Genomes and Genes
Summary: Total mass of all the organisms of a given type and/or in a given area. (From Concise Dictionary of Biology, 1990) It includes the yield of vegetative mass produced from any given crop.
Publications341 found, 100 shown here
- Biomass recalcitrance: engineering plants and enzymes for biofuels productionMichael E Himmel
Chemical and Biosciences Center, National Renewable Energy Laboratory, Golden, CO 80401, USA
Science 315:804-7. 2007Lignocellulosic biomass has long been recognized as a potential sustainable source of mixed sugars for fermentation to biofuels and other biomaterials...
- Metagenomic discovery of biomass-degrading genes and genomes from cow rumenMatthias Hess
Department of Energy, Joint Genome Institute, Walnut Creek, CA 94598, USA
Science 331:463-7. 2011..deconstruct plant polysaccharides represents a major bottleneck for industrial-scale conversion of cellulosic biomass into biofuels...
- Microbial cellulose utilization: fundamentals and biotechnologyLee R Lynd
Chemical and Biochemical Engineering, Thayer School of Engineering and Department of Biological Sciences, Dartmouth College, Hanover, New Hampshire 03755, USA
Microbiol Mol Biol Rev 66:506-77, table of contents. 2002..examined at successively higher levels of aggregation encompassing the structure and composition of cellulosic biomass, taxonomic diversity, cellulase enzyme systems, molecular biology of cellulase enzymes, physiology of ..
- Consolidated bioprocessing of cellulosic biomass: an updateLee R Lynd
Thayer School of Engineering, Dartmouth College, Hanover, New Hampshire 03755, USA
Curr Opin Biotechnol 16:577-83. 2005..mediated processes seem promising for energy conversion, in particular for the conversion of lignocellulosic biomass into fuels...
- Microbial production of fatty-acid-derived fuels and chemicals from plant biomassEric J Steen
Joint BioEnergy Institute, Emeryville, California 94608, USA
Nature 463:559-62. 2010..to this important class of chemicals would be through the microbial conversion of renewable feedstocks, such as biomass-derived carbohydrates...
- Insights into the oxidative degradation of cellulose by a copper metalloenzyme that exploits biomass componentsR Jason Quinlan
Novozymes, Inc, Davis, CA 95618, USA
Proc Natl Acad Sci U S A 108:15079-84. 2011The enzymatic degradation of recalcitrant plant biomass is one of the key industrial challenges of the 21st century. Accordingly, there is a continuing drive to discover new routes to promote polysaccharide degradation...
- Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: structure and function of a large, enigmatic familyPaul V Harris
Novozymes Inc, 1445 Drew Avenue, Davis, California 95618, USA
Biochemistry 49:3305-16. 2010..of a biorefinery capable of producing renewable transportable fuels such as ethanol from abundant lignocellulosic biomass. Among the many families of glycoside hydrolases that catalyze cellulose and hemicellulose hydrolysis, few are ..
- The biomass objective functionAdam M Feist
GT Life Sciences, Inc, 10520 Wateridge Circle, San Diego, CA 92122, USA
Curr Opin Microbiol 13:344-9. 2010..To computationally predict cell growth using FBA, one has to determine the biomass objective function that describes the rate at which all of the biomass precursors are made in the correct ..
- The path forward for biofuels and biomaterialsArthur J Ragauskas
School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, GA 30332, USA
Science 311:484-9. 2006b>Biomass represents an abundant carbon-neutral renewable resource for the production of bioenergy and biomaterials, and its enhanced use would address several societal needs...
- The worldwide leaf economics spectrumIan J Wright
Department of Biological Sciences, Macquarie University, New South Wales 2109, Australia
Nature 428:821-7. 2004..Reliable quantification of the leaf economics spectrum and its interaction with climate will prove valuable for modelling nutrient fluxes and vegetation boundaries under changing land-use and climate...
- Lignin modification improves fermentable sugar yields for biofuel productionFang Chen
Plant Biology Division, Samuel Roberts Noble Foundation, 2510 Sam Noble Parkway, Ardmore, Oklahoma 73401, USA
Nat Biotechnol 25:759-61. 2007Recalcitrance to saccharification is a major limitation for conversion of lignocellulosic biomass to ethanol...
- Effects of biodiversity on the functioning of trophic groups and ecosystemsBradley J Cardinale
Department of Ecology, Evolution and Marine Biology, University of California at Santa Barbara, Santa Barbara, California 93106, USA
Nature 443:989-92. 2006..and examine how this alters the efficiency by which communities capture resources and convert those into biomass. So far, the generality of patterns and processes observed in individual studies have been the subjects of ..
- Global analysis of nitrogen and phosphorus limitation of primary producers in freshwater, marine and terrestrial ecosystemsJames J Elser
School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
Ecol Lett 10:1135-42. 2007..Thus, contrary to some prevailing paradigms, freshwater, marine and terrestrial ecosystems are surprisingly similar in terms of N and P limitation...
- Rebuilding global fisheriesBoris Worm
Biology Department, Dalhousie University, Halifax, NS B3H 4J1, Canada
Science 325:578-85. 2009..Impacts of international fleets and the lack of alternatives to fishing complicate prospects for rebuilding fisheries in many poorer regions, highlighting the need for a global perspective on rebuilding marine resources...
- Biodiesel from microalgaeYusuf Chisti
Institute of Technology and Engineering, Massey University, Private Bag 11 222, Palmerston North, New Zealand
Biotechnol Adv 25:294-306. 2007..Oil productivity of many microalgae greatly exceeds the oil productivity of the best producing oil crops. Approaches for making microalgal biodiesel economically competitive with petrodiesel are discussed...
