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  • richardmitnick 8:04 am on July 7, 2017 Permalink | Reply
    Tags: , Biofuels, ,   

    From Rutgers: “Cutting the Cost of Ethanol, Other Biofuels and Gasoline” 

    Rutgers University
    Rutgers University

    July 5, 2017
    Todd B. Bates

    1
    Enzymes, genetically engineered to avoid sticking to the surfaces of biomass such as corn stalks, may lower costs in the production of cellulose-based biofuels like ethanol. Shishir Chundawat/Rutgers University and U.S. Department of Energy

    Biofuels like the ethanol in U.S. gasoline could get cheaper thanks to experts at Rutgers University-New Brunswick and Michigan State University.

    They’ve demonstrated how to design and genetically engineer enzyme surfaces so they bind less to corn stalks and other cellulosic biomass, reducing enzyme costs in biofuels production, according to a study published this month on the cover of the journal ACS Sustainable Chemistry & Engineering.

    “The bottom line is we can cut down the cost of converting biomass into biofuels,” said Shishir P. S. Chundawat, senior author of the study and an assistant professor in the Department of Chemical and Biochemical Engineering at Rutgers University-New Brunswick.

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  • richardmitnick 3:19 pm on June 28, 2017 Permalink | Reply
    Tags: Biofuels, IMAGINE neutron scattering diffractometer, LPMOs - lytic polysaccharide monooxygenases, , North Carolina State University, , ORNL’s High Flux Isotope Reactor   

    From ORNL: “‘On your mark, get set'” 

    i1

    Oak Ridge National Laboratory

    June 27, 2017
    Jeremy Rumsey
    rumseyjp@ornl.gov
    865.576.2038

    1
    A combination of X-ray and neutron scattering has revealed new insights into how a highly efficient industrial enzyme is used to break down cellulose. Knowing how oxygen molecules (red) bind to catalytic elements (illustrated by a single copper ion) will guide researchers in developing more efficient, cost-effective biofuel production methods. (Image credit: ORNL/Jill Hemman)

    Producing biofuels like ethanol from plant materials requires various enzymes to break down the cellulosic fibers. Scientists using neutron scattering have identified the specifics of an enzyme-catalyzed reaction that could significantly reduce the total amount of enzymes used, improving production processes and lowering costs.

    Researchers from the Department of Energy’s Oak Ridge National Laboratory and North Carolina State University used a combination of X-ray and neutron crystallography to determine the detailed atomic structure of a specialized fungal enzyme.

    A deeper understanding of the enzyme reactivity could also lead to improved computational models that will further guide industrial applications for cleaner forms of energy. Their results are published in the journal Angewandte Chemie International Edition.

    Part of a larger family known as lytic polysaccharide monooxygenases, or LPMOs, these oxygen-dependent enzymes act in tandem with hydrolytic enzymes—which chemically break down large complex molecules with water—by oxidizing and breaking the bonds that hold cellulose chains together. The combined enzymes can digest biomass more quickly than currently used enzymes and speed up the biofuel production process.

    “These enzymes are already used in industrial applications, but they’re not well understood,” said lead author Brad O’Dell, a graduate student from NC State working in the Biology and Soft Matter Division of ORNL’s Neutron Sciences Directorate. “Understanding each step in the LPMO mechanism of action will help industry use these enzymes to their full potential and, as a result, make final products cheaper.”

    In an LPMO enzyme, oxygen and cellulose arrange themselves through a sequence of steps before the biomass deconstruction reaction occurs. Sort of like “on your mark, get set, go,” says O’Dell.

    To better understand the enzyme’s reaction mechanism, O’Dell and coauthor Flora Meilleur, ORNL instrument scientist and an associate professor at NC State, used the IMAGINE neutron scattering diffractometer at ORNL’s High Flux Isotope Reactor to see how the enzyme and oxygen molecules were behaving in the steps leading up to the reaction—from the “resting state” to the “active state.”

    ORNL IMAGINE neutron scattering diffractometer

    The resting state, O’Dell says, is where all the critical components of the enzyme assemble to bind oxygen and carbohydrate. When electrons are delivered to the enzyme, the system moves from the resting state to the active state—i.e., from “on your mark” to “get set.”

    In the active state, oxygen binds to a copper ion that initiates the reaction. Aided by X-ray and neutron diffraction, O’Dell and Meilleur identified a previously unseen oxygen molecule being stabilized by an amino acid, histidine 157.

    Hydrogen is a key element of amino acids like histidine 157. Because neutrons are particularly sensitive to hydrogen atoms, the team was able to determine that histidine 157 plays a significant role in transporting oxygen molecules to the copper ion in the active site, revealing a vital detail about the first step of the LPMO catalytic reaction.

    “Because neutrons allow us to see hydrogen atoms inside the enzyme, we gained essential information in deciphering the protein chemistry. Without that data, the role of histidine 157 would have remained unclear,” Meilleur said. “Neutrons were instrumental in determining how histidine 157 stabilizes oxygen to initiate the first step of the LPMO reaction mechanism.”

    Their results were subsequently confirmed via quantum chemical calculations performed by coauthor Pratul Agarwal from ORNL’s Computing and Computational Sciences Directorate.

    Research material preparation was supported by the ORNL Center for Structural Molecular Biology. X-ray data were collected at the Argonne National Laboratory Advanced Photon Source through access provided by the Southeast Regional Collaborative Access Team.

