Joule Unlimited, a biofuels startup located in Bedford, MA, announced today that it has pocketed $70 million in financing to put toward a facility underway in Hobbs, NM, that will demonstrate Joule’s process for converting sunlight and carbon dioxide into fuels such as diesel and ethanol.

The new money brings Joule’s funding total to more than $110 million, and comes from founding Joule investor Flagship Ventures, as well as new and existing investors whose identities were not disclosed. Joule will also use the new funding for its technology development and global expansion, according to the announcement. In April 2010, Joule raised $30 million in second-round funding from Flagship and other institutional investors.

The Hobbs, NM, site is expected to be up and running later this year, and is designed to demonstrate how Joule’s technology could scale up to thousands of acres for commercial production. Joule now has 11 patents, covering technology such as  an engineered bacterium that produces liquid hydrocarbon fuels from sunlight and carbon dioxide, and a method for producing ethanol at high volumes and high efficiencies.

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It is a dark time for biofuels companies—and industrial biotech around Boston, more broadly.

Xconomy has learned that Qteros, a heavily funded developer of cellulosic ethanol technology based in Marlborough, MA, has laid off most of its staff, including its CEO John McCarthy. The news was reported earlier today by Dan Primack at Fortune. Xconomy received a tip yesterday from a source with knowledge of the company.

The source said that Qteros “couldn’t raise money” and was “reduced to a skeleton crew to sell anything of value.” Mick Sawka, who is listed on the company’s website as senior vice president, is the acting CEO, according to the source. Messages left with Qteros and Battery Ventures, one of the company’s lead investors, were not returned.

Qteros started in 2006 as SunEthanol (it changed its name in 2008), out of UMass Amherst. Its investors include Battery, Venrock Associates, Long River Ventures, Soros Fund Management, Camros Capital, Valero Energy, and BP. By our count, the company had raised nearly $30 million prior to its most recent financing, which was a $22 million Series C round announced at the beginning of this year.

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When Ecomotors International set out to change the way car and truck engines are built, it set up shop in Livonia, MI, a suburb of Detroit, in hopes of eventually licensing its technology to the big U.S. automakers. It was a calculated risk. As radical as Ecomotors’ opposed-piston engine design may be, at least the company’s founder, Peter Hofbauer, has unquestionable auto-industry credentials—he’s the guy who helped Volkswagen build its first mass-production diesel engine.

Pinnacle Engines isn’t even bothering with Detroit. The San Carlos, CA, startup, which recently won the backing of the world’s largest venture capital firm, is also developing an opposed-piston engine, one that promises to marry the fuel efficiency of diesel technology with the lower cost structure of gasoline-burning engines. But Pinnacle’s founder, James Montague “Monty” Cleeves, is a veteran of the semiconductor industry; for him, designing engines and tinkering with cars was always an avocation, not a profession. He’s pretty convinced that Detroit will never listen to his ideas—so Pinnacle is looking farther east for its first commercialization opportunities. Much farther east. To India, in fact.

“This ought to be music to Detroit’s ears, but to them I’m just some whacko in California,” says Cleeves. “This is Silicon Valley, and what does Silicon Valley know about making engines? Folks in Asia have almost zero ‘not-invented-here’ issues, whereas it’s pretty prevalent all over the U.S.”

Pinnacle won its first funding in 2007 and has been testing prototype engines based on its patented “Cleeves Cycle” since the spring of 2009. This year, Pinnacle struck a joint development agreement with an Indian scooter manufacturer—it can’t yet reveal which one—that could see the technology move to the test track by next year and into commercial production by 2013.

But to buy a Pinnacle-powered scooter, you’ll have to go to Mumbai or Bangalore. With gas prices here stable at around $3.50 per gallon, “I don’t know what it’s going to take to get somebody in the U.S. excited” about fundamental improvements to the venerable internal combustion engine, Cleeves says. “But most of Asia is sensitive enough about fuel economy that they get it.” For many families in India, a two-wheeler is the main mode of transportation, and a scooter engine that consumes 25 to 50 percent less fuel, as Pinnacle promises, could be a big boon for the household budget.

