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https://www.readbyqxmd.com/read/28334199/stepwise-inference-of-likely-dynamic-flux-distributions-from-metabolic-time-series-data
#1
Mojdeh Faraji, Eberhard O Voit
Motivation: Most metabolic pathways contain more reactions than metabolites and therefore have a wide stoichiometric matrix that corresponds to infinitely many possible flux distributions that are perfectly compatible with the dynamics of the metabolites in a given dataset. This under-determinedness poses a challenge for the quantitative characterization of flux distributions from time series data and thus for the design of adequate, predictive models. Here we propose a method that reduces the degrees of freedom in a stepwise manner and leads to a dynamic flux distribution that is, in a statistical sense, likely to be close to the true distribution...
March 7, 2017: Bioinformatics
https://www.readbyqxmd.com/read/28304245/kineothrix-alysoides-gen-nov-sp-nov-a-saccharolytic-butyrate-producer-within-the-family-lachnospiraceae
#2
Kelly Nicole Haas, Jeffrey L Blanchard
An anaerobic, saccharolytic, spore-forming, butyrate-producing bacterium, strain KNHs209T, was isolated from a switchgrass microcosm seeded with forest soil. Cells were highly motile rods, often forming long filamentous chains which were easily observed moving under the microscope. Its closest phylogenetic relative was Eisenbergiella tayi (16S rRNA gene sequence identity 94.2 %), although it was easily distinguishable based on its morphology and physiology. Whole-genome sequencing enabled development of a minimal medium, and also suggested that the organism is capable of fixing nitrogen...
February 2017: International Journal of Systematic and Evolutionary Microbiology
https://www.readbyqxmd.com/read/28264034/overexpression-of-the-wox-gene-stenofolia-improves-biomass-yield-and-sugar-release-in-transgenic-grasses-and-display-altered-cytokinin-homeostasis
#3
Hui Wang, Lifang Niu, Chunxiang Fu, Yingying Meng, Dajun Sang, Pengcheng Yin, Jinxia Wu, Yuhong Tang, Tiegang Lu, Zeng-Yu Wang, Million Tadege, Hao Lin
Lignocellulosic biomass can be a significant source of renewable clean energy with continued improvement in biomass yield and bioconversion strategies. In higher plants, the leaf blade is the central energy convertor where solar energy and CO2 are assimilated to make the building blocks for biomass production. Here we report that introducing the leaf blade development regulator STENOFOLIA (STF), a WOX family transcription factor, into the biofuel crop switchgrass, significantly improves both biomass yield and sugar release...
March 2017: PLoS Genetics
https://www.readbyqxmd.com/read/28211339/phytoextraction-of-contaminated-urban-soils-by-panicum-virgatum-l-enhanced-with-application-of-a-plant-growth-regulator-bap-and-citric-acid
#4
Matthew Aderholt, Dale L Vogelien, Marina Koether, Sigurdur Greipsson
Lead (Pb) contamination in soil represents a threat to human health. Phytoextraction has gained attention as a potential alternative to traditional remediation methods because of lower cost and minimal soil disruption. The North American native switchgrass (Panicum virgatum L.) was targeted due to its ability to produce high biomass and grow across a variety of ecozones. In this study switchgrass was chemically enhanced with applications of the soil-fungicide benomyl, chelates (EDTA and citric acid), and PGR to optimize phytoextraction of Pb and zinc (Zn) from contaminated urban soils in Atlanta, GA...
May 2017: Chemosphere
https://www.readbyqxmd.com/read/28209137/transcriptional-analysis-of-defense-mechanisms-in-upland-tetraploid-switchgrass-to-greenbugs
#5
Teresa Donze-Reiner, Nathan A Palmer, Erin D Scully, Travis J Prochaska, Kyle G Koch, Tiffany Heng-Moss, Jeffrey D Bradshaw, Paul Twigg, Keenan Amundsen, Scott E Sattler, Gautam Sarath
BACKGROUND: Aphid infestation of switchgrass (Panicum virgatum) has the potential to reduce yields and biomass quality. Although switchgrass-greenbug (Schizaphis graminum; GB) interactions have been studied at the whole plant level, little information is available on plant defense responses at the molecular level. RESULTS: The global transcriptomic response of switchgrass cv Summer to GB was monitored by RNA-Seq in infested and control (uninfested) plants harvested at 5, 10, and 15 days after infestation (DAI)...