- Spreading dead zones and consequences for marine ecosystemsRobert J Diaz
Virginia Institute of Marine Science, College of William and Mary, Gloucester Point, VA 23062, USA
Science 321:926-9. 2008..Dead zones have now been reported from more than 400 systems, affecting a total area of more than 245,000 square kilometers, and are probably a key stressor on marine ecosystems...
- Feedstocks for lignocellulosic biofuelsChris Somerville
Energy Biosciences Institute, The University of California Berkeley, Berkeley, CA 94720, USA
Science 329:790-2. 2010..However, there has been relatively little discussion of what types of plants may be useful as bioenergy crops...
- Hydrolysis of lignocellulosic materials for ethanol production: a reviewYe Sun
Department of Biological and Agricultural Engineering, North Carolina State University, Raleigh 27695 7625, USA
Bioresour Technol 83:1-11. 2002Lignocellulosic biomass can be utilized to produce ethanol, a promising alternative energy source for the limited crude oil...
- Estimation of the total parasite biomass in acute falciparum malaria from plasma PfHRP2Arjen M Dondorp
Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
PLoS Med 2:e204. 2005..P. falciparum releases a specific histidine-rich protein (PfHRP2) into plasma. Quantitative measurement of plasma PfHRP2 concentrations may reflect the total parasite biomass in falciparum malaria.
- Challenges in engineering microbes for biofuels productionGregory Stephanopoulos
Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
Science 315:801-4. 2007..There is justified optimism that the full potential of biofuel production from cellulosic biomass will be obtainable in the next 10 to 15 years.
- Biomass allocation to leaves, stems and roots: meta-analyses of interspecific variation and environmental controlHendrik Poorter
Plant Sciences IBG2, Forschungszentrum Julich, D 52425 Julich, Germany
New Phytol 193:30-50. 2012We quantified the biomass allocation patterns to leaves, stems and roots in vegetative plants, and how this is influenced by the growth environment, plant size, evolutionary history and competition...
- Genomics of cellulosic biofuelsEdward M Rubin
DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA
Nature 454:841-5. 2008The development of alternatives to fossil fuels as an energy source is an urgent global priority. Cellulosic biomass has the potential to contribute to meeting the demand for liquid fuel, but land-use requirements and process ..
- Targeted discovery of glycoside hydrolases from a switchgrass-adapted compost communityMartin Allgaier
Deconstruction Division, Joint BioEnergy Institute, Emeryville, California, United States of America
PLoS ONE 5:e8812. 2010....
- A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic informationAdam M Feist
Department of Bioengineering, University of California San Diego, La Jolla, CA 92093, USA
Mol Syst Biol 3:121. 2007..of EcoCyc leading to the inclusion of the activities of 1260 ORFs, (2) characterization and quantification of the biomass components and maintenance requirements associated with growth of E...
- Inhibition of ethanol-producing yeast and bacteria by degradation products produced during pre-treatment of biomassH B Klinke
Department of Plant Research, Risø National Laboratory, P O Box 49, 4000 Roskilde, Denmark
Appl Microbiol Biotechnol 66:10-26. 2004..The resulting hydrolyzsates contain substances inhibitory to fermentation-depending on both the raw material (biomass) and the pre-treatment applied...
- Partitioning selection and complementarity in biodiversity experimentsM Loreau
Laboratoire d Ecologie, UMR 7625, Ecole Normale Superieure, 46 rue d Ulm, 75230 Paris Cedex 05, France
Nature 412:72-6. 2001..experiments have provided evidence that reduced species diversity may impair ecosystem processes such as plant biomass production...
- From plant traits to plant communities: a statistical mechanistic approach to biodiversityBill Shipley
Departement de Biologie, Universite de Sherbrooke, Sherbrooke, Quebec J1K 2R1, Canada
Science 314:812-4. 2006....
- Features of promising technologies for pretreatment of lignocellulosic biomassNathan Mosier
Laboratory of Renewable Resources Engineering, Department of Agricultural and Biological Engineering, Purdue University, Potter Engineering Center, 500 Central Drive, West Lafayette, IN 47907 2022, USA
Bioresour Technol 96:673-86. 2005..structural and compositional factors hinder the enzymatic digestibility of cellulose present in lignocellulosic biomass. The goal of any pretreatment technology is to alter or remove structural and compositional impediments to ..
- Baselines and degradation of coral reefs in the Northern Line IslandsStuart A Sandin
Center for Marine Biodiversity and Conservation, Scripps Institution of Oceanography, La Jolla, California, USA
PLoS ONE 3:e1548. 2008..Sharks and other top predators overwhelmed the fish assemblages on Kingman and Palmyra so that the biomass pyramid was inverted (top-heavy)...
- From dwarves to giants? Plant height manipulation for biomass yieldMaria G Salas Fernandez
Department of Agronomy, 1126E Agronomy Hall, Iowa State University, Ames, IA 50011, USA
Trends Plant Sci 14:454-61. 2009The increasing demand for lignocellulosic biomass for the production of biofuels provides value to vegetative plant tissue and leads to a paradigm shift for optimizing plant architecture in bioenergy crops...
- Nitrogen additions and microbial biomass: a meta-analysis of ecosystem studiesKathleen K Treseder
Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697, USA
Ecol Lett 11:1111-20. 2008..In this meta-analysis, I synthesized responses of microbial biomass to N additions in 82 published field studies...
- Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725Phuongan Dam
Institute of Bioinformatics, Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
Nucleic Acids Res 39:3240-54. 2011..It is a promising anaerobic bacterium for studying high-temperature biomass conversion. Its genome contains 2666 protein-coding sequences organized into 1209 operons...
- Transcriptional regulation of biomass-degrading enzymes in the filamentous fungus Trichoderma reeseiPamela K Foreman
Genencor International, Inc, Palo Alto, California 94304, USA
J Biol Chem 278:31988-97. 2003..produces and secretes profuse quantities of enzymes that act synergistically to degrade cellulase and related biomass components. We partially sequenced over 5100 random T. reesei cDNA clones...
- Efficient degradation of lignocellulosic plant biomass, without pretreatment, by the thermophilic anaerobe "Anaerocellum thermophilum" DSM 6725Sung Jae Yang
Department of Biochemistry and Molecular Biology, University of Georgia, Athens, GA 30602, USA
Appl Environ Microbiol 75:4762-9. 2009Very few cultivated microorganisms can degrade lignocellulosic biomass without chemical pretreatment...
- Significant contribution of Archaea to extant biomass in marine subsurface sedimentsJulius S Lipp
Organic Geochemistry Group, Department of Geosciences and MARUM Center for Marine Environmental Sciences, University of Bremen, PO Box 330 440, 28334 Bremen, Germany
Nature 454:991-4. 2008..of live cells, are attributable to archaeal membranes, suggesting that Archaea constitute a major fraction of the biomass. Results obtained from modified quantitative polymerase chain reaction and slot-blot hybridization protocols ..
- Diversity and productivity in a long-term grassland experimentD Tilman
Department of Ecology, Evolution and Behavior, University of Minnesota, St Paul, MN 55108, USA
Science 294:843-5. 2001..7 times greater biomass than monocultures...
- Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnologyJacek Puchałka
Synthetic and Systems Biology Group, Helmholtz Center for Infection Research HZI, Braunschweig, Germany
PLoS Comput Biol 4:e1000210. 2008..revealed that the metabolic network structure is the main factor determining the accuracy of predictions, whereas biomass composition has negligible influence...
- An outlook on microalgal biofuelsRene H Wijffels
Wageningen University, Bioprocess Engineering, Post Office Box 8129, 6700 EV Wageningen, Netherlands
Science 329:796-9. 2010....
- Bioconversion of lignocellulosic biomass: biochemical and molecular perspectivesRaj Kumar
Radiation Biotechnology Unit, Division of Radiation Biology and Radiation Protection, Institute of Nuclear Medicine and Allied Sciences, New Delhi, 110054 India
J Ind Microbiol Biotechnol 35:377-91. 2008..Lignocelluloses as agricultural, industrial and forest residuals account for the majority of the total biomass present in the world...
- Positive interactions among alpine plants increase with stressRagan M Callaway
Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA
Nature 417:844-8. 2002..Here we show that the biomass, growth and reproduction of alpine plant species are higher when other plants are nearby...
- Absence of branches from xylan in Arabidopsis gux mutants reveals potential for simplification of lignocellulosic biomassJennifer C Mortimer
Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
Proc Natl Acad Sci U S A 107:17409-14. 2010..The results also demonstrate the potential for manipulating and simplifying the structure of xylan to improve the properties of lignocellulose for bioenergy and other uses...
- The 2010 Amazon droughtSimon L Lewis
School of Geography, University of Leeds, Leeds LS2 9JT, UK
Science 331:554. 2011..By using relationships between drying and forest biomass responses measured for 2005, we predict the impact of the 2010 drought as 2...
- Nutrient co-limitation of primary producer communitiesW Stanley Harpole
Department of Ecology, Evolution and Organismal Biology, Iowa State University, 133 Bessey Hall, Ames, IA 50010, USA
Ecol Lett 14:852-62. 2011..We found support for strict definitions of co-limitation in 28% of the studies: i.e. community biomass responded to only combined N and P addition, or to both N and P when added separately...
- Land clearing and the biofuel carbon debtJoseph Fargione
The Nature Conservancy, 1101 West River Parkway, Suite 200, Minneapolis, MN 55415, USA
Science 319:1235-8. 2008..In contrast, biofuels made from waste biomass or from biomass grown on degraded and abandoned agricultural lands planted with perennials incur little or no ..
- Global patterns and predictions of seafloor biomass using random forestsChih Lin Wei
Department of Oceanography, Texas A and M University, College Station, Texas, United States of America
PLoS ONE 5:e15323. 2010A comprehensive seafloor biomass and abundance database has been constructed from 24 oceanographic institutions worldwide within the Census of Marine Life (CoML) field projects...
- Emergent biogeography of microbial communities in a model oceanMichael J Follows
Department of Earth, Atmospheric and Planetary Sciences, Massachusetts Institute of Technology, 54 1514 MIT, Cambridge, MA 02139, USA
Science 315:1843-6. 2007..This flexible representation of community structure can be used to explore relations between ecosystems, biogeochemical cycles, and climate change...
- Plants integrate information about nutrients and neighborsJames F Cahill
Department of Biological Sciences, University of Alberta, Edmonton, AB T6G 2E9, Canada
Science 328:1657. 2010....