    O’Dell says their results refine the current understanding of LPMOs for science and industry researchers.

    “This is a big step forward in unraveling how LPMO’s initiate the breakdown of carbohydrates,” O’Dell said. “Now we need to characterize the enzyme’s activated state when the protein is also bound to a carbohydrate that mimics cellulose. Then we’ll have the chance to see what structural changes happen when the starting pistol is fired and the reaction takes off.”

    HFIR is a DOE Office of Science User Facility. UT-Battelle manages ORNL for the Office of Science. The Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time. For more information, please visit http://science.energy.gov/.

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    ORNL is managed by UT-Battelle for the Department of Energy’s Office of Science. DOE’s Office of Science is the single largest supporter of basic research in the physical sciences in the United States, and is working to address some of the most pressing challenges of our time.

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  • richardmitnick 11:56 am on June 20, 2017 Permalink | Reply
    Tags: , Biofuels, , , ,   

    From COSMOS: “Precision gene editing may deliver biofuel promise” 

    Cosmos Magazine bloc

    COSMOS

    20 June 2017
    Elizabeth Finkel

    1
    Biofuels from algae come with great promise. Santiago Urquijo/Getty Images

    For decades now, we’ve been promised cheap biofuels from algae. But there’s no free lunch. Growing these mini oil factories in vast ponds requires fertiliser and mechanical aeration; and then the oil has to be extracted. It all costs energy and money so the yields need to be high to make it worthwhile.

    One promising industrial species is Nannocholoropsis gaditana, which can produce a lipid – the oil and fat energy store – content up to about 60% of the algae’s ash-free dry weight. But Eric Moellering and colleagues at the company Synthetic Genomics Inc in California, wanted to do better.

    Starving the algae of nitrogen, paradoxically, boosts oil production. The problem is that the plants also curtail their growth so there’s no net gain. Ever since the 1970s, scientists have been trying to genetically engineer their way out of this quandary. But they’ve had to wait for the right tool: the bacterially derived CRISPR–Cas9 enzyme that has transformed ham-fisted genetic engineering into precision gene-editing.

    Moellering’s group identified a gene, called ZnCys, that was deactivated when the algae was starved of nitrogen. When the researchers completely disabled that gene, they saw oil production double, even without starving the algae.

    But the algae still grew poorly, so the scientists made use of the finesse of CRISPR–Cas9 to finely edit the DNA code of the ZnCys gene instead of disabling it competely. As they report in Nature Biotechnology this led to doubling oil yield without dampening algae growth.

    The final yield was up to five grams per square metre of algae per day.

    Amazing what a good editor can do!

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  • richardmitnick 5:53 am on May 23, 2017 Permalink | Reply
    Tags: , Biofuels, Discovery of an alga’s ‘dictionary of genes’ could lead to advances in biofuels and medicine, ,   

    From UCLA: “Discovery of an alga’s ‘dictionary of genes’ could lead to advances in biofuels, medicine” 

    UCLA bloc

    UCLA

    May 22, 2017
    Stuart Wolpert

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    Inside the alga’s cells, showing the nucleus (purple), mitochondria (red), chloroplast (green) and lipids (yellow). Melissa Roth/HHMI and Andreas Walters/Berkeley Lab

    Plant biologists and biochemists from UCLA, UC Berkeley and UC San Francisco have produced a gold mine of data by sequencing the genome of a green alga called Chromochloris zofingiensis.

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    Scientists have learned in the past decade that the tiny, single-celled organism could be used as a source of sustainable biofuel and that it produces a substance called astaxanthin, which may be useful for treating certain diseases. The new research could be an important step toward improving production of astaxanthin by algae and engineering its production in plants and other organisms.

    The study is published online in the journal Proceedings of the National Academy of Sciences.

    Chromochloris zofingiensis is one of the most prolific producers of a type of lipids called triacylglycerols, which are used in producing biofuels.

    Knowing the genome is like having a “dictionary” of the alga’s approximately 15,000 genes, said co-senior author Sabeeha Merchant, a UCLA professor of biochemistry. “From there, researchers can learn how to put the ‘words’ and ‘sentences’ together, and to target our research on important subsets of genes.”

    C. zofingiensis provides an abundant natural source for astaxanthin, an antioxidant found in salmon and other types of fish, as well as in some birds’ feathers. And because of its anti-inflammatory properties, scientists believe astaxanthin may have benefits for human health; it is being tested in treatments for cancer, cardiovascular disease, neurodegenerative diseases, inflammatory diseases, diabetes and obesity. Merchant said the natural version has stronger antioxidant properties than chemically produced ones, and only natural astaxanthin has been approved for human consumption.

    The study also revealed that an enzyme called beta-ketolase is a critical component in the production of astaxanthin.

    Algae absorb carbon dioxide and derive their energy from sunlight, and C. zofingiensis in particular can be cultivated on non-arable land and in wastewater. Harnessing it as a source for renewable and sustainable biofuels could lead to new ways to produce clean energy, said Krishna Niyogi, co-senior author of the paper and a scientist at the Department of Energy’s Lawrence Berkeley National Laboratory.

    Over the past decade-plus, Merchant said, research with algae, a small plant called rockcress, fruit flies and nematode worms — all so-called “model organisms” — has been advanced by other scientists’ determining their genome sequences.