Cleeves says his engine can also be scaled up for larger vehicles, and can easily be modified to run on diesel, ethanol, or even compressed natural gas, which means it could also turn up in light commercial vehicles or even cars in India or China. But the startup, which has raised $13.5 million from venture giant New Enterprise Associates (NEA) as well as Bessemer Venture Partners and Infield Capital, doesn’t see its engine as a cure for petroleum addiction. Instead, Cleeves describes it as a bridge technology, incrementally improving the efficiency and lowering the emissions of internal combustion engines as a warming world weans itself from carbon-spewing technologies.

“It’s going to take a long while for Detroit to adopt new technologies,” says Pinnacle CEO Ron Hoge, a veteran of diesel engine maker Cummins. “They may surprise us—it may happen faster than we think. But it’s not even important to us on a business level, because the opportunities we are uncovering in Asia are going to be massive and much more accelerated and have a bigger impact on world consumption of petroleum.”

The basic concept of an opposed-piston engine is so simple that it’s remarkable how long automakers have been ignoring it. In a traditional engine, each piston sits in its own cylinder, and combustion occurs inside the cylinder head, where intake and exhaust valves regulate the inflow of air and vaporized fuel and the outflow of exhaust. In an opposed-piston engine, there’s no cylinder head: two pistons move toward and away from one another inside the same cylinder, with … Next Page »

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Busy day for a couple of well-known cleantech companies around Boston. One public company has signed a big deal in China, while the other, an ambitious upstart, is carefully protecting its intellectual property as it heads toward large-scale commercialization.

—A123 Systems (NASDAQ: AONE), the Waltham, MA-based maker of lithium ion batteries, said today it has won a contract with China’s Dongfang Electric, a large manufacturer of wind turbines and power equipment. A123 will provide an energy storage system for Dongfang’s manufacturing facility in Hangzhou by the end of this year. Financial terms weren’t given. If all goes well, this will be A123’s first storage system installed in China.

A report in CNET today has more context on the deal: A123’s battery bank will be attached to a 1.5-megawatt wind turbine and diesel generator to test how well the batteries can smooth out the dips in wind energy production. A123 has car battery manufacturing facilities in China, but no grid storage systems there yet, the report says.

—Joule Unlimited, the Cambridge, MA-based biofuels startup, said today it has been awarded a pair of U.S. patents that cover its method for producing ethanol at high volumes and high efficiencies. The method involves genetically engineering “photosynthetic bacteria”—microorganisms that convert sunlight and carbon dioxide into ethanol without fermenting sugars from cellulose or other types of biomass. The patents (#7,981,647 and #7,968,321), which were granted in the past month, cover various enzymatic mechanisms that Joule has engineered into cells to maximize their ethanol productivity.

Joule has received plenty of media attention since it started in 2007. The company is also applying its method to produce energy in the form of diesel fuel, which could power trucks and planes. Joule has previously been awarded patents in the area of diesel production. The overarching idea is to replace fossil fuels, but most biofuels makers have found “they can’t compete on a cost basis,” said Joule senior vice president Troy Campione, on a panel at our XSITE conference last month. Joule, of course, believes it is different.

The company has a pilot plant in Texas that has been producing ethanol and is slated to start producing diesel later this year. Joule says it has also signed a lease for land in New Mexico on which it is building a demonstration-scale plant that will begin operations next year.

While the new patents should help distance Joule from some of its competitors, they don’t necessarily get the company to commercialization any faster. George Church, the Harvard geneticist (and chairman of Joule’s technical advisory board), was quoted in the New York Times in March saying, “It’s not a totally obvious organism and they’ve changed it pretty radically, so it’s not clear they can protect everything by patents.”

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We had a great time at our latest Xconomy Seattle event, “Separating Hype from Reality in Alternative Fuels,” held last night at the new Institute for Systems Biology headquarters in Seattle’s South Lake Union neighborhood.

The presenters sketched some meaty ideas about the drive to develop oil alternatives, challenged a bit of conventional thinking, and got the audience to dive in with great follow-up questions. Here are a few of the big themes that emerged as Luke moderated the main discussion with Ned David and Kristina Burow of Arch Venture Partners—two of the co-founders of San Diego-based Sapphire Energy—and Margaret McCormick, the co-founder and CEO of Seattle-based Matrix Genetics. If you want to see some images from the event, check out this Flickr gallery from Vinh Chung of Total Effects Video.

—Biofuels 3.0: David pointed to the U.S.’s last two attempts to develop biofuels—after the 1970s energy crunch and in the mid-2000s, when national policy ramped up the production of ethanol. Neither of those eras, of course, have delivered much in the way of energy independence.