- Recent changes in phytoplankton communities associated with rapid regional climate change along the western Antarctic PeninsulaMartin Montes-Hugo
Coastal Ocean Observation Lab, Institute of Marine and Coastal Sciences, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA
Science 323:1470-3. 2009..Regional changes in phytoplankton coincide with observed changes in krill (Euphausia superba) and penguin populations...
- Net energy of cellulosic ethanol from switchgrassM R Schmer
U S Department of Agriculture Agricultural Research Service, University of Nebraska, 314 Biochemistry Hall, P O Box 830737, Lincoln, NE 68583 0737, USA
Proc Natl Acad Sci U S A 105:464-9. 2008..We managed switchgrass as a biomass energy crop in field trials of 3-9 ha (1 ha = 10,000 m2) on marginal cropland on 10 farms across a wide ..
- Regulation of plant biomass productionTaku Demura
Graduate School of Biological Sciences, Nara Institute of Science and Technology, 8916 5 Takayama cho, Ikoma, Nara 630 0192, Japan
Curr Opin Plant Biol 13:299-304. 2010Plant biomass used for cellulosic biofuel production is primarily from vegetative tissues. Therefore, an increase in the vegetative growth of plants will lead to a higher production of plant biomass...
- Nitrogen limitation of net primary productivity in terrestrial ecosystems is globally distributedDavid S LeBauer
Department of Earth System Science, University of California, Irvine, California 92054, USA
Ecology 89:371-9. 2008..These results suggest that the global N and C cycles interact strongly and that geography can mediate ecosystem response to N within certain biome types...
- Rapid worldwide depletion of predatory fish communitiesRansom A Myers
Biology Department, Dalhousie University, Halifax, Nova Scotia, Canada B3H 4J1
Nature 423:280-3. 2003..We constructed trajectories of community biomass and composition of large predatory fishes in four continental shelf and nine oceanic systems, using all available ..
- An insect herbivore microbiome with high plant biomass-degrading capacityGarret Suen
Department of Energy Great Lakes Bioenergy Research Center, University of Wisconsin Madison, Madison, Wisconsin, United States of America
PLoS Genet 6:e1001129. 2010..the fungus garden microbiome of leaf-cutter ants is composed of a diverse community of bacteria with high plant biomass-degrading capacity...
- Soil carbon sequestration impacts on global climate change and food securityR Lal
Carbon Management and Sequestration Center, Ohio State University Columbus, OH 43210, USA
Science 304:1623-7. 2004..5 to 1 kg/ha for cowpeas. As well as enhancing food security, carbon sequestration has the potential to offset fossil fuel emissions by 0.4 to 1.2 gigatons of carbon per year, or 5 to 15% of the global fossil-fuel emissions...
- Ecosystem stability and compensatory effects in the Inner Mongolia grasslandYongfei Bai
Laboratory of Quantitative Vegetation Ecology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
Nature 431:181-4. 2004..First, that January-July precipitation is the primary climatic factor causing fluctuations in community biomass production; second, that ecosystem stability (conversely related to variability in community biomass production) ..
- Trends in biotechnological production of fuel ethanol from different feedstocksOscar J Sánchez
Department of Chemical Engineering, National University of Colombia at Manizales, Cra 27 No 64 60 Of F 505, Manizales, Caldas, Colombia
Bioresour Technol 99:5270-95. 2008..fuel ethanol from sucrose-containing feedstocks (mainly sugar cane), starchy materials and lignocellulosic biomass are described along with the major research trends for improving them...
- Comparison of dilute acid and ionic liquid pretreatment of switchgrass: Biomass recalcitrance, delignification and enzymatic saccharificationChenlin Li
Joint BioEnergy Institute, Physical Biosciences Division, Lawrence Berkeley National Laboratory, Emeryville, CA, USA
Bioresour Technol 101:4900-6. 2010The efficiency of two biomass pretreatment technologies, dilute acid hydrolysis and dissolution in an ionic liquid, are compared in terms of delignification, saccharification efficiency and saccharide yields with switchgrass serving as a ..
- Unraveling the complex trait of crop yield with quantitative trait loci mapping in Brassica napusJiaqin Shi
National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, China
Genetics 182:851-61. 2009..The idea of estimating indicator QTL for yield QTL and identifying potential candidate genes for yield provides an advance in methodology for complex traits...
- Expression of biomass-degrading enzymes is a major event during conidium development in Trichoderma reeseiBenjamin Metz
Institute of Chemical Engineering, University of Technology of Vienna, Vienna, Austria
Eukaryot Cell 10:1527-35. 2011..reesei, contributes to the hypothesis that the ability to hydrolyze plant biomass is a major trait of this fungus enabling it to break dormancy and reinitiate vegetative growth after a period of ..
- Determinants of woody cover in African savannasMahesh Sankaran
Natural Resource Ecology Laboratory, Colorado State University, Fort Collins, Colorado 80523, USA
Nature 438:846-9. 2005..These results provide insights into the nature of African savannas and suggest that future changes in precipitation may considerably affect their distribution and dynamics...
- Abrolhos bank reef health evaluated by means of water quality, microbial diversity, benthic cover, and fish biomass dataThiago Bruce
Department of Marine Biology, Universidade Federal do Rio de Janeiro UFRJ, Rio de Janeiro, Rio de Janeiro, Brazil
PLoS ONE 7:e36687. 2012..using measurements of four ecosystem components: (i) inorganic and organic nutrient concentrations,  fish biomass,  macroalgal and coral cover and (iv) microbial community composition and abundance...
