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    Japan's Marubeni Corp. plans to begin importing a bioethanol compound from Brazil for use in biogasoline sold by petroleum wholesalers in Japan. The trading firm will import ETBE, which is synthesized from petroleum products and ethanol derived from sugar cane. The compound will be purchased from Brazilian petrochemical company Companhia Petroquimica do Sul and in February, Marubeni will supply 6,500 kilolitres of the ETBE, worth around US$7 million, to a biogasoline group made up of petroleum wholesalers. Wholesalers have been introducing biofuels since last April by mixing 7 per cent ETBE into gasoline. Plans call for 840 million liters of ETBE to be procured annually from domestic and foreign suppliers by 2010. Trading Markets - January 24, 2007.

    Toyota Tsusho Corp., Ohta Oil Mill Co. and Toyota Chemical Engineering Co., say it and two other firms have jointly developed a technology to produce biodiesel fuel at lower cost. Biodiesel is made by blending methanol into plant-derived oil. The new technology requires smaller amounts of methanol and alkali catalysts than conventional technologies. In addition, the new technology makes water removal facilities unnecessary. JCN Network - January 22, 2007.

    Finland's Metso Paper and SWISS COMBI - W. Kunz dryTec A.G. have entered a licence agreement for the SWISS COMBI belt dryer KUVO, which allows biomass to be dried in a low temperature environment and at high capacity, both for pulp & paper and bioenergy applications. Kauppalehti - January 22, 2007.

    Record warm summers cause extreme ice melt in Greenland: an international team of scientists, led by Dr Edward Hanna at the University of Sheffield, has found that recent warm summers have caused the most extreme Greenland ice melting in 50 years. The new research provides further evidence of a key impact of global warming and helps scientists place recent satellite observations of Greenland´s shrinking ice mass in a longer-term climatic context. Findings are published in the 15 January 2008 issue of Journal of Climate. University of Sheffield - January 15, 2007.

    Japan's Tsukishima Kikai Co. and Marubeni Corp. have together clinched an order from Oenon Holdings Inc. for a plant that will make bioethanol from rice. The Oenon group will invest around 4.4 billion yen (US$40.17 million) in the project, half of which will be covered by a subsidy from the Ministry of Agriculture, Forestry and Fisheries. The plant will initially produce bioethanol from imported rice, with plans to use Hokkaido-grown rice in the future. It will produce 5 million liters per year starting in 2009, increasing output to 15m liters in 2011. The facility will be able to produce as much as 50,000 liters of bioethanol from 125 tons of rice each day. Trading Markets - January 11, 2007.

    PetroSun, Inc. announced today that its subsidiary, PetroSun BioFuels Refining, has entered into a JV to construct and operate a biodiesel refinery near Coolidge, Arizona. The feedstock for the refinery will be algal oil produced by PetroSun BioFuels at algae farms to be located in Arizona. The refinery will have a capacity of thirty million gallons and will produce 100% renewable biodiesel. PetroSun BioFuels will process the residual algae biomass into ethanol. MarketWire - January 10, 2007.

    BlueFire Ethanol Fuels Inc, which develops and operates carbohydrate-based transportation fuel production facilities, has secured capital liquidity for corporate overhead and continued project development in the value of US$15 million with Quercus, an environmentally focused trust. BlueFire Ethanol Fuels - January 09, 2007.

    Some $170 billion in new technology development projects, infrastructure equipment and construction, and biofuel refineries will result from the ethanol production standards contained the new U.S. Energy Bill, says BIO, the global Biotechnology Industry Organization. According to Brent Erickson, BIO's executive vice president "Such a new energy infrastructure has not occurred in more than 100 years. We are at the point where we were in the 1850s when kerosene was first distilled and began to replace whale oil. This technology will be coming so fast that what we say today won't be true in two years." Chemical & Engineering News - January 07, 2007.

    Scottish and Southern Energy plc, the UK's second largest power company, has completed the acquisition of Slough Heat and Power Ltd from SEGRO plc for a total cash consideration of £49.25m. The 101MW CHP plant is the UK’s largest dedicated biomass energy facility fueled by wood chips, biomass and waste paper. Part of the plant is contracted under the Non Fossil Fuel Obligation and part of it produces over 200GWH of output qualifying for Renewable Obligation Certificates (ROCs), which is equivalent to around 90MW of wind generation. Scottish & Southern Energy - January 2, 2007.

