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Sample records for evolved xylose transporter

  1. Directed evolution of xylose specific transporters to facilitate glucose-xylose co-utilization.

    Science.gov (United States)

    Wang, Meng; Yu, Chenzhao; Zhao, Huimin

    2016-03-01

    A highly active xylose specific transporter without glucose inhibition is highly desirable in cost-effective production of biofuels from lignocellulosic biomass. However, currently available xylose specific transporters suffer from low overall activity and most are inhibited by glucose. In this study, we applied a directed evolution strategy to engineer the xylose specific transporter AN25 from Neurospora crassa with improved xylose transportation capacity. After four rounds of directed evolution using two different strategies, we obtained an AN25 mutant AN25-R4.18 with 43-fold improvement in terms of xylose transportation capacity while maintaining its high xylose specificity. In addition, glucose inhibition was almost completely eliminated in the final evolved mutant. We demonstrated that improved xylose transportation of AN25 mutants in the exponential growth phase led to significant improvement of xylose consumption in high cell-density fermentation. Finally, we showed that AN25 mutant AN25-R4.18 can enable relatively efficient glucose-xylose co-utilization in high concentrations of mixed sugars. © 2015 Wiley Periodicals, Inc.

  2. Fermentation performance of engineered and evolved xylose-fermenting Saccharomyces cerevisiae strains

    DEFF Research Database (Denmark)

    Sonderegger, M.; Jeppsson, M.; Larsson, C.

    2004-01-01

    in the hydrolysate. A particular biological problem are the pentoses, which are not naturally metabolized by the main industrial ethanol producer Saccharomyces cerevisiae. Several recombinant, mutated, and evolved xylose fermenting S. cerevisiae strains have been developed recently. We compare here the fermentation...... performance and robustness of eight recombinant strains and two evolved populations on glucose/xylose mixtures in defined and lignocellulose hydrolysate-containing medium. Generally, the polyploid industrial strains depleted xylose faster and were more resistant to the hydrolysate than the laboratory strains...

  3. Transport of D-xylose in Lactobacillus pentosus, Lactobacillus casei, and Lactobacillus plantarum: Evidence for a mechanism of facilitated diffusion via the phosphoenolpyruvate:mannose phosphotransferase system

    NARCIS (Netherlands)

    Chaillou, S.; Pouwels, P.H.; Postma, P.W.

    1999-01-01

    We have identified and characterized the D-xylose transport system of Lactobacillus pentosus. Uptake of D-xylose was not driven by the proton motive force generated by malolactic fermentation and required D-xylose metabolism. The kinetics of D-xylose transport were indicative of a low- affinity

  4. Simultaneous fermentation of glucose and xylose at elevated temperatures co-produces ethanol and xylitol through overexpression of a xylose-specific transporter in engineered Kluyveromyces marxianus.

    Science.gov (United States)

    Zhang, Biao; Zhang, Jia; Wang, Dongmei; Han, Ruixiang; Ding, Rui; Gao, Xiaolian; Sun, Lianhong; Hong, Jiong

    2016-09-01

    Engineered Kluyveromyces marxianus strains were constructed through over-expression of various transporters for simultaneous co-fermentation of glucose and xylose. The glucose was converted into ethanol, whereas xylose was converted into xylitol which has higher value than ethanol. Over-expressing xylose-specific transporter ScGAL2-N376F mutant enabled yeast to co-ferment glucose and xylose and the co-fermentation ability was obviously improved through increasing ScGAL2-N376F expression. The production of glycerol was blocked and acetate production was reduced by disrupting gene KmGPD1. The obtained K. marxianus YZJ119 utilized 120g/L glucose and 60g/L xylose simultaneously and produced 50.10g/L ethanol and 55.88g/L xylitol at 42°C. The yield of xylitol from consumed xylose was over 98% (0.99g/g). Through simultaneous saccharification and co-fermentation at 42°C, YZJ119 produced a maximal concentration of 44.58g/L ethanol and 32.03g/L xylitol or 29.82g/L ethanol and 31.72g/L xylitol, respectively, from detoxified or non-detoxified diluted acid pretreated corncob. Copyright © 2016 Elsevier Ltd. All rights reserved.

  5. Bioprospecting and evolving alternative xylose and arabinose pathway enzymes for use in Saccharomyces cerevisiae.

    Science.gov (United States)

    Lee, Sun-Mi; Jellison, Taylor; Alper, Hal S

    2016-03-01

    Bioprospecting is an effective way to find novel enzymes from strains with desirable phenotypes. Such bioprospecting has enabled organisms such as Saccharomyces cerevisiae to utilize nonnative pentose sugars. Yet, the efficiency of this pentose catabolism (especially for the case of arabinose) remains suboptimal. Thus, further pathway optimization or identification of novel, optimal pathways is needed. Previously, we identified a novel set of xylan catabolic pathway enzymes from a superior pentose-utilizing strain of Ustilago bevomyces. These enzymes were used to successfully engineer a xylan-utilizing S. cerevisiae through a blended approach of bioprospecting and evolutionary engineering. Here, we expanded this approach to xylose and arabinose catabolic pathway engineering and demonstrated that bioprospected xylose and arabinose catabolic pathways from U. bevomyces offer alternative choices for enabling efficient pentose catabolism in S. cerevisiae. By introducing a novel set of xylose catabolic genes from U. bevomyces, growth rates were improved up to 85 % over a set of traditional Scheffersomyces stipitis pathway genes. In addition, we suggested an alternative arabinose catabolic pathway which, after directed evolution and pathway engineering, enabled S. cerevisiae to grow on arabinose as a sole carbon source in minimal medium with growth rates upwards of 0.05 h(-1). This pathway represents the most efficient growth of yeast on pure arabinose minimal medium. These pathways provide great starting points for further strain development and demonstrate the utility of bioprospecting from U. bevomyces.

  6. Stimulating effects of sorbitol and L-xylose on rat ileal Ca transport in vitro.

    Science.gov (United States)

    Lacour, B; Ohan, J; Aznag, A; Drüeke, T B

    1995-01-01

    The direct effect of sorbitol and L-xylose on net intestinal calcium transport was compared to that of lactose, by determining unidirectional steady state calcium fluxes in segments of rat ileum in vitro under short-circuited conditions. The iso-molar addition of either 100 mM sorbitol, L-xylose, or lactose in mucosal buffer fluid increased the absorptive flux of Ca from mucosa to serosa to a similar extent and thus reversed ileal net Ca transport from net secretion to a zero net movement. The three substances decreased tissue conductance and reversed tissue polarity. At 200 mM, sorbitol induced a stimulation of net Ca transport due to an enhancement of absorptive Ca flux but in addition due to a decrease of secretory Ca flux from serosa to mucosa. The presence of 1 mM N-ethylmaleimide abolished the effects of sorbitol on ileal Ca flux. In conclusion, the present result shows that sorbitol, L-xylose, and lactose increase net Ca absorption to a comparable extent, in the absence of electrochemical or osmotic gradients. Such an absence of specificity suggests a stimulation of transcellular Ca transport related to the decrease of Na concentration in mucosal solution.

  7. Analysis of metabolisms and transports of xylitol using xylose- and xylitol-assimilating Saccharomyces cerevisiae.

    Science.gov (United States)

    Tani, Tatsunori; Taguchi, Hisataka; Akamatsu, Takashi

    2017-05-01

    To clarify the relationship between NAD(P) + /NAD(P)H redox balances and the metabolisms of xylose or xylitol as carbon sources, we analyzed aerobic and anaerobic batch cultures of recombinant Saccharomyces cerevisiae in a complex medium containing 20 g/L xylose or 20 g/L xylitol at pH 5.0 and 30°C. The TDH3p-GAL2 or gal80Δ strain completely consumed the xylose within 24 h and aerobically consumed 92-100% of the xylitol within 96 h, but anaerobically consumed only 20% of the xylitol within 96 h. Cells of both strains grew well in aerobic culture. The addition of acetaldehyde (an effective oxidizer of NADH) increased the xylitol consumption by the anaerobically cultured strain. These results indicate that in anaerobic culture, NAD + generated in the NAD(P)H-dependent xylose reductase reaction was likely needed in the NAD + -dependent xylitol dehydrogenase reaction, whereas in aerobic culture, the NAD + generated by oxidation of NADH in the mitochondria is required in the xylitol dehydrogenase reaction. The role of Gal2 and Fps1 in importing xylitol into the cytosol and exporting it from the cells was analyzed by examining the xylitol consumption in aerobic culture and the export of xylitol metabolized from xylose in anaerobic culture, respectively. The xylitol consumptions of gal80Δ gal2Δ and gal80Δ gal2Δ fps1Δ strains were reduced by 81% and 88% respectively, relative to the gal80Δ strain. The maximum xylitol concentration accumulated by the gal80Δ, gal80Δ gal2Δ, and gal80Δ gal2Δ fps1Δ strains was 7.25 g/L, 5.30 g/L, and 4.27 g/L respectively, indicating that Gal2 and Fps1 transport xylitol both inward and outward. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  8. Improved xylose uptake in Saccharomyces cerevisiae due to directed evolution of galactose permease Gal2 for sugar co-consumption.

    Science.gov (United States)

    Reznicek, O; Facey, S J; de Waal, P P; Teunissen, A W R H; de Bont, J A M; Nijland, J G; Driessen, A J M; Hauer, B

    2015-07-01

    Saccharomyces cerevisiae does not express any xylose-specific transporters. To enhance the xylose uptake of S. cerevisiae, directed evolution of the Gal2 transporter was performed. Three rounds of error-prone PCR were used to generate mutants with improved xylose-transport characteristics. After developing a fast and reliable high-throughput screening assay based on flow cytometry, eight mutants were obtained showing an improved uptake of xylose compared to wild-type Gal2 out of 41 200 single yeast cells. Gal2 variant 2·1 harbouring five amino acid substitutions showed an increased affinity towards xylose with a faster overall sugar metabolism of glucose and xylose. Another Gal2 variant 3·1 carrying an additional amino acid substitution revealed an impaired growth on glucose but not on xylose. Random mutagenesis of the S. cerevisiae Gal2 led to an increased xylose uptake capacity and decreased glucose affinity, allowing improved co-consumption. Random mutagenesis is a powerful tool to evolve sugar transporters like Gal2 towards co-consumption of new substrates. Using a high-throughput screening system based on flow-through cytometry, various mutants were identified with improved xylose-transport characteristics. The Gal2 variants in this work are a promising starting point for further engineering to improve xylose uptake from mixed sugars in biomass. © 2015 The Society for Applied Microbiology.

  9. Improved xylose and arabinose utilization by an industrial recombinant Saccharomyces cerevisiae strain using evolutionary engineering

    DEFF Research Database (Denmark)

    Sanchez, R.G.; Karhumaa, Kaisa; Fonseca, C.

    2010-01-01

    Background: Cost-effective fermentation of lignocellulosic hydrolysate to ethanol by Saccharomyces cerevisiae requires efficient mixed sugar utilization. Notably, the rate and yield of xylose and arabinose co-fermentation to ethanol must be enhanced. Results: Evolutionary engineering was used...... to improve the simultaneous conversion of xylose and arabinose to ethanol in a recombinant industrial Saccharomyces cerevisiae strain carrying the heterologous genes for xylose and arabinose utilization pathways integrated in the genome. The evolved strain TMB3130 displayed an increased consumption rate...... prolonged continuous culture in xylose and arabinose medium resulted in the improved transport of xylose and arabinose as well as increased levels of the enzymes from the introduced fungal xylose pathway. No mutation was found in any of the genes from the pentose converting pathways. Conclusion: To the best...

  10. Engineering of an endogenous hexose transporter into a specific D-xylose transporter facilitates glucose-xylose co-consumption in Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Nijland, Jeroen G.; Shin, Hyun Yong; de Jong, Rene M.; De Waal, Paul P.; Klaassen, Paul; Driessen, Arnold J. M.

    2014-01-01

    Background: Engineering of Saccharomyces cerevisiae for the simultaneous utilization of hexose and pentose sugars is vital for cost-efficient cellulosic bioethanol production. This yeast lacks specific pentose transporters and depends on endogenous hexose transporters for low affinity pentose

  11. Novel transporters from Kluyveromyces marxianus and Pichia guilliermondii expressed in Saccharomyces cerevisiae enable growth on L-arabinose and D-xylose.

    Science.gov (United States)

    Knoshaug, Eric P; Vidgren, Virve; Magalhães, Frederico; Jarvis, Eric E; Franden, Mary Ann; Zhang, Min; Singh, Arjun

    2015-10-01

    Genes encoding L-arabinose transporters in Kluyveromyces marxianus and Pichia guilliermondii were identified by functional complementation of Saccharomyces cerevisiae whose growth on L-arabinose was dependent on a functioning L-arabinose transporter, or by screening a differential display library, respectively. These transporters also transport D-xylose and were designated KmAXT1 (arabinose-xylose transporter) and PgAXT1, respectively. Transport assays using L-arabinose showed that KmAxt1p has K(m) 263 mM and V(max) 57 nM/mg/min, and PgAxt1p has K(m) 0.13 mM and V(max) 18 nM/mg/min. Glucose, galactose and xylose significantly inhibit L-arabinose transport by both transporters. Transport assays using D-xylose showed that KmAxt1p has K(m) 27 mM and V(max) 3.8 nM/mg/min, and PgAxt1p has K(m) 65 mM and V(max) 8.7 nM/mg/min. Neither transporter is capable of recovering growth on glucose or galactose in a S. cerevisiae strain deleted for hexose and galactose transporters. Transport kinetics of S. cerevisiae Gal2p showed K(m) 371 mM and V(max) 341 nM/mg/min for L-arabinose, and K(m) 25 mM and V(max) 76 nM/mg/min for galactose. Due to the ability of Gal2p and these two newly characterized transporters to transport both L-arabinose and D-xylose, one scenario for the complete usage of biomass-derived pentose sugars would require only the low-affinity, high-throughput transporter Gal2p and one additional high-affinity general pentose transporter, rather than dedicated D-xylose or L-arabinose transporters. Additionally, alignment of these transporters with other characterized pentose transporters provides potential targets for substrate recognition engineering. Copyright © 2015 John Wiley & Sons, Ltd.

  12. In-Space Transportation for NASA's Evolvable Mars Campaign

    Science.gov (United States)

    Percy, Thomas K.; McGuire, Melissa; Polsgrove, Tara

    2015-01-01

    As the nation embarks on a new and bold journey to Mars, significant work is being done to determine what that mission and those architectural elements will look like. The Evolvable Mars Campaign, or EMC, is being evaluated as a potential approach to getting humans to Mars. Built on the premise of leveraging current technology investments and maximizing element commonality to reduce cost and development schedule, the EMC transportation architecture is focused on developing the elements required to move crew and equipment to Mars as efficiently and effectively as possible both from a performance and a programmatic standpoint. Over the last 18 months the team has been evaluating potential options for those transportation elements. One of the key aspects of the EMC is leveraging investments being made today in missions like the Asteroid Redirect Mission (ARM) mission using derived versions of the Solar Electric Propulsion (SEP) propulsion systems and coupling them with other chemical propulsion elements that maximize commonality across the architecture between both transportation and Mars operations elements. This paper outlines the broad trade space being evaluated including the different technologies being assessed for transportation elements and how those elements are assembled into an architecture. Impacts to potential operational scenarios at Mars are also investigated. Trades are being made on the size and power level of the SEP vehicle for delivering cargo as well as the size of the chemical propulsion systems and various mission aspects including Inspace assembly and sequencing. Maximizing payload delivery to Mars with the SEP vehicle will better support the operational scenarios at Mars by enabling the delivery of landers and habitation elements that are appropriately sized for the mission. The purpose of this investigation is not to find the solution but rather a suite of solutions with potential application to the challenge of sending cargo and crew to Mars

  13. EVOLVE

    CERN Document Server

    Deutz, André; Schütze, Oliver; Legrand, Pierrick; Tantar, Emilia; Tantar, Alexandru-Adrian

    2017-01-01

    This book comprises nine selected works on numerical and computational methods for solving multiobjective optimization, game theory, and machine learning problems. It provides extended versions of selected papers from various fields of science such as computer science, mathematics and engineering that were presented at EVOLVE 2013 held in July 2013 at Leiden University in the Netherlands. The internationally peer-reviewed papers include original work on important topics in both theory and applications, such as the role of diversity in optimization, statistical approaches to combinatorial optimization, computational game theory, and cell mapping techniques for numerical landscape exploration. Applications focus on aspects including robustness, handling multiple objectives, and complex search spaces in engineering design and computational biology.

  14. D-xylose absorption

    Science.gov (United States)

    ... this page: //medlineplus.gov/ency/article/003606.htm D-xylose absorption To use the sharing features on this page, please enable JavaScript. D-xylose absorption is a laboratory test to determine ...

  15. Improved Xylose Metabolism by a CYC8 Mutant of Saccharomyces cerevisiae.

    Science.gov (United States)

    Nijland, Jeroen G; Shin, Hyun Yong; Boender, Leonie G M; de Waal, Paul P; Klaassen, Paul; Driessen, Arnold J M

    2017-06-01

    Engineering Saccharomyces cerevisiae for the utilization of pentose sugars is an important goal for the production of second-generation bioethanol and biochemicals. However, S. cerevisiae lacks specific pentose transporters, and in the presence of glucose, pentoses enter the cell inefficiently via endogenous hexose transporters (HXTs). By means of in vivo engineering, we have developed a quadruple hexokinase deletion mutant of S. cerevisiae that evolved into a strain that efficiently utilizes d-xylose in the presence of high d-glucose concentrations. A genome sequence analysis revealed a mutation (Y353C) in the general corepressor CYC8, or SSN6, which was found to be responsible for the phenotype when introduced individually in the nonevolved strain. A transcriptome analysis revealed altered expression of 95 genes in total, including genes involved in (i) hexose transport, (ii) maltose metabolism, (iii) cell wall function (mannoprotein family), and (iv) unknown functions (seripauperin multigene family). Of the 18 known HXTs, genes for 9 were upregulated, especially the low or nonexpressed HXT10, HXT13, HXT15, and HXT16 Mutant cells showed increased uptake rates of d-xylose in the presence of d-glucose, as well as elevated maximum rates of metabolism (Vmax) for both d-glucose and d-xylose transport. The data suggest that the increased expression of multiple hexose transporters renders d-xylose metabolism less sensitive to d-glucose inhibition due to an elevated transport rate of d-xylose into the cell.IMPORTANCE The yeast Saccharomyces cerevisiae is used for second-generation bioethanol formation. However, growth on xylose is limited by pentose transport through the endogenous hexose transporters (HXTs), as uptake is outcompeted by the preferred substrate, glucose. Mutant strains were obtained with improved growth characteristics on xylose in the presence of glucose, and the mutations mapped to the regulator Cyc8. The inactivation of Cyc8 caused increased expression

  16. Heterologous xylose isomerase pathway and evolutionary engineering improve xylose utilization in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Xin eQi

    2015-10-01

    Full Text Available Xylose utilization is one key issue for the bioconversion of lignocelluloses. It is promising approach to engineer heterologous pathway for xylose utilization in Saccharomyces cerevisiae. Here, we constructed xylose-fermenting yeast SyBE001 by combinatorial fine-tuning the expression of XylA and endogenous XKS1. Overexpression of genes RKI1, RPE1, TKL1 and TAL1 in the non-oxidative pentose phosphate pathway in SyBE002 accelerated xylose utilization by 19%. By repetitive adaptation, the xylose utilization rate increased to about 10 folds in strain SyBE003 evolved from SyBE002. Gene expression analysis identified variety of genes with significantly different expressions in pentose phosphate pathway, glycolysis and tricarboxylic acid cycle in SyBE003.

  17. Alcoholic fermentation of xylose and mixed sugars using recombinant Saccharomyces cerevisiae engineered for xylose utilization.

    Science.gov (United States)

    Madhavan, Anjali; Tamalampudi, Sriappareddy; Srivastava, Aradhana; Fukuda, Hideki; Bisaria, Virendra S; Kondo, Akihiko

    2009-04-01

    Previously, a Saccharomyces cerevisiae strain was engineered for xylose assimilation by the constitutive overexpression of the Orpinomyces xylose isomerase, the S. cerevisiae xylulokinase, and the Pichia stipitis SUT1 sugar transporter genes. The recombinant strain exhibited growth on xylose, under aerobic conditions, with a specific growth rate of 0.025 h(-1), while ethanol production from xylose was achieved anaerobically. In the present study, the developed recombinant yeast was adapted for enhanced growth on xylose by serial transfer in xylose-containing minimal medium under aerobic conditions. After repeated batch cultivations, a strain was isolated which grew with a specific growth rate of 0.133 h(-1). The adapted strain could ferment 20 g l(-1) of xylose to ethanol with a yield of 0.37 g g(-1) and production rate of 0.026 g l(-1) h(-1). Raising the fermentation temperature from 30 degrees C to 35 degrees C resulted in a substantial increase in the ethanol yield (0.43 g g(-1)) and production rate (0.07 g l(-1) h(-1)) as well as a significant reduction in the xylitol yield. By the addition of a sugar complexing agent, such as sodium tetraborate, significant improvement in ethanol production and reduction in xylitol accumulation was achieved. Furthermore, ethanol production from xylose and a mixture of glucose and xylose was also demonstrated in complex medium containing yeast extract, peptone, and borate with a considerably high yield of 0.48 g g(-1).

  18. Xylose-induced dynamic effects on metabolism and gene expression in engineered Saccharomyces cerevisiae in anaerobic glucose-xylose cultures.

    Science.gov (United States)

    Alff-Tuomala, Susanne; Salusjärvi, Laura; Barth, Dorothee; Oja, Merja; Penttilä, Merja; Pitkänen, Juha-Pekka; Ruohonen, Laura; Jouhten, Paula

    2016-01-01

    Xylose is present with glucose in lignocellulosic streams available for valorisation to biochemicals. Saccharomyces cerevisiae has excellent characteristics as a host for the bioconversion, except that it strongly prefers glucose to xylose, and the co-consumption remains a challenge. Further, since xylose is not a natural substrate of S. cerevisiae, the regulatory response it induces in an engineered strain cannot be expected to have evolved for its utilisation. Xylose-induced effects on metabolism and gene expression during anaerobic growth of an engineered strain of S. cerevisiae on medium containing both glucose and xylose medium were quantified. The gene expression of S. cerevisiae with an XR-XDH pathway for xylose utilisation was analysed throughout the cultivation: at early cultivation times when mainly glucose was metabolised, at times when xylose was co-consumed in the presence of low glucose concentrations, and when glucose had been depleted and only xylose was being consumed. Cultivations on glucose as a sole carbon source were used as a control. Genome-scale dynamic flux balance analysis models were simulated to analyse the metabolic dynamics of S. cerevisiae. The simulations quantitatively estimated xylose-dependent flux dynamics and challenged the utilisation of the metabolic network. A relative increase in xylose utilisation was predicted to induce the bi-directionality of glycolytic flux and a redox challenge even at low glucose concentrations. Remarkably, xylose was observed to specifically delay the glucose-dependent repression of particular genes in mixed glucose-xylose cultures compared to glucose cultures. The delay occurred at a cultivation time when the metabolic flux activities were similar in the both cultures.

