UW-Madison Communications | June 26, 2009 | Margaret Broeren

Nestled within the twisting fungus gardens of leaf-cutter ants exists a complex symbiotic web that has evolved over millions of years. Now, with the help of a major genomic sequencing grant from Roche Applied Science, scientists at the University of Wisconsin-Madison will be able to analyze these interactions at the molecular scale.

Bacteriology professor Cameron Currie maintains an Acromyrmex volcanus colony in his UW-Madison laboratory.  The ants are located on a spongy fungus garden, which they grow themselves. Photo: B W Hoffmann

“By sequencing genomes of all the major players, we can study the evolution of the system,” says Cameron Currie, a UW-Madison bacteriology professor and one of the project’s lead researchers. “It would be one of the first, if not the first, genomic level study of a community of organisms over evolutionary time.”

As winners of Roche Applied Science’s 10 Gigabase Grant Program, UW-Madison and Great Lakes Bioenergy Research Center (GLBRC) scientists Currie, Steven Slater and Garret Suen will be part of a team that will use Roche technology to sequence the known members of the ant-fungus symbiosis, which includes three ant genomes and 14 ant-associated fungal and bacterial genomes.

“Three sequenced ant genomes will be truly spectacular,” says Ted Schultz, a research entomologist at the Smithsonian Institution National Museum of Natural History. “This is going to advance the field a quantum level beyond what is done now.

(more…)

From the July 2009 Scientific American Magazine 

Scientists are turning agricultural leftovers, wood and fast-growing grasses into a huge variety of biofuels—even jet fuel. But before these next-generation biofuels go mainstream, they have to compete with oil at $60 a barrel

By George W. Huber and Bruce E. Dale

Getty Images

Key Concepts

• Second-generation bio­fuels made from the inedible parts of plants are the most environmentally friendly and technologically promising near-term alternatives to oil.
• Most of this “grassoline” will come from agricultural residues such as cornstalks, weedlike energy crops and wood waste.
• The U.S. can grow enough of these feedstocks to replace about half the country’s total consumption of oil without affecting food supplies.

By now it ought to be clear that the U.S. must get off oil. We can no longer afford the dangers that our dependence on petroleum poses for our national security, our economic security or our environmental security. Yet civilization is not about to stop moving, and so we must invent a new way to power the world’s transportation fleet. Cellulosic biofuels—liquid fuels made from inedible parts of plants—offer the most environmentally attractive and technologically feasible near-term alternative to oil.

Biofuels can be made from anything that is, or ever was, a plant. First-generation biofuels derive from edible biomass, primarily corn and soybeans (in the U.S.) and sugarcane (in Brazil). They are the low-hanging fruits in a forest of possible biofuels, given that the technology to convert these feedstocks into fuels already exists (180 refineries currently process corn into ethanol in the U.S.). Yet first-generation biofuels are not a long-term solution. There is simply not enough available farmland to provide more than about 10 percent of developed countries’ liquid-fuel needs with first-generation biofuels. The additional crop demand raises the price of animal feed and thus makes some food items more expensive—though not nearly as much as the media hysteria last year would indicate. And once the total emissions of growing, harvesting and processing corn are factored into the ledger, it becomes clear that first-generation biofuels are not as environmentally friendly as we would like them to be. (more…)

Abstract
Radical coupling reactions between ethyl ferulate (Et-FA), a simple model for feruloyl polysaccharides in planta, and coniferyl alcohol (CA), a monolignol, were studied in order to better understand the polymer cross-coupling interactions among polysaccharides and monolignols or lignin, mediated by ferulate (FA), in plant cell walls. Cross-coupled FA/CA dimers produced in an aqueous buVer (pH 5.0) containing peroxidase/hydrogen peroxide were isolated and characterized by NMR. The total coupling products were characterized by 2D 13C–1H correlation (HSQC) NMR spectroscopy and GC–MS. Results from this study showed that ferulate readily cross-couples with coniferyl alcohol through free radical coupling mechanisms producing a series of cross-coupled FA/CA dimers with β-O-4-, β-5-/8-5-, and 8-β-linkages; the syntheses and isolation of β-5- and 8-5-cross-coupled dimers are reported here. The transformation from 8-β-coupled FA/CA hydroxyl esters into lactones through intramolecular transesterification is demonstrated for the Wrst time and mechanisms behind these transformations are discussed. The Wnding of both β-5- and 8-5-cross-coupled dimers in this study suggests that analogs of both may be present in plant cell walls. Finally it is suggested that ferulates in plants indeed react with monolignols through free radical mechanisms producing a more diverse array of cross-coupled dimers than previously reported.

