Novel gene expression profiles define the metabolic and physiological processes characteristic of wood and its extractive formation in a hardwood tree species,Robinia pseudoacacia

Wood is of critical importance to humans as a primary feedstock for biofuel, fiber, solid wood products, and various natural compounds including pharmaceuticals. The trunk wood of most tree species has two distinctly different regions: sapwood and heartwood. In addition to the major constituents, wood contains extraneous chemicals that can be removed by extraction with various solvents. The composition and the content of the extractives vary depending on such factors as, species, growth conditions, and time of year when the tree is cut. Despite the great commercial and keen scientific interest, little is known about the tree-specific biology of the formation of heartwood and its extractives. In order to gain insight on the molecular regulations of heartwood and its extractive formation, we carried out global examination of gene expression profiles across the trunk wood of black locust (Robinia pseudoacacia L.) trees. Of the 2,915 expressed sequenced tags (ESTs) that were generated and analyzed in the current study, 55.3% showed no match to known sequences. Cluster analysis of the ESTs identified a total of 2278 unigene sets, which were used to construct cDNA microarrays. Microarray hybridization analyses were then performed to survey the changes in gene expression profiles of trunk wood. The gene expression profiles of wood formation differ according to the region of trunk wood sampled, with highly expressed genes defining the metabolic and physiological processes characteristic of each region. For example, the gene encoding sugar transport had the highest expression in the sapwood, while the structural genes for flavonoid biosynthesis were up-regulated in the sapwood-heartwood transition zone. This analysis also established the expression patterns of 341 previously unknown genes.     

Dedicated Energy Crops and Crop Residues for Bioenergy Feedstocks in the Central and Eastern USA

Dedicated energy crops and crop residues will meet herbaceous feedstock demands for the new bioeconomy in the Central and Eastern USA. Perennial warm-season grasses and corn stover are well-suited to the eastern half of the USA and provide opportunities for expanding agricultural operations in the region. A suite of warm-season grasses and associated management practices have been developed by researchers from the Agricultural Research Service of the US Department of Agriculture (USDA) and collaborators associated with USDA Regional Biomass Research Centers. Second generation biofuel feedstocks provide an opportunity to increase the production of transportation fuels from recently fixed plant carbon rather than from fossil fuels. Although there is no “one-size-fits-all” bioenergy feedstock, crop residues like corn (Zea mays L.) stover are the most readily available bioenergy feedstocks. However, on marginally productive cropland, perennial grasses provide a feedstock supply while enhancing ecosystem services. Twenty-five years of research has demonstrated that perennial grasses like switchgrass (Panicum virgatum L.) are profitable and environmentally sustainable on marginally productive cropland in the western Corn Belt and Southeastern USA.     

The greenhouse gas intensity and potential biofuel production capacity of maize stover harvest in the US Midwest

Agricultural residues are important sources of feedstock for a cellulosic biofuels industry that is being developed to reduce greenhouse gas emissions and improve energy independence. While the US Midwest has been recognized as key to providing maize stover for meeting near‐term cellulosic biofuel production goals, there is uncertainty that such feedstocks can produce biofuels that meet federal cellulosic standards. Here, we conducted extensive site‐level calibration of the Environmental Policy Integrated Climate (EPIC) terrestrial ecosystems model and applied the model at high spatial resolution across the US Midwest to improve estimates of the maximum production potential and greenhouse gas emissions expected from continuous maize residue‐derived biofuels. A comparison of methodologies for calculating the soil carbon impacts of residue harvesting demonstrates the large impact of study duration, depth of soil considered, and inclusion of litter carbon in soil carbon change calculations on the estimated greenhouse gas intensity of maize stover‐derived biofuels. Using the most representative methodology for assessing long‐term residue harvesting impacts, we estimate that only 5.3 billion liters per year (bly) of ethanol, or 8.7% of the near‐term US cellulosic biofuel demand, could be met under common no‐till farming practices. However, appreciably more feedstock becomes available at modestly higher emissions levels, with potential for 89.0 bly of ethanol production meeting US advanced biofuel standards. Adjustments to management practices, such as adding cover crops to no‐till management, will be required to produce sufficient quantities of residue meeting the greenhouse gas emission reduction standard for cellulosic biofuels. Considering the rapid increase in residue availability with modest relaxations in GHG reduction level, it is expected that management practices with modest benefits to soil carbon would allow considerable expansion of potential cellulosic biofuel production.     