  19. Improved xylose uptake in Saccharomyces cerevisiae due to directed evolution of galactose permease Gal2 for sugar co-consumption

    NARCIS (Netherlands)

    Reznicek, Ondrej; Facey, Sandra J; de Waal, Paul P; Teunissen, Aloys W R H; de Bont, Jan A M; Nijland, J.G.; Driessen, A.J.M.; Hauer, Bernhard

    2015-01-01

    AIMS: S. cerevisiae does not express any xylose-specific transporters. To enhance the xylose uptake of S. cerevisiae, directed evolution of the Gal2 transporter was performed. METHODS AND RESULTS: Three rounds of error-prone PCR were used to generate mutants with improved xylose transport

  20. Xylose fermentation to ethanol

    Energy Technology Data Exchange (ETDEWEB)

    McMillan, J.D.

    1993-01-01

    The past several years have seen tremendous progress in the understanding of xylose metabolism and in the identification, characterization, and development of strains with improved xylose fermentation characteristics. A survey of the numerous microorganisms capable of directly fermenting xylose to ethanol indicates that wild-type yeast and recombinant bacteria offer the best overall performance in terms of high yield, final ethanol concentration, and volumetric productivity. The best performing bacteria, yeast, and fungi can achieve yields greater than 0.4 g/g and final ethanol concentrations approaching 5%. Productivities remain low for most yeast and particularly for fungi, but volumetric productivities exceeding 1.0 g/L-h have been reported for xylose-fermenting bacteria. In terms of wild-type microorganisms, strains of the yeast Pichia stipitis show the most promise in the short term for direct high-yield fermentation of xylose without byproduct formation. Of the recombinant xylose-fermenting microorganisms developed, recombinant E. coli ATTC 11303 (pLOI297) exhibits the most favorable performance characteristics reported to date.

  1. Ethanol production by recombinant and natural xylose-utilising yeasts

    Energy Technology Data Exchange (ETDEWEB)

    Eliasson, Anna

    2000-07-01

    from P. stipitis and the endogenous XKS1 gene under control of the PGKI promoter, into the HIS3 locus of S. cerevisiae CEN.PK 113-7A. The strain was stable for more than forty generations in continuous fermentation. The metabolic fluxes during xylose metabolism were quantitatively analysed and anaerobic ethanol formation from xylose in recombinant S. cerevisiae was demonstrated for the first time. The xylose uptake rate increased with increasing xylose concentration in the feed. However, with a feed of 15 g/l xylose and 5 g/l glucose, the xylose flux was 2.2 times lower than the glucose flux, indicating that transport limits the xylose flux. The role of mitochondria in ethanol formation from xylose was investigated using cells of recombinant xylose-utilising S. cerevisiae with two different respiratory capacities and cells from P. stipitis grown under conditions of optimal ethanol formation. Different inhibitors were used either to inhibit the electron transport chain and simulate oxygen limitation, or to inhibit the tricarboxylic acid cycle while not disturbing the electron transport chain. The response to the inhibitors differed significantly for glucose and xylose and the effect was more pronounced for S. cerevisiae. The results indicate that mitochondria play a significant role in the maintenance of the cytoplasmic redox balance during xylose fermentation, through the action of cytoplasmically directed NADH dehydrogenase activity. Thus, more carbon was directed towards ethanol in chemostat cultivations of xylose/glucose mixtures by S. cerevisiae TMB 3001, in the presence of low amounts of oxygen. P. stipitis possesses a second, cyanide-insensitive terminal oxidase, the alternative oxidase, which seems to be of particular importance for efficient ethanol formation from xylose. The highest activity of cyanide-insensitive respiration (CIR), the highest ethanol productivity and lowest xylitol formation were all observed with cells grown under oxygen-limited conditions

  2. Metabolic engineering of Propionibacterium freudenreichii subsp. shermanii for xylose fermentation.

    Science.gov (United States)

    Wei, Peilian; Lin, Meng; Wang, Zhongqiang; Fu, Hongxin; Yang, Hopen; Jiang, Wenyan; Yang, Shang-Tian

    2016-11-01

    Propionibacterium freudenreichii cannot use xylose, the second most abundant sugar in lignocellulosic biomass. Although Propionibacterium acidipropionici can use xylose as a carbon source, it is difficult to genetically modify, impeding further improvement through metabolic engineering. This study identified three xylose catabolic pathway genes encoding for xylose isomerase (xylA), xylose transporter (xylT), and xylulokinase (xylB) in P. acidipropionici and overexpressed them in P. freudenreichii subsp. shermanii via an expression plasmid pKHEM01, enabling the mutant to utilize xylose efficiently even in the presence of glucose without glucose-induced carbon catabolite repression. The mutant showed similar fermentation kinetics with glucose, xylose, and the mixture of glucose and xylose, respectively, as carbon source, and with or without the addition of antibiotic for selection pressure. The engineered P. shermanii thus can provide a novel cell factory for industrial production of propionic acid and other value-added products from lignocellulosic biomass. Copyright © 2016 Elsevier Ltd. All rights reserved.

  3. Transportation of volatile elements in thermally evolving planetesimals: An important role of metallic iron

    Science.gov (United States)

    Hashizume, K.; Sugiura, N.

    1994-01-01

    Ordinary chondrites are considered to have experienced thermal metamorphism in small bodies. We are interested in behaviors of volatile elements in such a kind of thermally evolving planetesimals. Volatile elements generally have high vapor pressures at high temperature. In porous bodies, with a high gas permeability, volatile elements are transported efficiently over a long range. Behavior of volatile elements transported by permeable gas flow can be handled by an equation whose form is similar to that of the equation of thermal diffusion. We can follow transportation of heats and volatile elements in planetesimals, when parameters in these equations, initial conditions and chemical behavior of volatile elements are given. Recently, we discovered that nitrogen in equilibrated H-chondrites is mainly trapped in taenite (f.c.c. Fe-Ni), probably dissolved in interstitial sites. Fegley suggests that metallic iron cannot trap nitrogen in the solar nebula gas due to its very low nitrogen partial pressure. Approximately 1 bar of nitrogen pressure is required to explain the nitrogen content in taenite. We may expect high nitrogen gas partial pressure (possibly produced by vaporization of nitrogen-bearing solids such as organic materials) at the interior of thermally evolving planetesimals. Kinetic behavior of nitrogen in taenite suggests that it can easily be equilibrated with the ambient nitrogen gas at temperatures of approximately 500 C or higher. We consider that nitrogen is trapped in taenite through a nitrogen redistribution process occurred during the thermal metamorphic event.

  4. Cis-Lunar Reusable In-Space Transportation Architecture for the Evolvable Mars Campaign

    Science.gov (United States)

    McVay, Eric S.; Jones, Christopher A.; Merrill, Raymond G.

    2016-01-01

    Human exploration missions to Mars or other destinations in the solar system require large quantities of propellant to enable the transportation of required elements from Earth's sphere of influence to Mars. Current and proposed launch vehicles are incapable of launching all of the requisite mass on a single vehicle; hence, multiple launches and in-space aggregation are required to perform a Mars mission. This study examines the potential of reusable chemical propulsion stages based in cis-lunar space to meet the transportation objectives of the Evolvable Mars Campaign and identifies cis-lunar propellant supply requirements. These stages could be supplied with fuel and oxidizer delivered to cis-lunar space, either launched from Earth or other inner solar system sources such as the Moon or near Earth asteroids. The effects of uncertainty in the model parameters are evaluated through sensitivity analysis of key parameters including the liquid propellant combination, inert mass fraction of the vehicle, change in velocity margin, and change in payload masses. The outcomes of this research include a description of the transportation elements, the architecture that they enable, and an option for a campaign that meets the objectives of the Evolvable Mars Campaign. This provides a more complete understanding of the propellant requirements, as a function of time, that must be delivered to cis-lunar space. Over the selected sensitivity ranges for the current payload and schedule requirements of the 2016 point of departure of the Evolvable Mars Campaign destination systems, the resulting propellant delivery quantities are between 34 and 61 tonnes per year of hydrogen and oxygen propellant, or between 53 and 76 tonnes per year of methane and oxygen propellant, or between 74 and 92 tonnes per year of hypergolic propellant. These estimates can guide future propellant manufacture and/or delivery architectural analysis.

  5. Multiplex growth rate phenotyping of synthetic mutants in selection to engineer glucose and xylose co-utilization in Escherichia coli.

    Science.gov (United States)

    Groot, Joost; Cepress-Mclean, Sidney C; Robbins-Pianka, Adam; Knight, Rob; Gill, Ryan T

    2017-04-01

    Engineering the simultaneous consumption of glucose and xylose sugars is critical to enable the sustainable production of biofuels from lignocellulosic biomass. In most major industrial microorganisms glucose completely inhibits the uptake of xylose, limiting efficient sugar mixture conversion. In E. coli removal of the major glucose transporter PTS allows for glucose and xylose co-consumption but only after prolonged adaptation, which is an effective process but hard to control and prone to co-evolving undesired traits. Here we synthetically engineer mutants to target sugar co-consumption properties; we subject a PTS- mutant to a short adaptive step and subsequently either delete or overexpress key genes previously suggested to affect sugar consumption. Screening the co-consumption properties of these mutants individually is very laborious. We show we can evaluate sugar co-consumption properties in parallel by culturing the mutants in selection and applying a novel approach that computes mutant growth rates in selection using chromosomal barcode counts obtained from Next-Generation Sequencing. We validate this multiplex growth rate phenotyping approach with individual mutant pure cultures, identify new instances of mutants cross-feeding on metabolic byproducts, and, importantly, find that the rates of glucose and xylose co-consumption can be tuned by altering glucokinase expression in our PTS- background. Biotechnol. Bioeng. 2017;114: 885-893. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  6. An efficient xylose-fermenting recombinant Saccharomyces cerevisiae strain obtained through adaptive evolution and its global transcription profile

    Energy Technology Data Exchange (ETDEWEB)

    Shen, Yu; Chen, Xiao; Peng, Bingyin; Chen, Liyuan; Hou, Jin; Bao, Xiaoming [Shandong Univ., Jinan (China). State Key Lab. of Microbial Technology

    2012-11-15

    Factors related to ethanol production from xylose in engineered Saccharomyces cerevisiae that contain an exogenous initial metabolic pathway are still to be elucidated. In the present study, a strain that expresses the xylose isomerase gene of Piromyces sp. Pi-xylA and overexpresses XKS1, RPE1, RKI1, TAL1, and TKL1, with deleted GRE3 and COX4 genes was constructed. The xylose utilization capacity of the respiratory deficiency strain was poor but improved via adaptive evolution in xylose. The {mu}{sub max} of the evolved strain in 20 gl{sup -1} xylose is 0.11 {+-} 0.00 h{sup -1}, and the evolved strain consumed 17.83 gl{sup -1} xylose within 72 h, with an ethanol yield of 0.43 gg{sup -1} total consumed sugars during glucose-xylose cofermentation. Global transcriptional changes and effect of several specific genes were studied. The result revealed that the increased xylose isomerase activity, the upregulation of enzymes involved in glycolysis and glutamate synthesis, and the downregulation of trehalose and glycogen synthesis, may have contributed to the improved xylose utilization of the strain. Furthermore, the deletion of PHO13 decreased the xylose growth in the respiration deficiency strain although deleting PHO13 can improve the xylose metabolism in other strains. (orig.)

  7. Enhanced production of xylitol from xylose by expression of Bacillus subtilis arabinose:H+ symporter and Scheffersomyces stipitis xylose reductase in recombinant Saccharomyces cerevisiae.

    Science.gov (United States)

    Kim, Hyoju; Lee, Hyun-Soo; Park, Haeseong; Lee, Dae-Hee; Boles, Eckhard; Chung, Donghwa; Park, Yong-Cheol

    2017-12-01

    Inefficient transport of xylose into Saccharomyces cerevisiae is a major hurdle for production of xylitol, a natural sweetener with five carbons. To facilitate the xylose transport and hence increase xylose conversion to xylitol, the araE gene encoding an arabinose:H+ symporter (AraE) from Bacillus subtilis and the XYL1 gene from Scheffersomyces stipitis were expressed in Saccharomyces cerevisiae EBY.VW4000, a hxt null mutant. The resulting strain of EXHA exhibited 4.1 fold increases in xylose consumption rate and xylitol productivity, relative to the control strain without AraE. Also, overexpression of AraE in wild type S. cerevisiae D452-2 having all hexose transporters and the XYL1 gene increased both xylose consumption and xylitol production considerably. In a glucose-limited fed-batch culture with intermittent addition of xylose, the DXXA strain with multiple copies of araE and XYL1 produced 177.8g/L xylitol with 2.47g/L-h productivity, which were 26.9 and 17.6 times higher than those for a batch culture of the DX strain expressing the XYL1 gene only, respectively. It was concluded that B. subtilis AraE might be a potent xylose transporter and conferred much higher xylose-consuming and xylitol-producing abilities to S. cerevisiae. Copyright © 2017 Elsevier Inc. All rights reserved.

  8. Regulation of xylose metabolism in recombinant Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Penttilä Merja

    2008-06-01

    Full Text Available Abstract Background Considerable interest in the bioconversion of lignocellulosic biomass into ethanol has led to metabolic engineering of Saccharomyces cerevisiae for fermentation of xylose. In the present study, the transcriptome and proteome of recombinant, xylose-utilising S. cerevisiae grown in aerobic batch cultures on xylose were compared with those of glucose-grown cells both in glucose repressed and derepressed states. The aim was to study at the genome-wide level how signalling and carbon catabolite repression differ in cells grown on either glucose or xylose. The more detailed knowledge whether xylose is sensed as a fermentable carbon source, capable of catabolite repression like glucose, or is rather recognised as a non-fermentable carbon source is important for further engineering this yeast for more efficient anaerobic fermentation of xylose. Results Genes encoding respiratory proteins, proteins of the tricarboxylic acid and glyoxylate cycles, and gluconeogenesis were only partially repressed by xylose, similar to the genes encoding their transcriptional regulators HAP4, CAT8 and SIP1-2 and 4. Several genes that are repressed via the Snf1p/Mig1p-pathway during growth on glucose had higher expression in the cells grown on xylose than in the glucose repressed cells but lower than in the glucose derepressed cells. The observed expression profiles of the transcription repressor RGT1 and its target genes HXT2-3, encoding hexose transporters suggested that extracellular xylose was sensed by the glucose sensors Rgt2p and Snf3p. Proteome analyses revealed distinct patterns in phosphorylation of hexokinase 2, glucokinase and enolase isoenzymes in the xylose- and glucose-grown cells. Conclusion The results indicate that the metabolism of yeast growing on xylose corresponds neither to that of fully glucose repressed cells nor that of derepressed cells. This may be one of the major reasons for the suboptimal fermentation of xylose by

  9. Xylose fermentation by Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Koetter, P.; Ciriacy, M. (Institut fuer Mikrobiologie, Univ. Duesseldorf (Germany))

    1993-03-01

    We have performed a comparative study of xylose utilization in Saccaromyces cerevisiae transformants expressing two key enzymes in xylose metabolism, xylose reductase (XR) and xylithol dehydrogenase (XDH), and in a prototypic xylose-utilizing yeast, Pichia stipitis. In the absence of respiration (see text), baker's yeast cells convert half of the xylose to xylitol and ethanol, whereas P. stipitis cells display rather a homofermentative conversion of xylose to ethanol. Xylitol production by baker's yeast is interpreted as a result of the dual cofactor dependence of the XR and the generation of NADPH by the pentose phosphate pathway. Further limitations of xylose utilization in S. cerevisiae cells are very likely caused by an insufficient capacity of the non-oxidative pentose phosphate pathway, as indicated by accumulation of sedoheptulose-7-phosphate and the absence of fructose-1,6-bisphosphate and pyruvate accumulation. By contrast, uptake at high substrate concentrations probably does not limit xylose conversion in S. cerevisiae XYL1/XYL2 transformants. (orig.).

  10. Transportation-Driven Mars Surface Operations Supporting an Evolvable Mars Campaign

    Science.gov (United States)

    Toups, Larry; Brown, Kendall; Hoffman, Stephen J.

    2015-01-01

    This paper describes the results of a study evaluating options for supporting a series of human missions to a single Mars surface destination. In this scenario the infrastructure emplaced during previous visits to this site is leveraged in following missions. The goal of this single site approach to Mars surface infrastructure is to enable "Steady State" operations by at least 4 crew for up to 500 sols at this site. These characteristics, along with the transportation system used to deliver crew and equipment to and from Mars, are collectively known as the Evolvable Mars Campaign (EMC). Information in this paper is presented in the sequence in which it was accomplished. First, a logical buildup sequence of surface infrastructure was developed to achieve the desired "Steady State" operations on the Mars surface. This was based on a concept of operations that met objectives of the EMC. Second, infrastructure capabilities were identified to carry out this concept of operations. Third, systems (in the form of conceptual elements) were identified to provide these capabilities. This included top-level mass, power and volume estimates for these elements. Fourth, the results were then used in analyses to evaluate three options (18t, 27t, and 40t landed mass) of Mars Lander delivery capability to the surface. Finally, Mars arrival mass estimates were generated based upon the entry, descent, and landing requirements for inclusion in separate assessments of in-space transportation capabilities for the EMC.

  11. Metabolic engineering and comparative performance studies of Synechocystis sp. PCC 6803 strains for effective utilization of xylose.

    Directory of Open Access Journals (Sweden)

    Saurabh eRanade

    2015-12-01

    Full Text Available Wood sugars such as xylose can be used as an inexpensive carbon source for biotechnological applications. The model cyanobacterium Synechocystis sp. PCC 6803 lacks the ability to catabolize wood sugars as an energy source. Here, we generated four Synechocystis strains that heterologously expressed XylAB enzymes, which mediate xylose catabolism, either in combination with or without one of three xylose transporters, namely XylE, GalP, or Glf. Except for glf, which is derived from the bacterium Zymomonas mobilis ZM4, the heterologous genes were sourced from Escherichia coli K-12. All of the recombinant strains were able to utilize xylose in the absence of catabolite repression. When xylose was the lone source of organic carbon, strains possessing the XylE and Glf transporters were most efficient in terms of dry biomass production and xylose consumption and the strain lacking a heterologous transporter was the least efficient. However, in the presence of a xylose-glucose mixed sugar source, the strains exhibited similar levels of growth and xylose consumption. This study demonstrates that various bacterial xylose transporters can boost xylose catabolism in transgenic Synechocystis strains, and paves the way for the sustainable production of bio-compounds and green fuels from lignocellulosic biomass.

  12. The Amino-Terminal Tail of Hxt11 Confers Membrane Stability to the Hxt2 Sugar Transporter and Improves Xylose Fermentation in the Presence of Acetic Acid

    NARCIS (Netherlands)

    Shin, Hyun Yong; Nijland, Jeroen G.; de Waal, Paul P.; Driessen, Arnold J. M.

    Hxt2 is a glucose repressed, high affinity glucose transporter of the yeast Saccharomyces cerevisiae and is subjected to high glucose induced degradation. Hxt11 is a sugar transporter that is stably expressed at the membrane irrespective the sugar concentration. To transfer this property to Hxt2,

  13. A multi-objective approach to evolving platooning strategies in intelligent transportation systems

    NARCIS (Netherlands)

    Illigen, W. van; Haasdijk, E.; Kester, L.J.H.M.

    2013-01-01

    The research in this paper is inspired by a vision of intelligent vehicles that autonomously move along motorways: they join and leave trains of vehicles (platoons), overtake other vehicles, etc. We propose a multi-objective evolutionary algorithm based on NEAT and SPEA2 that evolves highlevel

  14. Induction of D-xylose uptake and expression of NAD(P)H-linked xylose reductase and NADP + -linked xylitol dehydrogenase in the oleaginous microalga Chlorella sorokiniana.

    Science.gov (United States)

    Zheng, Yubin; Yu, Xiaochen; Li, Tingting; Xiong, Xiaochao; Chen, Shulin

    2014-01-01

    The heterotrophic and mixotrophic culture of oleaginous microalgae is a promising process to produce biofuel feedstock due to the advantage of fast growth. Various organic carbons have been explored for this application. However, despite being one of the most abundant and economical sugar resources in nature, D-xylose has never been demonstrated as a carbon source for wild-type microalgae. The purpose of the present work was to identify the feasibility of D-xylose utilization by the oleaginous microalga Chlorella sorokiniana. The sugar uptake kinetic analysis was performed with (14)C-labeled sugars and the data showed that the D-glucose induced algal cells (the alga was heterotrophically grown on D-glucose and then harvested as D-glucose induced cells) exhibited a remarkably increased D-xylose uptake rate. The maximum D-xylose transport rate was 3.8 nmol min(-1) mg(-1) dry cell weight (DCW) with K m value of 6.8 mM. D-xylose uptake was suppressed in the presence of D-glucose, D-galactose and D-fructose but not L-arabinose and D-ribose. The uptake of D-xylose activated the related metabolic pathway, and the activities of a NAD(P)H-linked xylose reductase (XR) and a unique NADP(+)-linked xylitol dehydrogenase (XDH) were detected in C. sorokiniana. Compared with the culture in the dark, the consumption of D-xylose increased 2 fold under light but decreased to the same level with addition of 3-(3,4-dichlorophenyl)-1,1-dimethylurea (DCMU), indicating that extra chemical energy from the light-dependent reaction contributed the catabolism of D-xylose for C. sorokiniana. An inducible D-xylose transportation system and a related metabolic pathway were discovered for microalga for the first time. The transportation of D-xylose across the cell membrane of C. sorokiniana could be realized by an inducible hexose symporter. The uptake of D-xylose subsequently activated the expression of key catalytic enzymes that enabled D-xylose entering central metabolism. Results of this

  15. Engineered xylose utilization enhances bio-products productivity in the cyanobacterium Synechocystis sp. PCC 6803

    Energy Technology Data Exchange (ETDEWEB)

    Lee, Tai-Chi; Xiong, Wei; Paddock, Troy; Carrieri, Damian; Chang, Ing-Feng; Chiu, Hui-Fen; Ungerer, Justin; Hank Juo, Suh-Hang; Maness, Pin-Ching; Yu, Jianping

    2015-06-12

    Hydrolysis of plant biomass generates a mixture of simple sugars that is particularly rich in glucose and xylose. Fermentation of the released sugars emits CO2 as byproduct due to metabolic inefficiencies. Therefore, the ability of a microbe to simultaneously convert biomass sugars and photosynthetically fix CO2 into target products is very desirable. In this work, the cyanobacterium, Synechocystis 6803, was engineered to grow on xylose in addition to glucose. Both the xylA (xylose isomerase) and xylB (xylulokinase) genes from Escherichia coli were required to confer xylose utilization, but a xylose-specific transporter was not required. Introducing xylAB into an ethylene-producing strain increased the rate of ethylene production in the presence of xylose. Additionally, introduction of xylAB into a glycogen-synthesis mutant enhanced production of keto acids. Moreover, isotopic tracer studies found that nearly half of the carbon in the excreted keto acids was derived from the engineered xylose metabolism, while the remainder was derived from CO2 fixation.