David said the 1970s saw the first big effort to cultivate algae as an alternative fuel source, but that fell short because the technology wasn’t advanced enough to get results. That wrongly led many to believe that algae wouldn’t work, he said.

The ethanol boomlet of the past decade was the 2.0 wave of biofuels for this country, but that hasn’t produced anything like what all those optimistic politicians pledged at the outset. “Forty percent of the U.S. corn crop goes to replacing 8 percent of our transportation fuel,” Burow said. “That is not sustainable.”

At present, David said, we’re in the 3.0 phase of U.S. biofuels. Algae was a big focus of this particular discussion, since all three of our panelists have direct experience with that field. With projects like Sapphire Energy’s drive to put a huge algae-fuel production facility in the Mexican desert, you’re seeing “the first building blocks of world-scale capability” for these fuels.

“I think that microorganisms can solve most of the problems of the world. If you go back, it was alcohol or it was cheese,” McCormick said. “There’s so much potential that can be harnessed out of these microorganisms and the DNA that’s in them, and we can look at them to solve all kinds of problems.”

—High stakes, but no quick fixes: McCormick said the latest phase of alternative fuels work is not purely driven by an economic need to reduce spending on oil, but is also by the need to address climate change and national security issues.

Burow added a fourth factor: “This has got to work. By 2020, we’ll have increased our need for energy by 40 percent as a world. And there’s simply no way to meet that increase without these types of alternative fuels.”

At the same time, Burow said, the cycle for developing such culture-shifting technologies is still much slower than we expect from other areas of innovation. “This isn’t Twitter. This isn’t … Next Page »

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Most people in the renewable fuel business will say that if you want to make ethanol, then corn is a lousy choice of raw material. The U.S. certainly has a lot of it, but corn is an inefficient source of energy, and it hogs up land that can be used to produce food.

But what if you could take municipal garbage—which our society produces plenty of—and transform it into ethanol?

That’s the idea Jeff Surma is pursuing at Bend, OR-based S4 Energy Solutions. I’m psyched to say that Surma, the company’s CEO, will be joining us for the next big Xconomy event “Separating Hype from Reality in Alternative Fuels” on May 19 at the Institute for Systems Biology’s new South Lake Union headquarters.

S4 is getting a lot of help from a big player in the trash business—Houston, TX-based Waste Management (NYSE: WM). S4 is a joint venture of Waste Management and Bend, OR-based InEnTec, which is developing a high-heat process that breaks down various kinds of waste (medical, commercial, someday the whole municipal smorgasbord of trash). The process creates a hydrogen-rich gas that can be converted into ethanol that powers motor vehicles.

This event is shaping up to be a diverse and provocative gathering of people pursuing different alternatives to fossil fuels. Here’s the lineup of confirmed speakers so far.

—Kristina Burow, partner, Arch Venture Partners; co-founder, Sapphire Energy

—Margaret McCormick, chief operating officer, Targeted Growth; CEO, Matrix Genetics

—Ned David, founder and president, Kilimanjaro Energy; venture partner, Arch Venture Partners

—John Gardner, incoming dean of academic affairs, Bainbridge Graduate Institute

—Tom Ranken, president, Washington Clean Technology Alliance

—Jan Allen, co-founder and VP of engineering, Harvest Power

—Michael Ramage, CEO, Asemblon

—Jeff Surma, CEO, S4 Energy Solutions

There should be plenty of room for debate in a gathering like there, where you have folks betting on algae-based biofuel (Sapphire, Matrix Genetics); natural gas from organic waste (Harvest Power); ethanol from industrial garbage (S4 Energy Solutions); and hydrogen fuel (Asemblon). We’ll also hear much more detail from Gardner about the new initiative that Boeing and Alaska Airlines have been pushing to create a cradle-to-grave system for producing and consuming aviation biofuels in the Northwest.

As always, this will be a first-rate opportunity to learn about the big challenges that remain in an important field of technology, and to network with some of the leading thinkers and doers in the business. I look forward to asking some hard questions on May 19, and inviting you to join in the conversation.