    PetroChina Co Ltd, the country's largest oil and gas producer, plans to invest 800 million yuan to build an ethanol plant in Nanchong, in the southwestern province of Sichuan, its parent China National Petroleum Corp said. The ethanol plant has a designed annual capacity of 100,000 tons. ABCMoneyNews - December 21, 2007.

    Mexico passed legislation to promote biofuels last week, offering unspecified support to farmers that grow crops for the production of any renewable fuel. Agriculture Minister Alberto Cardenas said Mexico could expand biodiesel faster than ethanol. More soon. Reuters - December 20, 2007.

    Oxford Catalysts has placed an order worth approximately €700,000 (US$1 million) with the German company Amtec for the purchase of two Spider16 high throughput screening reactors. The first will be used to speed up the development of catalysts for hydrodesulphurisation (HDS). The second will be used to further the development of catalysts for use in gas to liquid (GTL) and Fischer-Tropsch processes which can be applied to next generation biofuels. AlphaGalileo - December 18, 2007.

    According to the Instituto Brasileiro de Geografia e Estatística (IBGE), Brazil's production of sugarcane will increase from 514,1 million tonnes this season, to a record 561,8 million tonnes in the 2008/09 cyclus - an increase of 9.3%. New numbers are also out for the 2007 harvest in Brazil's main sugarcane growing region, the Central-South: a record 425 million tonnes compared to 372,7 million tonnes in 2006, or a 14% increase. The estimate was provided by Unica – the União da Indústria de Cana-de-Açúcar. Jornal Cana - December 16, 2007.

    The University of East Anglia and the UK Met Office's Hadley Centre have today released preliminary global temperature figures for 2007, which show the top 11 warmest years all occurring in the last 13 years. The provisional global figure for 2007 using data from January to November, currently places the year as the seventh warmest on records dating back to 1850. The announcement comes as the Secretary-General of the World Meteorological Organization (WMO), Michel Jarraud, speaks at the Conference of the Parties (COP) in Bali. Eurekalert - December 13, 2007.

    The Royal Society of Chemistry has announced it will launch a new journal in summer 2008, Energy & Environmental Science, which will distinctly address both energy and environmental issues. In recognition of the importance of research in this subject, and the need for knowledge transfer between scientists throughout the world, from launch the RSC will make issues of Energy & Environmental Science available free of charge to readers via its website, for the first 18 months of publication. This journal will highlight the important role that the chemical sciences have in solving the energy problems we are facing today. It will link all aspects of energy and the environment by publishing research relating to energy conversion and storage, alternative fuel technologies, and environmental science. AlphaGalileo - December 10, 2007.

    Dutch researcher Bas Bougie has developed a laser system to investigate soot development in diesel engines. Small soot particles are not retained by a soot filter but are, however, more harmful than larger soot particles. Therefore, soot development needs to be tackled at the source. Laser Induced Incandescence is a technique that reveals exactly where soot is generated and can be used by project partners to develop cleaner diesel engines. Terry Meyer, an Iowa State University assistant professor of mechanical engineering, is using similar laser technology to develop advanced sensors capable of screening the combustion behavior and soot characteristics specifically of biofuels. Eurekalert - December 7, 2007.

    Lithuania's first dedicated biofuel terminal has started operating in Klaipeda port. At the end of November 2007, the stevedoring company Vakaru krova (VK) started activities to manage transshipments. The infrastructure of the biodiesel complex allows for storage of up to 4000 cubic meters of products. During the first year, the terminal plans to transship about 70.000 tonnes of methyl ether, after that the capacities of the terminal would be increased. Investments to the project totaled €2.3 million. Agrimarket - December 5, 2007.

    New Holland supports the use of B100 biodiesel in all equipment with New Holland-manufactured diesel engines, including electronic injection engines with common rail technology. Overall, nearly 80 percent of the tractor and equipment manufacturer's New Holland-branded products with diesel engines are now available to operate on B100 biodiesel. Tractor and equipment maker John Deere meanwhile clarified its position for customers that want to use biodiesel blends up to B20. Grainnet - December 5, 2007.

    According to Wetlands International, an NGO, the Kyoto Protocol as it currently stands does not take into account possible emissions from palm oil grown on a particular type of land found in Indonesia and Malaysia, namely peatlands. Mongabay - December 5, 2007.