February 16, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28165761/bio-and-phytoremediation-of-total-petroleum-hydrocarbons-tph-under-various-conditions
#6
Patrick McIntosh, Cristian P Schulthess, Yulia A Kuzovkina, Karl Guillard
Remediation of contaminated soils is often studied using fine textured soils rather than low-fertility sandy soils, and few studies focus on recontamination events. This study compared aerobic and anaerobic treatments for remediation of freshly introduced used motor oil on a sandy soil previously phytoremediated and bioacclimated (microorganisms already adapted in the soil environment) with some residual total petroleum hydrocarbon (TPH) contamination. Vegetated and unvegetated conditions to remediate anthropogenic fill containing residual TPH that was spiked with non-aqueous phase liquids (NAPLs) were evaluated in a 90-day greenhouse pot study...
February 6, 2017: International Journal of Phytoremediation
https://www.readbyqxmd.com/read/28160678/phenoxy-herbicide-removal-from-aqueous-solutions-using-fast-pyrolysis-switchgrass-biochar
#7
Matthew Essandoh, Daniel Wolgemuth, Charles U Pittman, Dinesh Mohan, Todd Mlsna
The release of herbicides is known to negatively impact humans and the environment. We report the use of a low cost biochar (prepared through fast pyrolysis) to successfully remove phenoxy herbicides from aqueous solutions. The biochar was characterized using: FT-IR, SEM, pHpzc, elemental analysis, and surface area measurements. Sorption experiments were run at pH values from 2 to 10, adsorbate concentrations from 25 to 300 mg/L and temperatures from 25 to 45 °C. Adsorption isotherms were evaluated from 25 to 45 °C using both two parameter (Freundlich and Langmuir) and three parameter (Redlich-Peterson and Toth) adsorption isotherm models...
May 2017: Chemosphere
https://www.readbyqxmd.com/read/28115990/stochastic-techno-economic-analysis-of-alcohol-to-jet-fuel-production
#8
Guolin Yao, Mark D Staples, Robert Malina, Wallace E Tyner
BACKGROUND: Alcohol-to-jet (ATJ) is one of the technical feasible biofuel technologies. It produces jet fuel from sugary, starchy, and lignocellulosic biomass, such as sugarcane, corn grain, and switchgrass, via fermentation of sugars to ethanol or other alcohols. This study assesses the ATJ biofuel production pathway for these three biomass feedstocks, and advances existing techno-economic analyses of biofuels in three ways. First, we incorporate technical uncertainty for all by-products and co-products though statistical linkages between conversion efficiencies and input and output levels...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28092137/isolation-and-characterization-of-rhizobium-sp-strain-ys-1r-that-degrades-lignin-in-plant-biomass
#9
C A Jackson, M B Couger, M Prabhakaran, K D Ramachandriya, P Canaan, B Z Fathepure
AIMS: The aim of this work was to isolate novel lignin-degrading organisms. METHODS AND RESULTS: Several pure cultures of bacteria that degrade lignin were isolated from bacterial consortia developed from decaying biomass. Among the isolates, Rhizobium sp. strain YS-1r (closest relative of Rhizobium petrolearium strain SL-1) was explored for its lignin-degrading ability. Microcosm studies showed that strain YS-1r was able to degrade a variety of lignin monomers, dimers and also native lignin in switchgrass and alfalfa...