  16. Evolving Transport Networks With Cellular Automata Models Inspired by Slime Mould.

    Science.gov (United States)

    Tsompanas, Michail-Antisthenis I; Sirakoulis, Georgios Ch; Adamatzky, Andrew I

    2015-09-01

    Man-made transport networks and their design are closely related to the shortest path problem and considered amongst the most debated problems of computational intelligence. Apart from using conventional or bio-inspired computer algorithms, many researchers tried to solve this kind of problem using biological computing substrates, gas-discharge solvers, prototypes of a mobile droplet, and hot ice computers. In this aspect, another example of biological computer is the plasmodium of acellular slime mould Physarum polycephalum (P. polycephalum), which is a large single cell visible by an unaided eye and has been proven as a reliable living substrate for implementing biological computing devices for computational geometry, graph-theoretical problems, and optimization and imitation of transport networks. Although P. polycephalum is easy to experiment with, computing devices built with the living slime mould are extremely slow; it takes slime mould days to execute a computation. Consequently, mapping key computing mechanisms of the slime mould onto silicon would allow us to produce efficient bio-inspired computing devices to tackle with hard to solve computational intelligence problems like the aforementioned. Toward this direction, a cellular automaton (CA)-based, Physarum-inspired, network designing model is proposed. This novel CA-based model is inspired by the propagating strategy, the formation of tubular networks, and the computing abilities of the plasmodium of P. polycephalum. The results delivered by the CA model demonstrate a good match with several previously published results of experimental laboratory studies on imitation of man-made transport networks with P. polycephalum. Consequently, the proposed CA model can be used as a virtual, easy-to-access, and biomimicking laboratory emulator that will economize large time periods needed for biological experiments while producing networks almost identical to the tubular networks of the real-slime mould.

  17. Anaerobic xylose fermentation by Spathaspora passalidarum

    DEFF Research Database (Denmark)

    Hou, Xiaoru

    2012-01-01

    A cost-effective conversion of lignocellulosic biomass into bioethanol requires that the xylose released from the hemicellulose fraction (20–40% of biomass) can be fermented. Baker’s yeast, Saccharomyces cerevisiae, efficiently ferments glucose but it lacks the ability to ferment xylose. Xylose-fermenting...... yeast such as Pichia stipitis requires accurately controlled microaerophilic conditions during the xylose fermentation, rendering the process technically difficult and expensive. In this study, it is demonstrated that under anaerobic conditions Spathaspora passalidarum showed high ethanol production...

  18. Characterization of xylose reductase from Candida tropicalis ...

    African Journals Online (AJOL)

    USER

    2010-08-02

    Aug 2, 2010 ... which is found generally in various fruits and vegetables. Xylitol has been highly valued by the ... In xylose-assimilating yeast and fungi, XR catalyzes the reduction of xylose for xylitol at the first step .... activity of the immobilized XR in aqueous medium with standard method already mentioned. Preparation ...

  19. Xylose Fermentation by Saccharomyces cerevisiae: Challenges and Prospects

    Directory of Open Access Journals (Sweden)

    Danuza Nogueira Moysés

    2016-02-01

    Full Text Available Many years have passed since the first genetically modified Saccharomyces cerevisiae strains capable of fermenting xylose were obtained with the promise of an environmentally sustainable solution for the conversion of the abundant lignocellulosic biomass to ethanol. Several challenges emerged from these first experiences, most of them related to solving redox imbalances, discovering new pathways for xylose utilization, modulation of the expression of genes of the non-oxidative pentose phosphate pathway, and reduction of xylitol formation. Strategies on evolutionary engineering were used to improve fermentation kinetics, but the resulting strains were still far from industrial application. Lignocellulosic hydrolysates proved to have different inhibitors derived from lignin and sugar degradation, along with significant amounts of acetic acid, intrinsically related with biomass deconstruction. This, associated with pH, temperature, high ethanol, and other stress fluctuations presented on large scale fermentations led the search for yeasts with more robust backgrounds, like industrial strains, as engineering targets. Some promising yeasts were obtained both from studies of stress tolerance genes and adaptation on hydrolysates. Since fermentation times on mixed-substrate hydrolysates were still not cost-effective, the more selective search for new or engineered sugar transporters for xylose are still the focus of many recent studies. These challenges, as well as under-appreciated process strategies, will be discussed in this review.

  20. Xylose Fermentation by Saccharomyces cerevisiae: Challenges and Prospects

    Science.gov (United States)

    Moysés, Danuza Nogueira; Reis, Viviane Castelo Branco; de Almeida, João Ricardo Moreira; de Moraes, Lidia Maria Pepe; Torres, Fernando Araripe Gonçalves

    2016-01-01

    Many years have passed since the first genetically modified Saccharomyces cerevisiae strains capable of fermenting xylose were obtained with the promise of an environmentally sustainable solution for the conversion of the abundant lignocellulosic biomass to ethanol. Several challenges emerged from these first experiences, most of them related to solving redox imbalances, discovering new pathways for xylose utilization, modulation of the expression of genes of the non-oxidative pentose phosphate pathway, and reduction of xylitol formation. Strategies on evolutionary engineering were used to improve fermentation kinetics, but the resulting strains were still far from industrial application. Lignocellulosic hydrolysates proved to have different inhibitors derived from lignin and sugar degradation, along with significant amounts of acetic acid, intrinsically related with biomass deconstruction. This, associated with pH, temperature, high ethanol, and other stress fluctuations presented on large scale fermentations led the search for yeasts with more robust backgrounds, like industrial strains, as engineering targets. Some promising yeasts were obtained both from studies of stress tolerance genes and adaptation on hydrolysates. Since fermentation times on mixed-substrate hydrolysates were still not cost-effective, the more selective search for new or engineered sugar transporters for xylose are still the focus of many recent studies. These challenges, as well as under-appreciated process strategies, will be discussed in this review. PMID:26927067

  1. Xylose Fermentation by Saccharomyces cerevisiae: Challenges and Prospects.

    Science.gov (United States)

    Moysés, Danuza Nogueira; Reis, Viviane Castelo Branco; de Almeida, João Ricardo Moreira; de Moraes, Lidia Maria Pepe; Torres, Fernando Araripe Gonçalves

    2016-02-25

    Many years have passed since the first genetically modified Saccharomyces cerevisiae strains capable of fermenting xylose were obtained with the promise of an environmentally sustainable solution for the conversion of the abundant lignocellulosic biomass to ethanol. Several challenges emerged from these first experiences, most of them related to solving redox imbalances, discovering new pathways for xylose utilization, modulation of the expression of genes of the non-oxidative pentose phosphate pathway, and reduction of xylitol formation. Strategies on evolutionary engineering were used to improve fermentation kinetics, but the resulting strains were still far from industrial application. Lignocellulosic hydrolysates proved to have different inhibitors derived from lignin and sugar degradation, along with significant amounts of acetic acid, intrinsically related with biomass deconstruction. This, associated with pH, temperature, high ethanol, and other stress fluctuations presented on large scale fermentations led the search for yeasts with more robust backgrounds, like industrial strains, as engineering targets. Some promising yeasts were obtained both from studies of stress tolerance genes and adaptation on hydrolysates. Since fermentation times on mixed-substrate hydrolysates were still not cost-effective, the more selective search for new or engineered sugar transporters for xylose are still the focus of many recent studies. These challenges, as well as under-appreciated process strategies, will be discussed in this review.

  2. Comparison of the xylose reductase-xylitol dehydrogenase and the xylose isomerase pathways for xylose fermentation by recombinant Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Hahn-Hägerdal Bärbel

    2007-02-01

    Full Text Available Abstract Background Two heterologous pathways have been used to construct recombinant xylose-fermenting Saccharomyces cerevisiae strains: i the xylose reductase (XR and xylitol dehydrogenase (XDH pathway and ii the xylose isomerase (XI pathway. In the present study, the Pichia stipitis XR-XDH pathway and the Piromyces XI pathway were compared in an isogenic strain background, using a laboratory host strain with genetic modifications known to improve xylose fermentation (overexpressed xylulokinase, overexpressed non-oxidative pentose phosphate pathway and deletion of the aldose reductase gene GRE3. The two isogenic strains and the industrial xylose-fermenting strain TMB 3400 were studied regarding their xylose fermentation capacity in defined mineral medium and in undetoxified lignocellulosic hydrolysate. Results In defined mineral medium, the xylose consumption rate, the specific ethanol productivity, and the final ethanol concentration were significantly higher in the XR- and XDH-carrying strain, whereas the highest ethanol yield was achieved with the strain carrying XI. While the laboratory strains only fermented a minor fraction of glucose in the undetoxified lignocellulose hydrolysate, the industrial strain TMB 3400 fermented nearly all the sugar available. Xylitol was formed by the XR-XDH-carrying strains only in mineral medium, whereas in lignocellulose hydrolysate no xylitol formation was detected. Conclusion Despite by-product formation, the XR-XDH xylose utilization pathway resulted in faster ethanol production than using the best presently reported XI pathway in the strain background investigated. The need for robust industrial yeast strains for fermentation of undetoxified spruce hydrolysates was also confirmed.

  3. Quantitative metabolomics of a xylose-utilizing Saccharomyces cerevisiae strain expressing the Bacteroides thetaiotaomicron xylose isomerase on glucose and xylose.

    Science.gov (United States)

    Mert, M J; Rose, S H; la Grange, D C; Bamba, T; Hasunuma, T; Kondo, A; van Zyl, W H

    2017-10-01

    The yeast Saccharomyces cerevisiae cannot utilize xylose, but the introduction of a xylose isomerase that functions well in yeast will help overcome the limitations of the fungal oxido-reductive pathway. In this study, a diploid S. cerevisiae S288c[2n YMX12] strain was constructed expressing the Bacteroides thetaiotaomicron xylA (XI) and the Scheffersomyces stipitis xyl3 (XK) and the changes in the metabolite pools monitored over time. Cultivation on xylose generally resulted in gradual changes in metabolite pool size over time, whereas more dramatic fluctuations were observed with cultivation on glucose due to the diauxic growth pattern. The low G6P and F1,6P levels observed with cultivation on xylose resulted in the incomplete activation of the Crabtree effect, whereas the high PEP levels is indicative of carbon starvation. The high UDP-D-glucose levels with cultivation on xylose indicated that the carbon was channeled toward biomass production. The adenylate and guanylate energy charges were tightly regulated by the cultures, while the catabolic and anabolic reduction charges fluctuated between metabolic states. This study helped elucidate the metabolite distribution that takes place under Crabtree-positive and Crabtree-negative conditions when cultivating S. cerevisiae on glucose and xylose, respectively.

  4. Engineering xylose utilization in Yarrowia lipolytica by understanding its cryptic xylose pathway.

    Science.gov (United States)

    Rodriguez, Gabriel M; Hussain, Murtaza Shabbir; Gambill, Lauren; Gao, Difeng; Yaguchi, Allison; Blenner, Mark

    2016-01-01

    The oleaginous yeast, Yarrowia lipolytica, has been utilized as an industrial host for about 60 years for various applications. Recently, the metabolic engineering of this host has become increasingly popular due to its ability to accumulate lipids as well as improvements made toward developing new genetic tools. Y. lipolytica can robustly metabolize glucose, glycerol, and even different lipid classes. However, little is known about its xylose metabolizing capability. Given the desirability of having a robust xylose utilizing strain of Y. lipolytica, we performed a comprehensive investigation and elucidation of the existing components of its xylose metabolic pathway. A quick and efficient means of determining functionality of the candidate xylose pathway genes (XYR, XDH, and XKS) from Y. lipolytica was desirable. We challenged Escherichia coli mutants lacking either the xylose isomerase (xylA) gene or the xylulose kinase (xylB) gene to grow on xylose minimal media by expressing the candidate genes from Y. lipolytica. We showed that the XKS of Y. lipolytica is able to rescue xylose growth of E. coli ΔxylB, and the XDH enabled growth on xylitol, but not on xylose, of E. coli ΔxylA. Overexpression of XKS and XDH in Y. lipolytica improved growth on xylitol, indicating that expression of the native enzymes was limiting. Overexpression of XKS and XDH in Y. lipolytica also enables robust growth on xylose under high nitrogen conditions without the need for adaptation. These results prove that a complete xylose pathway exists in Y. lipolytica, but the pathway is poorly expressed. To elucidate the XYR gene, we applied the E. coli ΔxylA xylose growth challenge with 14 candidate XYR genes and XDH. The XYR2 candidate was able to rescue growth of E. coli ΔxylA xylose on minimal media. While a native xylose pathway exists in Y. lipolytica, the microorganism's inability to grow robustly on xylose is an effect of cryptic genetic circuits that control expression of key enzymes

  5. Xylose utilizing recombinant Saccharomyces cerevisiae strains

    Energy Technology Data Exchange (ETDEWEB)

    Walfridsson, M.

    1996-04-01

    Through metabolic engineering, S. cerevisiae was provided with the necessary enzymes required for xylose utilisation during ethanolic fermentation of xylose-rich lignocellulose raw materials. For xylitol production, S. cerevisiae was provided with the Pichia stipitis XYL1 gene encoding xylose reductase (XR). The in-vivo reduction and the following excretion of xylitol, requires a co-substrate for maintenance and cofactor regeneration. Xylitol yields close to 100% were obtained with the XYL1 containing S. cerevisiae. Introducing P. stipitis XYL1 and XYL2 genes, encoding XR and xylitol dehydrogenase (XDH), respectively, enabled S. cerevisiae to convert xylose to xylulose, via xylitol. During the screening work of P. stipitis XDH gene, another gene encoding a polyol dehydrogenase was isolated and cloned in S. cerevisiae. The gene was identified as a D-arabinitol dehydrogenase gene. In P. stipitis it may function as a redox sink by reducing D-ribulose to D-arabinitol. The metabolism through the pentose phosphate pathway (PPP) was enhanced by over-expressing the native genes TKL1 and TAL1 encoding transketolase and transaldolase, respectively, resulting in improved xylose utilisation. The XR and XDH activities in recombinant S. cerevisiae were produced at different levels by constructing yeast vectors in which the PGK1 and ADHI promoters controlled XYL1 and XYL2. With higher XDH than XR activities, less by-products, in the form of xylitol and glycerol, were formed by the recombinant S. cerevisiae strains. The Thermus thermophilus xylA gene encoding a thermostable xylose isomerase was cloned and expressed in S. cerevisiae. The recombinant xylose isomerase was actively produced and a new functional metabolic pathway was established in S. cerevisiae resulting in ethanol production from xylose. 150 refs, 3 figs, 4 tabs

  6. Xylose fermentation to ethanol. A review

    Energy Technology Data Exchange (ETDEWEB)

    McMillan, J D

    1993-01-01

    The past several years have seen tremendous progress in the understanding of xylose metabolism and in the identification, characterization, and development of strains with improved xylose fermentation characteristics. A survey of the numerous microorganisms capable of directly fermenting xylose to ethanol indicates that wild-type yeast and recombinant bacteria offer the best overall performance in terms of high yield, final ethanol concentration, and volumetric productivity. The best performing bacteria, yeast, and fungi can achieve yields greater than 0.4 g/g and final ethanol concentrations approaching 5%. Productivities remain low for most yeast and particularly for fungi, but volumetric productivities exceeding 1.0 g/L-h have been reported for xylose-fermenting bacteria. In terms of wild-type microorganisms, strains of the yeast Pichia stipitis show the most promise in the short term for direct high-yield fermentation of xylose without byproduct formation. Of the recombinant xylose-fermenting microorganisms developed, recombinant E. coli ATTC 11303 (pLOI297) exhibits the most favorable performance characteristics reported to date.

  7. Effect of xylose on the synthesis of phosphorylcholine and phosphorylethanolamine in rat lenses.

    Science.gov (United States)

    Jernigan, H M; Ekambaram, M C; Blum, P S; Blanchard, M S

    1993-03-01

    Choline, an essential phospholipid precursor, enters the lens by a facilitated transport system and is phosphorylated to form phosphorylcholine (P-choline). Intact lenses incubated with [3H]choline accumulate both [3H]choline and P-[3H]choline. The rate and extent of this accumulation have been used to study the effects of osmotic or oxidative cataractogenic stress, and also to test the ability of compounds to protect lenses from stress-related damage. The initial effect of oxidative stress on choline metabolism is decreased choline transport, but the mechanism by which osmotic stress affects the accumulation of [3H]choline is not understood. The effects of osmotic and oxidative stress on choline influx and metabolism were compared in rat lenses incubated in TC-199 medium. After osmotic stress by incubation with 30 mM xylose for up to 24 hr, lenses accumulated the same amount of radiolabel as controls during a 30 min pulse with [3H]choline. However, if the lenses were exposed to [3H]choline for 6 hr so that accumulation of radiolabel in the lenses was limited by the rate of P-choline synthesis, xylose treated lenses accumulated less choline than controls. Separation of the lenticular radiolabel into [3H]choline and P-[3H]choline confirmed that xylose decreased synthesis of P-choline, although adequate unphosphorylated [3H]choline was available in the lenses. A decrease in P-[3H]ethanolamine synthesis was also seen in xylose-treated lenses incubated with [3H]ethanolamine. Ethanolamine can enter lenses by a non-saturable process which is not dependent upon a transporter. Although xylose decreased P-choline synthesis in intact lenses, neither xylose nor xylitol inhibited choline kinase in lens homogenates.(ABSTRACT TRUNCATED AT 250 WORDS)

  8. Stoichiometric network constraints on xylose metabolism by recombinant Saccharomyces cerevisiae

    Science.gov (United States)

    Yong-Su Jin; Thomas W. Jeffries

    2004-01-01

    Metabolic pathway engineering is constrained by the thermodynamic and stoichiometric feasibility of enzymatic activities of introduced genes. Engineering of xylose metabolism in Saccharomyces cerevisiae has focused on introducing genes for the initial xylose assimilation steps from Pichia stipitis, a xylose-fermenting yeast, into S. cerevisiae, a yeast raditionally...

  9. Saccharomyces cerevisiae engineered for xylose metabolism exhibits a respiratory response

    Science.gov (United States)

    Yong-Su Jin; Jose M. Laplaza; Thomas W. Jeffries

    2004-01-01

    Native strains of Saccharomyces cerevisiae do not assimilate xylose. S. cerevisiae engineered for D-xylose utilization through the heterologous expression of genes for aldose reductase ( XYL1), xylitol dehydrogenase (XYL2), and D-xylulokinase ( XYL3 or XKS1) produce only limited amounts of ethanol in xylose medium. In recombinant S. cerevisiae expressing XYL1, XYL2,...

  10. Zymomonas with improved xylose utilization in stress conditions

    Science.gov (United States)

    Caimi, Perry G; Emptage, Mark; Li, Xu; Viitanen, Paul V; Chou, Yat-Chen; Franden, Mary Ann; Zhang, Min

    2013-06-18

    Strains of xylose utilizing Zymomonas with improved xylose utilization and ethanol production during fermentation in stress conditions were obtained using an adaptation method. The adaptation involved continuously growing xylose utilizing Zymomonas in media containing high sugars, acetic acid, ammonia, and ethanol.

  11. Metabolic control analysis of xylose catabolism in Aspergillus

    NARCIS (Netherlands)

    Prathumpai, W.; Gabelgaard, J.B.; Wanchanthuek, P.; Vondervoort, van de P.J.I.; Groot, de M.J.L.; McIntyre, M.; Nielsen, J.

    2003-01-01

    A kinetic model for xylose catabolism in Aspergillus is proposed. From a thermodynamic analysis it was found that the intermediate xylitol will accumulate during xylose catabolism. Use of the kinetic model allowed metabolic control analysis (MCA) of the xylose catabolic pathway to be carried out,

  12. Xylose reductase from the thermophilic fungus Talaromyces ...

    Indian Academy of Sciences (India)

    Given the potential application of xylose reductase enzymes that preferentially utilize the reduced form of nicotinamide adenine dinucleotide (NADH) rather than NADPH in the fermentation of five carbon sugars by genetically engineered microorganisms, the coenzyme selectivity of TeXR was altered by site-directed ...

  13. Fermentation of mixed glucose-xylose substrates by engineered strains of Saccharomyces cerevisiae: role of the coenzyme specificity of xylose reductase, and effect of glucose on xylose utilization

    Directory of Open Access Journals (Sweden)

    Klimacek Mario

    2010-03-01

    Full Text Available Abstract Background In spite of the substantial metabolic engineering effort previously devoted to the development of Saccharomyces cerevisiae strains capable of fermenting both the hexose and pentose sugars present in lignocellulose hydrolysates, the productivity of reported strains for conversion of the naturally most abundant pentose, xylose, is still a major issue of process efficiency. Protein engineering for targeted alteration of the nicotinamide cofactor specificity of enzymes catalyzing the first steps in the metabolic pathway for xylose was a successful approach of reducing xylitol by-product formation and improving ethanol yield from xylose. The previously reported yeast strain BP10001, which expresses heterologous xylose reductase from Candida tenuis in mutated (NADH-preferring form, stands for a series of other yeast strains designed with similar rational. Using 20 g/L xylose as sole source of carbon, BP10001 displayed a low specific uptake rate qxylose (g xylose/g dry cell weight/h of 0.08. The study presented herein was performed with the aim of analysing (external factors that limit qxylose of BP10001 under xylose-only and mixed glucose-xylose substrate conditions. We also carried out a comprehensive investigation on the currently unclear role of coenzyme utilization, NADPH compared to NADH, for xylose reduction during co-fermentation of glucose and xylose. Results BP10001 and BP000, expressing C. tenuis xylose reductase in NADPH-preferring wild-type form, were used. Glucose and xylose (each at 10 g/L were converted sequentially, the corresponding qsubstrate values being similar for each strain (glucose: 3.0; xylose: 0.05. The distribution of fermentation products from glucose was identical for both strains whereas when using xylose, BP10001 showed enhanced ethanol yield (BP10001 0.30 g/g; BP000 0.23 g/g and decreased yields of xylitol (BP10001 0.26 g/g; BP000 0.36 g/g and glycerol (BP10001 0.023 g/g; BP000 0.072 g/g as compared

  14. Experimental evidence of a xylose-catabolic pathway on the pAO1 megaplasmid of Arthrobacter nicotinovorans

    Directory of Open Access Journals (Sweden)

    Marius Mihasan

    2012-09-01

    Full Text Available The pAO1 megaplasmid of A. nicotinovorans consists of 165 ORF's related mainly to nicotine degradation, uptake and utilization of carbohydrates, amino acids and sarcosine. A putative sugar catabolic pathway consisting of 11 ORF's organized as a single operon were previously described. The current work brings experimental data supporting the existence of a D-Xylose catabolic pathway on the pAO1 megaplasmid. When grown on D-xylose containing media, the cells harboring the pAO1 megaplasmid grow to higher cell densities and also express the OxRe protein coded by the megaplasmid. A putative pathway similar to Weimberg pentose pathway is postulated, in which D-xylose is transported in the cell by the ABC-type transport system and then transformed using the putative sugar-dehidrogenase OxRe to D-xylonate, which is further degrated to 2-ketoglutarate and integrated into the general metabolism of the cell

  15. Proteomic analysis of the secretory response of Aspergillus niger to D-maltose and D-xylose.

    Directory of Open Access Journals (Sweden)

    José Miguel P Ferreira de Oliveira

    Full Text Available Fungi utilize polysaccharide substrates through extracellular digestion catalyzed by secreted enzymes. Thus far, protein secretion by the filamentous fungus Aspergillus niger has mainly been studied at the level of individual proteins and by genome and transcriptome analyses. To extend these studies, a complementary proteomics approach was applied with the aim to investigate the changes in secretome and microsomal protein composition resulting from a shift to a high level secretion condition. During growth of A. niger on D-sorbitol, small amounts of D-maltose or D-xylose were used as inducers of the extracellular amylolytic and xylanolytic enzymes. Upon induction, protein compositions in the extracellular broth as well as in enriched secretory organelle (microsomal fractions were analyzed using a shotgun proteomics approach. In total 102 secreted proteins and 1,126 microsomal proteins were identified in this study. Induction by D-maltose or D-xylose resulted in the increase in specific extracellular enzymes, such as glucoamylase A on D-maltose and β-xylosidase D on D-xylose, as well as of microsomal proteins. This reflects the differential expression of selected genes coding for dedicated extracellular enzymes. As expected, the addition of extra D-sorbitol had no effect on the expression of carbohydrate-active enzymes, compared to addition of D-xylose or D-maltose. Furthermore, D-maltose induction caused an increase in microsomal proteins related to translation (e.g., Rpl15 and vesicular transport (e.g., the endosomal-cargo receptor Erv14. Millimolar amounts of the inducers D-maltose and D-xylose are sufficient to cause a direct response in specific protein expression levels. Also, after induction by D-maltose or D-xylose, the induced enzymes were found in microsomes and extracellular. In agreement with our previous findings for D-xylose induction, D-maltose induction leads to recruitment of proteins involved in proteasome-mediated degradation.