    Malaysia's oil & gas giant Petronas considers entering the biofuels sector. Zamri Jusoh, senior manager of Petronas' petroleum development management unit told reporters "of course our focus is on oil and gas, but I think as we move into the future we cannot ignore the importance of biofuels." AFP - December 5, 2007.

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Friday, January 25, 2008

Coal's deep trouble makes biomass highly attractive

Coal is not well. Serious supply constraints in Australia, a major power crisis in South Africa shutting down big mines, and shortages in China on record domestic demand, prompting the country to halt all exports, have pushed up prices to records. Analysts are very bullish on coal not just for the immediate future, but for the coming years. This automatically makes biomass an attractive alternative. The green fuel is no longer merely interesting for its capacity to reduce carbon emissions, it has become a feasible alternative to coal on purely commercial grounds. Those who can tap into the niche market could be doing a good deal.

Let's do the math, but take into account that data for biomass price estimates are rudimentary and freight rates for the bulky fuel would be difficult to assess. We compare South African coal - more than a quarter of Europe's energy coal is shipped from Richards Bay - with prices for palm kernel shells, a biomass fuel that is being co-fired routinely by several European power producers. Palm kernel shells (PKS) are a waste residue from palm fruit processing; they are easy to ship, don't need to be densified and can be readily co-fired with coal (for PKS fuel properties, see the IEA Bioenergy Task 32 - Biomass Combustion and Co-firing and its databases on biomass fuels).

  • European contracts for South African coal from Richards Bay for delivery to Amsterdam-Rotterdam-Antwerp with settlement next year rose to $112.25 per metric ton today. Spot prices for FOB deals have been consistently hovering around $100/ton for months, and have been higher than that for most contracts since the beginning of this year.
  • Coal at Richards Bay has an average heating value of 25.1 Gj/ton. So today's price comes down to $4.427/Gj, which is high by any means, but still cheaper than continental natural gas.
  • Palm kernel shells from Nigeria, Africa's largest producer, fetch farmgate prices of $6.45/ton. Biopact has an FOB quote for 20,000 tons at $40 per ton, for dry PKS, shipped out from Port Harcourt. It would seem that $40 per ton is high, compared to such a low farmgate price, but we take it as an indicator of inefficient logistics in Nigeria - we can imagine it isn't easy to collect PKS from plantations inland and to transport it over bad roads to port. So we take the FOB price as such (negotiations would certainly push it down a bit).
  • Dry palm kernel shells have a heating value of around 21 Gj/ton. So the $40/ton price would be equivalent to $1.904/Gj. A major competitive edge over South African thermal coal.
  • However, freight rates would be considerably higher for PKS because of the much lower bulk density of the biomass fuel (750kg/m³) compared with Richards Bay coal (around 1300kg/m³).
  • Freight rates for dry bulk goods have seen records over the past year, but have crashed recently on fears of a global recession (see chart of the Baltic Dry Index, the most often quoted index for commodity freight rates; click to enlarge). So it's a bit tricky to estimate prices. We would however guesstimate, given the fact that the difference in the FOB price between coal and PKS is so big, even much higher freight rates would not close the price gap between the two fuels anywhere soon. We averaged shipping prices for grains with a similar bulk density (around 750kg/m³), and find PKS would still be considerably cheaper at their destination: Amsterdam-Rotterdam-Antwerp.
  • Add that the distance between Port Hartcourt and Antwerp (4419 nautical miles) is considerably shorter than that between Richards Bay and Antwerp (7,033 nautical miles). So this would largely offset higher freight rates for PKS. On the other hand, handling procedures and other supply chain steps for such a new fuel like PKS are probably untested and inefficient at the moment. This would add some to the price.
  • Finally, it is important to note that co-firing renewable biomass yields added value for power producers, because the fuel reduces carbon emissions - this added value can be expressed in many forms: green electricity certificates, carbon credits, etc...
In short, it seems like palm kernel shells from Nigeria could beat several contracts for coal from South Africa. If coal's problems persist over the coming years, similar forms of biomass could begin to find a niche as a commercially viable alternative fuel source. Supply chains and logistical infrastructures are virtually non-existent (some current biomass trade routes pictured in the map) which means a dedicated investment in these chains in places where a secure biomass supply is available, could lower prices still further.

References on which we based our guesstimation can be found below:
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Coal in trouble:
Bloomberg: Coal Rises the Most in Three Weeks as South African Mines Shut - January 25, 2008.