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Pleasanton, CA-based Fulcrum BioEnergy, a developer of technology for converting municipal solid waste into ethanol, said yesterday (PDF) that it has collected $75 million in Series C financing. The company declined to name the investors in the round, though it told Dow Jones VentureWire that existing shareholders Rustic Canyon Partners and U.S. Renewables Group participated. Fulcrum president and CEO James Macias said the new investment will allow the company to move forward with construction of a $120 million garbage-to-ethanol plant in McCarran, NV, near Reno. Expected to open in 2012, the plant will create 500 new “green jobs,” Fulcrum said.

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Lebanon, NH-based Mascoma has found a key piece of funding for a commercial-scale ethanol plant in northern Michigan. The oil firm Valero Energy has inked a non-binding agreement to invest up to $50 million to fund construction of a refinery that would use wood-based materials to make ethanol.

Frontier Renewable Resources, a joint venture of Mascoma and its Michigan-based partner J.M. Longyear, expects to break ground on the plant this year and to begin production of ethanol there in 2013, according to Mascoma. The plant is expected to be able to initially churn out 40 million gallons of ethanol per year, and it will be somewhat unique because it will rely on pulpwood as its main feedstock rather than food crops such as corn or soybeans.

This is a big deal for Mascoma, which has been working for years to bring its process for making cellulosic ethanol up to commercial scale. The company has showed its potential for commercial-scale production at its pilot facility in Rome, NY. Yet a lack of financing had delayed the project in Kinross Charter Township, MI, and last year Mascoma CEO Bill Brady told Xconomy that production would likely begin there in 2013 rather than the previous expected date in 2012.

Valero has agreed to provide a crucial equity piece to fund for the project, in addition to making a separate and unspecified investment in Mascoma, according to Mascoma. The firm says that the project has additional funding from the Michigan Economic Development Corporation and the U.S. Department of Energy. Valero, which says it owns 10 ethanol plants, has also agreed to take ethanol from the Kinross facility and sell it to its customers. Ethanol is a gasoline additive.

“Valero’s proposed investment in our first commercial-scale production facility proves the economic practicality of Mascoma’s technology for the conversion of woody biomass into ethanol,” said Mascoma’s Brady, in a statement. “We are also thrilled to have Valero as a shareholder in Mascoma Corporation as there are many synergies even beyond the Kinross facility, where the technologies we have developed could be helpful to Valero’s business.”

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The biofuels industry is still chugging along in Massachusetts. Marlborough, MA-based Qteros said today it has closed $22 million in the first tranche of its Series C financing. The investors in the round were not disclosed, but Qteros said both new and existing ones participated. The company’s previous backers include Battery Ventures, Venrock Associates, Long River Ventures, Soros Fund Management, Camros Capital, Valero Energy, and BP.

Qteros, formerly known as SunEthanol, had raised nearly $30 million before this latest financing round. The company has developed an experimental process for making ethanol from plant waste and other non-food sources—corn stalks, sugar cane leftovers, wood chips—that could someday make the cost of biofuels competitive with fossil fuels.

The cellulosic ethanol industry still faces many challenges, but here’s one promising bit of news: Qteros also said this week it has formed a strategic partnership with India’s Praj Industries, a major ethanol producer that has installed plants in more than 50 countries. Financial details weren’t given, but the deal exemplifies Qteros’s technology licensing approach—and it could be a big step forward for the firm.

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Enzymes make the world go around, if you spend much time listening to biochemists. Now one of the emerging players in the business of engineering industrial enzymes, Redwood City, CA-based Codexis, is starting to show it can make those biological workhorse proteins into something else important—money.

Codexis (NASDAQ: CDXS) made headlines back in April when it went public at $13 a share, as investors bought in to its story about enzyme technology and its potential use for the future of renewable biofuels. What fewer people realize is that while this is largely about technology, Codexis is on pace to generate almost $100 million in sales this year and to turn an operating profit, as measured by earnings before interest, taxes, depreciation and amortization (EBITDA). Tomorrow, the company will provide more color on where it stands in its third-quarter financial report.

The Codexis story is one of those rare tales in which a big science project finds its legs as a business. The company was founded in 2002 as a spinoff from Maxygen, which itself spun off from Affymax. The underlying technology is all about what’s known as “directed evolution,” in which scientists take an existing enzyme, or stretch of DNA to make an enzyme, and tweak properties here and there in a way that Mother Nature never intended, to get a useful product. Scientific imaginations can run wild with ideas of enzymes to run nifty processes that make active pharmaceutical ingredient for drugmakers; new catalysts that break down cellulosic biomass sugarcane into renewable fuel; or concentrate carbon dioxide so it can be stashed underground to limit the pollution from coal-fired power plants.

