In a previous post, I wrote about Coskata’s patent-pending ethanol production process.  The Illinois-based cellulosic ethanol company’s proprietary technology makes ethanol from various feedstocks by converting it to synthesis gas, or syngas, and then fermenting the gas using anaerobic microorganisms.

Coskata owns Patent Application Publication Nos. 2008/0305539 and 2008/0305540, directed to a membrane supported bioreactor system for converting syngas to biofuels (collectively “Bioreactor Applications”). 

According to the Bioreactor Applications, the disclosed processes boost efficiency by using one side of a membrane as the syngas contact surface and the opposite side as the surface for growing the microorganisms.  The gas is fed onto the contact side and transported through the membrane to a biofilm of anaerobic microorganisms, where it is fermented into biofuels.

Last month, Coskata opened a semi-commercial ethanol facility in Madison, Pennsylvania that makes ethanol using the company’s microorganisms and bioreactor technology.  According to the company’s press release, the flex facility will produce ethanol from numerous feedstocks, including wood biomass, agricultural waste, sustainable energy crops and construction waste.

To build the facility, Coskata teamed up with Westinghouse Plasma Corporation, which suppled the gasification technology for the project.

I had the opportunity to speak to Wes Bolsen, Coskata’s CMO, about the new facility, the company’s technology and the company’s IP.  He confirmed that the Pennsylvania facility uses Coskata’s patent-pending bioreactor technology.

Bolsen also told me that Coskata has patents directed to microorganisms used in the fermentation process, but that the company favors trade secret protection for some of the newer strains of “bugs,” including some of those used in the new facility.

According to Bolsen, Coskata ”will continue with patents, trade secrets and whatever combination of the two” the company needs.  “Our IP is the core of this business,” he said.  ”Our IP and innovation is what keeps us ahead in the industry.”

Synthetic Genomics, Inc. (SGI) is a San Diego biotech company that develops biofuels using genetic engineering and other genomic and microbiological techniques.

Last month SGI announced that it has entered a multi-year research and development agreement with ExxonMobil Research and Engineering Company (EMRE) to develop next generation biofuels using photosynthetic algae. According to SGI’s press release, total funding for R & D and milestone payments could total more than $300 million. 

SGI will use its proprietary tools and technologies in genomics, metagenomics, synthetic genomics and genome engineering to develop superior strains of algae for commercial scale production of biofuels.  SGI owns several pending patent applications relating to these tools and technologies. 

U.S. Application No. 2007/0264688 (’688 application) is entitled “Synthetic genomes” and is directed to methods of constructing synthetic genomes and introducing them into vesicles (cells or synthetic membrane-bound “cells”). 

The ’688 application describes generating small nucleic acid fragments, assembling them into cassettes, cloning the cassettes, assembling the cassettes into a genome, and transferring the synthetic genome into a biochemical system.  The end products produced by the biochemical systems have various applications such as energy sources (e.g., hydrogen or ethanol), therapeutics and industrial polymers.

According to the ’688 application, selection and construction of synthetic genome sequences (as opposed to conventional genetic engineering techniques) allows for easier manipulation of genetic sequences and construction of novel organisms and biological systems.

U.S. Application No. 2007/0269862 (’862 application) is directed to methods for installing a genome into a cell or cell-like system.  The genome may comprise supercoiled nucleic acid molecules (102) with scaffolding proteins (104).  The nucleic acids may also have ribosomes (106).

The supercoiled nucleic acid molecules (102) may be accompanied by small molecules (108) and single stranded nucleic acid molecules (110).  The genomes are introduced into a membrane bound aqueous volume (112) such as a lipid vesicle.

Claim 1 of the ’862 application is rather broad:

1.  A method for making a synthetic cell, the method comprising:

obtaining a genome that is not within a cell; and

introducing the genome into a cell or cell-like system.

U.S. Application No. 2009/0176280 is directed to a method for isothermal amplification of small amounts of DNA or cell-free cloning of the DNA.

Other SGI pending applications include U.S. Application Pub. No. 2007/0037196 and U.S. Application Pub. No. 2007/0037197 (relating to in vitro methods for joining two double-stranded DNA molecules) and U.S. Application No. 2007/0122826 (relating to a minimal essential gene set that codes for a free-living organism).

One theme that runs throughout SGI’s portfolio of patent applications is impatience with the limits of existing genetic engineering methods and a desire for better techniques to shatter those limits, which SGI may have found in its synthetic genome technology.  This “Description of the Related Art” from the ’688 application captures that sentiment:

Conventional genetic engineering techniques are limited to allowing manipulation of existing sequences.  It would thus be desirable to have the ability to implement dramatic alterations and arrangements of genetic content, beyond that made possible by conventional techniques.  Consequently, there is a need for synthetic genomes.

OriginOil, Inc. (OriginOil) is a Los Angeles company developing a full range of technologies to improve the processes of algae growth and oil extraction.  OriginOil’s methods may substantially reduce the amount of energy necessary to extract oil from algae (see the Matter Network story here).

Unlike some algae biodiesel companies who only focus on the extraction step, OriginOil’s innovations span a much broader approach.  The company’s suite of technologies is covered by several pending patent applications, which “apply to the whole life cycle of algae production, not just extraction” according to OriginOil’s President and CEO Riggs Eckelberry. 

OriginOil’s U.S. Patent Application Pub. No. 2009/0029445 (’445 application), is entitled “Algae growth system for oil production” and is directed to systems for growth and processing of microorganisms such as micro-algae. 