April 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/28077967/integrated-omics-analyses-reveal-the-details-of-metabolic-adaptation-of-clostridium-thermocellum-to-lignocellulose-derived-growth-inhibitors-released-during-the-deconstruction-of-switchgrass
#10
Suresh Poudel, Richard J Giannone, Miguel Rodriguez, Babu Raman, Madhavi Z Martin, Nancy L Engle, Jonathan R Mielenz, Intawat Nookaew, Steven D Brown, Timothy J Tschaplinski, David Ussery, Robert L Hettich
BACKGROUND: Clostridium thermocellum is capable of solubilizing and converting lignocellulosic biomass into ethanol. Although much of the work-to-date has centered on characterizing this microbe's growth on model cellulosic substrates, such as cellobiose, Avicel, or filter paper, it is vitally important to understand its metabolism on more complex, lignocellulosic substrates to identify relevant industrial bottlenecks that could undermine efficient biofuel production. To this end, we have examined a time course progression of C...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28053668/study-of-traits-and-recalcitrance-reduction-of-field-grown-comt-down-regulated-switchgrass
#11
Mi Li, Yunqiao Pu, Chang Geun Yoo, Erica Gjersing, Stephen R Decker, Crissa Doeppke, Todd Shollenberger, Timothy J Tschaplinski, Nancy L Engle, Robert W Sykes, Mark F Davis, Holly L Baxter, Mitra Mazarei, Chunxiang Fu, Richard A Dixon, Zeng-Yu Wang, C Neal Stewart, Arthur J Ragauskas
BACKGROUND: The native recalcitrance of plants hinders the biomass conversion process using current biorefinery techniques. Down-regulation of the caffeic acid O-methyltransferase (COMT) gene in the lignin biosynthesis pathway of switchgrass reduced the thermochemical and biochemical conversion recalcitrance of biomass. Due to potential environmental influences on lignin biosynthesis and deposition, studying the consequences of physicochemical changes in field-grown plants without pretreatment is essential to evaluate the performance of lignin-altered plants...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28034316/high-temperature-carbonized-grass-as-a-high-performance-sodium-ion-battery-anode
#12
Fang Zhang, Yonggang Yao, Jiayu Wan, Doug Henderson, Xiaogang Zhang, Liangbing Hu
Hard carbon is currently considered the most promising anode candidate for room temperature sodium ion batteries because of its relatively high capacity, low cost, and good scalability. In this work, switchgrass as a biomass example was carbonized under an ultrahigh temperature, 2050 °C, induced by Joule heating to create hard carbon anodes for sodium ion batteries. Switchgrass derived carbon materials intrinsically inherit its three-dimensional porous hierarchical architecture, with an average interlayer spacing of 0...
December 30, 2016: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28012044/a-survey-of-yeast-from-the-yarrowia-clade-for-lipid-production-in-dilute-acid-pretreated-lignocellulosic-biomass-hydrolysate
#13
Josh Quarterman, Patricia J Slininger, Cletus P Kurtzman, Stephanie R Thompson, Bruce S Dien
Yarrowia lipolytica is an oleaginous yeast species that has attracted attention as a model organism for synthesis of single cell oil. Among over 50 isolates of Y. lipolytica identified, only a few of the strains have been studied extensively. Furthermore, 12 other yeast species were recently assigned to the Yarrowia clade, and most are not well characterized in terms of cell growth and lipid accumulation, especially in industrially relevant conditions. In the present study, we investigated biomass and lipid production by 57 yeast isolates, representing all 13 species in the Yarrowia clade, on a non-detoxified dilute acid-pretreated switchgrass hydrolysate under highly aerobic conditions...
December 23, 2016: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28003194/laci-transcriptional-regulatory-networks-in-clostridium-thermocellum-dsm1313
#14
Charlotte M Wilson, Dawn M Klingeman, Caleb Schlachter, Mustafa H Syed, Chia-Wei Wu, Adam M Guss, Steven D Brown
Organisms regulate gene expression in response to the environment to coordinate metabolic reactions. Clostridium thermocellum expresses enzymes for both lignocellulose solubilization and its fermentation to produce ethanol. One LacI regulator termed GlyR3 in C. thermocellum ATCC 27405 was previously identified as a repressor of neighboring genes with repression relieved by laminaribiose (a β-1,3 disaccharide). To better understand the three C. thermocellum LacI regulons, deletion mutants were constructed using the genetically tractable DSM1313 strain...
March 1, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/27986076/transcriptome-analysis-in-switchgrass-discloses-ecotype-difference-in-photosynthetic-efficiency
#15
Desalegn D Serba, Srinivasa Rao Uppalapati, Nick Krom, Shreyartha Mukherjee, Yuhong Tang, Kirankumar S Mysore, Malay C Saha
BACKGROUND: Switchgrass, a warm-season perennial grass studied as a potential dedicated biofuel feedstock, is classified into two main taxa - lowland and upland ecotypes - that differ in morphology and habitat of adaptation. But there is limited information on their inherent molecular variations. RESULTS: Transcriptome analysis by RNA-sequencing (RNA-Seq) was conducted for lowland and upland ecotypes to document their gene expression variations. Mapping of transcriptome to the reference genome (Panicum virgatum v1...