Reuters: S.Africa export coal to be kept for domestic - January 24, 2008.

AP: China Halts Coal Exports Amid Shortage - January 26, 2008.

Times Online: Coal, and not gold, should be the real concern - January 26, 2008.

Mining Weekly: More coal price increases on the way, says senior analyst - January 25, 2008.

Fairfield (Australia): Spot the boom as coal price soars - January 25, 2008.

Reuters: China may delay coal exports on power shortages - January 24, 2008.

News about spot prices, discussion of several contracts:

Reuters: Richards Bay, DES ARA coal prices rise - January 8, 2008.

Reuters: RPT-PREVIEW-Japan-Australia '08 thermal coal price record-bound - January 24, 2008.

Freight costs:
Coal Portal: Freight rates [subscription req'd].

The Baltic Dry Index, which measures shipping costs for commodities.

Example list of concrete freight rates for grains, per ton, over the past months and years - one company; we compared prices over at different charterers.

Co-firing PKS and biomass in general:

Essent Energy's Amer power plant in the Netherlands is one of the facilities in Europe co-firing PKS and coal.

Two interesting case studies about this practise can be found here:

IEA Bioenergy Task 38: "Greenhouse Gas Balances of Biomass Import Chains for “Green” Electricity Production in The Netherlands" [*.pdf], IEA Bioenergy Task 38, Greenhouse Gas Balances of Biomass and Bioenergy Systems.

IEA Bioenergy Task 40: "Sustainable International Bioenergy Trade: securing an international supply and demand", IEA Bioenergy Task 40: international bioenergy trade, 2006.

On co-firing biomass in general, see the IEA's Bioenergy Task 32, entirely devoted to the topic. See especially its co-firing database of 150 major power producers who burn biomass alongside coal. Data about fuel properties for different types of biomass can be found in these databases.

Farmgate price estimates for crop residues in Nigeria can be found here:

S.O. Jekayinfa, and V. Scholz, "Assessment of Availability and Cost of Energetically Usable Crop Residues in Nigeria", Tropentag 2007, University of Kassel-Witzenhausen and University of Göttingen, October 9-11, 2007, Conference on International Agricultural Research for Development.

The quote we received for the 20,000 tons of PKS comes from a Nigerian agribusiness company based in Owerri in Imo State. Contact us for details.

Article continues

Pacific Gas & Electric Company to research large-scale biomethane resources for its customers

Pacific Gas and Electric Company (PG&E), one of the largest combination natural gas and electric utilities in the United States, announced that it has issued a Request for Information (RFI) to identify partners for a potential project to demonstrate technologies that could cost-effectively produce significant quantities of biomethane - pipeline-quality, renewable natural gas. The demonstration project is part of PG&E's commitment to increase the amount of clean energy it provides customers throughout its northern and central California service area. The company created an online biomethanation forum where interested parties can meet.

Biomethane is pipeline-quality gas derived from biomass as defined [*.pdf] by the California Energy Commission (CEC), which includes any organic material not derived from fossil fuels, including agricultural crops, agricultural and forestry wastes and residues, and construction wood wastes, among others. Biomethanation, also called anaerobic digestion, is the biochemical process of converting biomass to biogas via microorganisms. Alternatively, a thermochemical pathway based on the gasification of biomass can be used to yield socalled synthetic natural gas (called 'bio-SNG' or 'greengas' in Europe).

Renewable biogas is then purified and upgraded to pipeline quality and can be blended with natural gas in existing pipelines. This is done in Europe on an increasingly large scale. In the U.S., the first such project was announced only recently (previous post).

According to energy experts, the highly efficient gaseous biofuel holds a large potential across the world. In Europe, a comprehensive study showed that biogas can replace all of the continent's Russian gas imports by 2020. The EU could generate around 500 million cubic meters of biogas per year, sustainably. Estimates of the potential for China and the U.S. are even larger (previous post). PG&E is aware of this potential.
There is a tremendous opportunity in California to utilize biomass, which would otherwise go unused, to contribute significantly to meeting the state's climate goals. With this request for information, we hope to identify promising biomethanation technologies and understand what the market needs for support. Biomethanation is the latest example of how PG&E is planning for the future by exploring innovative technologies to produce and deliver clean energy. - Fong Wan, vice president of Energy Procurement for PG&E
California and the western region of North America contain large quantities of biomass, which could meaningfully contribute toward the state's renewable energy requirements while simultaneously providing other benefits, including greenhouse gas emission reduction, fire prevention, improved local air quality and landfill disposal reduction.