More than $400 million of investment has gone into the technology by Codexis and its two predecessors over the past two decades, and only now can Codexis say with confidence that it is off and running as a sustainable business with potential to really go after its biggest commercial ambitions.

“In the last two years we have been able to put hand on our hearts and say we now have a platform that works,” says Codexis CEO Alan Shaw. “It works in a time frame that matters in the real world.”

Alan Shaw

Enzymes can be finicky things in which seemingly small differences end up counting for a lot, so the key for a company like Codexis is to find the right combination and make it consistently and profitably. Without going too deep into the science, it starts with a template of DNA, and the company does high-powered screening of different mutations to see if it can get the properties of an enzyme it wants. What might take Mother Nature a millennium to evolve can be done in a matter of months through the high-speed screening technique, Shaw says.

The big question was always where this technology would be useful in a commercial setting. Codexis started with the pharmaceutical industry.

“When you try to deploy a new technology in a market, usually the best place to go is to look for natural innovators, you have to look for early adopters, and you find them in the life sciences industry,” Shaw says.

One of the important test cases for Codexis came through a contract it earned with the world’s largest drugmaker, Pfizer. The company makes the world’s best-selling … Next Page »

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Stephen Gatto focused much his career during the previous decade on the biofuels industry. But today, he’s betting on specialty chemicals as the highest-growth market for his Quincy, MA-based company’s fermentation technology.

Myriant Technologies is aiming to raise $60 million in a round of equity financing in the coming months, Gatto told Xconomy. The funding would help finance construction of the firm’s planned bio-chemical plant in Port of Lake Providence, LA. The plant, which is supported by a $50 million U.S. Department of Energy grant, will produce succinic acid in a fermentation process that uses plants as feedstock rather than gases or petrochemicals. It’s slated to begin producing the acid—which most people have never heard of but factors into goods like plastics, stretch fabrics, and perfumes—in 2011.

“This first plant will provide a significant earnings profile and revenue platform for the business going forward,” said Gatto, who is chairman and chief executive of Myriant. Myriant was spun off from Quincy-based BioEnergy International, which operates an ethanol plant in Pennsylvania, in June 2009 to apply BioEnergy’s fermentation technology to the specialty chemicals sector.

Myriant’s new round of financing will come from both previous investors and new backers, Gatto said. The firm’s existing investors include the Stamford, CT, hedge funds Plainfield Asset Management and Camulos Capital, Houston-based NGP Capital Resources, and Itera, a global holding company. Gatto declined to reveal the names of the new investors.

While I’ve heard CEOs talk up big financing deals that never bore fruit, it seems unlikely that will be the case with Gatto. Why? Bio-chemicals, meaning those chemicals made in sustainable processes, offer a lucrative opportunity to apply fermentation technologies like Myriant’s, especially when the products can be sold at prices that are competitive with petroleum-based chemicals. Gatto says his firm’s succinic acid will be priced as such.

Last week, Cambridge, MA-based Verenium (NASDAQ:VRNM) jumped out of the cellulosic biofuels game, selling its assets in that business to … Next Page »

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If only funding for biofuel startups were as omnipresent as spilt oil in the Gulf. That’s not the case, of course, as biofuel firms have struggled to find cash. Yet Qteros, a Marlborough, MA-based developer of cellulosic ethanol, has a plan to remove some of the typical financial aches from its business.

Qteros, which has raised nearly $30 million in venture capital to date, has developed an experimental process for making ethanol from plant waste and other non-food sources that could someday make the cost of biofuels competitive with fossil fuels. John McCarthy, CEO of the startup, joined the company in January after engineering a $90 million partnership between his previous employer, the Cambridge, MA-based biofuel developer Verenium (NASDAQ:VRNM), and the energy giant BP (which is, of course, at the center of the oil spill crisis in the Gulf of Mexico).

In an interview yesterday, McCarthy said that Qteros doesn’t need as much capital as some of its competitors to succeed.

Lebanon, NH-based Mascoma, for one, has fallen behind schedule in raising money to build a cellulosic ethanol plant in northern Michigan, company CEO Bill Brady told Xconomy last month. Brady said that such facilities cost north of $100 million, but he declined to reveal exactly how much his firm needs to finance the project.