Synergistic effects of floral phytochemicals against a bumble bee parasite

Floral landscapes comprise diverse phytochemical combinations. Individual phytochemicals in floral nectar and pollen can reduce infection in bees and directly inhibit trypanosome parasites. However, gut parasites of generalist pollinators, which consume nectar and pollen from many plant species, are exposed to phytochemical combinations. Interactions between phytochemicals could augment or decrease effects of single compounds on parasites. Using a matrix of 36 phytochemical treatment combinations, we assessed the combined effects of two floral phytochemicals, eugenol and thymol, against four strains of the bumblebee gut trypanosome Crithidia bombi. Eugenol and thymol had synergistic effects against C. bombi growth across seven independent experiments, showing that the phytochemical combination can disproportionately inhibit parasites. The strength of synergistic effects varied across strains and experiments. Thus, the antiparasitic effects of individual compounds will depend on both the presence of other phytochemicals and parasite strain identity. The presence of synergistic phytochemical combinations could augment the antiparasitic activity of individual compounds for pollinators in diverse floral landscapes.     

A model describing chemical interference caused by decomposing residues at different densities of growing plants

In literature, the biological response of plants to phytochemicals has been modelled and then used to simulate phytotoxicity caused by plant residues during decomposition. According to the resulting residue allelopathy model, stimulation dominates in the beginning of the residue decomposition process for a short while. Thereafter, severe inhibition is predicted to occur rapidly, until stimulation gradually re-emerges at the later stages of residue decomposition. Also in literature, direct chemical interference has been shown to be density-dependent; with increasing target plant density, the effects of phytochemicals are diluted. As a result, inhibition is the most probable outcome in density-dependent phytochemical interactions at low target plant densities, but phytotoxic effects often become stimulatory as target plant density increases. In this paper, these models that have been reported in literature are combined. While the original residue allelopathy model predicts inhibitory effects in most cases, the new density-dependent extension of the residue allelopathy model predicts that the density of target plants determines whether or not inhibition occurs. According to the new model, the intensity of inhibition decreases and the final stimulatory period begins earlier if target plant density increases. Therefore, combining the effects of density-dependency to the residue allelopathy model enhances our understanding of chemical interference. In addition, the new model may partially explain why several field studies have not observed chemically driven inhibitory effects similar to those observed in laboratory experiments.     

Triple bottom line study of a lignocellulosic biofuel industry

Growing concerns about energy security and climate change have prompted interest in Australia and worldwide to look for alternatives of fossil fuels. Among the renewable fuel sources, biofuels are one such alternative that have received unprecedented attention in the past decade. Cellulosic biofuels, derived from agricultural and wood biomass, could potentially increase Australia's oil self‐sufficiency. In this study, we carry out a hybrid life‐cycle assessment (LCA) of a future cellulose‐refining industry located in the Green Triangle region of South Australia. We assess both the upstream and downstream refining stages, and consider as well the life‐cycle effects occurring in conventional industries displaced by the proposed biofuel supply chains. We improve on conventional LCA method by utilising multi‐region input–output (IO) analysis that allows a comprehensive appraisal of the industry's supply chains. Using IO‐based hybrid LCA, we evaluate the social, economic and environmental impacts of lignocellulosic biofuel production. In particular, we evaluate the employment, economic stimulus, energy consumption and greenhouse gas impacts of the biofuel supply chain and also quantify the loss in economic activity and employment in the paper, pulp and paperboard industry resulting from the diversion of forestry biomass to biofuel production. Our results reveal that the loss in economic activity and employment will only account for 10% of the new jobs and additional stimulus generated in the economy. Lignocellulosic biofuel production will create significant new jobs and enhance productivity and economic growth by initiating the growth of new industries in the economy. The energy return on investment for cellulosic biofuel production lies between 2.7 and 5.2, depending on the type of forestry feedstock and the travel distance between the feedstock industry and the cellulose refinery. Furthermore, the biofuel industry will be a net carbon sequester.     