    “They are called model organisms because we use what we learn about the operation of their cells and proteins as a model for understanding the workings of more complex systems like humans or crops,” she said. “Today, we can sequence the genome of virtually any organism in the laboratory, as has been done over the past 10 to 15 years with other model organisms.”

    Merchant, Niyogi and Matteo Pellegrini, a UCLA professor of molecular, cell and developmental biology and a co-author of the study, maintain a website that shares a wealth of information about the alga’s genome.

    During the study, the scientists also used soft X-ray tomography, a technique similar to a CT scan, to get a 3-D view of the algae cells , which gave them more detailed insights about their biology.

    Niyogi is also a UC Berkeley professor of plant and microbial biology and a Howard Hughes Medical Institute Investigator.

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    The study’s other authors are researchers Shawn Cokus and Sean Gallaher and postdoctoral scholar David Lopez, all of UCLA; postdoctoral fellow Melissa Roth, and graduate students Erika Erickson, Benjamin Endelman and Daniel Westcott, all of Niyogi’s laboratory; and Carolyn Larabell, a professor of anatomy, and researcher Andreas Walter, both of UC San Francisco.

    The research was funded by the Department of Energy’s Office of Science, the Department of Agriculture’s National Institute of Food and Agriculture, the National Institute of General Medical Sciences of the National Institutes of Health, and the Gordon and Betty Moore Foundation.

    See the full article here .

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    For nearly 100 years, UCLA has been a pioneer, persevering through impossibility, turning the futile into the attainable.

    We doubt the critics, reject the status quo and see opportunity in dissatisfaction. Our campus, faculty and students are driven by optimism. It is not naïve; it is essential. And it has fueled every accomplishment, allowing us to redefine what’s possible, time after time.

    This can-do perspective has brought us 12 Nobel Prizes, 12 Rhodes Scholarships, more NCAA titles than any university and more Olympic medals than most nations. Our faculty and alumni helped create the Internet and pioneered reverse osmosis. And more than 100 companies have been created based on technology developed at UCLA.

     
  • richardmitnick 12:26 pm on August 8, 2016 Permalink | Reply
    Tags: , Biofuels, , MITEI   

    From MITEI at MIT: “Microbial engineering technique could reduce contamination in biofermentation plants” 

    MIT News
    MIT News
    MIT Widget

    1

    August 4, 2016
    Helen Knight

    Approach could lower cost and eliminate need for antibiotics during biofuel production.

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    The ability to ferment low-cost feedstocks under nonsterile conditions may enable new classes of biochemicals and biofuels, such as microbial oil produced by the yeast Yarrowia lipolytica (shown here, oil in lipid bodies is stained green and cells walls stained blue). Photo: Novogy, Inc.

    The cost and environmental impact of producing liquid biofuels and biochemicals as alternatives to petroleum-based products could be significantly reduced, thanks to a new metabolic engineering technique.

    Liquid biofuels are increasingly used around the world, either as a direct “drop-in” replacement for gasoline, or as an additive that helps reduce carbon emissions.

    The fuels and chemicals are often produced using microbes to convert sugars from corn, sugar cane, or cellulosic plant mass into products such as ethanol and other chemicals, by fermentation. However, this process can be expensive, and developers have struggled to cost-effectively ramp up production of advanced biofuels to large-scale manufacturing levels.

    One particular problem facing producers is the contamination of fermentation vessels with other, unwanted microbes. These invaders can outcompete the producer microbes for nutrients, reducing yield and productivity.

    Ethanol is known to be toxic to most microorganisms other than the yeast used to produce it,Saccharomyces cerevisiae, naturally preventing contamination of the fermentation process. However, this is not the case for the more advanced biofuels and biochemicals under development.

    To kill off invading microbes, companies must instead use either steam sterilization, which requires fermentation vessels to be built from expensive stainless steels, or costly antibiotics. Exposing large numbers of bacteria to these drugs encourages the appearance of tolerant bacterial strains, which can contribute to the growing global problem of antibiotic resistance.

    Now, in a paper published today in the journal Science, researchers at MIT and the Cambridge startup Novogy describe a new technique that gives producer microbes the upper hand against unwanted invaders, eliminating the need for such expensive and potentially harmful sterilization methods.

    The researchers engineered microbes, such as Escherichia coli, with the ability to extract nitrogen and phosphorous — two vital nutrients needed for growth — from unconventional sources that could be added to the fermentation vessels, according to Gregory Stephanopoulos, the Willard Henry Dow Professor of Chemical Engineering and Biotechnology at MIT, and Joe Shaw, senior director of research and development at Novogy, who led the research.

    What’s more, because the engineered strains only possess this advantage when they are fed these unconventional chemicals, the chances of them escaping and growing in an uncontrolled manner outside of the plant in a natural environment are extremely low.

    “We created microbes that can utilize some xenobiotic compounds that contain nitrogen, such as melamine,” Stephanopoulos says. Melamine is a xenobiotic, or artificial, chemical that contains 67 percent nitrogen by weight.

    Conventional biofermentation refineries typically use ammonium to supply microbes with a source of nitrogen. But contaminating organisms, such as Lactobacilli, can also extract nitrogen from ammonium, allowing them to grow and compete with the producer microorganisms.

    In contrast, these organisms do not have the genetic pathways needed to utilize melamine as a nitrogen source, says Stephanopoulos.