Qteros, conversely, doesn’t want to build or operate ethanol plants. The 50-person firm wants to make money from licensing its technology to other companies that have, at least in some cases, already invested in building ethanol facilities, McCarthy said. The startup needs capital to fund its research and development, but that amount will be way less than the amount needed to erect ethanol plants.

In Qteros’s licensing model, some ethanol producers would incorporate its technology into their existing plants. McCarthy said that retrofitting existing facilities to use his firm’s technology would be less expensive than … Next Page »

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Five companies ranging in focus from fueling to family planning will have a chance to compete for $50,000 in business acceleration services and a one-year incubator lease at SPARK East in Ypsilanti, MI, on June 4. Business incubator Ann Arbor SPARK, which first announced the competition at the end of April, listed the finalists today. Each of the following companies will have three minutes to make their case before a panel of “noted funding and business experts.”

• Urobiologics, based in Livonia, MI, has a product called the UroGender Test Kit aimed at couples that would like to know the gender of their children early in a pregnancy. The company claims a 95 percent success rate in detecting a fetus’s gender, based on the mother’s urine sample, between five weeks and 15 weeks after conception.
• Mobile Sign Language Systems, a University of Michigan startup, is developing smart phone software that translates spoken English into real-time sign language.
• Eco-Fueling is developing a way for diesel engines to run on a mix of renewable ethanol and diesel, aimed at the six million diesel trucks currently on the road that use no renewable fuel.
• Own, based at the TechArb incubator in Ann Arbor, MI, will present its combined Web and hardware point of sale (POS) system for coffeehouses. Own says its product replaces cash registers or software POS systems.
• Aeradigm will present an air conditioning appliance for data centers that it says fits in the same racks with servers, cooling adjacent equipment and reducing overall energy load by harvesting waste heat for power.

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Lebanon, NH-based Mascoma has made strides with its process for producing ethanol from non-food plants such as wood chips and grass. Yet the firm is likely to delay the start of production at its first planned commercial facility, in northern Michigan, company CEO Bill Brady says.

Mascoma had been aiming to open a plant in Kinross, MI, by 2012. Now, Brady says, the facility is more likely to open in 2013—and the company has not secured the debt and equity funding it seeks to pay for the project. Though he would not say how much it would cost to build the proposed Kinross plant, Brady says that such facilities typically cost more than $100 million.

To hear Brady tell it, the financial meltdown bears much of the blame for slowing down plans for the Michigan plant. “There’s no doubt that the financial crisis in 2009 was a setback to all of the cleantech world, and so the financing that’s ever so important to this first plant has definitely been delayed,” the CEO says. “So that’s really been the big issue in terms of timing.”

In October 2008, Mascoma said that it had garnered grants of $26 million from the U.S. Department of Energy and $23.5 million in grants from the Michigan Economic Development Corporation to help build and support the facility in Kinross. Brady, who joined the company as CEO in January, says that part of the state grant was to fund research and development of the firm’s technology, and that some of those funds have been spent. Yet the CEO declined to say how much of the state grant remained for building the production plant. The DOE grants also included funding for both research and plant construction.

Mascoma is working on multiple fronts to advance the project in Michigan. One big effort is to prove the commercial … Next Page »

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The Boston-area pollen count surged in April, but venture financings experienced a more modest increase. New England’s tech and life sciences startups raised a total of $202.9 million in 21 equity-based deals, compared to March’s $194.5 million raised in 17 deals, according to data provided by our partner, private company intelligence platform, CB Insights. (Note, I’m talking here about equity-based deals worth $1 million or more apiece; we’ll round up April’s smaller “under-the-radar” deals a little later on this month.)

Early-stage deals dominated the April list. Of the 21 deals, 15 were seed, A, or B funding rounds. And those early rounds weren’t necessarily small, either: four of the five top deals were early-stage financings.

The life sciences sector came in first for dollars raised in April, as it did in March. But the $75.5 million raised by life sciences firms in April made up less than 40 percent of the venture investing for the month, compared to $144.2 million that went to the sector in March, accounting for nearly three-quarters of the equity-based venture dollars raised that month. A biotech company still nabbed the top deal spot in April, though, with $39.6 million going to Catabasis Pharmaceuticals, a developer of treatments for inflammation-related diseases such as diabetes. The Cambridge-based startup secured the round from SV Life Sciences, Clarus Ventures, and MedImmune Ventures. (Luke first broke the news when the company filed for the first $7.7 million of the financing, and then caught up with the company’s CEO, a Sirtris Pharmaceuticals veteran, the following week.)