  16. Disruption of the cytochrome c gene in xylose-utilizing yeast Pichia stipitis leads to higher ethanol production

    Science.gov (United States)

    Nian-Qing. Shi; Brian. Davis; Fred. Sherman; Jose. Cruz; Thomas W. Jeffries

    1999-01-01

    The xylose-utilizing yeast, Pichia stipitis, has a complex respiratory system that contains cytochrome and non-cytochrome alternative electron transport chains in its mitochondria. To gain primary insights into the alternative respiratory pathway, a cytochrome c gene (PsCYC1, Accession No. AF030426) was cloned from wild-type P. stipitis CBS 6054 by cross-hybridization...

  17. Nutritional implications of D-xylose in pigs

    NARCIS (Netherlands)

    Schutte, J.B.; Jong, J.de; Polziehn, R.; Verstegen, M.W.A.

    1991-01-01

    Hemicellulose consists primarily of pentose sugars, joined together in a polysaccharide chain with D-xylose as the most abundant component. Ileal digestibility and urinary excretion of D-xylose and associated effects of this pentose sugar on ileal and faecal digestibility of dry matter (DM), organic

  18. Ethanol production in fermentation of mixed sugars containing xylose

    Science.gov (United States)

    Viitanen, Paul V [West Chester, PA; Mc Cutchen, Carol M [Wilmington, DE; Li,; Xu, [Newark, DE; Emptage, Mark [Wilmington, DE; Caimi, Perry G [Kennett Square, PA; Zhang, Min [Lakewood, CO; Chou, Yat-Chen [Lakewood, CO; Franden, Mary Ann [Centennial, CO

    2009-12-08

    Xylose-utilizing Z. mobilis strains were found to have improved ethanol production when grown in medium containing mixed sugars including xylose if sorbitol or mannitol was included in the medium. The effect was seen in concentrations of mixed sugars where no growth lag period occurs, as well as in higher sugars concentrations.

  19. Metabolic control analysis of xylose catabolism in Aspergillus

    DEFF Research Database (Denmark)

    Prathumpai, Wai; Gabelgaard, J.B.; Wanchanthuek, P.

    2003-01-01

    nidulans grown on media containing xylose, and a concentration up to 30 mM was found. Applying MCA showed that the first polyol dehydrogenase (XDH) in the catabolic pathway of xylose exerted the main flux control in the two strains of A. nidulans and A. niger NW324, but the flux control was exerted mainly...

  20. Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption

    DEFF Research Database (Denmark)

    Scalcinati, Gionata; Otero, José Manuel; Van Vleet, Jennifer R. H.

    2012-01-01

    Industrial biotechnology aims to develop robust microbial cell factories, such as Saccharomyces cerevisiae, to produce an array of added value chemicals presently dominated by petrochemical processes. Xylose is the second most abundant monosaccharide after glucose and the most prevalent pentose...... flux to biomass production. Such a platform may then be enhanced with complementary metabolic engineering strategies that couple biomass production with high value-added chemical. Saccharomyces cerevisiae, expressing xylose reductase, xylitol dehydrogenase and xylulose kinase, from the native xylose......-metabolizing yeast Pichia stipitis, was constructed, followed by a directed evolution strategy to improve xylose utilization rates. The resulting S. cerevisiae strain was capable of rapid growth and fast xylose consumption producing only biomass and negligible amount of byproducts. Transcriptional profiling...

  1. Homofermentative production of optically pure L-lactic acid from xylose by genetically engineered Escherichia coli B.

    Science.gov (United States)

    Zhao, Jinfang; Xu, Liyuan; Wang, Yongze; Zhao, Xiao; Wang, Jinhua; Garza, Erin; Manow, Ryan; Zhou, Shengde

    2013-06-07

    Polylactic acid (PLA), a biodegradable polymer, has the potential to replace (at least partially) traditional petroleum-based plastics, minimizing "white pollution". However, cost-effective production of optically pure L-lactic acid is needed to achieve the full potential of PLA. Currently, starch-based glucose is used for L-lactic acid fermentation by lactic acid bacteria. Due to its competition with food resources, an alternative non-food substrate such as cellulosic biomass is needed for L-lactic acid fermentation. Nevertheless, the substrate (sugar stream) derived from cellulosic biomass contains significant amounts of xylose, which is unfermentable by most lactic acid bacteria. However, the microorganisms that do ferment xylose usually carry out heterolactic acid fermentation. As a result, an alternative strain should be developed for homofermentative production of optically pure L-lactic acid using cellulosic biomass. In this study, an ethanologenic Escherichia coli strain, SZ470 (ΔfrdBC ΔldhA ΔackA ΔpflB ΔpdhR ::pflBp6-acEF-lpd ΔmgsA), was reengineered for homofermentative production of L-lactic acid from xylose (1.2 mole xylose = > 2 mole L-lactic acid), by deleting the alcohol dehydrogenase gene (adhE) and integrating the L-lactate dehydrogenase gene (ldhL) of Pediococcus acidilactici. The resulting strain, WL203, was metabolically evolved further through serial transfers in screw-cap tubes containing xylose, resulting in the strain WL204 with improved anaerobic cell growth. When tested in 70 g L-1 xylose fermentation (complex medium), WL204 produced 62 g L-1 L-lactic acid, with a maximum production rate of 1.631 g L-1 h-1 and a yield of 97% based on xylose metabolized. HPLC analysis using a chiral column showed that an L-lactic acid optical purity of 99.5% was achieved by WL204. These results demonstrated that WL204 has the potential for homofermentative production of L-lactic acid using cellulosic biomass derived substrates, which contain a

  2. Changing flux of xylose metabolites by altering expression of xylose reductase and xylitol dehydrogenase in recombinant Saccharomyces cerevisiae

    Science.gov (United States)

    Yong-Su Jin; Thomas W. Jeffries

    2003-01-01

    We changed the fluxes of xylose metabolites in recombinant Saccharomyces cerevisiae by manipulating expression of Pichia stipitis genes(XYL1 and XYL2) coding for xylose reductase (XR) and xylitol dehydrogenase (XDH), respectively. XYL1 copy number was kept constant by integrating it into the chromosome. Copy numbers of XYL2 were varied either by integrating XYL2 into...

  3. Xylose reductase from Pichia stipitis with altered coenzyme preference improves ethanolic xylose fermentation by recombinant Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Hahn-Hägerdal Bärbel

    2009-05-01

    Full Text Available Abstract Background Xylose reductase (XR and xylitol dehydrogenase (XDH from Pichia stipitis are the two enzymes most commonly used in recombinant Saccharomyces cerevisiae strains engineered for xylose utilization. The availability of NAD+ for XDH is limited during anaerobic xylose fermentation because of the preference of XR for NADPH. This in turn results in xylitol formation and reduced ethanol yield. The coenzyme preference of P. stipitis XR was changed by site-directed mutagenesis with the aim to engineer it towards NADH-preference. Results XR variants were evaluated in S. cerevisiae strains with the following genetic modifications: overexpressed native P. stipitis XDH, overexpressed xylulokinase, overexpressed non-oxidative pentose phosphate pathway and deleted GRE3 gene encoding an NADPH dependent aldose reductase. All overexpressed genes were chromosomally integrated to ensure stable expression. Crude extracts of four different strains overexpressing genes encoding native P. stipitis XR, K270M and K270R mutants, as well as Candida parapsilosis XR, were enzymatically characterized. The physiological effects of the mutations were investigated in anaerobic xylose fermentation. The strain overexpressing P. stipitis XR with the K270R mutation gave an ethanol yield of 0.39 g (g consumed sugars-1, a xylitol yield of 0.05 g (g consumed xylose-1 and a xylose consumption rate of 0.28 g (g biomass-1 h-1 in continuous fermentation at a dilution rate of 0.12 h-1, with 10 g l-1 glucose and 10 g l-1 xylose as carbon sources. Conclusion The cofactor preference of P. stipitis XR was altered by site-directed mutagenesis. When the K270R XR was combined with a metabolic engineering strategy that ensures high xylose utilization capabilities, a recombinant S. cerevisiae strain was created that provides a unique combination of high xylose consumption rate, high ethanol yield and low xylitol yield during ethanolic xylose fermentation.

  4. Maintaining evolvability.

    Science.gov (United States)

    Crow, James F

    2008-12-01

    Although molecular methods, such as QTL mapping, have revealed a number of loci with large effects, it is still likely that the bulk of quantitative variability is due to multiple factors, each with small effect. Typically, these have a large additive component. Conventional wisdom argues that selection, natural or artificial, uses up additive variance and thus depletes its supply. Over time, the variance should be reduced, and at equilibrium be near zero. This is especially expected for fitness and traits highly correlated with it. Yet, populations typically have a great deal of additive variance, and do not seem to run out of genetic variability even after many generations of directional selection. Long-term selection experiments show that populations continue to retain seemingly undiminished additive variance despite large changes in the mean value. I propose that there are several reasons for this. (i) The environment is continually changing so that what was formerly most fit no longer is. (ii) There is an input of genetic variance from mutation, and sometimes from migration. (iii) As intermediate-frequency alleles increase in frequency towards one, producing less variance (as p --> 1, p(1 - p) --> 0), others that were originally near zero become more common and increase the variance. Thus, a roughly constant variance is maintained. (iv) There is always selection for fitness and for characters closely related to it. To the extent that the trait is heritable, later generations inherit a disproportionate number of genes acting additively on the trait, thus increasing genetic variance. For these reasons a selected population retains its ability to evolve. Of course, genes with large effect are also important. Conspicuous examples are the small number of loci that changed teosinte to maize, and major phylogenetic changes in the animal kingdom. The relative importance of these along with duplications, chromosome rearrangements, horizontal transmission and polyploidy

  5. Genome sequence of the lignocellulose-bioconverting and xylose-fermenting yeast Pichia stipitis

    Science.gov (United States)

    Thomas W. Jeffries; Igor V. Grigroriev; Jane Grimwood; Jose M. Laplaza; Andrea Aerts; Asaf Salamov; Jeremy Schmutz; Erika Lindquist; Paramvir Dehal; Harris Shapiro; Yong-Su Jin; Volkmar Passoth; Paul M. Richardson

    2007-01-01

    Xylose is a major constituent of plant lignocellulose, and its fermentation is important for the bioconversion of plant biomass to fuels and chemicals. Pichia stipitis is a well-studied, native xylose-fermenting yeast. The mechanism and regulation of xylose metabolism in P. stipitis have been characterized and genes from P. stipitis have been used to engineer xylose...

  6. Engineering yeast hexokinase 2 for improved tolerance toward xylose-induced inactivation.

    Directory of Open Access Journals (Sweden)

    Basti Bergdahl

    Full Text Available Hexokinase 2 (Hxk2p from Saccharomyces cerevisiae is a bi-functional enzyme being both a catalyst and an important regulator in the glucose repression signal. In the presence of xylose Hxk2p is irreversibly inactivated through an autophosphorylation mechanism, affecting all functions. Consequently, the regulation of genes involved in sugar transport and fermentative metabolism is impaired. The aim of the study was to obtain new Hxk2p-variants, immune to the autophosphorylation, which potentially can restore the repressive capability closer to its nominal level. In this study we constructed the first condensed, rationally designed combinatorial library targeting the active-site in Hxk2p. We combined protein engineering and genetic engineering for efficient screening and identified a variant with Phe159 changed to tyrosine. This variant had 64% higher catalytic activity in the presence of xylose compared to the wild-type and is expected to be a key component for increasing the productivity of recombinant xylose-fermenting strains for bioethanol production from lignocellulosic feedstocks.

  7. Conversion of hemicelluloses and D-xylose into ethanol by the use of thermophilic anaerobic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1998-05-01

    Ethanol is a CO{sub 2} neutral liquid fuel that can substitute the use of fossil fuels in the transportation sector, thereby reducing the CO{sub 2} emission to the atmosphere. CO{sub 2} emission is suspected to contribute significantly to the so-called greenhouse effect, the global heating. Substrates for production of ethanol must be cheap and plentiful. This can be met by the use of lignocellulosic biomass such as willow, wheat straw, hardwood and softwood. However, the complexity of these polymeric substrates and the presence of several types of carbohydrates (glucose, xylose, mannose, galactose, arabinose) require additional treatment to release the useful carbohydrates and ferment the major carbohydrates fractions. The costs related to the ethanol-production must be kept at a minimum to be price competitive compared to gasoline. Therefore all of the carbohydrates present in lignocellulose need to be converted into ethanol. Glucose can be fermented to ethanol by yeast strains such as Saccharomyces cerevisiae, which, however, is unable to ferment the other major carbohydrate fraction, D-xylose. Thermophilic anaerobic ethanol producing bacteria can be used for fermentation of the hemicelluloses fraction of lignocellulosic biomass. However, physiological studies of thermophilic anaerobic bacteria have shown that the ethanol yield decreases at increasing substrate concentration. The biochemical limitations causing this phenomenon are not known in detail. Physiological and biochemical studies of a newly characterized thermophilic anaerobic ethanol producing bacterium, Thermoanaerobacter mathranii, was performed. This study included extraction of intracellular metabolites and enzymes of the pentose phosphate pathway and glycolysis. These studies revealed several bottlenecks in the D-xylose metabolism. This knowledge makes way for physiological and genetic engineering of this strain to improve the ethanol yield and productivity at high concentration of D-xylose. (au)

  8. Pnp gene modification for improved xylose utilization in Zymomonas

    Science.gov (United States)

    Caimi, Perry G G; Qi, Min; Tao, Luan; Viitanen, Paul V; Yang, Jianjun

    2014-12-16

    The endogenous pnp gene encoding polynucleotide phosphorylase in the Zymomonas genome was identified as a target for modification to provide improved xylose utilizing cells for ethanol production. The cells are in addition genetically modified to have increased expression of ribose-5-phosphate isomerase (RPI) activity, as compared to cells without this genetic modification, and are not limited in xylose isomerase activity in the absence of the pnp modification.

  9. Efficient xylose fermentation by the brown rot fungus Neolentinus lepideus.

    Science.gov (United States)

    Okamoto, Kenji; Kanawaku, Ryuichi; Masumoto, Masaru; Yanase, Hideshi

    2012-02-10

    The efficient production of bioethanol on an industrial scale requires the use of renewable lignocellulosic biomass as a starting material. A limiting factor in developing efficient processes is identifying microorganisms that are able to effectively ferment xylose, the major pentose sugar found in hemicellulose, and break down carbohydrate polymers without pre-treatment steps. Here, a basidiomycete brown rot fungus was isolated as a new biocatalyst with unprecedented fermentability, as it was capable of converting not only the 6-carbon sugars constituting cellulose, but also the major 5-carbon sugar xylose in hemicelluloses, to ethanol. The fungus was identified as Neolentinus lepideus and was capable of assimilating and fermenting xylose to ethanol in yields of 0.30, 0.33, and 0.34 g of ethanol per g of xylose consumed under aerobic, oxygen-limited, and anaerobic conditions, respectively. A small amount of xylitol was detected as the major by-product of xylose metabolism. N. lepideus produced ethanol from glucose, mannose, galactose, cellobiose, maltose, and lactose with yields ranging from 0.34 to 0.38 g ethanol per g sugar consumed, and also exhibited relatively favorable conversion of non-pretreated starch, xylan, and wheat bran. These results suggest that N. lepideus is a promising candidate for cost-effective and environmentally friendly ethanol production from lignocellulosic biomass. To our knowledge, this is the first report on efficient ethanol fermentation from various carbohydrates, including xylose, by a naturally occurring brown rot fungus. Copyright © 2011 Elsevier Inc. All rights reserved.

  10. Impact of overexpressing NADH kinase on glucose and xylose metabolism in recombinant xylose-utilizing Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Hou, Jin; Vemuri, G. N.; Bao, X. M.

    2009-01-01

    During growth of Saccharomyces cerevisiae on glucose, the redox cofactors NADH and NADPH are predominantly involved in catabolism and biosynthesis, respectively. A deviation from the optimal level of these cofactors often results in major changes in the substrate uptake and biomass formation....... However, the metabolism of xylose by recombinant S. cerevisiae carrying xylose reductase and xylitol dehydrogenase from the fungal pathway requires both NADH and NADPH and creates cofactor imbalance during growth on xylose. As one possible solution to overcoming this imbalance, the effect...... of overexpressing the native NADH kinase (encoded by the POS5 gene) in xylose-consuming recombinant S. cerevisiae directed either into the cytosol or to the mitochondria was evaluated. The physiology of the NADH kinase containing strains was also evaluated during growth on glucose. Overexpressing NADH kinase...

  11. The xylose reductase/xylitol dehydrogenase/xylulokinase ratio affects product formation in recombinant xylose-utilising Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Eliasson, Anna; Hofmeyr, J.H.S.; Pedler, S.

    2001-01-01

    Data simulations based on a kinetic model implied that under simplified simulation conditions a 1:greater than or equal to 10:greater than or equal to4 relation of the xylose reductase (XR)/xylitol dehydrogenase (XDH)/xylulokinase (XK) ratio was optimal in minimising xylitol formation during xylose...... utilisation in yeast. The steady-state level of the intermediary xylitol depended also, to a great extent, on the NADH and NAD(+) concentrations. Anaerobic xylose utilisation was investigated for three different recombinant. XR-, XDH- and XK-expressing Saccharomyces cerevisiae strains, TMB 3002, TMB 3003...... and TMB 3004, to verify the model predictions. Overexpression of XK was found to be necessary for ethanol formation from xylose. Furthermore, the xylitol formation decreased with decreasing XR/XDH ratio, while the ethanol formation increased. Of the three strains, TMB 3004, which was the strain with a XR/XDH...

  12. Conversion of hemicellulose and D-xylose into ethanol by the use of thermophilic anaerobic bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Sommer, Peter

    1998-02-01

    Ethanol is a CO{sub 2} neutral liquid fuel that can substitute the use of fossil fuels in the transportation sector, thereby reducing the CO{sub 2} emission to the atmoshpere. CO{sub 2} emission is suspected to contribute significantly to the so-called greenhouse effect, the global heating. Substrates for production of ethanol must be cheap and plentiful. This can be met by the use of lignocellulosic biomass such as willow, wheat straw, hardwood and softwood. However, the complexity of these polymeric substrates and the presence of several types of carbohydrates (glucose, xylose, mannose, galactose, arabinose) require additional treatment to release the useful carbohydrates and ferment the major carbohydrates fractions. The costs related to the ethanol-production must be kept at a minimum to be price competitive compared to gasoline. Therefore all of the carbohydrates present in lignocellulose need to be converted into ethanol. Glucose can be fermented to ethanol by yeast strains such as Saccharomyces cerevisiae, which, however, is unable to ferment the other major carbohydrate fraction, D-xylose. The need for a microorganism able to ferment D-xylose is therefore apparent. Thermophilic anaerobic ethanol producing bacteria can therefore be considered for fermentation of D-xylose. Screening of 130 thermophilic anaerobic bacterial strains, from hot-springs, mesophilic and thermophilic biogas plants, paper pulp industries and brewery waste, were examined for production of ethanol from D-xylose and wet-oxidized hemicellulose hydrolysate. Several strains were isolated and one particular strain was selected for best performance during the screening test. This strain was characterized as a new species, Thermoanaerobacter mathranii. However, the ethanol yield on wet-oxidized hemicellulose hydrolysate was not satisfactory. The bacterium was adapted by isolation of mutant strains, now resistant to the inhibitory compounds present in the hydrolysate. Growth and ethanol yield

  13. Construction of xylose dehydrogenase displayed on the surface of bacteria using ice nucleation protein for sensitive D-xylose detection.

    Science.gov (United States)

    Liang, Bo; Li, Liang; Mascin, Marco; Liu, Aihua

    2012-01-03

    A novel method was developed to detect d-xylose (INS 967) sensitively and selectively, which is based on a xylose dehydrogenase (XDH) cell-surface displaying system using a newly identified ice nucleation protein from Pseudomonas borealis DL7 as an anchoring motif. With coenzyme NAD(+), the XDH-displayed bacteria facilitates the catalysis of the oxidization of xylose and the resultant NADH can be detected spectrometrically at 340 nm. The fusion protein was characterized by proteinase accessibility, Western blot, and enzyme activity assays. The established XDH surface displaying system did not inhibit the growth of the recombinant Escherichia coli strain. The XDH was mainly displayed on the surface of host cells, which is of high XDH activity and high D-xylose specificity. The optimal temperature and pH of cell displayed XDH were found at 30 °C and pH 8.0, respectively. The XDH-displayed bacteria can be used directly without further enzyme extraction and purification, and it improved the stability of the enzyme. Moreover, the cell-surface-displayed-protein-based approach showed a wide linear range (5-900 μM) and a low detection limit of 2 μM of d-xylose. More importantly, the recombinant cells could be used for precise detection of D-xylose from the real samples such as foods and degradation products of lignocellulose. The method shown here provides a simple, rapid, and low-cost strategy for the sensitive and selective measurement of D-xylose. In addition, the XDH-displayed bacteria showed an interesting response in developing electrochemical biosensors. Thus, the genetically engineered cells may find broad application in such biosensors and biocatalysts. Similarly, this type of genetic approach may be used for the expression of other intracellular enzymes of interest for certain purposes. © 2011 American Chemical Society

  14. Xylose fermentation efficiency and inhibitor tolerance of the recombinant industrial Saccharomyces cerevisiae strain NAPX37.