Impact of agronomic uncertainty in biomass production and endogenous commodity prices on cellulosic biofuel feedstock composition

This study evaluates the effect of agronomic uncertainty on bioenergy crop production as well as endogenous commodity and biomass prices on the feedstock composition of cellulosic biofuels under a binding mandate in the United States. The county‐level simulation model focuses on both field crops (corn, soybean, and wheat) and biomass feedstocks (corn stover, wheat straw, switchgrass, and Miscanthus). In addition, pasture serves as a potential area for bioenergy crop production. The economic model is calibrated to 2022 in terms of yield, crop demand, and baseline prices and allocates land optimally among the alternative crops given the binding cellulosic biofuel mandate. The simulation scenarios differ in terms of bioenergy crop type (switchgrass and Miscanthus) and yield, biomass production inputs, and pasture availability. The cellulosic biofuel mandates range from 15 to 60 billion L. The results indicate that the 15 and 30 billion L mandates in the high production input scenarios for switchgrass and Miscanthus are covered entirely by agricultural residues. With the exception of the low production input for Miscanthus scenario, the share of agricultural residues is always over 50% for all other scenarios including the 60 billion L mandate. The largest proportion of agricultural land dedicated to either switchgrass or Miscanthus is found in the southern Plains and the southeast. Almost no bioenergy crops are grown in the Midwest across all scenarios. Changes in the prices for the three commodities are negligible for cellulosic ethanol mandates because most of the mandate is met with agricultural residues. The lessons learned are that (1) the share of agricultural residue in the feedstock mix is higher than previously estimated and (2) for a given mandate, the feedstock composition is relatively stable with the exception of one scenario.     

蜂胶对幽门螺杆菌的抑制作用

本试验通过对幽门螺杆菌 (Hp)培养的营养条件和微需氧环境的摸索 ,得出其较佳的培养方法是采用心脑浸液血琼脂培养基 ,选用焦性没食子酸法 ,焦性没食子酸的最佳用量为 0 .9g/ 10 0ml,使Hp的球形体仅为 10 % ,而且该方法具有操作方便 ,费用低廉等优点。蜂胶各种溶剂提取物对Hp都有很好的抑菌效果 ,以 95 %乙醇提取物的抑菌能力最强 ,6 0 %乙醇提取物次之 ,而水提取物的抑菌能力最差。     

Recovery and utilization of tree extractives

Economic Botany - Tree species vary in properties because of the chemical nature of their respective extractive components. So it is that some species yield sufficient quantities of extractives to...     

Mystery of mysteries: Darwin and the species problem

Darwin offered an intriguing answer to the species problem. He doubted the existence of the species category as a real category in nature, but he did not doubt the existence of those taxa called “species”. And despite his scepticism of the species category, Darwin continued using the word “species”. Many have said that Darwin did not understand the nature of species. Yet his answer to the species problem is both theoretically sound and practical. On the theoretical side, Darwin’s answer is confirmed by contemporary biology, and it offers a more satisfactory answer to the species problem than recent attempts to save the species category. On the practical side, Darwin’s answer frees us from the search for the correct theoretical definition of “species”. But at the same time it does not require that we banish the word “species” from biology as some recent sceptics of the species category advocate. © The Willi Hennig Society 2010.     