Abstract
Poplar lignins with exceedingly high syringyl monomer levels are produced by over-expression of the ferulate 5-hydroxlase (F5H) gene driven by a cinnamate 4-hydroxylase (C4H) promoter. Compositional data derived from both standard degradative methods and NMR analyses of the entire lignin component (as well as
isolated lignin fraction) indicated that the C4H::F5H transgenic lignin was comprised of as much as 97.5% syringyl units (derived from sinapyl alcohol), the remainder being guaiacyl units (derived from coniferyl alcohol); the syringyl level in the wild-type control was 68%. The resultant transgenic lignins are more linear, and display a lower degree of polymerization. Although the crucial β-ether content is similar, the distribution of other inter-unit linkages in the lignin polymer is markedly different, with higher resinol (β–β) and spirodienone (β–1) contents, but with virtually no phenylcoumarans (β–5, which can only be formed from guaiacyl units). p-Hydroxybenzoates, acylating the γ-positions of lignin sidechains, were reduced by over 50%, suggesting consequent impacts on related pathways. A model depicting the putative structure of the transgenic lignin resulting from the over-expression of F5H is presented. The altered structural features in the transgenic lignin polymer, as revealed here, support the contention that there are
significant opportunities to improve biomass utilization by exploiting the malleability of plant lignification processes.

Abstract
The amino sugars (e.g.,glucosamine, galactosamine, mannosamine, muramicacid) in soils are frequently employed as biomarkers of microbial residues. The analysis of amino sugars in environmental matrices, however, is expected to be more complicated than their determination in isolated microbial cells. In this study, we employed a widely used protocol for amino sugar analysis, and found that some amino glycoside antibiotics interfere with amino sugar quantification invitro. The method converts the amino glycosides to compounds that coelute with the aldononitrile acetate derivatives of the amino sugars. Specifically, streptomycin significantly interferes with muramicacid analysis, and kanamycin, tobramycin and amikacin hamper glucosamine measurement. Mass spectrometry confirmed that the interfering compounds from aminoglycosides are not actually genuine microbial amino sugar monomers (bacterial muramic acid or fungal glucosamine), and are most likely to be N-methylglucosamine or 3-amino-3-deoxy-glucopyranose. In contrast to their effects on muramic acid and glucosamine analyses, aminoglycosides do not interfere with galactosamine and mannosamin equantification. The few data that exist on the environmental occurrence of aminoglycoside antibiotics suggest they occur at only trace levels. Our findings may have implications for the qualitative and quantitative validity of results from amino sugar assays in some context. Application of the aldononitrile acetate derivatization method to samples (especially in selective microbial cultures using aminoglycosides as inhibitors) requires that potential interference be evaluated.

Abstract
Genome sequencing and subsequent global gene expression studies have advanced our understanding of the lignocellulose fermenting yeast Pichia stipitis. These studies have given insight into its central carbon metabolism, and analysis of its genome has revealed numerous functional gene clusters and tandem repeats. Specialized physiological traits are often the result of several gene products acting together. When co‐inheritance is necessary for the overall physiological function, recombination and selection favors co‐location of these genes in a cluster. These are particularly evident in strongly conserved and idiomatic traits. In some cases, the functional clusters consist of multiple gene families. Phylogenetic analyses of the members in each family show that once formed, functional clusters undergo duplication and differentiation. Genome‐wide expression analysis reveals that regulatory patterns of clusters are similar after they have duplicated and that the expression profiles evolve along with functional differentiation of the clusters. Orthologous gene families appear to arise through tandem gene duplication followed by differentiation in the regulatory and coding regions of the gene. Genome‐wide expression analysis combined with cross‐species comparisons of functional gene clusters should reveal many more aspects of eukaryotic physiology.

Abstract
This study investigated long-term agronomic management systems and precipitation level effects on soybean [Glycine max (L.) Merr.] total oil content and fatty acid composition. Management systems evaluated included conventional (CT), no-till (NT), low chemical input (LI), and zero chemical input (ORG). Total oil content and major fatty acids profi les were analyzed by accelerated solvent extractor (ASE 200) and gas chromatography with fl ame ionization detector (FID). The results showed these four management systems have limited infl uence on soybean grain total oil content and oleic acid (O) and linoleic acid (L) compositions. The NT management system signifi cantly improved soybean oil yield on a land-area basis as a result of higher annual grain yields. Soybeans grown under the NT management system had as high or higher palmitic acid (P) composition than the other three management systems; similarly, the CT treatments had as low or lower linolenic acid (LN) composition in soybean when compared with the other three management systems. The levels of stearic acid (S), O, L, and LN had a significant quadratic relationship (R2 = 0.64–0.75) with total (July–September) precipitation. The oil quality ratio of O/(L + LN) had a quadratic relation with precipitation.