    Science.gov (United States)

    Li, Yun-Cheng; Mitsumasu, Kanako; Gou, Zi-Xi; Gou, Min; Tang, Yue-Qin; Li, Guo-Ying; Wu, Xiao-Lei; Akamatsu, Takashi; Taguchi, Hisataka; Kida, Kenji

    2016-02-01

    Industrial yeast strains with good xylose fermentation ability and inhibitor tolerance are important for economical lignocellulosic bioethanol production. The flocculating industrial Saccharomyces cerevisiae strain NAPX37, harboring the xylose reductase-xylitol dehydrogenase (XR-XDH)-based xylose metabolic pathway, displayed efficient xylose fermentation during batch and continuous fermentation. During batch fermentation, the xylose consumption rates at the first 36 h were similar (1.37 g/L/h) when the initial xylose concentrations were 50 and 75 g/L, indicating that xylose fermentation was not inhibited even when the xylose concentration was as high as 75 g/L. The presence of glucose, at concentrations of up to 25 g/L, did not affect xylose consumption rate at the first 36 h. Strain NAPX37 showed stable xylose fermentation capacity during continuous ethanol fermentation using xylose as the sole sugar, for almost 1 year. Fermentation remained stable at a dilution rate of 0.05/h, even though the xylose concentration in the feed was as high as 100 g/L. Aeration rate, xylose concentration, and MgSO4 concentration were found to affect xylose consumption and ethanol yield. When the xylose concentration in the feed was 75 g/L, a high xylose consumption rate of 6.62 g/L/h and an ethanol yield of 0.394 were achieved under an aeration rate of 0.1 vvm, dilution rate of 0.1/h, and 5 mM MgSO4. In addition, strain NAPX37 exhibited good tolerance to inhibitors such as weak acids, furans, and phenolics during xylose fermentation. These findings indicate that strain NAPX37 is a promising candidate for application in the industrial production of lignocellulosic bioethanol.

  15. Stepwise metabolic adaption from pure metabolization to balanced anaerobic growth on xylose explored for recombinant Saccharomyces cerevisiae.

    Science.gov (United States)

    Klimacek, Mario; Kirl, Elisabeth; Krahulec, Stefan; Longus, Karin; Novy, Vera; Nidetzky, Bernd

    2014-03-08

    To effectively convert lignocellulosic feedstocks to bio-ethanol anaerobic growth on xylose constitutes an essential trait that Saccharomyces cerevisiae strains normally do not adopt through the selective integration of a xylose assimilation route as the rate of ATP-formation is below energy requirements for cell maintenance (mATP). To enable cell growth extensive evolutionary and/or elaborate rational engineering is required. However the number of available strains meeting demands for process integration are limited. In this work evolutionary engineering in just two stages coupled to strain selection under strict anaerobic conditions was carried out with BP10001 as progenitor. BP10001 is an efficient (Yethanol = 0.35 g/g) but slow (qethanol = 0.05 ± 0.01 g/gBM/h) xylose-metabolizing recombinant strain of Saccharomyces cerevisiae that expresses an optimized yeast-type xylose assimilation pathway. BP10001 was adapted in 5 generations to anaerobic growth on xylose by prolonged incubation for 91 days in sealed flasks. Resultant strain IBB10A02 displayed a specific growth rate μ of 0.025 ± 0.002 h-1 but produced large amounts of glycerol and xylitol. In addition growth was strongly impaired at pH below 6.0 and in the presence of weak acids. Using sequential batch selection and IBB10A02 as basis, IBB10B05 was evolved (56 generations). IBB10B05 was capable of fast (μ = 0.056 ± 0.003 h-1; qethanol = 0.28 ± 0.04 g/gBM/h), efficient (Yethanol = 0.35 ± 0.02 g/g), robust and balanced fermentation of xylose. Importantly, IBB10A02 and IBB10B05 displayed a stable phenotype. Unlike BP10001 both strains displayed an unprecedented biphasic formation of glycerol and xylitol along the fermentation time. Transition from a glycerol- to a xylitol-dominated growth phase, probably controlled by CO2/HCO3-, was accompanied by a 2.3-fold increase of mATP while YATP (= 87 ± 7 mmolATP/gBM) remained unaffected. As long as glycerol

  16. Expanding xylose metabolism in yeast for plant cell wall conversion to biofuels

    Science.gov (United States)

    Li, Xin; Yu, Vivian Yaci; Lin, Yuping; Chomvong, Kulika; Estrela, Raíssa; Park, Annsea; Liang, Julie M; Znameroski, Elizabeth A; Feehan, Joanna; Kim, Soo Rin; Jin, Yong-Su; Glass, N Louise; Cate, Jamie HD

    2015-01-01

    Sustainable biofuel production from renewable biomass will require the efficient and complete use of all abundant sugars in the plant cell wall. Using the cellulolytic fungus Neurospora crassa as a model, we identified a xylodextrin transport and consumption pathway required for its growth on hemicellulose. Reconstitution of this xylodextrin utilization pathway in Saccharomyces cerevisiae revealed that fungal xylose reductases act as xylodextrin reductases, producing xylosyl-xylitol oligomers as metabolic intermediates. These xylosyl-xylitol intermediates are generated by diverse fungi and bacteria, indicating that xylodextrin reduction is widespread in nature. Xylodextrins and xylosyl-xylitol oligomers are then hydrolyzed by two hydrolases to generate intracellular xylose and xylitol. Xylodextrin consumption using a xylodextrin transporter, xylodextrin reductases and tandem intracellular hydrolases in cofermentations with sucrose and glucose greatly expands the capacity of yeast to use plant cell wall-derived sugars and has the potential to increase the efficiency of both first-generation and next-generation biofuel production. DOI: http://dx.doi.org/10.7554/eLife.05896.001 PMID:25647728

  17. Production of Acetoin through Simultaneous Utilization of Glucose, Xylose, and Arabinose by Engineered Bacillus subtilis

    National Research Council Canada - National Science Library

    Zhang, Bo; Li, Xin-Li; Fu, Jing; Li, Ning; Wang, Zhiwen; Tang, Ya-Jie; Chen, Tao

    2016-01-01

    .... In our previous study, the recombinant Bacillus subtilis 168ARSRCPΔacoAΔbdhA strain was already shown to efficiently utilize xylose for production of acetoin, with a yield of 0.36 g/g xylose...

  18. The effect of CreA in glucose and xylose catabolism in Aspergillus nidulans

    DEFF Research Database (Denmark)

    Prathumpai, Wai; Mcintyre, Mhairi; Nielsen, Jens

    2004-01-01

    The catabolism of glucose and xylose was studied in a wild type and creA deleted (carbon catabolite de-repressed) strain of Aspergillus nidulans. Both strains were cultivated in bioreactors with either glucose or xylose as the sole carbon source, or in the presence of both sugars....... In the cultivations on single carbon sources, it was demonstrated that xylose acted as a carbon catabolite repressor (xylose cultivations), while the enzymes in the xylose utilisation pathway were also subject to repression in the presence of glucose (glucose cultivations). In the wild type strain growing...... on the sugar mixture, glucose repression of xylose utilisation was observed; with xylose utilisation occurring only after glucose was depleted. This phenomenon was not seen in the creA deleted strain, where glucose and xylose were catabolised simultaneously. Measurement of key metabolites and the activities...

  19. Co-fermentation of glucose, xylose and/or cellobiose by yeast

    Science.gov (United States)

    Jeffries, Thomas W.; Willis, Laura B.; Long, Tanya M.; Su, Yi-Kai

    2013-09-10

    Provided herein are methods of using yeast cells to produce ethanol by contacting a mixture comprising xylose with a Spathaspora yeast cell under conditions suitable to allow the yeast to ferment at least a portion of the xylose to ethanol. The methods allow for efficient ethanol production from hydrolysates derived from lignocellulosic material and sugar mixtures including at least xylose and glucose or xylose, glucose and cellobiose.

  20. Growth rate dispersion in seeded batch D-xylose crystallization

    Science.gov (United States)

    Gabas, N.; Biscans, B.; Laguérie, C.

    1990-01-01

    Laboratoire de Genie Chimique (URA CNRS 192), ENSIGC, Chemin de la Loge, F-31078 Toulouse Cedex, France Batch crystallization runs of D-xylose from aqueous solutions have been performed. Growth rate kinetics of xylose crystals have been evaluated from successive crystal size distribution records by means of a laser light scattering size analyser. The experiments have emphasized a broadening of the crystal size distribution during growth. Solutions to population balance equations have provided evidence for growth rate dispersion. A time-averaged growth rate equation as well as a growth rate diffusivity parameter have been identified.

  1. Convergent Synthesis of Pancratistatin from Piperonal and Xylose

    DEFF Research Database (Denmark)

    Dam, Johan Hygum; Madsen, Robert

    2009-01-01

    A synthesis of the antitumour agent pancratistatin is described from piperonal and D-xylose. Piperonal is converted into cinnamyl bromide 11 while methyl 5-iodoribofuranoside 12 is derived from xylose. The allylic bromide and the iodocarbohydrate are combined in a zinc-mediated tandem reaction...... to afford a highly functionalised 1,7-diene, which is then converted into the corresponding cyclohexene by ring-closing olefin metathesis. Subsequent Overman rearrangement, dihydroxylation and deprotection afford the natural product in a total of 25 steps from the two starting materials. The longest linear...

  2. Toward "homolactic" fermentation of glucose and xylose by engineered Saccharomyces cerevisiae harboring a kinetically efficient l-lactate dehydrogenase within pdc1-pdc5 deletion background.

    Science.gov (United States)

    Novy, Vera; Brunner, Bernd; Müller, Gerdt; Nidetzky, Bernd

    2017-01-01

    l-Lactic acid is an important platform chemical and its production from the lignocellulosic sugars glucose and xylose is, therefore, of high interest. Tolerance to low pH and a generally high robustness make Saccharomyces cerevisiae a promising host for l-lactic acid fermentation but strain development for effective utilization of both sugars is an unsolved problem. The herein used S. cerevisiae strain IBB10B05 incorporates a NADH-dependent pathway for oxidoreductive xylose assimilation within CEN.PK113-7D background and was additionally evolved for accelerated xylose-to-ethanol fermentation. Selecting the Plasmodium falciparum l-lactate dehydrogenase (pfLDH) for its high kinetic efficiency, strain IBB14LA1 was derived from IBB10B05 by placing the pfldh gene at the pdc1 locus under control of the pdc1 promotor. Strain IBB14LA1_5 additionally had the pdc5 gene disrupted. With both strains, continued l-lactic acid formation from glucose or xylose, each at 50 g/L, necessitated stabilization of pH. Using calcium carbonate (11 g/L), anaerobic shaken bottle fermentations at pH ≥ 5 resulted in l-lactic acid yields (YLA ) of 0.67 g/g glucose and 0.80 g/g xylose for strain IBB14LA1_5. Only little xylitol was formed (≤0.08 g/g) and no ethanol. In pH stabilized aerobic conversions of glucose, strain IBB14LA1_5 further showed excellent l-lactic acid productivities (1.8 g/L/h) without losses in YLA (0.69 g/g glucose). In strain IBB14LA1, the YLA was lower (≤0.18 g/g glucose; ≤0.27 g/g xylose) due to ethanol as well as xylitol formation. Therefore, this study shows that a S. cerevisiae strain originally optimized for xylose-to-ethanol fermentation was useful to implement l-lactic acid production from glucose and xylose; and with the metabolic engineering strategy applied, advance toward homolactic fermentation of both sugars was made. Biotechnol. Bioeng. 2017;114: 163-171. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  3. Xylitol synthesis mutant of xylose-utilizing zymomonas for ethanol production

    Science.gov (United States)

    Viitanen, Paul V.; Chou, Yat-Chen; McCutchen, Carol M.; Zhang, Min

    2010-06-22

    A strain of xylose-utilizing Zymomonas was engineered with a genetic modification to the glucose-fructose oxidoreductase gene resulting in reduced expression of GFOR enzyme activity. The engineered strain exhibits reduced production of xylitol, a detrimental by-product of xylose metabolism. It also consumes more xylose and produces more ethanol during mixed sugar fermentation under process-relevant conditions.

  4. Transposon mutagenesis to improve the growth of recombinant Saccharomyces cerevisiae on D-xylose

    Science.gov (United States)

    Haiying Ni; Jose M. Laplaza; Thomas W. Jeffries

    2007-01-01

    Saccharomyces cerevisiae L2612 transformed with genes for xylose reductase and xylitol dehydrogenase (XYL1 and XYL2) grows well on glucose but very poorly on D-xylose. When a gene for D-xylulokinase (XYL3 or XKS1) is overexpressed, growth on glucose is unaffected, but growth on xylose is blocked. Spontaneous or chemically induced mutants of this engineered yeast that...

  5. Engineering industrial Saccharomyces cerevisiae strains for xylose fermentation and comparison for switchgrass conversion

    Science.gov (United States)

    Saccharomyces physiology and fermentation related properties vary broadly among industrial strains. In this study, six industrial strains of varied genetic background were engineered to ferment xylose. Aerobic growth rates on xylose were 0.040 h**-1 to 0.167 h**-1. Fermentation of xylose, glucose/xy...

  6. On the pull: periplasmic trapping of sugars before transport.

    Science.gov (United States)

    Thomas, Gavin H

    2017-06-01

    Bacteria have evolved many routes for taking up nutrients, demonstrating great versatility in the types and mechanism of uptake used in different physiological conditions. The discovery of a single transporter in the bacterium Advenella mimigardefordensis for the uptake of five different sugars, including L-glucose and D-xylose, is described in this issue (Meinert et al., ), providing yet another example of the surprising adaptability of bacterial transport strategies. The transporter identified is a tripartite ATP-independent (TRAP) transporter, not previously associated with sugar transport, and in fact does not transport the sugars directly at all, rather requiring them to be converted in the periplasm to their respective sugar acid forms before transport through what appears to be a novel general sugar acid transporter. In this commentary, I describe how this process is consistent with the known mechanisms of TRAP transporters and consider how the role of sugar oxidation, or oxidative fermentation, operates with multiple hexose and pentose sugars. Finally I suggest that the periplasmic conversion of nutrients acquired across the outer membrane, before transport across the inner membrane, could have potentially useful biological functions in Gram negative bacteria. © 2017 John Wiley & Sons Ltd.

  7. Production of xylitol from D-xylose by Debaryomyces hansenii

    Energy Technology Data Exchange (ETDEWEB)

    Dominguez, J.M. [Univ. of Vigo, Ornese (Spain); Gong, Cheng S.; Tsao, G.T. [Purdue Univ., West Lafayette, IN (United States)

    1997-12-31

    Xylitol, a naturally occurring five-carbon sugar alcohol, can be produced from D-xylose through microbial hydrogenation. Xylitol has found increasing use in the food industries, especially in confectionary. It is the only so-called {open_quotes}second-generation polyol sweeteners{close_quotes} that is allowed to have the specific health claims in some world markets. In this study, the effect of cell density on the xylitol production by the yeast Debaryomyces hansenii NRRL Y-7426 from D-xylose under microaerobic conditions was examined. The rate of xylitol production increased with increasing yeast cell density to 3 g/L. Beyond this amount there was no increase in the xylitol production with increasing cell density. The optimal pH range for xylitol production was between 4.5 and 5.5. The optimal temperature was between 28 and 37{degrees}C, and the optimal shaking speed was 300 rpm. The rate of xylitol production increased linearly with increasing initial xylose concentration. A high concentration of xylose (279 g/L) was converted rapidly and efficiently to produce xylitol with a product concentration of 221 g/L was reached after 48 h of incubation under optimum conditions. 18 refs., 5 figs.

  8. Xylose reductase from the thermophilic fungus Talaromyces emersonii

    Indian Academy of Sciences (India)

    Prakash

    National University of Ireland, Galway, University Road, Galway, Ireland. 2Shannon Applied Biotechnology Centre, Limerick Institute Technology, Moylish Park, Limerick, Ireland. *Corresponding authors (Fax, 0035361208208; Email, patrick.murray@lit.ie). Xylose reductase is involved in the first step of the fungal pentose ...

  9. Enabling xylose utilization in Yarrowia lipolytica for lipid production.

    Science.gov (United States)

    Li, Haibo; Alper, Hal S

    2016-09-01

    The conversion of lignocellulosic sugars, in particular xylose, is important for sustainable fuels and chemicals production. While the oleaginous yeast Yarrowia lipolytica is a strong candidate for lipid production, it is currently unable to effectively utilize xylose. By introducing a heterologous oxidoreductase pathway and enabling starvation adaptation, we obtained a Y. lipolytica strain, E26 XUS, that can use xylose as a sole carbon source and produce over 15 g/L of lipid in bioreactor fermentations (29.3% of theoretical yield) with a maximal lipid productivity of 0.19 g/L/h. Genomic sequencing and genetic analysis pointed toward increases in genomic copy number of the pathway and resulting elevated expression levels as the causative mutations underlying this improved phenotype. More broadly, many regions of the genome were duplicated during starvation of Yarrowia. This strain can form the basis for further engineering to enhance xylose catabolic rates and conversion. Finally, this study also reveals the flexibility and dynamic nature of the Y. lipolytica genome, and the means at which starvation can be used to induce genomic duplications. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. 21 CFR 862.1820 - Xylose test system.

    Science.gov (United States)

    2010-04-01

    ... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Xylose test system. 862.1820 Section 862.1820 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL... treatment of gastrointestinal malabsorption syndrome (a group of disorders in which there is subnormal...

  11. Biofuel from D-xylose-the Second Most Abundant Sugar

    Indian Academy of Sciences (India)

    Home; Journals; Resonance – Journal of Science Education; Volume 7; Issue 5. Biofuel from D-xylose – the Second Most Abundant Sugar. Anil Lachke. General Article Volume 7 Issue 5 May 2002 pp 50-58. Fulltext. Click here to view fulltext PDF. Permanent link: http://www.ias.ac.in/article/fulltext/reso/007/05/0050-0058 ...

  12. Fermentation of xylose to ethanol by genetically modified enteric bacteria

    Energy Technology Data Exchange (ETDEWEB)

    Tolan, J.S.

    1987-01-01

    This thesis describes the fermentation of D-xylose by wild type and recombinant Klebsiella planticola ATCC 33531 and Erwinia chrysanthemi B374. The recombinant strains bear multi-copy plasmids containing the pdc gene inserted from Zymomonas mobilis. Expression of the gene in K. planticola markedly increased the yield of ethanol, up to 1.3 mole/mole xylose, or 25.1 g/L. Concurrently, there were significant decreases in the yields of formation acetate, lactate, and butanediol. Transconjugant Klebsiella grew almost as fast as the wild type and tolerated up to 4% ethanol. The plasmid was retained by the cells during at least one batch culture, even in the absence of selective pressure by antibiotics to maintain the plasmid. The cells produced 31.6 g/L ethanol from 79.6 g/L of a D-glucose-D-xylose-L-arabinose mixture designed to simulate hydrolyzed hemicellulose. The physiology of the wild type K. planticola is described in more detail than in the original report of its isolation. E. chrysanthemi PDC transconjugants also produced ethanol in high yield (up to 1.45 mole/mole xylose). However, transconjugant E. chrysanthemi grew only 1/4 as rapidly as the wild type and tolerated only 2% ethanol. The plasmid PZM15 apparently exhibits pleiotropic effects when inserted into K. planticola and into E. chrysanthemi.

  13. Alcohol Fermentation and Biomass formation from xylose, glucose ...

    African Journals Online (AJOL)

    This paper addresses the potential for utilizing xylose fermenting yeasts in fermenting pentoses from lignocellulosic materials obtained from saw dust and agricultural based products such as post harvest straws from maize, rice, sorghum, millet and bagasse from the sugar industries. Key words: wort, hydrolyzate, glucose, ...

  14. Evolutionary engineering of Saccharomyces cerevisiae for efficient aerobic xylose consumption

    Science.gov (United States)

    Gionata Scalcinati; Jose´ Manuel Otero; Jennifer R.H. Van Vleet; Thomas W. Jeffries; Lisbeth Olsson; Jens. Nielsen

    2012-01-01

    Industrial biotechnology aims to develop robust microbial cell factories, such as , to produce an array of added value chemicals presently dominated by petrochemical processes. Xylose is the second most abundant monosaccharide after glucose and the most prevalent pentose sugar found in lignocelluloses. Significant research...

  15. Screening of oleaginous yeast with xylose assimilating capacity for ...

    African Journals Online (AJOL)

    ... in industrial-scale production. In our preliminary study, 57 oleaginous yeast with xylose assimilating capacity were isolated from 13 soil samples, 16 strains were identified as potential lipid biomass producer. Four strains which showed higher lipid content were used for further ethanol fermentation at different conditions.

  16. Recycling carbon dioxide during xylose fermentation by engineered Saccharomyces cerevisiae

    Science.gov (United States)

    In this study, we introduced the ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) and phosphoribulokinase (PRK) into an engineered S. cerevisiae (SR8) harboring the XR/XDH pathway and up-regulated PPP 10, to enable CO2 recycling through a synthetic rPPP during xylose fermentation (Fig. 1). ...

  17. Evolvable synthetic neural system

    Science.gov (United States)

    Curtis, Steven A. (Inventor)

    2009-01-01

    An evolvable synthetic neural system includes an evolvable neural interface operably coupled to at least one neural basis function. Each neural basis function includes an evolvable neural interface operably coupled to a heuristic neural system to perform high-level functions and an autonomic neural system to perform low-level functions. In some embodiments, the evolvable synthetic neural system is operably coupled to one or more evolvable synthetic neural systems in a hierarchy.

  18. Comparative xylose metabolism among the Ascomycetes C. albicans, S. stipitis and S. cerevisiae.

    Science.gov (United States)

    Harcus, Doreen; Dignard, Daniel; Lépine, Guylaine; Askew, Chris; Raymond, Martine; Whiteway, Malcolm; Wu, Cunle

    2013-01-01

    The ascomycetes Candida albicans, Saccharomyces cerevisiae and Scheffersomyces stipitis metabolize the pentose sugar xylose very differently. S. cerevisiae fails to grow on xylose, while C. albicans can grow, and S. stipitis can both grow and ferment xylose to ethanol. However, all three species contain highly similar genes that encode potential xylose reductases and xylitol dehydrogenases required to convert xylose to xylulose, and xylulose supports the growth of all three fungi. We have created C. albicans strains deleted for the xylose reductase gene GRE3, the xylitol dehydrogenase gene XYL2, as well as the gre3 xyl2 double mutant. As expected, all the mutant strains cannot grow on xylose, while the single gre3 mutant can grow on xylitol. The gre3 and xyl2 mutants are efficiently complemented by the XYL1 and XYL2 from S. stipitis. Intriguingly, the S. cerevisiae GRE3 gene can complement the Cagre3 mutant, while the ScSOR1 gene can complement the Caxyl2 mutant, showing that S. cerevisiae contains the enzymatic capacity for converting xylose to xylulose. In addition, the gre3 xyl2 double mutant of C. albicans is effectively rescued by the xylose isomerase (XI) gene of either Piromyces or Orpinomyces, suggesting that the XI provides an alternative to the missing oxido-reductase functions in the mutant required for the xylose-xylulose conversion. Overall this work suggests that C. albicans strains engineered to lack essential steps for xylose metabolism can provide a platform for the analysis of xylose metabolism enzymes from a variety of species, and confirms that S. cerevisiae has the genetic potential to convert xylose to xylulose, although non-engineered strains cannot proliferate on xylose as the sole carbon source.

