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https://www.readbyqxmd.com/read/28319856/systems-biology-solutions-for-biochemical-production-challenges
#1
REVIEW
Anne Sofie Lærke Hansen, Rebecca M Lennen, Nikolaus Sonnenschein, Markus J Herrgård
There is an urgent need to significantly accelerate the development of microbial cell factories to produce fuels and chemicals from renewable feedstocks in order to facilitate the transition to a biobased society. Methods commonly used within the field of systems biology including omics characterization, genome-scale metabolic modeling, and adaptive laboratory evolution can be readily deployed in metabolic engineering projects. However, high performance strains usually carry tens of genetic modifications and need to operate in challenging environmental conditions...
March 16, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28319371/expression-of-heterologous-sigma-factor-expands-the-searchable-space-for-biofuel-tolerance-mechanisms
#2
Timothy A Tomko, Mary J Dunlop
Microorganisms can produce hydrocarbons that can serve as replacements or additions to conventional liquid fuels for use in the transportation sector. However, a common problem in the microbial synthesis of biofuels is that these compounds often have toxic effects on the cell. In this study, we focused on mitigating the toxicity of the bio-jet fuel precursor pinene on Escherichia coli. We used genomic DNA from Pseudomonas putida KT2440, which has innate solvent-tolerance properties, to create transgenic libraries in an E...
March 20, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28317006/proteomic-data-on-enzyme-secretion-and-activity-in-the-bacterium-chitinophaga-pinensis
#3
Johan Larsbrink, Tina R Tuveng, Phillip B Pope, Vincent Bulone, Vincent G H Eijsink, Harry Brumer, Lauren S McKee
The secretion of carbohydrate-degrading enzymes by a bacterium sourced from a softwood forest environment has been investigated by mass spectrometry. The findings are discussed in full in the research article "Proteomic insights into mannan degradation and protein secretion by the forest floor bacterium Chitinophaga pinensis" in Journal of Proteomics by Larsbrink et al. ([1], doi: 10.1016/j.jprot.2017.01.003). The bacterium was grown on three carbon sources (glucose, glucomannan, and galactomannan) which are likely to be nutrient sources or carbohydrate degradation products found in its natural habitat...
April 2017: Data in Brief
https://www.readbyqxmd.com/read/28314665/bioflocculation-an-alternative-strategy-for-harvesting-of-microalgae-an-overview
#4
Sabeela Beevi Ummalyma, Edgard Gnansounou, Rajeev K Sukumaran, Raveendran Sindhu, Ashok Pandey, Dinabandhu Sahoo
Microalgae based research has been extensively progressed for the production of value added products and biofuels. Potential application of microalgae for biofuel is recently gained more attention for possibilities of biodiesel and other high value metabolites. However, high cost of production of biomass associated with harvesting technologies is one of the major bottleneck for commercialization of algae based industrial product. Based on the operation economics, harvesting efficiency, technological possibilities, flocculation of algal biomass is a superior method for harvesting microalgae from the growth medium...
February 27, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28303457/lipid-metabolism-and-potentials-of-biofuel-and-high-added-value-oil-production-in-red-algae
#5
REVIEW
Naoki Sato, Takashi Moriyama, Natsumi Mori, Masakazu Toyoshima
Biomass production is currently explored in microalgae, macroalgae and land plants. Microalgal biofuel development has been performed mostly in green algae. In the Japanese tradition, macrophytic red algae such as Pyropia yezoensis and Gelidium crinale have been utilized as food and industrial materials. Researches on the utilization of unicellular red microalgae such as Cyanidioschyzon merolae and Porphyridium purpureum started only quite recently. Red algae have relatively large plastid genomes harboring more than 200 protein-coding genes that support the biosynthetic capacity of the plastid...
