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News and Trendshttp://www.pnas.org/content/early/2008/12/10/0811011106.full.pdf+html (open access article at PNAS website) http://www.jcvi.org/cms/press/press-releases/full-text/article/j-craig-venter-institute-researchers-publish-significant-advance-in-genome-assembly-technology/?tx_ttnews%5BbackPid%5D=67&cHash=37e7fe3794 The J. Craig Venter Institute (JCVI, a leading genome research organization in the United States) recently announced that its scientists have developed a new, single-step method for the assembly of the whole bacterial genome of Mycoplasma genitalium, from 25 fragments of DNA. The assembly method for creating the “synthetic bacterial genome” (from the 25 DNA fragments) uses a natural cellular repair process called “homologous recombination” in the yeast, Saccharomyces cerevisiae. A technical paper describing the method appears in the online early edition of the Proceedings of the National Academy of Sciences (PNAS) (URL above). The improved method, which harnesses the DNA assembly capability in yeast, streamlines an otherwise tedious method for the construction of the synthetic bacterial genome. According to the JCVI website, this advance will be harnessed for making more efficient next-generation biofuels and biochemicals. Related information: “Venter Talks about “Synthetic Life” and Its Application for 4th Generation Biofuels” (Crop Biotech Update, 13 June 2008) http://www.isaaa.org/kc/cropbiotechupdate/biofuels/default.asp?Date=6/13/2008#2672 Homologous recombination http://en.wikipedia.org/wiki/Homologous_recombination http://www3.interscience.wiley.com/journal/121536533/abstract (may require paid access to full paper) http://www.eurekalert.org/pub_releases/2008-12/wwf-bpo120108.php A recent study by a group of seven international scientists showed that replacing tropical forestland by biofuel plantations reduces biodiversity, and is not a good option to mitigate climate change. The study (published in the journal, Conservation Biology) explored the impacts of the spread of oil palm plantations (arising from cleared tropical rain forests) on greenhouse gas emissions and biodiversity. Vegetation in forest lands contribute to climate change mitigation, by capturing carbon dioxide (a greenhouse gas) from the atmosphere. Clearing these forest lands for bioenergy crop plantations inevitably results in a net loss of “carbon capture capability”. According to the study, the loss of carbon capture capability (from replacing these forest lands with biofuel farms) does not balance well with the savings in carbon emissions resulting from biofuel use. It would take “between 75 and 93 years for the carbon emissions saved through use of biofuel to compensate for the carbon lost through forest conversion”. Biofuel plantations from converted forest land were also found to “support species-poor communities containing few forest species”. As countries strive to meet international commitments to reduce carbon emissions, the conversion of forest lands for biofuel plantations could actually hasten climate change. The study concludes that forest conservation, rather than conversion to biofuel farms, would be a better option for climate-change mitigation.. Energy Crops and Feedstocks for Biofuels Productionhttp://www.jgi.doe.gov/News/news_12_08_08.html http://www.phytozome.net/soybean The United States Department of Energy’s Joint Genome Institute (DOE-JGI) recently announced the complete draft assembly of the soybean (Glycine max) genetic code. It will be made widely available to the research community “to advance breeding strategies” of the crop for food, feed and biodiesel feedstock. The DOE-JGI’s interest in sequencing the soybean genome is for biodiesel applications. Soybean is said to account for 56% of the world’s oilseed production and 80% of biodiesel production in the United States in 2007. It is also “one of the largest and most complex plant genomes sequenced by the whole genome shotgun strategy”, according to Dan Rokhsar of the DOE-JGI. (“shotgun sequencing” involves the random breaking-up (“shearing”) of the DNA into small fragments so that the sequence of nucleotides can be analyzed and interpreted). Preliminary scientific details on the sequence analysis will have been reported at the Conference on Legume Genomics and Genetics in (Puerto Vallarta, Mexico, 8 December 2008). The soybean genome sequence can also be browsed at the phytozome website (URL above). Related information: Shotgun sequencing (shockwave flash presentation): http://smcg.cifn.unam.mx/enp-unam/03-EstructuraDelGenoma/animaciones/humanShot.swf http://en.wikipedia.org/wiki/Shotgun_sequencing Biofuels Processinghttp://www.innovation-america.org/archive.php?articleID=402 http://www.ca.sandia.gov/podcast/episodes/200810/2008-5709W/ http://www.ca.sandia.gov/casite/research/energy.php Scientists from the Sandia National