    “They need that special pathway to be able to utilize melamine, and if they don’t have it they cannot incorporate nitrogen, so they cannot grow,” he says.

    The researchers engineered E. coli with a synthetic six-step pathway that allows it to express enzymes needed to convert melamine to ammonia and carbon dioxide, in a strategy they have dubbed ROBUST (Robust Operation By Utilization of Substrate Technology).

    When they experimented with a mixed culture of the engineered E. coli strain and a naturally occurring strain, they found the engineered type rapidly outcompeted the control, when fed on melamine.

    They then investigated engineering the yeast Saccharomyces cerevisiae to express a gene that allowed it to convert the nitrile-containing chemical cyanamide into urea, from which it could obtain nitrogen.

    The engineered strain was then able to grow with cyanamide as its only nitrogen source.

    Finally, the researchers engineered both S. cerevisiae and the yeast Yarrowia lipolytica to use potassium phosphite as a source of phosphorous.

    Like the engineered E. coli strain, both the engineered yeasts were able to outcompete naturally occurring strains when fed on these chemicals.

    “So by engineering the strains to make them capable of utilizing these unconventional sources of phosphorous and nitrogen, we give them an advantage that allows them to outcompete any other microbes that may invade the fermenter without sterilization,” Stephanopoulos says.

    The microbes were tested successfully on a variety of biomass feedstocks, including corn mash, cellulosic hydrolysate, and sugar cane, where they demonstrated no loss of productivity when compared to naturally occurring strains.

    The paper provides a novel approach to allow companies to select for their productive microbes and select against contaminants, according to Jeff Lievense, a senior engineering fellow at the San Diego-based biotechnology company Genomatica who was not involved in the research.

    “In theory you could operate a fermentation plant with much less expensive equipment and lower associated operating costs,” Lievense says. “I would say you could cut the capital and capital-related costs [of fermentation] in half, and for very large-volume chemicals, that kind of saving is very significant,” he says.

    The ROBUST strategy is now ready for industrial evaluation, Shaw says. The technique was developed with Novogy researchers, who have tested the engineered strains at laboratory scale and trials with 1,000-liter fermentation vessels, and with Felix Lam of the MIT Whitehead Institute for Biomedical Research, who led the cellulosic hydrosylate testing.

    Novogy now hopes to use the technology in its own advanced biofuel and biochemical production, and is also interested in licensing it for use by other manufacturers, Shaw says.

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  • richardmitnick 8:36 am on July 1, 2016 Permalink | Reply
    Tags: , Biofuels,   

    From BNL: “Study Shows Trees with Altered Lignin are Better for Biofuels” 

    Brookhaven Lab

    June 28, 2016
    Karen McNulty Walsh
    (631) 344-8350
    kmcnulty@bnl.gov

    Peter Genzer
    (631) 344-3174
    genzer@bnl.gov

    Fundamental enzyme study leads to increased access to bioenergy feedstocks and improves ethanol yield by modifying plant cell wall structures.

    1
    Postdoctoral associate Yuanheng Cai, biological research associate Xuebin Zhang, and plant biochemist Chang-Jun Liu in the Brookhaven Lab greenhouse with transgenic trees designed to improve biofuel production.

    Lignin is a natural component of plant cell walls, the scaffolding that surrounds each cell and plays a pivotal role in plants’ ability to grow against gravity and reach heights ranging from stubbly grasses to the sky-scraping splendor of redwoods. But lignin is a problem for scientists interested in converting plant biomass to biofuels and other sustainable bio-based products. Lignin makes it hard to break down the plant matter so its carbon-rich building blocks can be converted into forms suitable for generating energy or running automobiles.

    A simple solution might be to engineer plants with less lignin. But previous attempts to do this have often resulted in weaker plants and stunted growth—essentially putting the brakes on biomass production.

    Now, by engineering a novel enzyme involved in lignin synthesis, scientists at the U.S. Department of Energy’s Brookhaven National Laboratory and collaborators have altered the lignin in aspen trees in a way that increases access to biofuel building blocks without inhibiting plant growth. Their research, described in Nature Communications, resulted in an almost 50 percent increase in ethanol yield from healthy aspen trees whose woody biomass released 62 percent more simple sugars than native plants.

    “Our study provides a useful strategy for tailoring woody biomass for bio-based applications,” said Brookhaven biologist Chang-Jun Liu, the lead author on the project.

    Lignin makes up about 20 percent of aspen’s woody structures, with cellulose and hemicellulose polymers making up approximately 45 and 25 percent, along with other minor components.

    “The lignin forms a barrier of sorts around the other polymers,” Liu explained. “Digestive enzymes can’t get through to break down the cellulose and hemicellulose to release their simple sugars.”

    Prior work, including Liu’s own research manipulating enzymes involved in lignin synthesis, has shown that reducing or altering plants’ lignin content can make woody biomass more digestible. But many of these approaches, particularly those that dramatically reduced lignin content, resulted in weaker plants and severe reductions in biomass yield, rendering these plants unsuitable for large-scale cultivation.

    In this study the scientists explored a creative new strategy for modifying lignin’s structure based on detailed analysis of enzyme structures that were previously solved by Liu’s group using x-rays at the National Synchrotron Light Source (NSLS)—a DOE Office of Science User Facility at Brookhaven Lab, now replaced by a much brighter NSLS-II.