- Transition of cellulose crystalline structure and surface morphology of biomass as a function of ionic liquid pretreatment and its relation to enzymatic hydrolysisGang Cheng
Joint BioEnergy Institute, Emeryville, California, USA
Biomacromolecules 12:933-41. 2011..and eucalyptus ( Eucalyptus globulus ), and its influence on cellulose hydrolysis kinetics of the resultant biomass. These feedstocks were pretreated using 1-ethyl-3-methyl imidazolium acetate ([C2mim][OAc]) at 120 and 160 °C ..
- Extremely thermophilic microorganisms for biomass conversion: status and prospectsSara E Blumer-Schuette
Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, NC 27695 7905, United States
Curr Opin Biotechnol 19:210-7. 2008..temperatures are able to utilize a variety of carbohydrates pertinent to the conversion of lignocellulosic biomass to bioenergy. The range of substrates utilized depends on growth temperature optimum and biotope...
- Deconstruction of lignocellulosic biomass to fuels and chemicalsShishir P S Chundawat
Great Lakes Bioenergy Research Center, East Lansing, MI 48824, USA
Annu Rev Chem Biomol Eng 2:121-45. 2011..To produce infrastructure-compatible fuels from biomass, two challenges remain: overcoming plant cell wall recalcitrance to extract sugar and phenolic intermediates, and ..
- Comparative genomic analysis of the thermophilic biomass-degrading fungi Myceliophthora thermophila and Thielavia terrestrisRandy M Berka
Novozymes, Inc, Davis, CA, USA
Nat Biotechnol 29:922-7. 2011..enzymes and thermophilic cell factories may afford economic advantages in the production of many chemicals and biomass-based fuels...
- Phylogenetic, microbiological, and glycoside hydrolase diversities within the extremely thermophilic, plant biomass-degrading genus CaldicellulosiruptorSara E Blumer-Schuette
Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina 27695 7905, USA
Appl Environ Microbiol 76:8084-92. 2010..toward the capacity of these extremely thermophilic bacteria to degrade the complex carbohydrate content of plant biomass. Seven species from this genus (C. saccharolyticus, C. bescii, C. hydrothermalis, C. owensensis, C...
- OptStrain: a computational framework for redesign of microbial production systemsPriti Pharkya
Department of Chemical Engineering, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
Genome Res 14:2367-76. 2004..In summary, OptStrain provides a useful tool to aid microbial strain design and, more importantly, it establishes an integrated framework to accommodate future modeling developments...
- Loss of plant species after chronic low-level nitrogen deposition to prairie grasslandsChristopher M Clark
Department of Ecology, Evolution and Behavior, 100 Ecology, 1987 Upper Buford Circle, University of Minnesota, St Paul, Minnesota 55108, USA
Nature 451:712-5. 2008..A second experiment showed that a decade after cessation of nitrogen addition, relative plant species number, although not species abundances, had recovered, demonstrating that some effects of nitrogen addition are reversible...
- Woodsmoke health effects: a reviewLuke P Naeher
Department of Environmental Health Science, College of Public Health, University of Georgia, Athens, Georgia, USA
Inhal Toxicol 19:67-106. 2007..of smoke from wildland fires and agricultural burning, and related controlled human laboratory exposures to biomass smoke; the epidemiology of outdoor and indoor woodsmoke exposures from residential woodburning in developed ..
- Plant species richness and functional composition drive overyielding in a six-year grassland experimentElisabeth Marquard
Max Planck Institute for Biogeochemistry, Hans Knöll Strasse 10, 07745 Jena, Germany
Ecology 90:3290-302. 2009Plant diversity has been shown to increase community biomass in experimental communities, but the mechanisms resulting in such positive biodiversity effects have remained largely unknown...
- Climate-driven trends in contemporary ocean productivityMichael J Behrenfeld
Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon 97331, USA
Nature 444:752-5. 2006..The distribution of phytoplankton biomass and NPP is defined by the availability of light and nutrients (nitrogen, phosphate, iron)...
- Soil biota and exotic plant invasionRagan M Callaway
Division of Biological Sciences, The University of Montana, Missoula, Montana 59812, USA
Nature 427:731-3. 2004..But in soils from North America, Centaurea cultivates soil biota with increasingly positive effects on itself, which may contribute to the success of this exotic species in North America...
- Flux balance analysis of primary metabolism in Chlamydomonas reinhardtiiNanette R Boyle
School of Chemical Engineering, Purdue University, West Lafayette, Indiana 47907, USA
BMC Syst Biol 3:4. 2009..organisms convert atmospheric carbon dioxide into numerous metabolites along the pathways to make new biomass. Aquatic photosynthetic organisms, which fix almost half of global inorganic carbon, have great potential: as a ..
- The carbon balance of terrestrial ecosystems in ChinaShilong Piao
Department of Ecology, College of Urban and Environmental Science, and Key Laboratory for Earth Surface Processes of the Ministry of Education, Peking University, Beijing 100871, China
Nature 458:1009-13. 2009..carbon balance of China and its driving mechanisms during the 1980s and 1990s using three different methods: biomass and soil carbon inventories extrapolated by satellite greenness measurements, ecosystem models and atmospheric ..
- Shifts in caterpillar biomass phenology due to climate change and its impact on the breeding biology of an insectivorous birdMarcel E Visser
Netherlands Institute of Ecology NIOO KNAW, P O Box 40, 6666 ZG, Heteren, The Netherlands
Oecologia 147:164-72. 2006..We measured caterpillar biomass over a 20-year period and showed that the annual peak date is correlated with temperatures from 8 March to 17 May...