Emerging biomethanation technologies and processes may increase conversion efficiency, expand the range of usable feedstock, and improve the quality of biomethane products. To accelerate the commercial availability of these emerging biomethanation technologies, PG&E is seeking partners to develop and operate a facility that will demonstrate the technical and economic feasibility of emerging technologies for developing significant quantities of biomethane:
:: :: :: :: :: :: :: :: :: :: :: ::

Through the proposed biomethanation demonstration project, PG&E intends to promote viable biomethanation technologies that convert CEC-approved sources of biomass into biomethane that could be injected into PG&E's gas transmission system and delivered for high-value uses such as dispatchable power generation.

PG&E will hold a networking forum on March 5 from 10 a.m. to 4 p.m. at its San Francisco headquarters to answer questions about the RFI and provide an opportunity for potential project partners to meet. Parties interested in attending the forum must register online by February 22, 2008, here [*.pdf]. For more information about the RFI, or to participate in PG&E's online biomethanation RFI forum, please visit: www.pge.com/rfi.

PG&E is a leader in utilizing biomethane. The utility recently received approval by the California Public Utilities Commission of its gas purchase agreements with Microgy, Inc. and with BioEnergy Solutions to deliver up to 8,000 MMBtu per day each of pipeline quality biomethane captured from cow manure.

PG&E currently supplies 12 percent of its power from qualifying renewable sources under California's Renewable Portfolio Standard (RPS) program. PG&E continues to aggressively add renewable electric power resources to its supply and is on target to exceed 20 percent under contract or delivered by 2010. On average, more than 50 percent of the energy PG&E delivers to its customers comes from generating sources that emit no carbon dioxide, providing among the cleanest energy in the nation.

PG&E: Pacific Gas and Electric Company Seeks to Research Biomethane Resources for its Customers - January 24, 2008.

PG&E: biomethanation forum.

Biopact: Germany considers opening natural gas network to biogas - major boost to sector - August 11, 2007

Biopact: Market study tracks global boom in biogas, Germany technology leader - July 13, 2007

Biopact: Report: biogas can replace all EU natural gas imports - January 04, 2008

Biopact: A first for the U.S.: company feeds biomethane into natural gas pipeline - January 22, 2008

Biopact: EU research project looks at feeding biogas into the main natural gas grid - April 08, 2007

Biopact: Schmack Biogas and E.ON to build Europe's largest biogas plant, will feed gas into natural gas grid - July 18, 2007

Article continues

Green partnerships: bioenergy entrepreneurs looking for investors, partners, advice

Biopact often receives requests from entrepreneurs, small companies and NGOs looking for partners to invest in a bioenergy project in the South. We try to link these organisations and individuals to potential interested parties. But our 'matchmaking' efforts might have more effect when we put the projects online.

For this reason we will be presenting these requests in the side-bar, under the 'green partnership' logo. We will describe the project's location, size and subject very briefly. Interested investors, service providers, consultants or entrepreneurs can then contact Biopact, after which we will link them up with the project. Note that we will only present medium, small and micro-scale projects (we keep the big ones for ourselves!)