  19. Saccharomyces cerevisiae engineered for xylose metabolism requires gluconeogenesis and the oxidative branch of the pentose phosphate pathway for aerobic xylose assimilation

    Science.gov (United States)

    Saccharomyces strains engineered to ferment xylose using Scheffersomyces stipitis xylose reductase (XR) and xylitol dehydrogenase (XDH) genes appear to be limited by metabolic imbalances due to differing cofactor specificities of XR and XDH. The S. stipitis XR, which uses nicotinamide adenine dinucl...

  20. Mutations in PMR1 stimulate xylose isomerase activity and anaerobic growth on xylose of engineered Saccharomyces cerevisiae by influencing manganese homeostasis

    NARCIS (Netherlands)

    Verhoeven, Maarten D; Lee, Misun; Kamoen, Lycka; van den Broek, Marcel; Janssen, Dick B; Daran, Jean-Marc G; van Maris, Antonius J A; Pronk, Jack T

    2017-01-01

    Combined overexpression of xylulokinase, pentose-phosphate-pathway enzymes and a heterologous xylose isomerase (XI) is required but insufficient for anaerobic growth of Saccharomyces cerevisiae on d-xylose. Single-step Cas9-assisted implementation of these modifications yielded a yeast strain

  1. Bypassing the Pentose Phosphate Pathway: Towards Modular Utilization of Xylose.

    Directory of Open Access Journals (Sweden)

    Kulika Chomvong

    Full Text Available The efficient use of hemicellulose in the plant cell wall is critical for the economic conversion of plant biomass to renewable fuels and chemicals. Previously, the yeast Saccharomyces cerevisiae has been engineered to convert the hemicellulose-derived pentose sugars xylose and arabinose to d-xylulose-5-phosphate for conversion via the pentose phosphate pathway (PPP. However, efficient pentose utilization requires PPP optimization and may interfere with its roles in NADPH and pentose production. Here, we developed an alternative xylose utilization pathway that largely bypasses the PPP. In the new pathway, d-xylulose is converted to d-xylulose-1-phosphate, a novel metabolite to S. cerevisiae, which is then cleaved to glycolaldehyde and dihydroxyacetone phosphate. This synthetic pathway served as a platform for the biosynthesis of ethanol and ethylene glycol. The use of d-xylulose-1-phosphate as an entry point for xylose metabolism opens the way for optimizing chemical conversion of pentose sugars in S. cerevisiae in a modular fashion.

  2. Functional architecture of MFS d-glucose transporters

    National Research Council Canada - National Science Library

    M. Gregor Madej; Linfeng Sun; Nieng Yan; H. Ronald Kaback

    2014-01-01

    .... The recently solved crystallographic models of the D-xylose permease XylE from Escherichia coli and GlcP from Staphylococcus epidermidus, homologs of the human D-glucose transporters, the GLUTs (SLC2...

  3. Combined enzyme mediated fermentation of cellulous and xylose to ethanol by Schizosaccharoyces pombe, cellulase, .beta.-glucosidase, and xylose isomerase

    Science.gov (United States)

    Lastick, Stanley M.; Mohagheghi, Ali; Tucker, Melvin P.; Grohmann, Karel

    1994-01-01

    A process for producing ethanol from mixed sugar streams from pretreated biomass comprising xylose and cellulose using enzymes to convert these substrates to fermentable sugars; selecting and isolating a yeast Schizosaccharomyces pombe ATCC No. 2476, having the ability to ferment these sugars as they are being formed to produce ethanol; loading the substrates with the fermentation mix composed of yeast, enzymes and substrates; fermenting the loaded substrates and enzymes under anaerobic conditions at a pH range of between about 5.0 to about 6.0 and at a temperature range of between about 35.degree. C. to about 40.degree. C. until the fermentation is completed, the xylose being isomerized to xylulose, the cellulose being converted to glucose, and these sugars being concurrently converted to ethanol by yeast through means of the anaerobic fermentation; and recovering the ethanol.

  4. Combined enzyme mediated fermentation of cellulose and xylose to ethanol by Schizosaccharomyces pombe, cellulase, [beta]-glucosidase, and xylose isomerase

    Science.gov (United States)

    Lastick, S.M.; Mohagheghi, A.; Tucker, M.P.; Grohmann, K.

    1994-12-13

    A process for producing ethanol from mixed sugar streams from pretreated biomass comprising xylose and cellulose using enzymes to convert these substrates to fermentable sugars; selecting and isolating a yeast Schizosaccharomyces pombe ATCC No. 2476, having the ability to ferment these sugars as they are being formed to produce ethanol; loading the substrates with the fermentation mix composed of yeast, enzymes and substrates; fermenting the loaded substrates and enzymes under anaerobic conditions at a pH range of between about 5.0 to about 6.0 and at a temperature range of between about 35 C to about 40 C until the fermentation is completed, the xylose being isomerized to xylulose, the cellulose being converted to glucose, and these sugars being concurrently converted to ethanol by yeast through means of the anaerobic fermentation; and recovering the ethanol. 2 figures.

  5. Effect of in situ acids removal on mixed glucose and xylose fermentation by Clostridium tyrobutyricum

    DEFF Research Database (Denmark)

    Baroi, George Nabin; V. Skiadas, Ioannis; Westermann, Peter

    2015-01-01

    . tyrobutyricum has a lower affinity for xylose than for glucose. Potassium ions negatively affected the effective maximum growth rate of C. tyrobutyricum at concentrations higher than 5 g L-1 exhibiting a non-competitive type of inhibition. Continuous fermentation of a glucose and xylose mixture......In the present study, the effect of potassium ions and increasing concentrations of glucose and xylose on the growth of a strain of Clostridium tyrobutyricum, adapted to wheat straw hydrolysate, was investigated. Application of continuous fermentation of a mixture of glucose and xylose and in situ...... of 50 and 37 g L-1 respectively, and that they were consumed at comparable rates when fermented alone. However, continuous fermentation of a mixture of glucose and xylose resulted in a significantly decreased xylose consumption rate compared to that of glucose alone, supporting the conclusion that C...

  6. Engineering of carbon catabolite repression in recombinant xylose fermenting Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Roca, Christophe Francois Aime; Haack, Martin Brian; Olsson, Lisbeth

    2004-01-01

    Two xylose-fermenting glucose-derepressed Saccharomyces cerevisiae strains were constructed in order to investigate the influence of carbon catabolite repression on xylose metabolism. S. cerevisiae CPB.CR2 (Deltamig1, XYL1, XYL2, XKS1) and CPB.MBH2 (Deltamig1, Deltamig2, XYL1, XYL2, XKS1) were...... analysed for changes in xylose consumption rate and ethanol production rate during anaerobic batch and chemostat cultivations on a mixture of 20 g l(-1) glucose and 50 g l(-1) xylose, and their characteristics were compared to the parental strain S. cerevisiae TMB3001 (XYL1, XYL2, XKS1). Improvement...... of CPB.CR2, where the cells are assumed to grow under non-repressive conditions as they sense almost no glucose, invertase activity was lower during growth on xylose and glucose than on glucose only. The 3-fold reduction in invertase activity could only be attributed to the presence of xylose, suggesting...

  7. Engineering of the redox imbalance of Fusarium oxysporum enables anaerobic growth on xylose

    DEFF Research Database (Denmark)

    Panagiotou, Gianni; Christakopoulos, Paul; Grotkjær, Thomas

    2006-01-01

    Dissimilatory nitrate reduction metabolism, of the natural xylose-fermenting fungus Fusarium oxysporum, was used as a strategy to achieve anaerobic growth and ethanol production from xylose. Beneficial alterations of the redox fluxes and thereby of the xylose metabolism were obtained by taking ad...... of this poorly described microorganism. It was demonstrated that dissimilatory nitrate reduction allows F oxysporum to exhibit typical respiratory metabolic behaviour with a highly active TCA cycle and a large demand for NADPH....

  8. Selection of yeast Saccharomyces cerevisiae promoters available for xylose cultivation and fermentation.

    Science.gov (United States)

    Nambu-Nishida, Yumiko; Sakihama, Yuri; Ishii, Jun; Hasunuma, Tomohisa; Kondo, Akihiko

    2017-08-28

    To efficiently utilize xylose, a major sugar component of hemicelluloses, in Saccharomyces cerevisiae requires the proper expression of varied exogenous and endogenous genes. To expand the repertoire of promoters in engineered xylose-utilizing yeast strains, we selected promoters in S. cerevisiae during cultivation and fermentation using xylose as a carbon source. To select candidate promoters that function in the presence of xylose, we performed comprehensive gene expression analyses using xylose-utilizing yeast strains both during xylose and glucose fermentation. Based on microarray data, we chose 29 genes that showed strong, moderate, and weak expression in xylose rather than glucose fermentation. The activities of these promoters in a xylose-utilizing yeast strain were measured by lacZ reporter gene assays over time during aerobic cultivation and microaerobic fermentation, both in xylose and glucose media. In xylose media, PTDH3, PFBA1, and PTDH1 were favorable for high expression, and PSED1, PHXT7, PPDC1, PTEF1, PTPI1, and PPGK1 were acceptable for medium-high expression in aerobic cultivation, and moderate expression in microaerobic fermentation. PTEF2 allowed moderate expression in aerobic culture and weak expression in microaerobic fermentation, although it showed medium-high expression in glucose media. PZWF1 and PSOL4 allowed moderate expression in aerobic cultivation, while showing weak but clear expression in microaerobic fermentation. PALD3 and PTKL2 showed moderate promoter activity in aerobic cultivation, but showed almost no activity in microaerobic fermentation. The knowledge of promoter activities in xylose cultivation obtained in this study will permit the control of gene expression in engineered xylose-utilizing yeast strains that are used for hemicellulose fermentation. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  9. Minimal metabolic engineering of Saccharomyces cerevisiae for efficient anaerobic xylose fermentation: a proof of principle.

    Science.gov (United States)

    Kuyper, Marko; Winkler, Aaron A; van Dijken, Johannes P; Pronk, Jack T

    2004-03-01

    When xylose metabolism in yeasts proceeds exclusively via NADPH-specific xylose reductase and NAD-specific xylitol dehydrogenase, anaerobic conversion of the pentose to ethanol is intrinsically impossible. When xylose reductase has a dual specificity for both NADPH and NADH, anaerobic alcoholic fermentation is feasible but requires the formation of large amounts of polyols (e.g., xylitol) to maintain a closed redox balance. As a result, the ethanol yield on xylose will be sub-optimal. This paper demonstrates that anaerobic conversion of xylose to ethanol, without substantial by-product formation, is possible in Saccharomyces cerevisiae when a heterologous xylose isomerase (EC 5.3.1.5) is functionally expressed. Transformants expressing the XylA gene from the anaerobic fungus Piromyces sp. E2 (ATCC 76762) grew in synthetic medium in shake-flask cultures on xylose with a specific growth rate of 0.005 h(-1). After prolonged cultivation on xylose, a mutant strain was obtained that grew aerobically and anaerobically on xylose, at specific growth rates of 0.18 and 0.03 h(-1), respectively. The anaerobic ethanol yield was 0.42 g ethanol x g xylose(-1) and also by-product formation was comparable to that of glucose-grown anaerobic cultures. These results illustrate that only minimal genetic engineering is required to recruit a functional xylose metabolic pathway in Saccharomyces cerevisiae. Activities and/or regulatory properties of native S. cerevisiae gene products can subsequently be optimised via evolutionary engineering. These results provide a gateway towards commercially viable ethanol production from xylose with S. cerevisiae.

  10. Engineering of a matched pair of xylose reductase and xylitol dehydrogenase for xylose fermentation by Saccharomyces cerevisiae.

    Science.gov (United States)

    Krahulec, Stefan; Klimacek, Mario; Nidetzky, Bernd

    2009-05-01

    Metabolic engineering of Saccharomyces cerevisiae for xylose fermentation has often relied on insertion of a heterologous pathway consisting of nicotinamide adenine dinucleotide (phosphate) NAD(P)H-dependent xylose reductase (XR) and NAD(+)-dependent xylitol dehydrogenase (XDH). Low ethanol yield, formation of xylitol and other fermentation by-products are seen for many of the S. cerevisiae strains constructed in this way. This has been ascribed to incomplete coenzyme recycling in the steps catalyzed by XR and XDH. Despite various protein-engineering efforts to alter the coenzyme specificity of XR and XDH individually, a pair of enzymes displaying matched utilization of NAD(H) and NADP(H) was not previously reported. We have introduced multiple site-directed mutations in the coenzyme-binding pocket of Galactocandida mastotermitis XDH to enable activity with NADP(+), which is lacking in the wild-type enzyme. We describe four enzyme variants showing activity for xylitol oxidation by NADP(+) and NAD(+). One of the XDH variants utilized NADP(+) about 4 times more efficiently than NAD(+). This is close to the preference for NADPH compared with NADH in mutants of Candida tenuis XR. Compared to an S. cerevisiae-reference strain expressing the genes for the wild-type enzymes, the strains comprising the gene encoding the mutated XDH in combination a matched XR mutant gene showed up to 50% decreased glycerol yield without increase in ethanol during xylose fermentation.

  11. Enhanced biofuel production through coupled acetic acid and xylose consumption by engineered yeast

    National Research Council Canada - National Science Library

    Wei, Na; Quarterman, Josh; Kim, Soo Rin; Cate, Jamie H D; Jin, Yong-Su

    2013-01-01

    .... However, commercial production of cellulosic biofuel has been hampered by inefficient fermentation of xylose and the toxicity of acetic acid, which constitute substantial portions of cellulosic biomass...

  12. Enhancing ethanol yields through d-xylose and l-arabinose co-fermentation after construction of a novel high efficient l-arabinose-fermenting Saccharomyces cerevisiae strain.

    Science.gov (United States)

    Caballero, Antonio; Ramos, Juan Luis

    2017-04-01

    Lignocellulose contains two pentose sugars, l-arabinose and d-xylose, neither of which is naturally fermented by first generation (1G) ethanol-producing Saccharomyces cerevisiae yeast. Since these sugars are inaccessible to 1G yeast, a significant percentage of the total carbon in bioethanol production from plant residues, which are used in second generation (2G) ethanol production, remains unused. Recombinant Saccharomyces cerevisiae strains capable of fermenting d-xylose are available on the market; however, there are few examples of l-arabinose-fermenting yeasts, and commercially, there are no strains capable of fermenting both d-xylose and l-arabinose because of metabolic incompatibilities when both metabolic pathways are expressed in the same cell. To attempt to solve this problem we have tested d-xylose and l-arabinose co-fermentation. To find efficient alternative l-arabinose utilization pathways to the few existing ones, we have used stringent methodology to screen for new genes (metabolic and transporter functions) to facilitate l-arabinose fermentation in recombinant yeast. We demonstrate the feasibility of this approach in a successfully constructed yeast strain capable of using l-arabinose as the sole carbon source and capable of fully transforming it to ethanol, reaching the maximum theoretical fermentation yield (0.43 g g-1). We demonstrate that efficient co-fermentation of d-xylose and l-arabinose is feasible using two different co-cultured strains, and observed no fermentation delays, yield drops or accumulation of undesired byproducts. In this study we have identified a technically efficient strategy to enhance ethanol yields by 10 % in 2G plants in a process based on C5 sugar co-fermentation.

  13. Butyric acid production from lignocellulosic biomass hydrolysates by engineered Clostridium tyrobutyricum overexpressing xylose catabolism genes for glucose and xylose co-utilization.

    Science.gov (United States)

    Fu, Hongxin; Yang, Shang-Tian; Wang, Minqi; Wang, Jufang; Tang, I-Ching

    2017-06-01

    Clostridium tyrobutyricum can utilize glucose and xylose as carbon source for butyric acid production. However, xylose catabolism is inhibited by glucose, hampering butyric acid production from lignocellulosic biomass hydrolysates containing both glucose and xylose. In this study, an engineered strain of C. tyrobutyricum Ct-pTBA overexpressing heterologous xylose catabolism genes (xylT, xylA, and xylB) was investigated for co-utilizing glucose and xylose present in hydrolysates of plant biomass, including soybean hull, corn fiber, wheat straw, rice straw, and sugarcane bagasse. Compared to the wild-type strain, Ct-pTBA showed higher xylose utilization without significant glucose catabolite repression, achieving near 100% utilization of glucose and xylose present in lignocellulosic biomass hydrolysates in bioreactor at pH 6. About 42.6g/L butyrate at a productivity of 0.56g/L·h and yield of 0.36g/g was obtained in batch fermentation, demonstrating the potential of C. tyrobutyricum Ct-pTBA for butyric acid production from lignocellulosic biomass hydrolysates. Copyright © 2017 Elsevier Ltd. All rights reserved.

  14. Reaction mechanisms and kinetics of processing glucose, xylose and glucose-xylose mixtures under hot compressed water conditions for predicting bio-crude composition

    DEFF Research Database (Denmark)

    Grigoras, Ionela; Toor, Saqib Sohail; Rosendahl, Lasse Aistrup

    Mechanisms for bio-crude formation during the conversion of glucose, xylose and glucose-xylose mixtures as biomass model compounds under hot compressed water conditions are investigated. Studies in literature have shown that the diverse products formed at the early stages of glucose or xylose...... conversion are 5-HMF, erythrose, glyceraldehyde, dihydroxyacetone, pyruvaldehyde, and saccharinic acids resulted through reactions such as dehydration, retro-aldol condensation and isomerization. However, these compounds are mostly water soluble compounds and lack the final steps towards formation of water...

  15. Engineering Saccharomyces pastorianus for the co-utilisation of xylose and cellulose from biomass.

    Science.gov (United States)

    Kricka, William; James, Tharappel C; Fitzpatrick, James; Bond, Ursula

    2015-04-28

    Lignocellulosic biomass is a viable source of renewable energy for bioethanol production. For the efficient conversion of biomass into bioethanol, it is essential that sugars from both the cellulose and hemicellulose fractions of lignocellulose be utilised. We describe the development of a recombinant yeast system for the fermentation of cellulose and xylose, the most abundant pentose sugar in the hemicellulose fraction of biomass. The brewer's yeast Saccharomyces pastorianus was chosen as a host as significantly higher recombinant enzyme activities are achieved, when compared to the more commonly used S. cerevisiae. When expressed in S. pastorianus, the Trichoderma reesei xylose oxidoreductase pathway was more efficient at alcohol production from xylose than the xylose isomerase pathway. The alcohol yield was influenced by the concentration of xylose in the medium and was significantly improved by the additional expression of a gene encoding for xylulose kinase. The xylose reductase, xylitol dehydrogenase and xylulose kinase genes were co-expressed with genes encoding for the three classes of T. reesei cellulases, namely endoglucanase (EG2), cellobiohydrolysase (CBH2) and β-glucosidase (BGL1). The initial metabolism of xylose by the engineered strains facilitated production of cellulases at fermentation temperatures. The sequential metabolism of xylose and cellulose generated an alcohol yield of 82% from the available sugars. Several different types of biomass, such as the energy crop Miscanthus sinensis and the industrial waste, brewer's spent grains, were examined as biomass sources for fermentation using the developed yeast strains. Xylose metabolism and cell growth were inhibited in fermentations carried out with acid-treated spent grain liquor, resulting in a 30% reduction in alcohol yield compared to fermentations carried out with mixed sugar substrates. Reconstitution of complete enzymatic pathways for cellulose hydrolysis and xylose utilisation in S

  16. Cross-reactions between engineered xylose and galactose pathways in recombinant Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Garcia Sanchez Rosa

    2010-09-01

    Full Text Available Abstract Background Overexpression of the PGM2 gene encoding phosphoglucomutase (Pgm2p has been shown to improve galactose utilization both under aerobic and under anaerobic conditions. Similarly, xylose utilization has been improved by overexpression of genes encoding xylulokinase (XK, enzymes from the non-oxidative pentose phosphate pathway (non-ox PPP and deletion of the endogenous aldose reductase GRE3 gene in engineered Saccharomyces cerevisiae strains carrying either fungal or bacterial xylose pathways. In the present study, we investigated how the combination of these traits affect xylose and galactose utilization in the presence or absence of glucose in S. cerevisiae strains engineered with the xylose reductase (XR-xylitol dehydrogenase (XDH pathway. Results In the absence of PGM2 overexpression, the combined overexpression of XK, the non-ox PPP and deletion of the GRE3 gene significantly delayed aerobic growth on galactose, whereas no difference was observed between the control strain and the xylose-engineered strain when the PGM2 gene was overexpressed. Under anaerobic conditions, the overexpression of the PGM2 gene increased the ethanol yield and the xylose consumption rate in medium containing xylose as the only carbon source. The possibility of Pgm2p acting as a xylose isomerase (XI could be excluded by measuring the XI activity in both strains. The additional copy of the PGM2 gene also resulted in a shorter fermentation time during the co-consumption of galactose and xylose. However, the effect was lost upon addition of glucose to the growth medium. Conclusions PGM2 overexpression was shown to benefit xylose and galactose fermentation, alone and in combination. In contrast, galactose fermentation was impaired in the engineered xylose-utilizing strain harbouring extra copies of the non-ox PPP genes and a deletion of the GRE3 gene, unless PGM2 was overexpressed. These cross-reactions are of particular relevance for the fermentation

  17. [Fermentations of xylose and arabinose by Kluyveromyces marxianus].

    Science.gov (United States)

    Hou, Shengbo; Feng, Hualiang; Gao, Jiaoqi; Li, Yimin; Yuan, Wenjie; Bai, Fengwu

    2017-06-25

    Kluyveromyces marxianus, as unconventional yeast, attracts more and more attention in the biofuel fermentation. Although this sort of yeasts can ferment pentose sugars, the fermentation capacity differs largely. Xylose and arabinose fermentation by three K. marxianus strains (K. m 9009, K. m 1911 and K. m 1727) were compared at different temperatures. The results showed that the fermentation performance of the three strains had significant difference under different fermentation temperatures. Especially, the sugar consumption rate and alcohol yield of K. m 9009 and K. m 1727 at 40 ℃ were better than 30 ℃. This results fully reflect the fermentation advantages of K. marxianus yeast under high-temperature. On this basis, five genes (XR, XDH, XK, AR and LAD) coding key metabolic enzymes in three different yeasts were amplified by PCR, and the sequence were compared by Clustalx 2.1. The results showed that the amino acid sequences coding key enzymes have similarity of over 98% with the reference sequences reported in the literature. Furthermore, the difference of amino acid was not at the key site of its enzyme, so the differences between three stains were not caused by the gene level, but by transcribed or translation regulation level. By real-time PCR experiment, we determined the gene expression levels of four key enzymes (XR, XDH, XK and ADH) in the xylose metabolism pathway of K. m 1727 and K. m 1911 at different fermentation time points. The results showed that, for thermotolerant yeast K. m 1727, the low expression level of XDH and XK genes was the main factors leading to accumulation of xylitol. In addition, according to the pathway of Zygosaccharomyces bailii, which have been reported in NCBI and KEGG, the xylose and arabinose metabolic pathways of K. marxianus were identified, which laid foundation for further improving the pentose fermentation ability by metabolic engineering.

  18. X-ray Laue diffraction from crystals of xylose isomerase.

    OpenAIRE

    Farber, G. K.; Machin, P; Almo, S C; Petsko, G A; Hajdu, J.