Simulated impact of the renewable fuels standard on US Conservation Reserve Program enrollment and conversion

A socioeconomic model is used to estimate the land‐use implications on the U.S. Conservation Reserve Program from potential increases in second‐generation biofuel production. A baseline scenario with no second‐generation biofuel production is compared to a scenario where the Renewable Fuels Standard (RFS2) volumes are met by 2022. We allow for the possibility of converting expiring CRP lands to alternative uses such as conventional crops, dedicated second‐generation biofuel crops, or harvesting existing CRP grasses for biomass. Results indicate that RFS2 volumes (RFS2‐v) can be met primarily with crop residues (78% of feedstock demand) and woody residues (19% of feedstock demand) compared with dedicated biomass (3% of feedstock demand), with only minimal conversion of cropland (0.27 million hectares, <1% of total cropland), pastureland (0.28 million hectares of pastureland, <1% of total pastureland), and CRP lands (0.29 million hectares of CRP lands, 3% of existing CRP lands) to biomass production. Meeting RFS2 volumes would reduce CRP re‐enrollment by 0.19 million hectares, or 4%, below the baseline scenario where RFS2 is not met. Yet under RFS2‐v scenario, expiring CRP lands are more likely to be converted to or maintain perennial cover, with 1.78 million hectares of CRP lands converting to hay production, and 0.29 million hectares being harvested for existing grasses. A small amount of CRP is harvested for existing biomass, but no conversion of CRP to dedicated biomass crops, such as switchgrass, are projected to occur. Although less land is enrolled in CRP under RFS2‐v scenario, total land in perennial cover increases by 0.15 million hectares, or 2%, under RFS2‐v. Sensitivity to yield, payment and residue retention assumptions are evaluated.     

The MIDAS database system

The Molecular Interactive Display and Simulation (MIDAS) database system is a hierarchical database specifically designed for complex macromolecular models, such as proteins and nucleic acids. Each molecular model consists of one or more molecules made up of a linear sequence of smaller units that we refer to loosely as “residues.” Each of these residue units, in turn, is composed of one or more even smaller units called “atoms.” The complete model might consist of a single component molecule, as in the case of a water molecule, or it might be a long chain of more complex residue components, such as in the case of amino acid and nucleic acid sequences. Complex functional groups, such as heme and NADH, can also be specified as single subunit components, and the user can then incorporate these groups into a larger model to form a single complex.The various model component types are defined as arbitrary graphs of atoms with defined starting and ending points. The component type thus defines the connectivity of atoms for that component, as well as the linkage atoms to adjacent model components. Molecular “data” are stored in the “leaves” of the database hierarchy and are therefore directly associated with the atoms of a particular residue component, the component having been specified by type and position in the sequence of residues making up the chain. Individual atom data, however, are not restricted to a specific format or quantity, thereby allowing both flexibility and future extensions to easily be made to the database.     

Crop Residue Removal for Bioenergy Reduces Soil Carbon Pools: How Can We Offset Carbon Losses?

Crop residue removal for bioenergy can deplete soil organic carbon (SOC) pools. Management strategies to counteract the adverse effects of residue removal on SOC pools have not been, however, widely discussed. This paper reviews potential practices that can be used to offset the SOC lost with residue removal. Literature indicates that practices including no-till cover crops, manure and compost application, and return of biofuel co-products increase SOC pools and may thus be used to offset some SOC loss. No-till rotations that include semi-perennial grasses or legumes also offer a promise to promote soil-profile C sequestration and improve soil resilience after residue removal. No-till cover crops can sequester between 0.10 and 1 Mg ha^?1 per year of SOC relative to no-till without cover crops, depending on cover crop species, soil type, and precipitation input. Animal manure and compost contain about 15 % of C and thus their addition to soil can enhance SOC pools and boost soil biological activity. Similarly, application of biofuel co-products such as biochar, which contain between 45 % and 85 % of C depending on the feedstock source and processing method, can enhance long-term C sequestration. These mitigation strategies may maintain SOC pools under partial residue removal in no-till soils but are unlikely to replace all the SOC lost if residue is removed at excessive rates. More field research and modeling efforts are needed to assess the magnitude at which the different mitigation strategies can overcome SOC loss with crop residue removal.     