- Multiple controls of community structure and dynamics in a sublittoral marine environmentBernat Hereu
Departament d Ecologia, Facultat de Biologia, Universitat de Barcelona, Diagonal 645, 08028 Barcelona, Spain
Ecology 89:3423-35. 2008..Most algae showed a marked annual cycle, with a biomass peak in late spring/summer and low biomass in winter, following seasonal fluctuations in resource availability, ..
- Shifts in lake N:P stoichiometry and nutrient limitation driven by atmospheric nitrogen depositionJames J Elser
School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
Science 326:835-7. 2009....
- Ethanol fermentation from biomass resources: current state and prospectsYan Lin
Asian Center for Environmental Research, Meisei University, Tokyo, Japan
Appl Microbiol Biotechnol 69:627-42. 2006In recent years, growing attention has been devoted to the conversion of biomass into fuel ethanol, considered the cleanest liquid fuel alternative to fossil fuels...
- Application of a high-density oligonucleotide microarray approach to study bacterial population dynamics during uranium reduction and reoxidationEoin L Brodie
Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA 94720, USA
Appl Environ Microbiol 72:6288-98. 2006..High-density phylogenetic microarrays constitute a powerful tool, enabling the detection and monitoring of a substantial portion of the microbial population in a routine, accurate, and reproducible manner...
- Plant species traits are the predominant control on litter decomposition rates within biomes worldwideWilliam K Cornwell
Faculty of Earth and Life Sciences, Department of Systems Ecology, Institute of Ecological Science, Vrije Universiteit, De Boelelaan 1085, 1081 HV Amsterdam, The Netherlands
Ecol Lett 11:1065-71. 2008..This connection between plant strategies and decomposability is crucial for both understanding vegetation-soil feedbacks, and for improving forecasts of the global carbon cycle...
- Network analysis of enzyme activities and metabolite levels and their relationship to biomass in a large panel of Arabidopsis accessionsRonan Sulpice
Max Planck Institute of Molecular Plant Physiology, 14476 Potsdam Golm, Germany
Plant Cell 22:2872-93. 2010..metabolism and generate a matrix to investigate species-wide connectivity between metabolites, enzymes, and biomass. Most enzyme activities change in a highly coordinated manner, especially those in the Calvin-Benson cycle...
- Flux balance analysis of photoautotrophic metabolismAvantika A Shastri
School of Chemical Engineering, Purdue University, 480 Stadium Mall Dr, West Lafayette, Indiana 47907, USA
Biotechnol Prog 21:1617-26. 2005..We also theoretically evaluated the effect of gene deletions or additions on biomass yield and metabolic flux distributions.
- A global perspective on belowground carbon dynamics under nitrogen enrichmentLingli Liu
Environmental Media Assessment Group MD B243 01, National Center for Environmental Assessment, Office of Research and Development, U S EPA, Research Triangle Park, NC 27711, USA
Ecol Lett 13:819-28. 2010..N addition inhibited microbial activity as indicated by a reduction in microbial respiration (-8%) and microbial biomass carbon (-20%)...
- Automated assay for screening the enzymatic release of reducing sugars from micronized biomassDavid Navarro
Architecture et Fonction des Macromolecules Biologiques, UMR 6098, CNRS et Université d Aix Marseille I et II, 163 avenue de Luminy CP 925, 13288 Marseille Cedex 09, France
Microb Cell Fact 9:58. 2010..production cost of bioethanol obtained from fermentation of the sugars provided by degradation of lignocellulosic biomass (i.e...
- Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environmentsKai Zhuang
Department of Chemical Engineering and Applied Chemistry, Institute of Biomaterials and Biomedical Engineering, University of Toronto, Toronto, Ontario, Canada
ISME J 5:305-16. 2011..that under nitrogen fixation, higher carbon and electron fluxes would be diverted toward respiration rather than biomass formation in Geobacter, providing a potential explanation for enhanced in situ U(VI) reduction in low-ammonium ..
- Biodiversity and ecosystem stability in a decade-long grassland experimentDavid Tilman
Department of Ecology, Evolution and Behavior, University of Minnesota, 1987 Upper Buford Circle, St Paul, Minnesota 55108, USA
Nature 441:629-32. 2006..Ecosystem stability was also positively dependent on root mass, which is a measure of perenniating biomass. Temporal stability of the ecosystem increased with diversity, despite a lower temporal stability of individual ..
- Impacts of plant diversity on biomass production increase through time because of species complementarityBradley J Cardinale
Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, CA 93106, USA
Proc Natl Acad Sci U S A 104:18123-8. 2007..experiments that have manipulated the richness of plants to examine how plant diversity affects the production of biomass. We show that mixtures of species produce an average of 1...
- HeterosisJames A Birchler
Division of Biological Sciences, University of Missouri, Columbia, Missouri 65211, USA
Plant Cell 22:2105-12. 2010..to the phenomenon that progeny of diverse varieties of a species or crosses between species exhibit greater biomass, speed of development, and fertility than both parents...
- Synthetic enzyme mixtures for biomass deconstruction: production and optimization of a core setGoutami Banerjee
Department of Energy, Great Lakes Bioenergy Research Center, Michigan State University, E Lansing, Michigan 48824, USA
Biotechnol Bioeng 106:707-20. 2010..Commercial enzyme cocktails for the conversion of plant biomass to fermentable sugars are complex mixtures containing more than 80 proteins of suboptimal activities and relative ..