December 16, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27981239/ionic-liquids-impact-the-bioenergy-feedstock-degrading-microbiome-and-transcription-of-enzymes-relevant-to-polysaccharide-hydrolysis
#16
Yu-Wei Wu, Brendan Higgins, Chaowei Yu, Amitha P Reddy, Shannon Ceballos, Lawrence D Joh, Blake A Simmons, Steven W Singer, Jean S VanderGheynst
Ionic liquid (IL) pretreatment is a promising approach for the conversion of lignocellulose to biofuels. The toxicity of residual IL, however, negatively impacts the performance of industrial enzymes and microorganisms in hydrolysis and fermentation. In this study, a thermophilic microbial community was cultured on switchgrass amended with various levels of the ionic liquid 1-ethyl-3-methylimidazolium acetate. Changes in the microbial community composition and transcription of genes relevant to IL tolerance and lignocellulose hydrolysis were quantified...
November 2016: MSystems
https://www.readbyqxmd.com/read/27976872/evaluating-the-potential-of-marginal-land-for-cellulosic-feedstock-production-and-carbon-sequestration-in-the-united-states
#17
Isaac Emery, Steffen Mueller, Zhangcai Qin, Jennifer B Dunn
Land availability for growing feedstocks at scale is a crucial concern for the bioenergy industry. Feedstock production on land not well-suited to growing conventional crops, or marginal land, is often promoted as ideal, although there is a poor understanding of the qualities, quantity, and distribution of marginal lands in the United States. We examine the spatial distribution of land complying with several key marginal land definitions at the United States county, agro-ecological zone, and national scales, and compare the ability of both marginal land and land cover data sets to identify regions for feedstock production...
January 3, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/27966736/identification-and-characterization-of-the-14-3-3-gene-family-in-switchgrass
#18
S Wu, H D Yan, A L Zhang, L K Huang, G H Yin, S Lee
Members of the 14-3-3 family of proteins are conserved regulatory proteins that are widely found in eukaryotes and play crucial roles in diverse physiological processes, including responses to different stresses. Although genome-wide analysis of 14-3-3 proteins has been performed in a few plant species, it has not been performed in switchgrass. In this study, we identified 21 switchgrass 14-3-3 proteins (designated PvGF14a to PvGF14u) and examined genes for improved stress tolerance in this species. A phylogenetic tree was constructed to demonstrate that PvGF14 proteins can be divided into six groups, and that PvGF14 proteins belonging to each class exhibit similar gene structure...
December 2, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/27957693/adsorption-of-metribuzin-from-aqueous-solution-using-magnetic-and-nonmagnetic-sustainable-low-cost-biochar-adsorbents
#19
Matthew Essandoh, Daniel Wolgemuth, Charles U Pittman, Dinesh Mohan, Todd Mlsna
Switchgrass biochar (SGB) was made by fast pyrolysis in an auger-fed reactor at 425 °C with a solid residence time of 60 s in the pyrolysis zone during bio-oil production. Magnetic switchgrass biochar (MSGB) was prepared by iron oxide precipitation onto the biochar surface using an aqueous Fe(3+)/Fe(2+) solution followed by NaOH treatment. Both the SGB and the MSGB were characterized by FTIR, SEM, SEM-EDX, TGA, pHpzc, elemental analysis, and surface area measurements. Batch sorption studies of metribuzin from aqueous solutions were carried out at different pH values, adsorbate concentrations, and temperatures...
December 12, 2016: Environmental Science and Pollution Research International
https://www.readbyqxmd.com/read/27930996/stabilization-of-mercury-in-sediment-by-using-biochars-under-reducing-conditions
#20
Peng Liu, Carol J Ptacek, David W Blowes, Y Zou Finfrock, Robert A Gordon
Mercury (Hg) is widely distributed in different localities around the world and poses a serious health threat to humans, especially when ingested in the form of methylmercury (MeHg). Efforts have been directed toward decreasing the production of MeHg by converting Hg to stable forms. Activated carbon and biochar have been evaluated as stabilization agents for Hg in contaminated sediments. However, the long-term fate of Hg stabilized by these materials remains unclear. Here, we compare the effectiveness of Hg stabilization using two biochars prepared from switchgrass at 300°C (lowT) and 600°C (highT)...
March 5, 2017: Journal of Hazardous Materials
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