April 2017: World Journal of Microbiology & Biotechnology
https://www.readbyqxmd.com/read/28300661/high-efficiency-extracellular-release-of-free-fatty-acids-from-aspergillus-oryzae-using-non-ionic-surfactants
#6
Koichi Tamano, Ai Miura, Hideaki Koike, Yasushi Kamisaka, Myco Umemura, Masayuki Machida
Free fatty acids (FFAs) are useful for generating biofuel compounds and functional lipids. Microbes are increasingly exploited to produce FFAs via metabolic engineering. However, in many microorganisms, FFAs accumulate in the cytosol, and disrupting cells to extract them is energy intensive. Thus, a simple cost-effective extraction technique must be developed to remove this drawback. We found that FFAs were released from cells of the filamentous fungus Aspergillus oryzae with high efficiency when they were cultured or incubated with non-ionic surfactants such as Triton X-100...
March 12, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28300180/systems-level-understanding-of-ethanol-induced-stresses-and-adaptation-in-e-coli
#7
Huansheng Cao, Du Wei, Yuedong Yang, Yu Shang, Gaoyang Li, Yaoqi Zhou, Qin Ma, Ying Xu
Understanding ethanol-induced stresses and responses in biofuel-producing bacteria at systems level has significant implications in engineering more efficient biofuel producers. We present a computational study of transcriptomic and genomic data of both ethanol-stressed and ethanol-adapted E. coli cells with computationally predicated ethanol-binding proteins and experimentally identified ethanol tolerance genes. Our analysis suggests: (1) ethanol damages cell wall and membrane integrity, causing increased stresses, particularly reactive oxygen species, which damages DNA and reduces the O2 level; (2) decreased cross-membrane proton gradient from membrane damage, coupled with hypoxia, leads to reduced ATP production by aerobic respiration, driving cells to rely more on fatty acid oxidation, anaerobic respiration and fermentation for ATP production; (3) the reduced ATP generation results in substantially decreased synthesis of macromolecules; (4) ethanol can directly bind 213 proteins including transcription factors, altering their functions; (5) all these changes together induce multiple stress responses, reduced biosynthesis, cell viability and growth; and (6) ethanol-adapted E...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28295166/engineering-oxidative-stress-defense-pathways-to-build-a-robust-lipid-production-platform-in-yarrowia-lipolytica
#8
Peng Xu, Kangjian Qiao, Gregory Stephanopoulos
Microbially-derived lipids have recently attracted renewed interests due to their broad applications in production of green diesels, cosmetic additives and oleochemicals. Metabolic engineering efforts have targeted a large portfolio of biosynthetic pathways to efficiently convert sugar to lipids in oleaginous yeast. In the engineered overproducing strains, endogenous cell metabolism typically generates harmful electrophilic molecules that compromise cell fitness and productivity. Lipids, particularly unsaturated fatty acids, are highly susceptible to oxygen radical attack and the resulting oxidative species are detrimental to cell metabolism and limit lipid productivity...
March 14, 2017: Biotechnology and Bioengineering
https://www.readbyqxmd.com/read/28294227/raman-spectroscopy-compatible-pdms-droplet-microfluidic-culture-and-analysis-platform-towards-on-chip-lipidomics
#9
Hyun Soo Kim, Sergio C Waqued, Dawson T Nodurft, Timothy P Devarenne, Vladislav V Yakovlev, Arum Han
Lipids produced by microalgae are viewed as a potential renewable alternative to fossil fuels, however, significant improvements in productivity are required for microalgal biofuels to become economically feasible. Here we present a method that allows for the use of Raman spectroscopy with poly(dimethylsiloxane) (PDMS) droplet microfluidic devices, which not only overcomes the high Raman background of PDMS, but also achieves pairing of the high-throughput single-cell resolution advantages of droplet microfluidics with the direct, chemically specific, label-free, and non-destructive nature of Raman spectroscopy...