The second-biggest deal went to North Billerica, MA’s Xos Digital, a provider of content management software and digital media services for sports organizations and athletic marketers. The company, which also has headquarters in Orlando, FL, announced in April that it had completed its Series B round of financing, but didn’t disclose the amount. An SEC filing shows that $37.16 million had been raised in equity and options and warrants, but that the round could total as much as $41.92 million.

Energy investing came back on the grid in April, with $30 million in second round funding for Joule Unlimited. The Cambridge-based company, which is developing technology for turning carbon dioxide into ethanol, nabbed the third-biggest venture deal last month. The energy sector was a no-show on March’s deals list.

Venture investing in the Web companies grew by more than 50 percent in April, compared to March. The sector took the second-largest pot of money for the month, $39.4 million, and the highest number of deals, at eight. The biggest deal in the Internet space went to Brightcove, a Cambridge-based online video hosting company that pulled in $12 million in Series D funding.

Companies in the retail arena accounted for a good chunk of the Internet cash raised last month, with Searchandise Commerce, an online media network for manufacturers and retail partners, and online e-commerce storefront provider Demandware taking $7 million apiece. E-commerce jewelry customization site Gemvara raised $5.2 million in Series B funding, and Daily Grommet, a site peddling unusual gift items with online videos, announced the first tranche of its Series A round, at $3.4 million.

Here’s the full list of April’s equity-based deals:
April also saw several startups raising cash through deals based on debt, options, and/or warrants, rather than equity. Those 6 transactions, worth a combined $21 million, are listed below.

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Paris-based oil company Total has joined General Motors as an investor in Coskata, according to an announcement by the cellulosic biofuels company based in Warrenville, IL.

GM invested an undisclosed amount in early 2008 and said in February this year that some of Coskata’s ethanol is being tested at the automaker’s proving grounds in Milford, MI.

“We invested in Coskata so that we could enable the rapid deployment of commercially viable and environmentally sustainable ethanol globally,” Bob Babik, GM Vehicle Emissions director, said in a statement.

The Detroit automaker says that, so far, it has produced more than 5.5 million flex-fuel vehicles, or cars and trucks that can run on a combination of gasoline and ethanol. Chevrolet, Cadillac, Buick, and GMC have produced flex-fuel-capable cars and trucks for the 2010 model year and GM says it is on track to make more than half of its vehicle production flex-fuel capable by 2012.

Coskata, which is funded in part by Waltham, MA-based Advanced Technology Ventures, uses microorganisms developed at the University of Oklahoma, along with the company’s bioreactor designs, to produce ethanol from practically any renewable source.

Other investors include Blackstone Cleantech Venture Partners, Khosla Ventures, Globespan Capital Partners, and Arancia. The company said previous investors joined this latest round, but would not disclose any amounts.

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News of financings, partnerships, royalties, and acquisitions among New England’s video game, transportation, biotech, and energy companies have kept us buzzing in the last week.

—Westwood, MA-based online games maker Turbine was purchased by the Home Entertainment Group of Warner Bros. Interactive Entertainment, a unit of Time Warner (NYSE: TWX). Turbine produces the massively multiplayer online game franchise Lord of the Rings Online, based on the books by J.R.R. Tolkien. Time Warner didn’t disclose the terms of the deal, but a source in a Boston Globe story pegged the transaction at $160 million, which would represent a modest return for Turbine investors, who have put slightly more than $100 million into the 16-year-old company.

—Zipcar, the Cambridge, MA-based car-sharing service, announced it had acquired Streetcar, a U.K.-based company with a similar business model. The terms of the deal weren’t disclosed, but Zipcar said it brought the companies’ combined memberships to more than 400,000 and gives it the opportunity to further expand in Europe.

—Qualtré, a Marlborough, MA, maker of motion sensors for consumer electronics, announced it closed an $8 million Series B round of funding, which included contributions from Matrix Partners and Pilot House Ventures. The money brings the company’s total funding pot to $13 million, and will go to operations, sales, and development of its products, which have applications in cellular handsets, navigation devices, and gaming controllers.