Laboratories (a “premier science and engineering lab for national security and technology innovation” in the United States) are looking into enzymes produced by microorganisms that survive in harsh environments (“extremophiles”). These enzymes could be harnessed for biofuel (cellulose ethanol) applications. Extremophiles are a class of microorganisms that can survive extreme temperature or extreme acid/alkaline environments. They have the potential to produce robust “extreme enzymes” that could withstand extreme temperature and pH conditions that could be used for industrial applications. The discovery and improvement of “extreme” cellulases (enzymes that degrade cellulose from plant biomass into simple sugars for ethanol fermentation) could contribute to the advancement of low cost cellulose ethanol production technology. A common method for cellulose breakdown is acid treatment, followed by neutralization and addition of cellulases to convert the cellulose to glucose. The neutralization step is needed because conventional cellulases cannot withstand extreme acidic environments after acid treatment. “Extreme cellulose” could make neutralization unnecessary and contribute to reducing the cost of cellulose ethanol production. Sandia researchers are presently using the “computational tools and enzyme engineering’ to develop the biofuel-relevant enzymes produced from extremophiles.. http://www.cleantech.com/news/3932/thar-technologies-plans-indian-biodiesel-plant http://jazz.nist.gov/atpcf/prjbriefs/prjbrief.cfm?ProjectNumber=00-00-7781 A $2 million grant from the Advanced Technology Program (ATP) of the National Institute of Standard and Technology (NIST, United States) has been awarded to an American company (Thar Technologies), to “develop and demonstrate continuous processing technology for environmentally friendly and cost-effective production of diesel-grade biofuel” from jatropha and karanj. An alternative to the solvent extraction process based on supercritical fluid technology will be developed. According to the Cleantech website, the company is working on a single step biodiesel process which uses supercritical carbon dioxide, instead of hexane, “to extract the oil from the seeds, and to create biodiesel with 25% less energy and 14% reduced cost. The setting up of a biodiesel plant is being planned in India, where jatropha and karanj (common biodiesel feedstocks) are abundantly available.. http://biofuelsdigest.com/blog2/2008/12/05/biofuels-market-snapshots-for-eu-brazil-china-and-us-available/ http://www.garbrook.com/welcome/globe.html?source=bd Biofuels Digest reports the availability of free “’market snapshots’ of ethanol and biodiesel industry activity in the US, China, Brazil and the EU” at the Garbrook Advanced Biofuels Resource website (URL above). Market key facts (arranged in a “wiki”-type format) for each of the above-mentioned countries include topics/keyword, such as Feedstock Availability/Production, Biofuel Policy/Incentives/Mandates, Trade, Fuel Consumption Profiles, etc.. http://www.ars.usda.gov/is/AR/archive/oct08/fuel1008.htm http://www.sciencedaily.com/releases/2008/10/081031212844.htm http://www.biomassmagazine.com/article.jsp?article_id=1605 Biobutanol, or butanol produced by biochemical means, is a 4-carbon alcohol which is considered an “advanced biofuel” or the ‘biofuel of the future” (replacing ethanol). Compared to ethanol, which is a 2-carbon alcohol, butanol offers many advantages: (1) a higher energy content, (2) less corrosion, (3) can be used as stand-alone fuel or in higher blends in gasoline without the need for engine modification and (4) can be easily transported in existing pipelines. However, there are many bottlenecks that need to be ironed out before large scale, low cost production of biobutanol can be realized. Like ethanol, butanol can also be produced from lignocellulosic biomass through a sequence of 4 steps: (1) pretreatment (removes the “lignin barrier” and “liberates” cellulose), (2) saccharification (enzymatic conversion of cellulose to simple sugars), (3) fermentation of sugars to ethanol, and (4) recovery of butanol from fermentation broth. And like ethanol, the bottlenecks are the cost of steps 1 to 3, and the problem of low yields due to toxicity of butanol to the fermenting organisms at high concentrations. Scientists at the United States Department of Agriculture (USDA) Agricultural Research Service (ARS) are developing modifications in the process for low cost, high yielding biobutanol production. The modifications involve combining steps 1 to 3 into a single step using bacteria and enzymes, utilizing a fed batch mode of feeding, and “gas stripping” (removal of the butanol from the fermentation product) to eliminate its toxic effects on the fermenting organism. Details of their work can be access at the USDA-ARS website (URL above).. |
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