Some of the past two weeks' requests for partners, investors and advice include:
  • A Dutch entrepreneur is building a medium scale (1 million liter per year) multi-feedstock biodiesel pilot plant in Mozambique and is looking for a partner/investor to expand the model to other African countries. Brochure about the project available.
  • The owners of a cultural tourism park in East Africa that is integrated into forests that have arisen out of the rehabilitation of a former municipal dumpsite quarry, are looking to sell carbon credits for a new afforestation effort. The rehabilitation was achieved by planting trees into a formerly desolate quarry, which won the project several international awards. The forests were planted from 1993 onwards and are now fairly well grown; they are a mix of indigenous and casuarina trees, with a total acreage of 16 acres. They would like to sell carbon credits for the purpose of completing the plantation of the remaining acres of unreclaimed quarry. They are looking for advice on how to take the project forward and on how to receive carbon credits.
  • The operators of a family-run tourist lodge in South Africa, specialising in horse-riding safaris and polo, are establishing 16 holiday homes on a game farm. They are looking into utilizing alternative energy to power the homes, more specifically biogas which could be made from the manure from 20 horses. They are looking for advice from biogas experts.
  • An entrepreneur in Kenya wants to establish a Jatropha plantation to produce seeds for biodiesel and is looking for a partner. He has access to agricultural resources and is a trained mechanical engineering technician who has worked in a medium sized biodiesel factory.
  • A U.S. based company is looking to start exporting hardwood pellet fuel. No info about quantities involved, but it is looking for potential buyers in Europe (we referred this company to the European biomass trading floor).
  • A company based in Nigeria's Rivers State has access to 20,000 metric tons of palm kernel shells, which it wants to export as a biomass source for co-firing or for the production of fuel pellets. (Info about the quality of the shells and farmgate price per ton provided to Biopact.)
  • An entrepeneur wants to 'experiment' with Jatropha plantations in Pakistan and Afghanistan and is looking for information and contacts to procure seeds. He is looking for a partner to carry out a feasibility study. The individual thinks "this may provide an alternate source of income to the very poor who give their sons away to the radicals as they cannot afford feeding them, especially in Norhern Pakistan & Southern Afganistan."
Contact us for more information.

Biopact itself does not invest in any concrete bioenergy projects, but we do have a growing set of references that allows us to connect people interested in doing so. In the future we might develop a dedicated matchmaking website focusing on bioenergy projects in developing countries, in Africa in particular [entry ends here].
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Polish energy company to bring 460MW coal-biomass power plant on line in 2009

Poland's second largest power group, Poludniowy Koncern Energetyczny (PKE), announces it will put on line a new coal and biomass fired 460 MW power station in Bedzin in the first quarter of 2009. Construction on the €500 (US$735) million plant began in January 2006 and is now in its final stages. The power station will burn 1.2 million tonnes of coal and renewable biomass per year. The biomass component and an efficient combustion system ensures that emissions are reduced by 25 per cent compared with the country's most efficient generators.

Bedzin is a small city located in the South-West of Poland, in the Silesian Voivodship, a forest-rich area, from where biomass will be supplied for co-firing. The electricity generated will be fed into a new 400kV power line being built by Energoprojekt Kraków S.A. servicing the large urban agglomeration of Krakow.

The cleaner coal plant will be the least polluting in Poland because it utilizes an efficient fluidized bed combustion (FBC) system, which allows for the flexible use of both coal and biomass. FBCs suspend solid fuels on upward-blowing jets of air during the combustion process. The result is a turbulent mixing of gas and solids. The tumbling action, much like a bubbling fluid, provides more effective chemical reactions and heat transfer.

Partly due to co-firing biomass and to the efficiency of the FBC, both SO2 and NOx emissions will not exceed 200mg/m³, which is in line with EU regulations. The lowered emissions will count as part of Poland's obligations to lower greenhouse gas emissions from industry and energy.

The company created a dedicated website showing progress at the construction site live. In november last year, the last important block of the plant was added, its 133,2 meter high cooling tower. A successful test with cooling water was conducted on 23 November. This allowed for the start of the construction of the boiler segment. The next milestone was the construction of a 60 tonne impeller, as well as the 288 tonne generator, the biggest single element on the block. This year in August the first full firing tests will take place, with synchronisation trials beginning in december:
:: :: :: :: :: :: :: :: :: ::

The investment in the biomass-coal plant is the first step in PKE's strategy to phase out its older coal power stations. PKE planning to build another two power stations, with capacity of 800 and 1000 MW each. Company spokesman Pawel Gniadek said that by the end of March, PKE would decide on the sites of these and possibly select partners to build them. Partners being included are E.ON, RWE, ESB International, Sempra Energy and JES Energy:

In the long run, PKE plans to maintain its capacity close to the current level, at around 5 GW, but needs to replace old capacity, which does not meet environmental standards.


Poludniowy Koncern Energetyczny: W przyszłym roku popłynie prąd z nowego bloku PKE - January 23, 2008.

Nowy Blok dedicated website.

Nowy Blok presentation 1 [*.pdf] and presentation 2 [*.pdf].

Presentation of the new 400kV power line project.