March 15, 2017: Analyst
https://www.readbyqxmd.com/read/28293290/nitrogen-starvation-induced-cellular-crosstalk-of-ros-scavenging-antioxidants-and-phytohormone-enhanced-the-biofuel-potential-of-green-microalga-acutodesmus-dimorphus
#10
Kaumeel Chokshi, Imran Pancha, Arup Ghosh, Sandhya Mishra
BACKGROUND: Microalgae accumulate a considerable amount of lipids and carbohydrate under nutrient-deficient conditions, which makes them one of the promising sustainable resources for biofuel production. In the present study, to obtain the biomass with higher lipid and carbohydrate contents, we implemented a short-term nitrogen starvation of 1, 2, and 3 days in a green microalga Acutodesmus dimorphus. Few recent reports suggest that oxidative stress-tolerant microalgae are highly efficient for biofuel production...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28292659/reassessing-escherichia-coli-as-a-cell-factory-for-biofuel-production
#11
REVIEW
Chonglong Wang, Brian F Pfleger, Seon-Won Kim
Via metabolic engineering, industrial microorganisms have the potential to convert renewable substrates into a wide range of biofuels that can address energy security and environmental challenges associated with current fossil fuels. The user-friendly bacterium, Escherichia coli, remains one of the most frequently used hosts for demonstrating production of biofuel candidates including alcohol-, fatty acid- and terpenoid-based biofuels. In this review, we summarize the metabolic pathways for synthesis of these biofuels and assess enabling technologies that assist in regulating biofuel synthesis pathways and rapidly assembling novel E...
March 11, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28286551/systems-analysis-of-ethanol-production-in-the-genetically-engineered-cyanobacterium-synechococcus-sp-pcc-7002
#12
Joachim Kopka, Stefanie Schmidt, Frederik Dethloff, Nadin Pade, Susanne Berendt, Marco Schottkowski, Nico Martin, Ulf Dühring, Ekaterina Kuchmina, Heike Enke, Dan Kramer, Annegret Wilde, Martin Hagemann, Alexandra Friedrich
BACKGROUND: Future sustainable energy production can be achieved using mass cultures of photoautotrophic microorganisms, which are engineered to synthesize valuable products directly from CO2 and sunlight. As cyanobacteria can be cultivated in large scale on non-arable land, these phototrophic bacteria have become attractive organisms for production of biofuels. Synechococcus sp. PCC 7002, one of the cyanobacterial model organisms, provides many attractive properties for biofuel production such as tolerance of seawater and high light intensities...
2017: Biotechnology for Biofuels
https://www.readbyqxmd.com/read/28281670/visualising-recalcitrance-by-colocalisation-of-cellulase-lignin-and-cellulose-in-pretreated-pine-biomass-using-fluorescence-microscopy
#13
Lloyd Donaldson, Alankar Vaidya
Mapping the location of bound cellulase enzymes provides information on the micro-scale distribution of amenable and recalcitrant sites in pretreated woody biomass for biofuel applications. The interaction of a fluorescently labelled cellulase enzyme cocktail with steam-exploded pine (SEW) was quantified using confocal microscopy. The spatial distribution of Dylight labelled cellulase was quantified relative to lignin (autofluorescence) and cellulose (Congo red staining) by measuring their colocalisation using Pearson correlations...
March 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28280815/lyotropic-liquid-crystal-engineering-moving-beyond-binary-compositional-space-ordered-nanostructured-amphiphile-self-assembly-materials-by-design
#14
REVIEW
Leonie van 't Hag, Sally L Gras, Charlotte E Conn, Calum J Drummond
Ordered amphiphile self-assembly materials with a tunable three-dimensional (3D) nanostructure are of fundamental interest, and crucial for progressing several biological and biomedical applications, including in meso membrane protein crystallization, as drug and medical contrast agent delivery vehicles, and as biosensors and biofuel cells. In binary systems consisting of an amphiphile and a solvent, the ability to tune the 3D cubic phase nanostructure, lipid bilayer properties and the lipid mesophase is limited...
March 10, 2017: Chemical Society Reviews
https://www.readbyqxmd.com/read/28273953/plasticity-elasticity-and-adhesion-energy-of-plant-cell-walls-nanometrology-of-lignin-loss-using-atomic-force-microscopy
#15
R H Farahi, A M Charrier, A Tolbert, A L Lereu, A Ragauskas, B H Davison, A Passian
The complex organic polymer, lignin, abundant in plants, prevents the efficient extraction of sugars from the cell walls that is required for large scale biofuel production. Because lignin removal is crucial in overcoming this challenge, the question of how the nanoscale properties of the plant cell ultrastructure correlate with delignification processes is important. Here, we report how distinct molecular domains can be identified and how physical quantities of adhesion energy, elasticity, and plasticity undergo changes, and whether such quantitative observations can be used to characterize delignification...