—France-based bioMérieux shelled out $5 million for an equity stake in Cambridge-based genomics analysis company Knome, as part of a partnership deal in which it will use Knome’s technology to develop diagnostics. BioMérieux appointed its CEO Stéphane Bancel as a director on the Knome board as part of the deal.

—I rounded up the top 10 largest venture deals inked in the first three months of 2010, with data from Dow Jones VentureSource, CB Insights, and the MoneyTree Report. Healthcare companies took seven of the 10 top slots, with the biggest transaction going to Andover, MA-based TransMedics at $36 million.

—Pluromed, a Woburn, MA-based maker of medical devices designed to stop bleeding during surgery, raised $1.1 million of a planned $3.9 million equity offering. Last year the company received a $500,000 loan as part of a Massachusetts initiative to further the life sciences industry in the state.

—Lebanon, NH-based Mascoma, a company developing methods for converting wood fiber and other non-edible plant material into ethanol, has raised $3.4 million of a planned $10 million round of convertible debt, an SEC filing showed. The company received a $15 million grant from the Michigan Economic Development Corporation in June 2008 to build an ethanol plant in Kinross, in Chippewa County, and the state later pledged another $8.5 million toward the site. The new funding, which came from … Next Page »

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Cambridge, MA-based Joule Unlimited, which is developing a technology that mimics photosynthesis by turning carbon dioxide into ethanol, has collected $30 million in a second round of funding from Flagship Ventures and unnamed additional investors, according to a report today in VentureWire. Formerly known as Joule Biotechnologies, the company launched last summer and is building a pilot plant near Austin, TX.

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There were a bunch of small deals in the Northwest this week. Some hot spots were mobile, business software, and alternative fuels.

—Portland, OR-based Urban Airship, a mobile software startup, raised $1.1 million in a deal led by True Ventures. Seattle-based Founder’s Co-op also participated in the round. Urban Airship makes infrastructure for mobile messaging services that lets companies send news and alerts to iPhones and other mobile devices.

—Seattle-based Kashless, an online classifieds and local promotions startup, acquired the patent portfolio of Mercata, the former Bellevue, WA-based volume discount dot-com owned by Paul Allen’s Vulcan Capital. Terms of the deal weren’t announced, but Vulcan has gained an equity stake in Kashless. Using the technology, Kashless has rolled out a sister site, Tippr, focused on group-buying deals from local merchants.

—Seattle-based Swype, a mobile text-input software firm, raised $1 million in a deal led by Docomo Capital. The funding is an extension of Swype’s recent $5.6 million Series B round led by Nokia Growth Partners and Samsung Ventures. The new investment should help the company continue to expand into international markets and mobile platforms.

—Bothell, WA-based Winshuttle, a business software firm, acquired German company A1 Professional Software, whose team will remain in place as a subsidiary. Financial terms of the deal weren’t given. Winshuttle sells software to help corporations shuttle data and bridge the gap between Excel spreadsheets and other familiar programs and German giant SAP’s business-management software.

—Bellevue, WA-based SinglePoint acquired M2Junction, a mobile advertising startup based in Hyderabad, India, for an undisclosed price. SinglePoint makes a mobile software platform for delivering things like brand messages and interactive coupons within text messages. The deal should help the company sell its services to Indian content publishers, mobile operators, brands, and ad agencies.

—Propel Fuels, the alternative fuel company founded in Seattle and now based in Sacramento, CA, raised $12 million in Series C equity financing led by new investor Craton Equity Partners, along with $8 million in debt financing. Existing investors Nth Power and @Ventures also participated in the equity round. The cash will help Propel expand its network of stations, which sell ethanol and biodiesel fuels, around California.

—Seattle-based RealNetworks and MTV Networks are spinning off their digital music service joint venture, Rhapsody, as a separate company. RealNetworks (NASDAQ: RNWK) will no longer be the majority owner and operator of Rhapsody; the new company will not have a single majority owner. The move looks to be a significant step in making Real more focused and profitable.

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Propel Fuels, the alternative fuel company founded in Seattle but now based in Sacramento, CA, announced today it has raised $12 million in Series C equity financing led by new investor Craton Equity Partners, along with $8 million in debt financing. Previous investors Nth Power and @Ventures also participated in the equity round. The money will be used to help Propel expand its network of fuel stations around California. The company currently owns and operates 11 stations around Seattle and Sacramento, selling ethanol and biodiesel fuels.

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