    BNL NSLS Interior
    NSLS

    BNL NSLS-II Interior
    NSLS-II

    That work, described in papers published in Plant Cell (2012) and the Journal of Biological Chemistry (2010 and 2015), was part of an effort to understand the enzymes’ mechanism of selectivity. In those studies, the scientists also sought to engineer a series of variations of the enzyme, called monolignol 4-O-methyltransferase, some of which effectively modified the structure of lignin building blocks so they would no longer be incorporated into the lignin polymer.

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    Cross-sections of wild type (a,c) and transgenic (b,d) aspen stems stained with lignin detection agents. The violet red color in the upper images indicates no dramatic change in total lignin content between the wild type (a) and transgenic (b) plants. The red color staining specific for one particular lignin structural unit shown in the lower images, however, indicates a significantly lower level of this component in the transgenic aspen (d) compared with the wild type (c). These findings suggest that lignin in the transgenic aspen has significantly altered composition and structure.

    In the new work, the scientists used biochemical analyses to identify a variant of monolignol 4-O-methyltransferase that had a slight chemical “preference” for reacting with one specific type of lignin precursor. The scientists reasoned that this variant had the potential to depress the formation of a particular lignin component.

    To test this idea, they transplanted the gene for this variant into a strain of fast-growing aspen trees—a model for other trees in the poplar family, which have widespread potential for bioenergy production because of their ability to grow in many regions and on non-agricultural land. The scientists grew the altered aspen trees alongside untreated control trees in a greenhouse on Brookhaven’s property.

    Modified cell walls, more sugar

    The trees that produced the engineered enzyme had slightly less total lignin in their cell walls. But on further analysis, the scientists found that these trees also had dramatically altered lignin structure, with a significant reduction in the level of one of the two major types of lignin components normally found in aspen trees. These findings were further confirmed using two-dimensional nuclear magnetic resonance spectroscopic imaging by a team led by John Ralph of the University of Wisconsin and the Great Lakes Bioenergy Research Center, a DOE Bioenergy Research Center. Specifically, the engineered trees had less “labile” lignin, while the remaining lignin components became structurally more condensed, forming an increased number of cross-linkages among the polymers.

    “We expected that this condensed, more cross-linked lignin might make the plants even harder to digest, but found that wood containing these structures released up to 62 percent more simple sugars when treated with digestive enzymes,” Liu said. The yield of ethanol from this modified wood was almost 50 percent higher than the ethanol yield of wood derived from untreated control trees.

    3
    Microscopic images of wood tissues from wild type (a) and transgenic (b) aspen trees show similar anatomical and structural features, suggesting that the transgenic plant maintains normal growth and wood formation even with altered lignin composition.

    Interestingly, by imaging aspen wood samples using infrared light at NSLS, the scientists found that their approach for altering lignin content and composition also increased the production of cellulose fibers, the major source of fermentable sugars in the cell wall. This increased cellulose content might partially contribute to the increased release of simple sugars, they said.

    Importantly, the changes in lignin and cell wall structures did not affect the growth of the engineered aspens. The wood densities and the biomass yields were comparable to those of the control trees.

    “These data suggest that lignin condensation itself is not a critical factor affecting the digestibility of the cell wall,” said Liu. “The findings also support the idea that engineering the enzymes that modify lignin precursors represents a useful biotechnological solution for effectively tailoring the digestibility of poplar-family woody biomass to generate feedstocks for biofuel production.

    “It’s gratifying when fundamental studies of enzyme function, such as the findings that underpin this work, can be translated to contribute to solving real-world problems,” he added.

    This work was supported by the DOE Office of Science.

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    One of ten national laboratories overseen and primarily funded by the Office of Science of the U.S. Department of Energy (DOE), Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world.Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University, the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.
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  • richardmitnick 11:32 am on June 9, 2016 Permalink | Reply
    Tags: , Biofuels, Chemistry lessons from bacteria may improve biofuel production,   

    From Wisconsin: “Chemistry lessons from bacteria may improve biofuel production” 

    U Wisconsin

    University of Wisconsin

    June 8, 2016
    Chris Barncard

    If you’re made of carbon, precious few things are as important to life as death.

    A dead tree may represent a literal windfall of the building blocks necessary for making new plants and animals and the energy to sustain them.

    “The recycling of plant carbon is fundamental to the function of our ecosystems,” says Cameron Currie, professor of bacteriology at the University of Wisconsin–Madison. “We get food, water, air, energy — almost everything — through those ecosystem services. It’s how our planet operates.”

    But the component parts of a dead tree were carefully assembled in the first place, and don’t just fall apart for easy recycling.

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    The ability to break down the cellulose in plant material is rare in Streptomyces bacteria, except in strains that live alongside insects — honeybees, leaf-cutter ants (above), some beetles —that eat or make use of the woody parts of plants. Courtesy of Don Parsons/UW-Madison

    In the case of cellulose — a key structural component in plant cell walls and the most abundant organic compound in life on land — a world of specialized microbes handles this careful deconstruction. Much of that work is done by fungi growing on decaying plants, but bacteria in the soil, in the guts of animals like cows and working alongside insects, get the job done, too.

    A new analysis of a group of bacteria called Streptomyces reveals the way some strains of the microbe developed advanced abilities to tear up cellulose, and points out more efficient ways we might mimic those abilities to make fuel from otherwise unusable plant material.