Article continues

Scientists create first synthetic bacterial genome - importance for biofuels

A team of 17 researchers at the J. Craig Venter Institute (JCVI) has created the largest man-made DNA structure by synthesizing and assembling the 582,970 base pair genome of a bacterium, Mycoplasma genitalium JCVI-1.0. This work, published online in the journal Science by Dan Gibson, Ph.D., et al, is the second of three key steps toward the team’s goal of creating a fully synthetic organism. The first step was achieved last year when a genome was successfully transplanted from one organism to another (previous post). In the next step, which is ongoing at the JCVI, the team will attempt to create a living bacterial cell based entirely on the synthetically made genome.

The new and potentially disruptive science field of synthetic biology is seen by many as one that promises valuable applications in medicine, chemistry, biology, materials science, climate change and energy. The handful of synthetic biologists creating life in the lab often refer to the production of highly efficient biofuels as a key application: by designing task-specific artificial microorganisms that can convert abundant biomass into fuels with ease, our energy worries could be alleviated (more here, here and here). After the new breakthrough, the scientists repeat the relevance of their work for the field of bioenergy:
When we started this work several years ago, we knew it was going to be difficult because we were treading into unknown territory. Through dedicated teamwork we have shown that building large genomes is now feasible and scalable so that important applications such as biofuels can be developed. - Hamilton Smith, M.D., senior author on the publication
The JCVI team achieved its new technical feat by chemically making DNA fragments in the lab and developing new methods for the assembly and reproduction of the DNA segments. After several years of work perfecting chemical assembly, the team found they could use homologous recombination (a process that cells use to repair damage to their chromosomes) in the yeast Saccharomyces cerevisiae to rapidly build the entire bacterial chromosome from large subassemblies.

The building blocks of DNA—adenine (A), guanine (G), cytosine (C) and thiamine (T) are not easy chemicals to artificially synthesize into chromosomes. As the strands of DNA get longer they get increasingly brittle, making them more difficult to work with. Prior to today’s publication the largest synthesized DNA contained only 32,000 base pairs. Thus, building a synthetic version of the genome of the bacteria M. genitalium genome that has more than 580,000 base pairs presented a formidable challenge. However, the JCVI team has expertise in many technical areas and a keen biological understanding of several species of mycoplasmas.

Methods for Creating the Synthetic M. genitalium

The process to synthesize and assemble the synthetic version of the M. genitalium chromosome began first by resequencing the native M. genitalium genome to ensure that the team was starting with an error free sequence. After obtaining this correct version of the native genome, the team specially designed fragments of chemically synthesized DNA to build 101 “cassettes” of 5,000 to 7,000 base pairs of genetic code. As a measure to differentiate the synthetic genome versus the native genome, the team created “watermarks” in the synthetic genome. These are short inserted or substituted sequences that encode information not typically found in nature. Other changes the team made to the synthetic genome included disrupting a gene to block infectivity. To obtain the cassettes the JCVI team worked primarily with the DNA synthesis company Blue Heron Technology, as well as DNA 2.0 and GENEART.:
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From here, the team devised a five stage assembly process where the cassettes were joined together in subassemblies to make larger and larger pieces that would eventually be combined to build the whole synthetic M. genitalium genome. In the first step, sets of four cassettes were joined to create 25 subassemblies, each about 24,000 base pairs (24kb). These 24kb fragments were cloned into the bacterium Escherichia coli to produce sufficient DNA for the next steps, and for DNA sequence validation.

The next step involved combining three 24kb fragments together to create 8 assembled blocks, each about 72,000 base pairs. These 1/8th fragments of the whole genome were again cloned into E. coli for DNA production and DNA sequencing. Step three involved combining two 1/8th fragments together to produce large fragments approximately 144,000 base pairs or 1/4th of the whole genome.

At this stage the team could not obtain half genome clones in E. coli, so the team experimented with yeast and found that it tolerated the large foreign DNA molecules well, and that they were able to assemble the fragments together by homologous recombination. This process was used to assemble the last cassettes, from 1/4 genome fragments to the final genome of more than 580,000 base pairs. The final chromosome was again sequenced in order to validate the complete accurate chemical structure.

The synthetic M. genitalium has a molecular weight of 360,110 kilodaltons (kDa). Printed in 10 point font, the letters of the M. genitalium JCVI-1.0 genome span 147 pages.
This is an exciting advance for our team and the field. However, we continue to work toward the ultimate goal of inserting the synthetic chromosome into a cell and booting it up to create the first synthetic organism. - Dan Gibson, lead author.
The research to create the synthetic M. genitalium JCVI-1.0 was funded by Synthetic Genomics, Inc.