- Progress and challenges in enzyme development for biomass utilizationSandra T Merino
Novozymes Inc, 1445 Drew Ave, CA 95618, Davis, USA
Adv Biochem Eng Biotechnol 108:95-120. 2007..Here we describe advances in enzyme technology for use in the production of biofuels and the challenges that remain...
- Ecosystem energetic implications of parasite and free-living biomass in three estuariesArmand M Kuris
Department of Ecology, Evolution and Marine Biology and Marine Science Institute, University of California, Santa Barbara, California 93106, USA
Nature 454:515-8. 2008Parasites can have strong impacts but are thought to contribute little biomass to ecosystems. We quantified the biomass of free-living and parasitic species in three estuaries on the Pacific coast of California and Baja California...
- A large and persistent carbon sink in the world's forestsYude Pan
U S Department of Agriculture Forest Service, Newtown Square, PA 19073, USA
Science 333:988-93. 2011..Our total forest sink estimate is equivalent in magnitude to the terrestrial sink deduced from fossil fuel emissions and land-use change sources minus ocean and atmospheric sinks...
- Anaerobic digestion of microalgae as a necessary step to make microalgal biodiesel sustainableBruno Sialve
INRA, UR050, Laboratoire de Biotechnologie de l Environnement, Avenue des Etangs, Narbonne F 11100, France
Biotechnol Adv 27:409-16. 2009..In the perspective of setting up massive cultures, the management of large quantities of residual biomass and the high amounts of fertilizers must be considered...
- Chloroplast-derived enzyme cocktails hydrolyse lignocellulosic biomass and release fermentable sugarsDheeraj Verma
Department of Molecular Biology and Microbiology, Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, FL 32816 2364, USA
Plant Biotechnol J 8:332-50. 2010..first report of using plant-derived enzyme cocktails for production of fermentable sugars from lignocellulosic biomass. Limitations of higher cost and lower production capacity of fermentation systems are addressed by chloroplast-..
- Reconstruction and analysis of genome-scale metabolic model of a photosynthetic bacteriumArnau Montagud
Instituto Universitario de Matemática Pura y Aplicada, Universidad Politecnica de Valencia, Camino de Vera 14, Valencia, Spain
BMC Syst Biol 4:156. 2010..In order to enable efficient use of metabolic potential of Synechocystis sp. PCC6803, it is of importance to develop tools for uncovering stoichiometric and regulatory principles in the Synechocystis metabolic network...
- Interactions among predators and the cascading effects of vertebrate insectivores on arthropod communities and plantsKailen A Mooney
Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697 2525, USA
Proc Natl Acad Sci U S A 107:7335-40. 2010Theory on trophic interactions predicts that predators increase plant biomass by feeding on herbivores, an indirect interaction called a trophic cascade...
- Agriculture. Sustainable biofuels reduxG Philip Robertson
W K Kellogg Biological Station and Department of Crop and Soil Sciences, Michigan State University, Hickory Corners, MI 49060, USA
Science 322:49-50. 2008
- Global response patterns of terrestrial plant species to nitrogen additionJianyang Xia
State Key Laboratory of Vegetation and Environmental Change, Institute of Botany, Chinese Academy of Sciences, Xiangshan, Beijing 100093, China
New Phytol 179:428-39. 2008..Across 456 terrestrial plant species included in the analysis, biomass and N concentration were increased by 53.6 and 28.5%, respectively, under N enrichment...
- Biomass content governs fermentation rate in nitrogen-deficient wine mustsCristian Varela
Departamento de Ingeniería Química y Bioprocesos, Escuela de Ingeniería, Pontificia Universidad Catolica de Chile, Santiago, Chile
Appl Environ Microbiol 70:3392-400. 2004..A lack of nitrogen diminishes a yeast's metabolic activity, as well as the biomass yield, although it has not been clear which of these two interdependent factors is more significant in sluggish ..
- Grassland responses to global environmental changes suppressed by elevated CO2M Rebecca Shaw
Department of Global Ecology, Carnegie Institution of Washington, 260 Panama Street, Stanford, CA 94305, USA
Science 298:1987-90. 2002..These findings indicate the importance of a multifactor experimental approach to understanding ecosystem responses to global change...
- How do plants respond to nutrient shortage by biomass allocation?Christian Hermans
Laboratoire de Physiologie et de Génétique Moléculaire des Plantes, Universite Libre de Bruxelles, Boulevard du Triomphe CP 242, 1050 Brussels, Belgium
Trends Plant Sci 11:610-7. 2006..changes in their environment; when mineral elements are scarce, they often allocate a greater proportion of their biomass to the root system...
- A Plant-Derived Recombinant Bioscavenger to Prevent Insecticide NeurotoxicityYvonne Rosenberg; Fiscal Year: 2007..rBChE using the plant expression system which is versatile and inexpensive due to its ability to yield a large biomass in GMP conditions (Phase I) and (2) as a result of their unsialyted and atypical glycans, these recombinant plant ..
- INDOOR AIR POLLUTION AND CHILD ARI: A RANDOMIZED TRIALKirk Smith; Fiscal Year: 2004..Such conditions are common in less-developed countries (LDCs), where some two-thirds of households rely on biomass fuels (wood, dung, crop residues)...
- Indoor woodsmoke PM and asthma: a randomized trialAnthony Ward; Fiscal Year: 2009..The results from this project will be translatable to other regions in the US and the world where biomass burning is commonly used for heating and cooking. Relevance: This study will determine if reductions in PM2...