Bioenergy by‐products as soil amendments? Implications for carbon sequestration and greenhouse gas emissions

An important but little understood aspect of bioenergy production is its overall impact on soil carbon (C) and nitrogen (N) cycling. Increased energy production from biomass will inevitably lead to higher input of its by‐products to the soil as amendments or fertilizers. However, it is still unclear how these by‐products will influence microbial transformation processes in soil, and thereby its greenhouse gas (GHG) balance and organic C stocks. In this study, we assess C and N dynamics and GHG emissions following application of different bioenergy by‐products to soil. Ten by‐products were selected from different bioenergy chains: anaerobic digestion (manure digestates), first generation biofuel by‐products (rapeseed meal, distilled dried grains with solubles), second‐generation biofuel by‐products (nonfermentables from hydrolysis of different lignocellulosic materials) and pyrolysis (biochars). These by‐products were added at a constant N rate (150 kg N ha^?1) to a sandy soil and incubated at 20 °C. After 60 days, >80% of applied C had been emitted as CO₂ in the first‐generation biofuel residue treatments. For second‐generation biofuel residues this was approximately 60%, and for digestates 40%. Biochars were the most stable residues with the lowest CO₂ loss (between 0.5% and 5.8% of total added C). Regarding N₂O emissions, addition of first‐generation biofuel residues led to the highest total N₂O emissions (between 2.5% and 6.0% of applied N). Second‐generation biofuel residues emitted between 1.0% and 2.0% of applied N, with the original feedstock material resulting in similar N₂O emissions and higher C mineralization rates. Anaerobic digestates resulted in emissions <1% of applied N. The two biochars used in this study decreased N₂O emissions below background values. We conclude that GHG dynamics of by‐products after soil amendment cannot be ignored and should be part of the lifecycle analysis of the various bioenergy production chains.     

The Impact of Molecular Methods on the Systematics of Angiosperms

A comparison is made between the systematics of selected orders and families based on morphology and other “classical” characters on the one hand, and the results of molecular methods on the other hand. It can be shown that taxa defined by a broad array of characters from morphology, anatomy, embryology and phytochemistry usually are confirmed by molecular results. On the other hand a family like the Saxifragaceae s.l. delimited solely on the basis of floral morphology has been shown to be grossly polyphyletic. Some quite surprising results of the molecular analyses usually agree with some embryological or phytochemical characters, and sometimes even with characters of vegetative morphology and anatomy. As a special case “unequal ancient splits” are discussed, where one clade contains few genera and species usually retaining many primitive characters, and the other shows great diversity and contains the more advanced members.     

Binding of the Human “Electron Transferring Flavoprotein” (ETF) to the Medium Chain Acyl-CoA Dehydrogenase (MCAD) Involves an Arginine and Histidine Residue

The interaction between the “electron transferring flavoprotein” (ETF) and medium chain acyl-CoA dehydrogenase (MCAD) enables successful flavin to flavin electron transfer, crucial for the β-oxidation of fatty acids. The exact biochemical determinants for ETF binding to MCAD are unknown. Here we show that binding of human ETF, to MCAD, was inhibited by 2,3-butanedione and diethylpyrocarbonate (DEPC) and reversed by incubation with free arginine and hydroxylamine respectively. Spectral analyses of native ETF vs modified ETF suggested that flavin binding was not affected and that the loss of ETF activity with MCAD involved modification of one ETF arginine residue and one ETF histidine residue respectively. MCAD and octanoyl-CoA protected ETF against inactivation by both 2,3-butanedione and DEPC indicating that the arginine and histidine residues are present in or around the MCAD binding site. Comparison of exposed arginine and histidine residues among different ETF species, however, indicates that arginine residues are highly conserved but that histidine residues are not. These results lead us to conclude that this single arginine residue is essential for the binding of ETF to MCAD, but that the single histidine residue, although involved, is not.     

The influence of feedstock supply risk on location of stover‐based bio‐gasoline plants

This study models and quantifies spatially referenced probability distributions of corn residue cost and assesses their influence on comparative advantages of different areas of the Corn Belt to attract biofuel plants. Results suggest that irrigated areas of the Corn Belt, despite their relatively low planting density, may result more attractive than some of their rainfed counterparts in the eastern Corn Belt due to low risk in feedstock cost resulting from stability of yields. Therefore, agricultural districts in the Great Plains of the US may not need to pay high subsidies to compete with those in the eastern Corn Belt to attract biofuel firms. Policy restrictions on irrigation due to concerns over groundwater depletion may, however, diminish the relative comparative advantage of the irrigated Corn Belt for biofuel production.     

