants are heteroplasmic, that is, contain large amounts of residual wild type plastid genome copies. To obtain genetically stable transplastomic lines (i.e., plants with transgenic plastid genomes), primary transformants must be purified to a state of homoplasmy by repeated cycles of plant regeneration under selective pressure^4,5. The impossibility of conducting such successive regeneration rounds in monocot species due to the lack (or extremely low efficiency) of leaf-based regeneration systems is the main reason for the failure to generate genetically stable chloroplast transformants in cereals. While rice chloroplast transformants could be readily obtained, all lines remained heteroplasmic and eventually lost the plastid transgenes in the absence of a protocol for carrying out repeated regeneration cycles².

A leaf-based callus induction and plant regeneration system for maize
We sought to overcome the limitations of the existing tissue culture systems by developing a plastid transformation protocol for maize (Zea mays L.). Currently, the source material used in maize (nuclear) transformation experiments comes nearly exclusively from callus cultures induced from immature zygotic embryos and propagated in the dark. We were interested in establishing a tissue culture and plant regeneration system that uses maize leaf tissue and thus is independent of zygotic embryos and greenhouse facilities. Earlier work had shown that cereals can undergo callus induction and plant regeneration via somatic embryogenesis from leaf explants, although the efficiency is often very low.

To develop an efficient leaf-based system for maize, we first systematically tested leaf explants of differing size, age, and developmental stage for their responsiveness to callus induction on different tissue culture media. An approximately 2 cm long section at the leaf base of young seedlings (Fig. 1A) sectioned into 1-2 mm × 1 mm pieces (Fig. 1B) was found to provide the most suitable source material for callus induction from maize leaves. In addition to optimizing the concentrations for known critical components of maize tissue culture media, such as proline, the auxin 2,4-dichlorophenoxyacetic acid (2,4-D), and silver nitrate, we tested a number of other chemicals for their effect on callus induction from leaves and found the polyamine spermidine has a stimulatory effect. The fully optimized protocol resulted in efficient callus induction from leaf segments, with a substantial proportion of yellow embryogenic type I-like callus⁶ (Fig. 1C,D). This callus type proved to be highly regenerable (Fig. 1E,F) and produced plants that grew normally and were fully fertile (Fig. 1G,H).

FLAVONOIDS FOR ENVIRONMENTAL EQUIVALENCE PROFILING OF GE PLANTS
Christof Sautter & Bartosz Urbaniak

Substantial equivalence (SE) is a parameter of biosafety concerning health and environmental interactions of genetically engineered plants (GEP), even though legally it is not a part of the deregulation procedure. SE in this context means that the expression profile, protein content, and metabolome of the GEP is exactly the same as the respective wild type (wt) plant, regardless of the desired effect of the transgene(s). Although SE might be an essential aspect of biosafety, it excludes a priori any undesired side effect on the health of a consumer, be it a human being or an animal, and moreover, any unintended interaction with the biotic or abiotic environment. Theoretically, SE should fulfil the strong criteria of even the over interpreted "precautionary principle."

In the European public debate about GEP, biosafety is a prominent topic. Highly sceptical parties and non-governmental organizations usually consider small differences between a GEP and its corresponding wt as a potential hazard, often regardless of the small scale of these differences and even lack of their significance. In none of these cases has the variation between conventionally bred varieties or the different environmental conditions been taken into account. However, scientifically sound risk assessments require such comparisons. Theoretically, the ability to judge a risk is limited when no direct effect is detectable. Instead, when assessing risks or indirect effects of a new technology, we can only compare them with risks associated with conventional systems, which are familiar to us. Only such a comparison makes rational decisions possible.

The main difficulty of SE is the uncountable number of compounds that constitute a plant and the impossibility of detecting them all. Therefore, recently published profiling studies focused on the parts of plant metabolism that the authors considered particularly important, such as the proteome or the metabolome^1,2,3. Our main goal was to study environmental interactions. Therefore, we choose the flavonoids, since these metabolites contribute to plant-environment interactions. These include defence against insects or microbes as well as abiotic stress reactions like photoprotection. Phenyl ammonium lyase and chalcone synthase are the enzymes catalyzing the first reactions of the flavonoid biosynthesis pathway. These are among the first enzymatic activities induced upon a microbe attack⁴.

Data
Varieties
For our studies we used three different Swiss spring wheat varieties: Golin, Greina, and Frisal. From all three varieties, genetically engineered lines were derived. Golin and Greina have been engineered with KP4, a viral protein that increases the resistance against seed transmitted fungal pathogens, known as smuts and bunts⁵. From the variety Frisal, we used two lines with a broad spectrum resistance against powdery mildew. The first one contained a chitinase and a glucanase from barley (line A5), the latter a barley ribosomal inhibiting protein (line B12)^6,7.

Grown under the same greenhouse conditions, the varieties exhibited significant differences in their flavonoid profile, whereas the differences between wt and genetically engineered lines were comparably negligible⁸. Principal component analysis revealed that the samples clustered according to the varieties. We therefore concluded that the differences between the conventional varieties are by far greater than the differences between wt and the respective genetically engineered lines⁸.