    1988-01-01

    The Laue method (stationary crystal, polychromatic x-rays) was used to collect native and heavy-atom-derivative data on crystals of xylose isomerase (EC 5.3.1.5). These data were used to find the heavy-atom positions. The positions found by use of Laue data are the same as those found by use of monochromatic data collected on a diffractometer. These results confirm that Laue diffraction data sets, which can be obtained on a millisecond time scale, can be used to locate small molecules bound t...

  19. Xylose fermentation to biofuels (hydrogen and ethanol) by extreme thermophilic (70 C) mixed culture

    DEFF Research Database (Denmark)

    Chenxi, Zhao; Karakashev, Dimitar Borisov; Lu, W.

    2010-01-01

    Combined biohydrogen and bioethanol (CHE) production from xylose was achieved by an extreme thermophilic (70 degrees C) mixed culture. Effect of initial pH, xylose, peptone, FeSO4, NaHCO3, yeast extract, trace mineral salts, vitamins, and phosphate buffer concentrations on bioethanol and biohydro...

  20. Ethanol production using xylitol synthesis mutant of xylose-utilizing zymomonas

    Science.gov (United States)

    Viitanen, Paul V.; McCutchen, Carol M.; Emptage, Mark; Caimi, Perry G.; Zhang, Min; Chou, Yat-Chen

    2010-06-22

    Production of ethanol using a strain of xylose-utilizing Zymomonas with a genetic modification of the glucose-fructose oxidoreductase gene was found to be improved due to greatly reduced production of xylitol, a detrimental by-product of xylose metabolism synthesized during fermentation.

  1. Electricity production from xylose using a mediator-less microbial fuel cell

    DEFF Research Database (Denmark)

    Huang, Liping; Zeng, Raymond Jianxiong; Angelidaki, Irini

    2008-01-01

    Electricity generation integrated with xylose degradation was investigated in a two-chamber mediator-less microbial fuel cell (MFC). Voltage output followed saturation kinetics as a function of xylose concentration for concentration below 9.7 mM, with a predicted maximum of 86 mV (6.3 mW m(-2...

  2. Cofermentation of Glucose, Xylose, and Cellobiose by the Beetle-Associated Yeast Spathaspora passalidarum

    Science.gov (United States)

    Tanya M. Long; Yi-Kai Su; Jennifer Headman; Alan Higbee; Laura B. Willis; Thomas W. Jeffries

    2012-01-01

    Fermentation of cellulosic and hemicellulosic sugars from biomass could resolve food-versus-fuel conflicts inherent in the bioconversion of grains. However, the inability to coferment glucose and xylose is a major challenge to the economical use of lignocellulose as a feedstock. Simultaneous cofermentation of glucose, xylose, and cellobiose is problematic for most...

  3. Continuous xylose fermentation by Clostridium acetobutylicum – Kinetics and energetics issues under acidogenesis conditions

    NARCIS (Netherlands)

    Procentese, A.; Raganati, F.; Olivieri, G.; Russo, M.E.; Salatino, P.; Marzocchella, A.

    2014-01-01

    The paper reports the assessment of the growth kinetics of Clostridium acetobutylicum DSM 792 adopting xylose as carbon source. Xylose is the fundamental component of hemicellulose hydrolysis, a relevant fraction of lignocellulosic feedstocks for biofuel production. Tests were carried out in a CSTR

  4. Transcriptional activator Cat8 is involved in regulation of xylose alcoholic fermentation in the thermotolerant yeast Ogataea (Hansenula) polymorpha

    OpenAIRE

    Ruchala, Justyna; Kurylenko, Olena O.; Soontorngun, Nitnipa; Dmytruk, Kostyantyn V.; Sibirny, Andriy A.

    2017-01-01

    Background Efficient xylose alcoholic fermentation is one of the key to a successful lignocellulosic ethanol production. However, regulation of this process in the native xylose-fermenting yeasts is poorly understood. In this work, we paid attention to the transcriptional factor Cat8 and its possible role in xylose alcoholic fermentation in Ogataea (Hansenula) polymorpha. In Saccharomyces cerevisiae, organism, which does not metabolize xylose, gene CAT8 encodes a Zn-cluster transcriptional ac...

  5. Engineering of xylose reductase and overexpression of xylitol dehydrogenase and xylulokinase improves xylose alcoholic fermentation in the thermotolerant yeast Hansenula polymorpha

    Directory of Open Access Journals (Sweden)

    Voronovsky Andriy Y

    2008-07-01

    Full Text Available Abstract Background The thermotolerant methylotrophic yeast Hansenula polymorpha is capable of alcoholic fermentation of xylose at elevated temperatures (45 – 48°C. Such property of this yeast defines it as a good candidate for the development of an efficient process for simultaneous saccharification and fermentation. However, to be economically viable, the main characteristics of xylose fermentation of H. polymorpha have to be improved. Results Site-specific mutagenesis of H. polymorpha XYL1 gene encoding xylose reductase was carried out to decrease affinity of this enzyme toward NADPH. The modified version of XYL1 gene under control of the strong constitutive HpGAP promoter was overexpressed on a Δxyl1 background. This resulted in significant increase in the KM for NADPH in the mutated xylose reductase (K341 → R N343 → D, while KM for NADH remained nearly unchanged. The recombinant H. polymorpha strain overexpressing the mutated enzyme together with native xylitol dehydrogenase and xylulokinase on Δxyl1 background was constructed. Xylose consumption, ethanol and xylitol production by the constructed strain were determined for high-temperature xylose fermentation at 48°C. A significant increase in ethanol productivity (up to 7.3 times was shown in this recombinant strain as compared with the wild type strain. Moreover, the xylitol production by the recombinant strain was reduced considerably to 0.9 mg × (L × h-1 as compared to 4.2 mg × (L × h-1 for the wild type strain. Conclusion Recombinant strains of H. polymorpha engineered for improved xylose utilization are described in the present work. These strains show a significant increase in ethanol productivity with simultaneous reduction in the production of xylitol during high-temperature xylose fermentation.

  6. Mutations in PMR1 stimulate xylose isomerase activity and anaerobic growth on xylose of engineered Saccharomyces cerevisiae by influencing manganese homeostasis

    Science.gov (United States)

    Verhoeven, Maarten D.; Lee, Misun; Kamoen, Lycka; van den Broek, Marcel; Janssen, Dick B.; Daran, Jean-Marc G.; van Maris, Antonius J. A.; Pronk, Jack T.

    2017-01-01

    Combined overexpression of xylulokinase, pentose-phosphate-pathway enzymes and a heterologous xylose isomerase (XI) is required but insufficient for anaerobic growth of Saccharomyces cerevisiae on d-xylose. Single-step Cas9-assisted implementation of these modifications yielded a yeast strain expressing Piromyces XI that showed fast aerobic growth on d-xylose. However, anaerobic growth required a 12-day adaptation period. Xylose-adapted cultures carried mutations in PMR1, encoding a Golgi Ca2+/Mn2+ ATPase. Deleting PMR1 in the parental XI-expressing strain enabled instantaneous anaerobic growth on d-xylose. In pmr1 strains, intracellular Mn2+ concentrations were much higher than in the parental strain. XI activity assays in cell extracts and reconstitution experiments with purified XI apoenzyme showed superior enzyme kinetics with Mn2+ relative to other divalent metal ions. This study indicates engineering of metal homeostasis as a relevant approach for optimization of metabolic pathways involving metal-dependent enzymes. Specifically, it identifies metal interactions of heterologous XIs as an underexplored aspect of engineering xylose metabolism in yeast. PMID:28401919

  7. A Novel Technique that Enables Efficient Conduct of Simultaneous Isomerization and Fermentation (SIF) of Xylose

    Science.gov (United States)

    Rao, Kripa; Chelikani, Silpa; Relue, Patricia; Varanasi, Sasidhar

    Of the sugars recovered from lignocellulose, D-glucose can be readily converted into ethanol by baker's or brewer's yeast (Saccharomyces cerevisiae). However, xylose that is obtained by the hydrolysis of the hemicellulosic portion is not fermentable by the same species of yeasts. Xylose fermentation by native yeasts can be achieved via isomerization of xylose to its ketose isomer, xylulose. Isomerization with exogenous xylose isomerase (XI) occurs optimally at a pH of 7-8, whereas subsequent fermentation of xylulose to ethanol occurs at a pH of 4-5. We present a novel scheme for efficient isomerization of xylose to xylulose at conditions suitable for the fermentation by using an immobilized enzyme system capable of sustaining two different pH microenvironments in a single vessel. The proof-of-concept of the two-enzyme pellet is presented, showing conversion of xylose to xylulose even when the immobilized enzyme pellets are suspended in a bulk solution whose pH is sub-optimal for XI activity. The co-immobilized enzyme pellets may prove extremely valuable in effectively conducting "simultaneous isomerization and fermentation" (SIF) of xylose. To help further shift the equilibrium in favor of xylulose formation, sodium tetraborate (borax) was added to the isomerization solution. Binding of tetrahydroxyborate ions to xylulose effectively reduces the concentration of xylulose and leads to increased xylose isomerization. The formation of tetrahydroxyborate ions and the enhancement in xylulose production resulting from the complexation was studied at two different bulk pH values. The addition of 0.05 M borax to the isomerization solution containing our co-immobilized enzyme pellets resulted in xylose to xylulose conversion as high as 86% under pH conditions that are suboptimal for XI activity. These initial findings, which can be optimized for industrial conditions, have significant potential for increasing the yield of ethanol from xylose in an SIF approach.

  8. Enhanced xylose fermentation by engineered yeast expressing NADH oxidase through high cell density inoculums.

    Science.gov (United States)

    Zhang, Guo-Chang; Turner, Timothy L; Jin, Yong-Su

    2017-03-01

    Accumulation of reduced byproducts such as glycerol and xylitol during xylose fermentation by engineered Saccharomyces cerevisiae hampers the economic production of biofuels and chemicals from cellulosic hydrolysates. In particular, engineered S. cerevisiae expressing NADPH-linked xylose reductase (XR) and NAD + -linked xylitol dehydrogenase (XDH) produces substantial amounts of the reduced byproducts under anaerobic conditions due to the cofactor difference of XR and XDH. While the additional expression of a water-forming NADH oxidase (NoxE) from Lactococcus lactis in engineered S. cerevisiae with the XR/XDH pathway led to reduced glycerol and xylitol production and increased ethanol yields from xylose, volumetric ethanol productivities by the engineered yeast decreased because of growth defects from the overexpression of noxE. In this study, we introduced noxE into an engineered yeast strain (SR8) exhibiting near-optimal xylose fermentation capacity. To overcome the growth defect caused by the overexpression of noxE, we used a high cell density inoculum for xylose fermentation by the SR8 expressing noxE. The resulting strain, SR8N, not only showed a higher ethanol yield and lower byproduct yields, but also exhibited a high ethanol productivity during xylose fermentation. As noxE overexpression elicits a negligible growth defect on glucose conditions, the beneficial effects of noxE overexpression were substantial when a mixture of glucose and xylose was used. Consumption of glucose led to rapid cell growth and therefore enhanced the subsequent xylose fermentation. As a result, the SR8N strain produced more ethanol and fewer byproducts from a mixture of glucose and xylose than the parental SR8 strain without noxE overexpression. Our results suggest that the growth defects from noxE overexpression can be overcome in the case of fermenting lignocellulose-derived sugars such as glucose and xylose.

  9. Impact of xylose and mannose on central metabolism of yeast Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Pitkaenen, J.P.

    2005-07-01

    In this study, understanding of the central metabolism was improved by quantification of metabolite concentrations, enzyme activities, protein abundances, and gene transcript concentrations. Intracellular fluxes were estimated by applying stoichiometric models of metabolism. The methods were applied in the study of yeast Saccharomyces cerevisiae in two separate projects. A xylose project aimed at improved utilization of D- xylose as a substrate for, e.g., producing biomaterial- based fuel ethanol. A mannose project studied the production of GDP-mannose from D-mannose in a strain lacking the gene for phosphomannose isomerase (PMI40 deletion). Hexose, D-glucose is the only sugar more abundant than pentose D-xylose. D-xylose is common in hardwoods (e.g. birch) and crop residues (ca. 25% of dry weight). However, S. cerevisiae is unable to utilize D- xylose without a recombinant pathway where D-xylose is converted to Dxylulose. In this study D-xylose was converted in two steps via xylitol: by D-xylose reductase and xylitol dehydrogenase encoded by XYL1 and XYL2 from Pichia stipitis, respectively. Additionally, endogenous xylulokinase (XKS1) was overexpressed in order to increase the consumption of D-xylose by enhancing the phosphorylation of D-xylulose. Despite of the functional recombinant pathway the utilization rates of D xylose still remained low. This study proposes a set of limitations that are responsible for the low utilization rates of D-xylose under microaerobic conditions. Cells compensated for the cofactor imbalance, caused by the conversion of D-xylose to D- xylulose, by increasing the flux through the oxidative pentose phosphate pathway and by shuttling NADH redox potential to mitochondrion to be oxidized in oxidative phosphorylation. However, mitochondrial NADH inhibits citrate synthase in citric acid cycle, and consequently lower flux through citric acid cycle limits oxidative phosphorylation. Further, limitations in the uptake of D- xylose, in the

  10. Evolving digital ecological networks.

    Directory of Open Access Journals (Sweden)

    Miguel A Fortuna

    Full Text Available "It is hard to realize that the living world as we know it is just one among many possibilities" [1]. Evolving digital ecological networks are webs of interacting, self-replicating, and evolving computer programs (i.e., digital organisms that experience the same major ecological interactions as biological organisms (e.g., competition, predation, parasitism, and mutualism. Despite being computational, these programs evolve quickly in an open-ended way, and starting from only one or two ancestral organisms, the formation of ecological networks can be observed in real-time by tracking interactions between the constantly evolving organism phenotypes. These phenotypes may be defined by combinations of logical computations (hereafter tasks that digital organisms perform and by expressed behaviors that have evolved. The types and outcomes of interactions between phenotypes are determined by task overlap for logic-defined phenotypes and by responses to encounters in the case of behavioral phenotypes. Biologists use these evolving networks to study active and fundamental topics within evolutionary ecology (e.g., the extent to which the architecture of multispecies networks shape coevolutionary outcomes, and the processes involved.

  11. Comparative genomics of xylose-fermenting fungi for enhanced biofuel production

    Energy Technology Data Exchange (ETDEWEB)

    Wohlbach, Dana J.; Kuo, Alan; Sato, Trey K.; Potts, Katlyn M.; Salamov, Asaf A.; LaButti, Kurt M.; Sun, Hui; Clum, Alicia; Pangilinan, Jasmyn L.; Lindquist, Erika A.; Lucas, Susan; Lapidus, Alla; Jin, Mingjie; Gunawan, Christa; Balan, Venkatesh; Dale, Bruce E.; Jeffries, Thomas W.; Zinkel, Robert; Barry, Kerrie W.; Grigoriev, Igor V.; Gasch, Audrey P.

    2011-02-24

    Cellulosic biomass is an abundant and underused substrate for biofuel production. The inability of many microbes to metabolize the pentose sugars abundant within hemicellulose creates specific challenges for microbial biofuel production from cellulosic material. Although engineered strains of Saccharomyces cerevisiae can use the pentose xylose, the fermentative capacity pales in comparison with glucose, limiting the economic feasibility of industrial fermentations. To better understand xylose utilization for subsequent microbial engineering, we sequenced the genomes of two xylose-fermenting, beetle-associated fungi, Spathaspora passalidarum and Candida tenuis. To identify genes involved in xylose metabolism, we applied a comparative genomic approach across 14 Ascomycete genomes, mapping phenotypes and genotypes onto the fungal phylogeny, and measured genomic expression across five Hemiascomycete species with different xylose-consumption phenotypes. This approach implicated many genes and processes involved in xylose assimilation. Several of these genes significantly improved xylose utilization when engineered into S. cerevisiae, demonstrating the power of comparative methods in rapidly identifying genes for biomass conversion while reflecting on fungal ecology.

  12. A Burkholderia sacchari cell factory: production of poly-3-hydroxybutyrate, xylitol and xylonic acid from xylose-rich sugar mixtures.

    Science.gov (United States)

    Raposo, Rodrigo S; de Almeida, M Catarina M D; de Oliveira, M da Conceição M A; da Fonseca, M Manuela; Cesário, M Teresa

    2017-01-25

    Efficient production of poly-3-hydroxybutyrate (P(3HB)) based on glucose-xylose mixtures simulating different types of lignocellulosic hydrolysate (LCH) was addressed using Burkholderia sacchari, a wild strain capable of metabolizing both sugars and producing P(3HB). Carbon catabolite repression was avoided by maintaining glucose concentration below 10g/L. Xylose concentrations above 30g/L were inhibitory for growth and production. In fed-batch cultivations, pulse size and feed addition rate were controlled in order to reach high productivities and efficient sugar consumptions. High xylose uptake and P(3HB) productivity were attained with glucose-rich mixtures (glucose/xylose ratio in the feed=1.5w/w) using high feeding rates, while with xylose-richer feeds (glucose/xylose=0.8w/w), a lower feeding rate is a robust strategy to avoid xylose build-up in the medium. Xylitol production was observed with xylose concentrations in the medium above 30-40g/L. With sugar mixtures featuring even lower glucose/xylose ratios, i.e. xylose-richer feeds (glucose/xylose=0.5), xylonic acid (a second byproduct) was produced. This is the first report of the ability of Burkholderia sacchari to produce both xylitol and xylonic acid. Copyright © 2016 Elsevier B.V. All rights reserved.

  13. Kinetics of growth and ethanol production on different carbon substrates using genetically engineered xylose-fermenting yeast

    Energy Technology Data Exchange (ETDEWEB)

    Govindaswamy, S.; Vane, L.M. [National Risk Management Research Laboratory, US Environmental Protection Agency, Cincinnati, OH (United States)

    2007-02-15

    Saccharomyces cerevisiae 424A (LNH-ST) strain was used for fermentation of glucose and xylose. Growth kinetics and ethanol productivity were calculated for batch fermentation on media containing different combinations of glucose and xylose to give a final sugar concentration of 20 {+-} 0.8 g/L. Growth rates obtained in pure xylose-based medium were less than those for media containing pure glucose and glucose-xylose mixtures. A maximum specific growth rate {mu}{sub max} of 0.291 h{sup -1} was obtained in YPD medium containing 20 g/L glucose as compared to 0.206 h{sup -1} in YPX medium containing 20 g/L xylose. In media containing combinations of glucose and xylose, glucose was exhausted first followed by xylose. Ethanol production on pure xylose entered log phase during the 12-24 h period as compared to the 4-10 h for pure glucose based medium using 2% inoculum. When glucose was added to fermentation flasks which had been initiated on a pure xylose-based medium, the rate of xylose usage was reduced indicating cosubstrate inhibition of xylose consumption by glucose. (author)

  14. Lactic acid production from xylose by engineered Saccharomyces cerevisiae without PDC or ADH deletion.

    Science.gov (United States)

    Turner, Timothy L; Zhang, Guo-Chang; Kim, Soo Rin; Subramaniam, Vijay; Steffen, David; Skory, Christopher D; Jang, Ji Yeon; Yu, Byung Jo; Jin, Yong-Su

    2015-10-01

    Production of lactic acid from renewable sugars has received growing attention as lactic acid can be used for making renewable and bio-based plastics. However, most prior studies have focused on production of lactic acid from glucose despite that cellulosic hydrolysates contain xylose as well as glucose. Microbial strains capable of fermenting both glucose and xylose into lactic acid are needed for sustainable and economic lactic acid production. In this study, we introduced a lactic acid-producing pathway into an engineered Saccharomyces cerevisiae capable of fermenting xylose. Specifically, ldhA from the fungi Rhizopus oryzae was overexpressed under the control of the PGK1 promoter through integration of the expression cassette in the chromosome. The resulting strain exhibited a high lactate dehydrogenase activity and produced lactic acid from glucose or xylose. Interestingly, we observed that the engineered strain exhibited substrate-dependent product formation. When the engineered yeast was cultured on glucose, the major fermentation product was ethanol while lactic acid was a minor product. In contrast, the engineered yeast produced lactic acid almost exclusively when cultured on xylose under oxygen-limited conditions. The yields of ethanol and lactic acid from glucose were 0.31 g ethanol/g glucose and 0.22 g lactic acid/g glucose, respectively. On xylose, the yields of ethanol and lactic acid were <0.01 g ethanol/g xylose and 0.69 g lactic acid/g xylose, respectively. These results demonstrate that lactic acid can be produced from xylose with a high yield by S. cerevisiae without deleting pyruvate decarboxylase, and the formation patterns of fermentations can be altered by substrates.

  15. Fermentation performance and intracellular metabolite patterns in laboratory and industrial xylose-fermenting Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Zaldivar, Jesus; Borges, A.; Johansson, B.

    2002-01-01

    Heterologous genes for xylose utilization were introduced into an industrial Saccharomyces cerevisiae, strain A, with the aim of producing fuel ethanol from lignocellulosic feedstocks. Two transformants, A4 and A6, were evaluated by comparing the performance in 4-1 anaerobic batch cultivations...... to both the parent strain and a laboratory xylose-utilizing strain: S. cerevisiae TMB 3001. During growth in a minimal medium containing a mixture of glucose and xylose (50 g/l each), glucose was preferentially consumed. During the first growth phase on glucose, the specific growth rates were 0.26, 0...

  16. Altering the coenzyme preference of xylose reductase to favor utilization of NADH enhances ethanol yield from xylose in a metabolically engineered strain of Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Nidetzky Bernd

    2008-03-01

    Full Text Available Abstract Background Metabolic engineering of Saccharomyces cerevisiae for xylose fermentation into fuel ethanol has oftentimes relied on insertion of a heterologous pathway that consists of xylose reductase (XR and xylitol dehydrogenase (XDH and brings about isomerization of xylose into xylulose via xylitol. Incomplete recycling of redox cosubstrates in the catalytic steps of the NADPH-preferring XR and the NAD+-dependent XDH results in formation of xylitol by-product and hence in lowering of the overall yield of ethanol on xylose. Structure-guided site-directed mutagenesis was previously employed to change the coenzyme preference of Candida tenuis XR about 170-fold from NADPH in the wild-type to NADH in a Lys274→Arg Asn276→Asp double mutant which in spite of the structural modifications introduced had retained the original catalytic efficiency for reduction of xylose by NADH. This work was carried out to assess physiological consequences in xylose-fermenting S. cerevisiae resulting from a well defined alteration of XR cosubstrate specificity. Results An isogenic pair of yeast strains was derived from S. cerevisiae Cen.PK 113-7D through chromosomal integration of a three-gene cassette that carried a single copy for C. tenuis XR in wild-type or double mutant form, XDH from Galactocandida mastotermitis, and the endogenous xylulose kinase (XK. Overexpression of each gene was under control of the constitutive TDH3 promoter. Measurement of intracellular levels of XR, XDH, and XK activities confirmed the expected phenotypes. The strain harboring the XR double mutant showed 42% enhanced ethanol yield (0.34 g/g compared to the reference strain harboring wild-type XR during anaerobic bioreactor conversions of xylose (20 g/L. Likewise, the yields of xylitol (0.19 g/g and glycerol (0.02 g/g were decreased 52% and 57% respectively in the XR mutant strain. The xylose uptake rate per gram of cell dry weight was identical (0.07 ± 0.02 h-1 in both strains

  17. Transportation

    Science.gov (United States)

    2006-01-01

    container. It now permits free transit of shipping containers from their western ports, if transported by rail directly to the U.S. ( Mireles , 2005, p...Transportation Industry Study Seminar. Mireles , Richard, Castillo. (2005, January). A Cure for West Coast Congestion. Logistics Today, Vol. 46, Issue 1. 1

  18. Mentoring: An Evolving Relationship.

    Science.gov (United States)

    Block, Michelle; Florczak, Kristine L

    2017-04-01

    The column concerns itself with mentoring as an evolving relationship between mentor and mentee. The collegiate mentoring model, the transformational transcendence model, and the humanbecoming mentoring model are considered in light of a dialogue with mentors at a Midwest university and conclusions are drawn.