    Streptomyces were long thought to be prominent contributors at work in breaking down cellulose, and to be equally active in the cause across hundreds or thousands of strains of the bacteria.

    2
    Researchers tried to grow different strains of Streptomyces bacteria on dead plant material (in this case, filter paper). Successful cellulose processing strains tapped special genes to produce enzymes that break down cellulose. Courtesy of Currie Lab/UW-Madison

    “The strains that aren’t good at degrading cellulose mostly express the same genes whether we grow them on glucose or on plant material,” says Gina Lewin, a bacteriology graduate student and study co-author. “The strains that are really good at degrading cellulose totally change their gene expression when we grow them on plant material.”

    The successful Streptomyces strains — which were typically those found living in communities with insects — ramp up production of certain enzymes, the proteins that do the cleaving and dissolving and picking apart of cellulose.

    “There are families — six or eight or maybe 10 of these enzymes — that all of the active Streptomyces have,” Fox says. “And this paper shows that the most abundant one of them has to be there or the whole thing collapses.”

    It’s the particular combinations of enzymes that makes the research useful to scientists working on biofuels.

    4
    Counter to long-held belief about the bacteria Streptomyces, seen growing here in a petri dish, the ability to break down a stubborn molecule in plant cell walls called cellulose may be limited to just a few gifted strains. Courtesy of Adam Book/UW-Madison

    Biofuels are typically made from the sugars easily extracted from the same parts of plants we eat.

    “We eat the kernels off the corn cob,” Currie says. “But most of the energy in that corn plant is in the part which is not digestible to us. It’s not in the cob. It’s in the green parts, like the stalk and the leaves.”

    Evolving microbes like Streptomyces have been sharpening the way they make use of those parts of plants almost as long as the plants themselves have been growing on land. That’s hundreds of millions of years. On the other hand, the Department of Energy’s UW–Madison-based Great Lakes Bioenergy Research Center, which funded the Streptomyces study, was established in 2007.

    “The natural world is responding to the same kind of things that humans are,” Fox says. “We need to get food. We need to get energy. And different types of organisms are achieving their needs in different ways. It’s worth looking at how they do it.”

    The new study identifies important enzymes, and new groups of enzymes, produced when Streptomyces flex particular genes. If they represent an improvement over current industrial processes, the microbes’ tricks could make for a great boon to bioenergy production.

    “For a cellulosic biofuel plant, enzymes are one of the most expensive parts of making biofuels,” Lewin says. “So, if you can identify enzymes that work even just slightly better, that could mean a difference of millions of dollars in costs and cheaper energy.”

    See the full article here .

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    In achievement and prestige, the University of Wisconsin–Madison has long been recognized as one of America’s great universities. A public, land-grant institution, UW–Madison offers a complete spectrum of liberal arts studies, professional programs and student activities. Spanning 936 acres along the southern shore of Lake Mendota, the campus is located in the city of Madison.

     
  • richardmitnick 7:40 am on March 31, 2016 Permalink | Reply
    Tags: , Biofuels, Ee-Been Goh, , woman scientist   

    From LBL: “From Near-Dropout to PhD, Berkeley Lab Scientist Now at Forefront of Biofuels Revolution” 

    Berkeley Logo

    Berkeley Lab

    March 30, 2016
    Julie Chao
    (510) 486-6491
    JHChao@lbl.gov

    1
    Ee-Been Goh works with summer intern Joshua Borrajo in 2013. (Credit: Roy Kaltschmidt/Berkeley Lab)

    To see biochemist Ee-Been Goh in the lab today, figuring out how to rewire bacteria to produce biofuels, one would never guess she was once so uninterested in school that she barely made it through junior high.

    “My mom would say, ‘You used to be the worst in school—why would you want to go for more school?’” Goh said. “That was the joke when I was going into grad school.”

    Today Goh is a project scientist at the Joint BioEnergy Institute (JBEI), a Department of Energy Bioenergy Research Center led by Lawrence Berkeley National Laboratory (Berkeley Lab). She has been lead author on two important publications on methyl ketones, a compound found in blue cheese that has also turned out be one of the most promising and high-performing biofuels at JBEI.

    Her path into science is an object lesson she likes to share with the high school students she mentors through a JBEI summer program called Introductory College Level Experience in Microbiology (iCLEM). “I always tell the iCLEM kids how I was a terrible student in Singapore,” she said. “I was a tomboy, and I just loved goofing off on the streets and playing sports. I really hated school. I would’ve loved to have had a career in professional sports.”

    At the age of 14, her parents moved the entire family to Vancouver, largely for a better educational experience for Goh and her two sisters. Getting to do hands-on science activities in high school, such as animal dissections, sparked her interest in science. “When you do it yourself, you understand things a lot better than when you’re being bombarded with words on a board or an overhead projector,” she said. “That’s something that really caught on for me.”

    Likewise, she encourages students to take advantage of any opportunity they might have. “I think some of these students get really dejected when they don’t do well in school, and as you get more dejected, you just don’t want to put in any more effort,” she said. “That’s how I felt when I was a little kid. The most important thing for me is to fan their interest.”

    As an undergrad at the University of British Columbia, her opportunity was an internship in the microbiology lab of Julian Davies, a renowned scientist in the field of antibiotics and drug resistance. “He was retired and in his 70s, but he really loved science so he was still taking on undergrad students who liked to do research,” she said. “He was very hands-on and got very excited even with small results, and it got me excited too.”