Key Milestones in JCVI’s Synthetic Genomics Research
The work described by Gibson et al. has its genesis in research by Dr. Venter and colleagues in the mid-1990s after sequencing M. genitalium and beginning work on the minimal genome project. This area of research, trying to understand the minimal genetic components necessary to sustain life, began with M. genitalium because it is a bacterium with the smallest genome that we know of that can be grown in pure culture. That work was published in the journal Science in 1995.

In 2003 Drs. Venter, Smith and Hutchison made the first significant strides in the development of a synthetic genome by their work in assembling the 5,386 base pair bacteriophage ΦX174 (phi X). They did so using short, single strands of synthetically produced, commercially available DNA (known as oligonucleotides) and using an adaptation of polymerase chain reaction (PCR), known as polymerase cycle assembly (PCA), to build the phi X genome. The team produced the synthetic phi X in just 14 days.

In June 2007 another major advance was achieved when JCVI researchers led by Carole Lartigue, Ph.D., announced the results of work on genome transplantation methods allowing them to transform one type of bacteria into another type dictated by the transplanted chromosome. The work was published in the journal Science, and outlined the methods and techniques used to change one bacterial species, Mycoplasma capricolum, into another, Mycoplasma mycoides Large Colony (LC), by replacing one organism’s genome with the other one’s genome (previous post).

Genome transplantation was the first essential enabling step in the field of synthetic genomics as it is a key mechanism by which chemically synthesized chromosomes can be activated into viable living cells. Today’s announcement of the successful synthesis of the M. genitalium genome is the second step leading to the next experiments to transplant a fully synthetic bacterial chromosome into a living organism and “boot up” the cell.

Ethical Considerations

Since the beginning of the quest to understand and build a synthetic genome, Dr. Venter and his team have been concerned with the societal issues surrounding the work. In 1995 while the team was doing the research on the minimal genome, the work underwent significant ethical review by a panel of experts at the University of Pennsylvania (Cho et al, Science December 1999:Vol. 286. no. 5447, pp. 2087 – 2090). The bioethical group's independent deliberations, published at the same time as the scientific minimal genome research, resulted in a unanimous decision that there were no strong ethical reasons why the work should not continue as long as the scientists involved continued to engage public discussion.

Dr. Venter and the team at JCVI continue to work with bioethicists, outside policy groups, legislative members and staff, and the public to encourage discussion and understanding about the societal implications of their work and the field of synthetic genomics generally. As such, the JCVI’s policy team, along with the Center for Strategic & International Studies (CSIS), and the Massachusetts Institute of Technology (MIT), were funded by a grant from the Alfred P. Sloan Foundation for a 20-month study that explored the risks and benefits of this emerging technology, as well as possible safeguards to prevent abuse, including bioterrorism. After several workshops and public sessions the group published a report in October 2007 outlining options for the field and its researchers.

Civil society organisations responded to this report critically, asking questions about ownership, monopoly practices or intellectual property claims arising from synthetic biology (previous post).


Daniel G. Gibson, Gwynedd A. Benders, Cynthia Andrews-Pfannkoch, Evgeniya A. Denisova, Holly Baden-Tillson, Jayshree Zaveri, Timothy B. Stockwell, Anushka Brownley, David W. Thomas, Mikkel A. Algire, Chuck Merryman, Lei Young, Vladimir N. Noskov, John I. Glass, J. Craig Venter, Clyde A. Hutchison III, Hamilton O. Smith, "Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome", Science, Published Online January 24, 2008, DOI: 10.1126/science.115172

JCVI: Venter Institute Scientists Create First Synthetic Bacterial Genome - January 24, 2007.

Biopact: Scientists take major step towards 'synthetic life': first bacterial genome transplantation changing one species to another - June 29, 2007

Biopact: Breakthrough in synthetic biology: scientists synthesize DNA-based memory in yeast cells, guided by mathematical model - September 17, 2007

Biopact: Scientists call for global push to advance synthetic biology - biofuels to benefit - June 25, 2007

Biopact: Scientists patent synthetic life - promise for 'endless' biofuels - June 09, 2007

Biopact: Synthetic Genomics and Asiatic Centre for Genome Technology to sequence oil palm genome - July 11, 2007

Biopact: Agrivida and Codon Devices to partner on third-generation biofuels - August 03, 2007

Biopact: Civil society organizations respond to report on synthetic biology governance - October 18, 2007

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