The systems attempt to duplicate the optimum natural growth promoting environment for algae, including thorough exposure to carbon dioxide, growth promoting admixtures, exposure to light and extraction.

The key to this Quantum Fracturing process is breaking down water, carbon dioxide and other nutrients into micron-sized bubbles.  The increased surface area of these bubbles facilitates high absorption of carbon dioxide and nutrients by micro-algae during the growth phase.

Several as yet unpublished patent applications are directed to other aspects of OriginOil’s algae technology, including:

an application filed in 2008 directed to the Helix Bioreactor, which optimizes delivery of light to algae by providing light at closely spaced intervals within a photobioreactor;

an application filed in 2008 directed to the company’s Modular and Scalable Growth System, which facilitates large scale algae production through stacking of multiple Helix Bioreactors into an integrated network; and

an application filed this year directed to a Single-step Extraction Process, which combines Quantum Fracturing with electromagnetics and pH modification to break down cell walls and extract oil in one step.

OriginOil recently announced the filing of an international or PCT patent application, which Mr. Eckelberry said combines several of the company’s technologies and is now its consolidated “lead application” going forward. 

With this holistic approach, Eckelberry said OriginOil’s business model is to help other companies make algae and provide full support for its customers producing the oil.  The company’s new partnerships include one with Desmet Ballestra and one with the U.S. Department of Energy’s Idaho National Laboratory, wherein the latter will team with OriginOil on algae scalability issues.

In a previous post I wrote about parties to a biodiesel processor dispute battling over home court advantage.  There, Agri-Process Innovations (API) succeeded in getting its case against Greenline Industries heard in API’s home state of Arkansas.

The most common litigation tool for getting a case heard on your home turf is the declaratory judgment action (DJ).  In the patent infringement context, this means the accused infringer (or DJ plaintiff) beats the patent holder (or DJ defendant) to the punch by filing suit first and asking the court for a judgment of no infringement or patent invalidity.

The DJ plaintiff in a patent case must show that an actual controversy exists between the parties having adverse legal interests and that the DJ plaintiff is engaging in infringement or concrete steps with the intent to engage in infringement.

As in all lawsuits, the DJ plaintiff also has to establish personal jurisdiction (PJ) over the DJ Defendants.  Personal jurisdiction can be either general (i.e., the defendant has sufficient contacts in the forum state generally to justify PJ regardless of whether there was a connection between the acts leading to the lawsuit and the state) or specific (there was a connection between the specific acts leading to the lawsuit and the forum state).

Idaho Energy LP, dba Energy Products of Idaho (EPI) is an Idaho company that designs, manufactures and sells fluidized bed energy systems.  Harris Contracting Company (Harris), Alliant Energy Corporate Services and Von Roll, Inc. (collectively DJ Defendants) are co-holders of U.S. Patent No. 7,263,934 (’934 patent), entitled “Methods for generating energy using agricultural biofuel.” 

The ’934 patent is directed to a process for producing steam from ethanol byproducts such as grain stillage syrup by combusting the byproducts in a fluidized bed reactor.

After several communications and license offers between Harris and EPI and one alleged instance of Harris threatening one of EPI’s potential customers about the ’934 patent, EPI filed a DJ action in federal court in Boise, Idaho seeking a declaratory judgment of patent invalidity and making other claims including business defamation, unfair competition, trade libel and interference with prospective economic advantage.

The DJ Defendants moved to dismiss the case for lack of DJ jurisdiction and lack of PJ.  Recently, Judge Edward J. Lodge issued an order (epi_order.pdf) in which he found that there was DJ jurisdiction, but EPI had failed to establish PJ over the DJ defendants.  

The court found that none of the DJ Defendants did business in Idaho or had any other continuous presence in the state, so there was no general jurisidiction over them. 

As to specific jurisdiction, the court held that none of the alleged actions leading to the lawsuit had a connection to Idaho.  The alleged improper statement made to EPI’s potential customer did not involve Idaho customers and was not directed to the state.

The court also noted that letters threatening infringement litigation or the need for a license are insufficient to confer personal jurisdiction without other actions directed to the forum state.  So EPI’s DJ was dismissed for lack of PJ.

Solazyme is a South San Francisco biotech company that makes oil from algae.  While most algal oil makers harness the ability of algae to use energy from sunlight, Solazyme uses algae that grow in the dark and feed on sugar.

The company has identified natural strains of algae that thrive in the dark and is developing its own strains through genetic engineering.

Currently the company is operating in the cosmetics market where its oil will be used in anti-wrinkle products.

Solazyme recently announced that it will enter the jet fuel market (see the greentechmedia article here).  Its oil has been tested for viability as jet fuel by an independent lab, the Southwest Research Institute (SRI).

SRI tested many elements of Solazyme’s algal oil, including density, thickness and freezing point, and determined that the oil meets the ASTM D1655 standard for aviation turbine fuel.

Solazyme owns one issued patent and eleven published patent applications relating to genetic engineering methods, gene sequences and protein sequences that cause microbes to perform various biochemical functions.

Those functions include generating hydrogen (U.S. Patent No. 7,135,290) and boosting photosynthetic energy production by increasing a microorganism’s ability to harvest photons of light (U.S. Patent Application Pub No. 2008/124756).

Biofuel for air travel has the potential to be a huge market, and commercial airlines are looking to algae and other renewables to reduce their reliance on traditional jet fuel.