    With encouragement from Davies, Goh decided to pursue an advanced career in science. She did her graduate work in microbiology at UC Davis, where her research focused on understanding how bacteria communicate with each other. This work in the basic sciences taught Goh useful research techniques, but she realized she wanted to pursue a career in the applied sciences.

    “With applied science it impacts more people and has broader reach,” she said. “People can take it and use it. That’s what science is about, right?”

    Landing a job at JBEI fit that requirement perfectly.

    From blue cheese to climate change

    “Many valuable commodity chemicals and fragrances are often derived from petroleum,” Goh said. “At JBEI we’re aiming not just to make biofuels but also to replace a lot of everyday products that come from that barrel of crude oil. We’re trying to do our part in slowing down climate change—that’s the ultimate goal.”

    The focus of her research has been methyl ketones, which are derived from fatty acids and show great promise for biodiesel fuels. Not only are methyl ketones a potential biodiesel, there is a market for these compounds as flavors and fragrances. Working with Harry Beller, director of Biofuels Pathways at JBEI, Goh’s research is aimed at engineering E. coli bacteria to produce methyl ketones as efficiently as possible.

    “Ee-Been has made significant scientific contributions to the development of new biofuels at JBEI,” Beller said. “Her two first-author publications on engineering and optimizing a novel methyl ketone pathway in E. coli have made a notable impact in the area of fatty acid-derived biofuels—medium-chain methyl ketones are among our best performing biofuels at JBEI.”

    Beller elaborated on what made Goh good at what she does: “Qualities that have helped Ee-Been be a successful scientist are her persistence and intelligent approach to troubleshooting. In biotechnology, as in many areas of science and technology, only a fraction of scientific avenues we follow lead to clear success. Ee-Been has the fortitude and ability to learn from things that didn’t work to eventually pursue things that do.”

    And although she occasionally likes to pull pranks in the lab—switching out medium-sized gloves for small ones is a perennial favorite—her JBEI colleagues have voted her “JBEI Citizen” for two consecutive years for “fostering a positive working environment through helping colleagues.”

    “Perhaps Ee-Been’s most lasting legacy at JBEI is all the people she has helped along the way,” Beller said. “She’s been very generous with her time, including ongoing involvement in the iCLEM summer internship program for economically disadvantaged high-school students.”

    See the full article here .

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    A U.S. Department of Energy National Laboratory Operated by the University of California

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  • richardmitnick 10:53 am on February 3, 2016 Permalink | Reply
    Tags: , Biofuels, ,   

    From Sandia: “Algae raceway paves path from lab to real-world applications” 


    Sandia Lab

    February 2, 2016
    Patti Koning
    pkoning@sandia.gov
    (925) 294-4911

    Sandia algae raceway testing facility

    In a twist of geometry, an oval can make a line. The new algae raceway testing facility at Sandia National Laboratories may be oval in shape, but it paves a direct path between laboratory research and solving the demand for clean energy.

    As the nation and California adopt policies to promote clean transportation fuels, that path could help bring the promise of algal biofuels closer to reality. As one of the fastest growing organisms on the planet, algae are an ideal source of biomass, but researchers have not yet found a cost-competitive way to use algae for fuels.

    “This facility helps bridge the gap from the lab to the real world by giving us an environmentally controlled raceway that we can monitor to test and fine tune discoveries,” said Ben Wu, Sandia’s Biomass Science and Conversion Technology manager.

    “The success of moving technologies from a research lab to large outdoor facilities is tenuous. The scale-up from flask to a 150,000-liter outdoor raceway pond is just too big.”

    The new Sandia algae testing facility consists of three 1,000-liter raceway ponds with advanced monitoring provides new advantages to researchers:

    Easy scale-up to larger, outdoor raceways
    Customizable lighting and temperature controls, operational by year end, to simulate the conditions of locations across the country
    Fully contained for testing genetic strains and crop protection strategies
    Advanced hyperspectral monitoring 24 hours a day

    Several ongoing projects will use the algae raceway right away. Researchers Todd Lane and Anne Ruffing will test genetically modified algae strains as part of a project funded by Sandia’s Laboratory Directed Research and Development (LDRD) program. The algae raceway will allow the researchers to more quickly identify strains that promise improved performance.

    Lane is also part of a project partnership with Lawrence Livermore National Laboratory funded by the Department of Energy’s Bioenergy Technologies Office (BETO) that is investigating a probiotic approach to algae crop protection.

    Another BETO project seeks to convert algae proteins into useful chemical compounds such as butanol. Wu expects the facility will expand opportunities for Sandia researchers to develop algae as a robust source of biofuels and increase collaborations and partnerships with the private sector, particularly in California where efforts to transform transportation energy are prevalent.

    “The bioeconomy is gaining momentum,” he said. “Biofuels from algae may be further off, but algae has sugar and proteins that can make fuel or higher valued products, such as butanol or nylon — products that currently come from fossil fuels.”

    See the full article here .