Douglas-Fir Seedlings Exhibit Metabolic Responses to Increased Temperature and Atmospheric Drought

In the future, periods of strongly increased temperature in concert with drought (heat waves) will have potentially detrimental effects on trees and forests in Central Europe. Norway spruce might be at risk in the future climate of Central Europe. However, Douglas-fir is often discussed as an alternative for the drought and heat sensitive Norway spruce, because some provenances are considered to be well adapted to drier and warmer conditions. In this study, we identified the physiological and growth responses of seedlings from two different Douglas-fir provenances to increased temperature and atmospheric drought during a period of 92 days. We analysed (i) plant biomass, (ii) carbon stable isotope composition as an indicator for time integrated intrinsic water use efficiency, (iii) apparent respiratory carbon isotope fractionation as well as (iv) the profile of polar low molecular metabolites. Plant biomass was only slightly affected by increased temperatures and atmospheric drought but the more negative apparent respiratory fractionation indicated a temperature-dependent decrease in the commitment of substrate to the tricarboxylic acid cycle. The metabolite profile revealed that the simulated heat wave induced a switch in stress protecting compounds from proline to polyols. We conclude that metabolic acclimation successfully contributes to maintain functioning and physiological activity in seedlings of both Douglas-fir provenances under conditions that are expected during heat waves (i.e. elevated temperatures and atmospheric drought). Douglas-fir might be a potentially important tree species for forestry in Central Europe under changing climatic conditions.     

Improving sugarcane for biofuel: engineering for an even better feedstock

Sugarcane is a proven biofuel feedstock and accounts for about 40% of the biofuel production worldwide. It has a more favorable energy input/output ratio than that of corn, the other major biofuel feedstock. The rich resource of genetic diversity and the plasticity of autopolyploid genomes offer a wealth of opportunities for the application of genomics and technologies to address fundamental questions in sugarcane towards maximizing biomass production. In a workshop on sugarcane engineering held at Rutgers University, we identified research areas and emerging technologies that could have significant impact on sugarcane improvement. Traditional plant physiological studies and standardized phenotypic characterization of sugarcane are essential for dissecting the developmental processes and patterns of gene expression in this complex polyploid species. Breeder friendly DNA markers associated with target traits will enhance selection efficiency and shorten the long breeding cycles. Integration of cold tolerance from Saccharum spontaneum and Miscanthus has the potential to expand the geographical range of sugarcane production from tropical and subtropical regions to temperate zones. The Flex-stock and mix-stock concepts could be solutions for sustaining local biorefineries where no single biofuel feedstock could provide consistent year-round supplies. The ever increasing capacities of genomics and biotechnologies pave the way for fully exploring these potentials to optimize sugarcane for biofuel production.     

Chemical composition of Hypericum species from the Taeniocarpium and Drosanthe sections

The presence of several phytochemicals, namely naphthodianthrones hypericin and pseudohypericin, phloroglucinol derivatives hyperforin and adhyperforin, the phenolic acids as chlorogenic acid, neochlorogenic acid, caffeic acid and 2,4-dihydroxybenzoic acid, the flavonols, hyperoside, isoquercitrin, quercitrin, quercetin, avicularin, rutin, and flavanols (+)-catechin and (?)-epicatechin, as well as biflavonoid amentoflavone was investigated in seven Turkish species of Hypericum from Taeniocarpium and Drosanthe sections. Plants were harvested at flowering, dried at room temperature, dissected into different tissues and assayed for chemical contents by HPLC. All chemicals were detected at various levels depending on species and plant parts. Despite the observed quantitative variation in the chemical content of plant material, it was found that phytochemical profiles of the species from the same section were very similar. The present data could be helpful in selecting the future targets for phytochemical and biological studies as well as enriching our current chemical knowledge about Hypericum species. Such kind of data could also be useful for elucidation of the chemotaxonomical relationships among the sections of Hypericum genus.