Abstract
The reactions leading to triacylglycerol (TAG) synthesis in oilseeds have been well characterized. However, quantitative analyses of acyl group and glycerol backbone fluxes that comprise extraplastidic phospholipid and TAG synthesis, including acyl editing and phosphatidylcholine-diacylglycerol interconversion, are lacking. To investigate these fluxes, we rapidly labeled developing soybean (Glycine max) embryos with [14C]acetate and [14C]glycerol. Cultured intact embryos that mimic in planta growth were used. The initial kinetics of newly synthesized acyl chain and glycerol backbone incorporation into phosphatidylcholine (PC), 1,2-sn-diacylglycerol (DAG), and TAG were analyzed along with their initial labeled molecular species and positional distributions. Almost 60% of the newly synthesized fatty acids first enter glycerolipids through PC acyl editing, largely at the sn-2 position. This flux, mostly of oleate, was over three times the flux of nascent [14C]fatty acids incorporated into the sn-1 and sn-2 positions of DAG through glycerol-3-phosphate acylation. Furthermore, the total flux for PC acyl editing, which includes both nascent and preexisting fatty acids, was estimated to be 1.5 to 5 times the flux of fatty acid synthesis. Thus, recycled acyl groups (16:0, 18:1, 18:2, and 18:3) in the acyl-coenzyme A pool provide most of the acyl chains for de novo glycerol-3-phosphate acylation. Our results also show kinetically distinct DAG pools. DAG used for TAG synthesis is mostly derived from PC, whereas de novo synthesized DAG is mostly used for PC synthesis. In addition, two kinetically distinct sn-3 acylations of DAG were observed, providing TAG molecular species enriched in saturated or polyunsaturated fatty acids.

One lab’s use of modern computers speeds up research on enzymes that break down the cellulose of feedstocks to produce ethanol.

Great Lakes Bioenergy Research Center (GLBRC) project co-leader and Associate Scientist, David Keating, is part of a research team focusing on improving the ability of microorganisms to convert cellulose to ethanol.

“This project is exciting to me because this is a deeply important problem and it also makes good use of skills I developed in graduate school and beyond.”

Keating has studied the metabolisms and physiology of microorganisms and views this research project as an opportunity for him to help benefit the country.

“The big picture is to develop microorganisms that are better in converting cellulose…whether it’s from corn stover or switch grass or whatever (feedstock) we choose.” (more…)

Science 22 May 2009:
Vol. 324. no. 5930, pp. 1019 - 1020
DOI: 10.1126/science.1171740

The development of the internal combustion engine (ICE) vehicle dramatically influenced American society during the 20th century by providing affordable, reliable transportation. However, the ICE vehicle is an inherently inefficient converter of chemical energy to mechanical power; less than 20% of the energy in gasoline is transformed into mechanical work, and the remainder is lost as heat. With seemingly unlimited supplies of low-cost petroleum in the last century, the poor efficiency of the ICE was initially less important than the power, convenience, and reliability it provided. However, two major factors make it likely that electric vehicles, rather than the ICE, will be the power source of choice for passenger vehicles in the 21st century. First, heightened world petroleum demand coupled with more expensive oil recovery will continue to increase gasoline costs. Second, concerns over the environmental impact of CO₂ production are leading toward carbon taxes, cap-and-trade limits, and other strategies that will impact the ICE.

In response to escalating monetary and political costs of imported petroleum and the existence of surplus U.S. agricultural capacity in the 20th century, the U.S. government instituted policies to support the conversion of the chemical energy stored in plantderived starch to ethanol. This conversion now consumes almost 30% of U.S. corn production. Starch is a simple polymer of glucose that is easily converted to ethanol with existing technology, yet almost one-third of the chemical energy of starch is lost in producing ethanol (1). Concerns about fuel competing with food, fertilizer runoff, and potent greenhouse gases such as NO₂ released from microbial conversion of fertilizer in agricultural fields have brought into question the sustainability of corn-based ethanol production (2). Therefore, a major effort has begun to develop alternative feedstocks for ethanol (or other liquid fuels) by using crop residues, forest by-products, perennial grasses, and other forms of plant biomass that are collectively termed “lignocellulosics.” The 2005 “billion-ton vision” (3) proposed by the U.S. Departments of Energy (DOE) and Agriculture (USDA) has set a goal of replacing 30% of U.S. petroleum consumption with lignocellulosic-derived liquid fuels—a goal that would require the production of ~60 billion gallons of ethanol annually by 2030. Several billion dollars have been invested for research and development toward this goal, and tax advantages and other subsidies for ethanol and biodiesel production have been estimated at $9 billion for 2008 and could increase to over $30 billion annually under current legislation (4).

Read the entire paper here.