- Cookstove Replacement for Prevention of ARI and Low Birthweight in NepalJames M Tielsch; Fiscal Year: 2010..for poor, rural areas in developing countries and the strong observational association between open burning of biomass fuel sources and ARI in young children and low birth weight, we have designed a community-based randomized trial ..
- Cookstove Replacement for Prevention of ARI and Low Birthweight in NepalJames Tielsch; Fiscal Year: 2009..for poor, rural areas in developing countries and the strong observational association between open burning of biomass fuel sources and ARI in young children and low birth weight, we have designed a community-based randomized trial ..
- Microbial Mediation of Habitat Selection and ProductionEdward Walker; Fiscal Year: 2006..Secondly, we will quantify microbial processing of nutrients and accrual of microbial biomass in larval habitats, and link them to adult production...
- Research Training on Chronic Lung Diseases in Southern AfricaThomas Robins; Fiscal Year: 2009..g., ambient air pollution, burning of biomass fuels in domiciles, indoor and outdoor exposure to bioaerosols, environmental tobacco smoke)and occupational (e.g...
- Novel accelerated in vitro breeding for phytoremediationMIHALY CZAKO; Fiscal Year: 2007..built on the successful demonstration of the feasibility of our novel technology for in vitro breeding of a large biomass plant for field-scale phytoremediation...
- Indoor woodsmoke PM and asthma: a randomized trialANTHONY JOHN contact WARD; Fiscal Year: 2010..The results from this project will be translatable to other regions in the US and the world where biomass burning is commonly used for heating and cooking. Relevance: This study will determine if reductions in PM2...
- LARVAL MOSQUITO FEEDING AND MICROBIAL INTERACTIONSEdward Walker; Fiscal Year: 1993..tree holes, tires); (2) to examine experimentally the relationships between limiting nutrients, microbial biomass and diversity, and surface microlayer water fractions to mosquito growth and adult mosquito production for Aedes ..
- Model-driven Media Optimization in Hybridoma Cell LineIman Famili; Fiscal Year: 2006..to microbial systems, productivity and product titers in mammalian cell cultures are low mainly due to the low biomass concentration achievable in standard mammalian cell culture...
- COMMUNITY COMPOSITION AND PHYSIOLOGY OF ORAL BIOFILMSDavid White; Fiscal Year: 2001..define a species-composition measurement using phospholipid-bound fatty-acid (PLFA) profiles of whole-community biomass, and will validate that measurement by correlation with checkerboard hybridization and cultivable flora methods...
- LARVAL MOSQUITO FEEDING AND MICROBIAL INTERACTIONSEdward Walker; Fiscal Year: 2007..but it is constrained by conversion of refractile organic material into ingestible and digestible microbial biomass. The tree hole habitat of several mosquito species is our model system to study this phenomenon...
- Nano-scale Mechanisms of Metal(loid) Rhizostabilization in Desert Mine TailingsJONATHAN CHOROVER; Fiscal Year: 2009..with the goal of root zone metal accumulation to avoid metals from entering the food chain through above-ground biomass. The role of plant roots and microbes in promoting mineral dissolution-precipitation reactions and associated ..
- Nano-scale Mechanisms of Metal(loid) Rhizostabilization in Desert Mine TailingsJONATHAN D CHOROVER; Fiscal Year: 2010..with the goal of root zone metal accumulation to avoid metals from entering the food chain through above-ground biomass. The role of plant roots and microbes in promoting mineral dissolution-precipitation reactions and associated ..
- Nano-scale Mechanisms of Metal(loid) Rhizostabilization in Desert Mine TailingsJONATHAN D CHOROVER; Fiscal Year: 2011..with the goal of root zone metal accumulation to avoid metals from entering the food chain through above-ground biomass. The role of plant roots and microbes in promoting mineral dissolution-precipitation reactions and associated ..
- Discovery of genes that extend yeast lifespan: Aging in immobilized cell reactorsRAPHAEL ROSENZWEIG; Fiscal Year: 2007..These reactors continue to produce close-to-theoretical yields of ethanol but very little biomass, relative to substrate input...
- Expression of Human Therapeutic Proteins in ChloroplastsHenry Daniell; Fiscal Year: 2005..Tobacco is an ideal choice because of its large biomass, ease of scale-up (million seeds pen plant), genetic manipulation and an impending need to explore alternative ..
- Metabolic Engineering Studies of Extreme ThermoacidophilyRobert Kelly; Fiscal Year: 2009..the Crenarcheaota (not all of which are extreme thermoacidophiles) comprise a significant fraction of the global biomass, and are relevant beyond extreme niches...
- Discovery of Anticancer Drugs from CyanobacteriaFrederick Valeriote; Fiscal Year: 2007..collected and cultured tropical marine microalgae, mainly cyanobacteria, with a focus on those of low natural biomass or found in symbiosis with marine invertebrates, such as sponges and tunicates and to characterize "super-..
- Effects of cooking smoke on healthVinod Mishra; Fiscal Year: 2004..heating causes substantial ill health in developing countries where a majority of households rely on unprocessed biomass fuels such as wood, crop residues, and dung cakes, but research on this subject is limited and many uncertainties ..
- REGULATION OF THE HEAT SHOCK RESPONSE IN E. COLICarol Gross; Fiscal Year: 2009..PUBLIC HEALTH RELEVANCE: Project relevance Microbes account for fully half of the world's biomass and are of immense importance to life on earth, for reasons as diverse as performing mineral recycling in our ..