December 2017: Scientific Reports
https://www.readbyqxmd.com/read/28273364/a-multidomain-enzyme-with-glycerol-3-phosphate-dehydrogenase-and-phosphatase-activities-is-involved-in-a-chloroplastic-pathway-for-glycerol-synthesis-in-chlamydomonas-reinhardtii
#16
Daniela Morales-Sánchez, Yeongho Kim, Ee Leng Terng, Laura Peterson, Heriberto Cerutti
Understanding the unique features of algal metabolism may be necessary to realize the full potential of algae as feedstock for the production of biofuels and biomaterials. Under nitrogen deprivation, the green alga C. reinhardtii showed substantial triacylglycerol (TAG) accumulation and up-regulation of a gene, GPD2, encoding a multidomain enzyme with a putative phosphoserine phosphatase (PSP) motif fused to glycerol-3-phosphate dehydrogenase (GPD) domains. Canonical GPD enzymes catalyze the synthesis of glycerol-3-phosphate (G3P) by reduction of dihydroxyacetone phosphate (DHAP)...
March 8, 2017: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/28267957/germline-development-and-fertilization-mechanisms-in-maize
#17
REVIEW
Liang-Zi Zhou, Martina Juranić, Thomas Dresselhaus
Maize is the most important agricultural crop used for food, feed, and biofuel as well as a raw material for industrial products such as packaging material. To increase yield and to overcome hybridization barriers, studies of maize gamete development, the pollen tube journey, and fertilization mechanisms were initiated more than a century ago. In this review, we summarize and discuss our current understanding of the regulatory components for germline development including sporogenesis and gametogenesis, the progamic phase of pollen germination and pollen tube growth and guidance, as well as fertilization mechanisms consisting of pollen tube arrival and reception, sperm cell release, fusion with the female gametes, and egg cell activation...
March 6, 2017: Molecular Plant
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
#18
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/28259016/self-assembly-of-an-electronically-conductive-network-through-microporous-scaffolds
#19
H Bri Sebastian, Steven L Bryant
Electron transfer spanning significant distances through a microporous structure was established via the self-assembly of an electronically conductive iridium oxide nanowire matrix enveloping the pore walls. Microporous formations were simulated using two scaffold materials of varying physical and chemical properties; paraffin wax beads, and agar gel. Following infiltration into the micropores, iridium nanoparticles self-assembled at the pore wall/ethanol interface. Subsequently, cyclic voltammetry was employed to electrochemically crosslink the metal, erecting an interconnected, and electronically conductive metal oxide nanowire matrix...
February 21, 2017: Journal of Colloid and Interface Science
https://www.readbyqxmd.com/read/28257170/downregulation-of-rwa-genes-in-hybrid-aspen-affects-xylan-acetylation-and-wood-saccharification
#20
Prashant Mohan-Anupama Pawar, Christine Ratke, Vimal K Balasubramanian, Sun-Li Chong, Madhavi Latha Gandla, Mathilda Adriasola, Tobias Sparrman, Mattias Hedenström, Klaudia Szwaj, Marta Derba-Maceluch, Cyril Gaertner, Gregory Mouille, Ines Ezcurra, Maija Tenkanen, Leif J Jönsson, Ewa J Mellerowicz
High acetylation of angiosperm wood hinders its conversion to sugars by glycoside hydrolases, subsequent ethanol fermentation and (hence) its use for biofuel production. We studied the REDUCED WALL ACETYLATION (RWA) gene family of the hardwood model Populus to evaluate its potential for improving saccharification. The family has two clades, AB and CD, containing two genes each. All four genes are expressed in developing wood but only RWA-A and -B are activated by master switches of the secondary cell wall PtNST1 and PtMYB21...
March 3, 2017: New Phytologist
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