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    Sandia Campus
    Sandia National Laboratory

    Sandia National Laboratories is a multiprogram laboratory operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Department of Energy’s National Nuclear Security Administration. With main facilities in Albuquerque, N.M., and Livermore, Calif., Sandia has major R&D responsibilities in national security, energy and environmental technologies, and economic competitiveness.
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  • richardmitnick 6:20 pm on January 4, 2016 Permalink | Reply
    Tags: , Biofuels, Indiana U   

    From IU: “IU scientists create ‘nano-reactor’ for the production of hydrogen biofuel” 

    Indiana U bloc

    Indiana University

    Jan. 4, 2016
    Kevin Fryling
    Office 812-856-2988
    kfryling@iu.edu

    Temp 1
    An artist’s rendering of P22-Hyd, a new biomaterial created by encapsulating a hydrogen-producing enzyme within a virus shell. | Photo by Trevor Douglas

    Temp 2
    Illustration showing the release of NiFe-hydrogenase from inside the virus shell, or “capsid,” of bacteriophage P22. | Photo by Trevor Douglas

    Scientists at Indiana University have created a highly efficient biomaterial that catalyzes the formation of hydrogen — one half of the “holy grail” of splitting H2O to make hydrogen and oxygen for fueling cheap and efficient cars that run on water.

    A modified enzyme that gains strength from being protected within the protein shell — or capsid — of a bacterial virus, this new material is 150 times more efficient than the unaltered form of the enzyme.

    The process of creating the material was recently reported in Self-assembling biomolecular catalysts for hydrogen production in the journal Nature Chemistry.

    “Essentially, we’ve taken a virus’s ability to self-assemble myriad genetic building blocks and incorporated a very fragile and sensitive enzyme with the remarkable property of taking in protons and spitting out hydrogen gas,” said Trevor Douglas, the Earl Blough Professor of Chemistry in the IU Bloomington College of Arts and Sciences’ Department of Chemistry, who led the study.

    3
    Trevor Douglas | Photo by Montana State University

    “The end result is a virus-like particle that behaves the same as a highly sophisticated material that catalyzes the production of hydrogen.”

    Other IU scientists who contributed to the research were Megan C. Thielges, an assistant professor of chemistry; Ethan J. Edwards, a Ph.D. student; and Paul C. Jordan, a postdoctoral researcher at Alios BioPharma, who was an IU Ph.D. student at the time of the study.

    The genetic material used to create the enzyme, hydrogenase, is produced by two genes from the common bacteria Escherichia coli, inserted inside the protective capsid using methods previously developed by these IU scientists. The genes, hyaA and hyaB, are two genes in E. coli that encode key subunits of the hydrogenase enzyme. The capsid comes from the bacterial virus known as bacteriophage P22.

    The resulting biomaterial, called “P22-Hyd,” is not only more efficient than the unaltered enzyme but also is produced through a simple fermentation process at room temperature.

    The material is potentially far less expensive and more environmentally friendly to produce than other materials currently used to create fuel cells. The costly and rare metal platinum, for example, is commonly used to catalyze hydrogen as fuel in products such as high-end concept cars.

    “This material is comparable to platinum, except it’s truly renewable,” Douglas said. “You don’t need to mine it; you can create it at room temperature on a massive scale using fermentation technology; it’s biodegradable. It’s a very green process to make a very high-end sustainable material.”

    In addition, P22-Hyd both breaks the chemical bonds of water to create hydrogen and also works in reverse to recombine hydrogen and oxygen to generate power. “The reaction runs both ways — it can be used either as a hydrogen production catalyst or as a fuel cell catalyst,” Douglas said.

    The form of hydrogenase is one of three occurring in nature: di-iron (FeFe)-, iron-only (Fe-only)- and nitrogen-iron (NiFe)-hydrogenase. The third form was selected for the new material due to its ability to easily integrate into biomaterials and tolerate exposure to oxygen.

    NiFe-hydrogenase also gains significantly greater resistance upon encapsulation to breakdown from chemicals in the environment, and it retains the ability to catalyze at room temperature. Unaltered NiFe-hydrogenase, by contrast, is highly susceptible to destruction from chemicals in the environment and breaks down at temperatures above room temperature — both of which make the unprotected enzyme a poor choice for use in manufacturing and commercial products such as cars.

    These sensitivities are “some of the key reasons enzymes haven’t previously lived up to their promise in technology,” Douglas said. Another is their difficulty to produce.

    “No one’s ever had a way to create a large enough amount of this hydrogenase despite its incredible potential for biofuel production. But now we’ve got a method to stabilize and produce high quantities of the material — and enormous increases in efficiency,” he said.

    The development is highly significant according to Seung-Wuk Lee, professor of bioengineering at the University of California-Berkeley, who was not a part of the study.

    “Douglas’ group has been leading protein- or virus-based nanomaterial development for the last two decades. This is a new pioneering work to produce green and clean fuels to tackle the real-world energy problem that we face today and make an immediate impact in our life in the near future,” said Lee, whose work has been cited in a U.S. Congressional report on the use of viruses in manufacturing.

    Beyond the new study, Douglas and his colleagues continue to craft P22-Hyd into an ideal ingredient for hydrogen power by investigating ways to activate a catalytic reaction with sunlight, as opposed to introducing elections using laboratory methods.

    “Incorporating this material into a solar-powered system is the next step,” Douglas said.

    This research was supported by the U.S. Department of Energy.

    See the full article here .

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    Indiana University students get it all—the storybook experience of what college should be like, and the endless opportunities that come with it. Top-ranked academics. Awe-inspiring faculty. Dynamic campus life. International culture. Phenomenal music and arts events. The excitement of IU Hoosier sports. And a jaw-droppingly beautiful campus.

     
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