  19. Measurably evolving populations

    DEFF Research Database (Denmark)

    Drummond, Alexei James; Pybus, Oliver George; Rambaut, Andrew

    2003-01-01

    processes through time. Populations for which such studies are possible � measurably evolving populations (MEPs) � are characterized by sufficiently long or numerous sampled sequences and a fast mutation rate relative to the available range of sequence sampling times. The impact of sequences sampled through...... understanding of evolutionary processes in diverse organisms, from viruses to vertebrates....

  20. Optimized Production of Xylitol from Xylose Using a Hyper-Acidophilic Candida tropicalis

    Directory of Open Access Journals (Sweden)

    Elena Tamburini

    2015-08-01

    Full Text Available The yeast Candida tropicalis DSM 7524 produces xylitol, a natural, low-calorie sweetener, by fermentation of xylose. In order to increase xylitol production rate during the submerged fermentation process, some parameters-substrate (xylose concentration, pH, aeration rate, temperature and fermentation strategy-have been optimized. The maximum xylitol yield reached at 60–80 g/L initial xylose concentration, pH 5.5 at 37 °C was 83.66% (w/w on consumed xylose in microaerophilic conditions (kLa = 2·h−1. Scaling up on 3 L fermenter, with a fed-batch strategy, the best xylitol yield was 86.84% (w/w, against a 90% of theoretical yield. The hyper-acidophilic behaviour of C. tropicalis makes this strain particularly promising for industrial application, due to the possibility to work in non-sterile conditions.

  1. Genes related to xylose fermentation and methods of using same for enhanced biofuel production

    Energy Technology Data Exchange (ETDEWEB)

    Wohlbach, Dana J.; Gasch, Audrey P.

    2015-09-29

    The present invention provides isolated gene sequences involved in xylose fermentation and related recombinant yeast which are useful in methods of enhanced biofuel production, particularly ethanol production. Methods of bioengineering recombinant yeast useful for biofuel production are also provided.

  2. Genes related to xylose fermentation and methods of using same for enhanced biofuel production

    Science.gov (United States)

    Wohlbach, Dana J.; Gasch, Audrey P.

    2014-08-05

    The present invention provides isolated gene sequences involved in xylose fermentation and related recombinant yeast which are useful in methods of enhanced biofuel production, particularly ethanol production. Methods of bioengineering recombinant yeast useful for biofuel production are also provided.

  3. Genes related to xylose fermentation and methods of using same for enhanced biofuel production

    Energy Technology Data Exchange (ETDEWEB)

    Wohlbach, Dana J.; Gasch, Audrey P.

    2016-11-29

    The present invention provides isolated gene sequences involved in xylose fermentation and related recombinant yeast which are useful in methods of enhanced biofuel production, particularly ethanol production. Methods of bioengineering recombinant yeast useful for biofuel production are also provided.

  4. Genomic sequence of the xylose fermenting, insect-inhabitingyeast, Pichia stipitis

    Energy Technology Data Exchange (ETDEWEB)

    Jeffries, Thomas W.; Grigoriev, Igor; Grimwood, Jane; Laplaza,Jose M.; Aerts, Andrea; Salamov, Asaf; Schmutz, Jeremy; Lindquist, Erika; Dehal, Paramvir; Shapiro, Harris; Jin, Yong-Su; Passoth, Volkmar; Richardson, Paul M.

    2007-06-25

    Xylose is a major constituent of angiosperm lignocellulose,so its fermentation is important for bioconversion to fuels andchemicals. Pichia stipitis is the best-studied native xylose fermentingyeast. Genes from P. stipitis have been used to engineer xylosemetabolism in Saccharomycescerevisiae, and the regulation of the P.stipitis genome offers insights into the mechanisms of xylose metabolismin yeasts. We have sequenced, assembled and finished the genome ofP.stipitis. As such, it is one of only a handful of completely finishedeukaryotic organisms undergoing analysis and manual curation. Thesequence has revealed aspects of genome organization, numerous genes forbiocoversion, preliminary insights into regulation of central metabolicpathways, numerous examples of co-localized genes with related functions,and evidence of how P. stipitis manages to achieve redox balance whilegrowing on xylose under microaerobic conditions.

  5. Bulk segregant analysis by high-throughput sequencing reveals a novel xylose utilization gene from Saccharomyces cerevisiae.

    Directory of Open Access Journals (Sweden)

    Jared W Wenger

    2010-05-01

    Full Text Available Fermentation of xylose is a fundamental requirement for the efficient production of ethanol from lignocellulosic biomass sources. Although they aggressively ferment hexoses, it has long been thought that native Saccharomyces cerevisiae strains cannot grow fermentatively or non-fermentatively on xylose. Population surveys have uncovered a few naturally occurring strains that are weakly xylose-positive, and some S. cerevisiae have been genetically engineered to ferment xylose, but no strain, either natural or engineered, has yet been reported to ferment xylose as efficiently as glucose. Here, we used a medium-throughput screen to identify Saccharomyces strains that can increase in optical density when xylose is presented as the sole carbon source. We identified 38 strains that have this xylose utilization phenotype, including strains of S. cerevisiae, other sensu stricto members, and hybrids between them. All the S. cerevisiae xylose-utilizing strains we identified are wine yeasts, and for those that could produce meiotic progeny, the xylose phenotype segregates as a single gene trait. We mapped this gene by Bulk Segregant Analysis (BSA using tiling microarrays and high-throughput sequencing. The gene is a putative xylitol dehydrogenase, which we name XDH1, and is located in the subtelomeric region of the right end of chromosome XV in a region not present in the S288c reference genome. We further characterized the xylose phenotype by performing gene expression microarrays and by genetically dissecting the endogenous Saccharomyces xylose pathway. We have demonstrated that natural S. cerevisiae yeasts are capable of utilizing xylose as the sole carbon source, characterized the genetic basis for this trait as well as the endogenous xylose utilization pathway, and demonstrated the feasibility of BSA using high-throughput sequencing.

  6. Increased expression of the oxidative pentose phosphate pathway and gluconeogenesis in anaerobically growing xylose-utilizing Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Hahn-Hägerdal Bärbel

    2009-09-01

    Full Text Available Abstract Background Fermentation of xylose to ethanol has been achieved in S. cerevisiae by genetic engineering. Xylose utilization is however slow compared to glucose, and during anaerobic conditions addition of glucose has been necessary for cellular growth. In the current study, the xylose-utilizing strain TMB 3415 was employed to investigate differences between anaerobic utilization of glucose and xylose. This strain carried a xylose reductase (XYL1 K270R engineered for increased NADH utilization and was capable of sustained anaerobic growth on xylose as sole carbon source. Metabolic and transcriptional characterization could thus for the first time be performed without addition of a co-substrate or oxygen. Results Analysis of metabolic fluxes showed that although the specific ethanol productivity was an order of magnitude lower on xylose than on glucose, product yields were similar for the two substrates. In addition, transcription analysis identified clear regulatory differences between glucose and xylose. Respiro-fermentative metabolism on glucose during aerobic conditions caused repression of cellular respiration, while metabolism on xylose under the same conditions was fully respiratory. During anaerobic conditions, xylose repressed respiratory pathways, although notably more weakly than glucose. It was also observed that anaerobic xylose growth caused up-regulation of the oxidative pentose phosphate pathway and gluconeogenesis, which may be driven by an increased demand for NADPH during anaerobic xylose catabolism. Conclusion Co-factor imbalance in the initial twp steps of xylose utilization may reduce ethanol productivity by increasing the need for NADP+ reduction and consequently increase reverse flux in glycolysis.

  7. Design of Xylose-Based Semisynthetic Polyurethane Tissue Adhesives with Enhanced Bioactivity Properties.

    Science.gov (United States)

    Balcioglu, Sevgi; Parlakpinar, Hakan; Vardi, Nigar; Denkbas, Emir Baki; Karaaslan, Merve Goksin; Gulgen, Selam; Taslidere, Elif; Koytepe, Suleyman; Ates, Burhan

    2016-02-01

    Developing biocompatible tissue adhesives with high adhesion properties is a highly desired goal of the tissue engineering due to adverse effects of the sutures. Therefore, our work involves synthesis, characterization, adhesion properties, protein adsorption, in vitro biodegradation, in vitro and in vivo biocompatibility properties of xylose-based semisynthetic polyurethane (NPU-PEG-X) bioadhesives. Xylose-based semisynthetic polyurethanes were developed by the reaction among 4,4'-methylenebis(cyclohexyl isocyanate) (MCI), xylose and polyethylene glycol 200 (PEG). Synthesized polyurethanes (PUs) showed good thermal stability and high adhesion strength. The highest values in adhesion strength were measured as 415.0 ± 48.8 and 94.0 ± 2.8 kPa for aluminum substrate and muscle tissue in 15% xylose containing PUs (NPU-PEG-X-15%), respectively. The biodegradation of NPU-PEG-X-15% was also determined as 19.96 ± 1.04% after 8 weeks of incubation. Relative cell viability of xylose containing PU was above 86%. Moreover, 10% xylose containing NPU-PEG-X (NPU-PEG-X-10%) sample has favorable tissue response, and inflammatory reaction between 1 and 6 weeks implantation period. With high adhesiveness and biocompatibility properties, NPU-PEG-X can be used in the medical field as supporting materials for preventing the fluid leakage after abdominal surgery or wound closure.

  8. The effect of sedation on D(+)-xylose absorption tests in 6 normal horses.

    Science.gov (United States)

    Fintl, C; Ihler, C F

    2011-08-01

    D(+)-xylose absorption tests are commonly performed when investigating suspected small intestinal malabsorption in the horse. The test involves the administration of a D(+)-xylose solution via a nasogastric tube followed by serial blood sampling to determine its rate of absorption. In some horses, nasogastric intubation cannot be safely performed without prior administration of a sedative. Due to its short duration of action, the α(2) agonist xylazine is commonly used for this purpose. However, α(2) agonists have also been reported to influence the rate of gastric emptying as well as small intestinal motility patterns. To evaluate if prior sedation with xylazine would influence the rate of absorption of D(+)-xylose in 6 normal Standardbred horses in a randomised cross-over study. D(+)-xylose was administered by nasogastric intubation at a dose rate of 0.5 g/kg bwt given as a 10% solution with water while xylazine was administered iv at a dose rate of 0.5 mg/kg bwt. A heparinised blood sample was collected prior to administration of D(+)-xylose (and xylazine when used) and then at 30, 45, 60, 75, 90, 120, 150, 180 and 240 min following administration. Samples were immediately analysed using a modified colorimetric micro method. The cumulative amount of D(+)-xylose absorbed at each time point with and without prior sedation were. The significance rate was set at Pabsorption test in the normal horse. © 2011 EVJ Ltd.

  9. Metabolic Engineering of Escherichia coli K12 for Homofermentative Production of L-Lactate from Xylose.

    Science.gov (United States)

    Jiang, Ting; Zhang, Chen; He, Qin; Zheng, Zhaojuan; Ouyang, Jia

    2018-02-01

    The efficient utilization of xylose is regarded as a technical barrier to the commercial production of bulk chemicals from biomass. Due to the desirable mechanical properties of polylactic acid (PLA) depending on the isomeric composition of lactate, biotechnological production of lactate with high optical pure has been increasingly focused in recent years. The main objective of this work was to construct an engineered Escherichia coli for the optically pure L-lactate production from xylose. Six chromosomal deletions (pflB, ldhA, ackA, pta, frdA, adhE) and a chromosomal integration of L-lactate dehydrogenase-encoding gene (ldhL) from Bacillus coagulans was involved in construction of E. coli KSJ316. The recombinant strain could produce L-lactate from xylose resulting in a yield of 0.91 g/g xylose. The chemical purity of L-lactate was 95.52%, and the optical purity was greater than 99%. Moreover, three strategies, including overexpression of L-lactate dehydrogenase, intensification of xylose catabolism, and addition of additives to medium, were designed to enhance the production. The results showed that they could increase the concentration of L-lactate by 32.90, 20.13, and 233.88% relative to the control, respectively. This was the first report that adding formate not only could increase the xylose utilization but also led to the fewer by-product levels.

  10. Utilization of xylose as a carbon source for mixotrophic growth of Scenedesmus obliquus.

    Science.gov (United States)

    Yang, Suling; Liu, Guijun; Meng, Youting; Wang, Ping; Zhou, Sijing; Shang, Hongzhong

    2014-11-01

    Mixotrophic cultivation is one potential mode for microalgae production, and an economically acceptable and environmentally sustainable organic carbon source is essential. The potential use of xylose for culturing Scenedesmus obliquus in a mixotrophic mode and physiological features of xylose-grown S. obliquus were studied. S. obliquus had a certain xylose tolerance, and was capable of utilizing xylose for growth. At a xylose concentration of 4gL(-1), the maximal cell density was 2.2gL(-1), being 2.9-fold of that under photoautotrophic condition and arriving to the level of mixotrophic growth using 4gL(-1) glucose. No changes in cellular morphology of the cells grown with or without xylose were detected. Fluorescence emission from photosystem II (PS II) relative to photosystem I (PS I) was decreased in mixotrophic cells, implying that the PSII activity was decreased. The biomass lipid content was enhanced and carbohydrate concentration was decreased, in relation to photoautotrophic controls. Copyright © 2014 Elsevier Ltd. All rights reserved.

  11. Transcriptome analysis of Rhizopus oryzae in response to xylose during fumaric acid production.

    Science.gov (United States)

    Xu, Qing; Liu, Ying; Li, Shuang; Jiang, Ling; Huang, He; Wen, Jianping

    2016-08-01

    Xylose is one of the most abundant lignocellulosic components, but it cannot be used by R. oryzae for fumaric acid production. Here, we applied high-throughput RNA sequencing to generate two transcriptional maps of R. oryzae following fermentation in glucose or xylose. The differential expression analysis showed that, genes involved in amino acid metabolism, fatty acid metabolism, and gluconeogenesis, were up-regulated in response to xylose. Moreover, we discovered the potential presence of oxidative stress in R. oryzae during xylose fermentation. To adapt to this unfavorable condition, R. oryzae displayed reduced growth and induce of a number of antioxidant enzymes, including genes involved in glutathione, trehalose synthesis, and the proteasomal pathway. These responses might divert the flow of carbon required for the accumulation of fumaric acid. Furthermore, using high-throughput RNA sequencing, we identified a large number of novel transcripts and a substantial number of genes that underwent alternative splicing. Our analysis provides remarkable insight into the mechanisms underlying xylose fermentation by R. oryzae. These results may reveal potential target genes or strategies to improve xylose fermentation.

  12. EVOLVE 2014 International Conference

    CERN Document Server

    Tantar, Emilia; Sun, Jian-Qiao; Zhang, Wei; Ding, Qian; Schütze, Oliver; Emmerich, Michael; Legrand, Pierrick; Moral, Pierre; Coello, Carlos

    2014-01-01

    This volume encloses research articles that were presented at the EVOLVE 2014 International Conference in Beijing, China, July 1–4, 2014.The book gathers contributions that emerged from the conference tracks, ranging from probability to set oriented numerics and evolutionary computation; all complemented by the bridging purpose of the conference, e.g. Complex Networks and Landscape Analysis, or by the more application oriented perspective. The novelty of the volume, when considering the EVOLVE series, comes from targeting also the practitioner’s view. This is supported by the Machine Learning Applied to Networks and Practical Aspects of Evolutionary Algorithms tracks, providing surveys on new application areas, as in the networking area and useful insights in the development of evolutionary techniques, from a practitioner’s perspective. Complementary to these directions, the conference tracks supporting the volume, follow on the individual advancements of the subareas constituting the scope of the confe...

  13. Evolvable Neural Software System

    Science.gov (United States)

    Curtis, Steven A.

    2009-01-01

    The Evolvable Neural Software System (ENSS) is composed of sets of Neural Basis Functions (NBFs), which can be totally autonomously created and removed according to the changing needs and requirements of the software system. The resulting structure is both hierarchical and self-similar in that a given set of NBFs may have a ruler NBF, which in turn communicates with other sets of NBFs. These sets of NBFs may function as nodes to a ruler node, which are also NBF constructs. In this manner, the synthetic neural system can exhibit the complexity, three-dimensional connectivity, and adaptability of biological neural systems. An added advantage of ENSS over a natural neural system is its ability to modify its core genetic code in response to environmental changes as reflected in needs and requirements. The neural system is fully adaptive and evolvable and is trainable before release. It continues to rewire itself while on the job. The NBF is a unique, bilevel intelligence neural system composed of a higher-level heuristic neural system (HNS) and a lower-level, autonomic neural system (ANS). Taken together, the HNS and the ANS give each NBF the complete capabilities of a biological neural system to match sensory inputs to actions. Another feature of the NBF is the Evolvable Neural Interface (ENI), which links the HNS and ANS. The ENI solves the interface problem between these two systems by actively adapting and evolving from a primitive initial state (a Neural Thread) to a complicated, operational ENI and successfully adapting to a training sequence of sensory input. This simulates the adaptation of a biological neural system in a developmental phase. Within the greater multi-NBF and multi-node ENSS, self-similar ENI s provide the basis for inter-NBF and inter-node connectivity.

  14. Xylitol production from xylose mother liquor: a novel strategy that combines the use of recombinant Bacillus subtilis and Candida maltosa

    Directory of Open Access Journals (Sweden)

    Jiang Mingguo

    2011-02-01

    Full Text Available Abstract Background Xylose mother liquor has high concentrations of xylose (35%-40% as well as other sugars such as L-arabinose (10%-15%, galactose (8%-10%, glucose (8%-10%, and other minor sugars. Due to the complexity of this mother liquor, further isolation of xylose by simple method is not possible. In China, more than 50,000 metric tons of xylose mother liquor was produced in 2009, and the management of sugars like xylose that present in the low-cost liquor is a problem. Results We designed a novel strategy in which Bacillus subtilis and Candida maltosa were combined and used to convert xylose in this mother liquor to xylitol, a product of higher value. First, the xylose mother liquor was detoxified with the yeast C. maltosa to remove furfural and 5-hydromethylfurfural (HMF, which are inhibitors of B. subtilis growth. The glucose present in the mother liquor was also depleted by this yeast, which was an added advantage because glucose causes carbon catabolite repression in B. subtilis. This detoxification treatment resulted in an inhibitor-free mother liquor, and the C. maltosa cells could be reused as biocatalysts at a later stage to reduce xylose to xylitol. In the second step, a recombinant B. subtilis strain with a disrupted xylose isomerase gene was constructed. The detoxified xylose mother liquor was used as the medium for recombinant B. subtilis cultivation, and this led to L-arabinose depletion and xylose enrichment of the medium. In the third step, the xylose was further reduced to xylitol by C. maltosa cells, and crystallized xylitol was obtained from this yeast transformation medium. C. maltosa transformation of the xylose-enriched medium resulted in xylitol with 4.25 g L-1·h-1 volumetric productivity and 0.85 g xylitol/g xylose specific productivity. Conclusion In this study, we developed a biological method for the purification of xylose from xylose mother liquor and subsequent preparation of xylitol by C. maltosa

  15. Transcriptional activator Cat8 is involved in regulation of xylose alcoholic fermentation in the thermotolerant yeast Ogataea (Hansenula) polymorpha.

    Science.gov (United States)

    Ruchala, Justyna; Kurylenko, Olena O; Soontorngun, Nitnipa; Dmytruk, Kostyantyn V; Sibirny, Andriy A

    2017-02-28

    Efficient xylose alcoholic fermentation is one of the key to a successful lignocellulosic ethanol production. However, regulation of this process in the native xylose-fermenting yeasts is poorly understood. In this work, we paid attention to the transcriptional factor Cat8 and its possible role in xylose alcoholic fermentation in Ogataea (Hansenula) polymorpha. In Saccharomyces cerevisiae, organism, which does not metabolize xylose, gene CAT8 encodes a Zn-cluster transcriptional activator necessary for expression of genes involved in gluconeogenesis, respiration, glyoxylic cycle and ethanol utilization. Xylose is a carbon source that could be fermented to ethanol and simultaneously could be used in gluconeogenesis for hexose synthesis. This potentially suggests involvement of CAT8 in xylose metabolism. Here, the role of CAT8 homolog in the natural xylose-fermenting thermotolerant yeast O. polymorpha was characterized. The CAT8 ortholog was identified in O. polymorpha genome and deleted both in the wild-type strain and in advanced ethanol producer from xylose. Constructed cat8Δ strain isolated from wild strain showed diminished growth on glycerol, ethanol and xylose as well as diminished respiration on the last substrate. At the same time, cat8Δ mutant isolated from the best available O. polymorpha ethanol producer showed only visible defect in growth on ethanol. CAT8 deletant was characterized by activated transcription of genes XYL3, DAS1 and RPE1 and slight increase in the activity of several enzymes involved in xylose metabolism and alcoholic fermentation. Ethanol production from xylose in cat8Δ mutants in the background of wild-type strain and the best available ethanol producer from xylose increased for 50 and 30%, respectively. The maximal titer of ethanol during xylose fermentation was 12.5 g ethanol/L at 45 °C. Deletion of CAT8 did not change ethanol production from glucose. Gene CAT8 was also overexpressed under control of the strong constitutive

  16. Dynamic metabolomics differentiates between carbon and energy starvation in recombinant Saccharomyces cerevisiae fermenting xylose

    Directory of Open Access Journals (Sweden)

    Bergdahl Basti

    2012-05-01

    Full Text Available Abstract Background The concerted effects of changes in gene expression due to changes in the environment are ultimately reflected in the metabolome. Dynamics of metabolite concentrations under a certain condition can therefore give a description of the cellular state with a high degree of functional information. We used this potential to evaluate the metabolic status of two recombinant strains of Saccharomyces cerevisiae during anaerobic batch fermentation of a glucose/xylose mixture. Two isogenic strains were studied, differing only in the pathways used for xylose assimilation: the oxidoreductive pathway with xylose reductase (XR and xylitol dehydrogenase (XDH or the isomerization pathway with xylose isomerase (XI. The isogenic relationship between the two strains ascertains that the observed responses are a result of the particular xylose pathway and not due to unknown changes in regulatory systems. An increased understanding of the physiological state of these strains is important for further development of efficient pentose-utilizing strains for bioethanol production. Results Using LC-MS/MS we determined the dynamics in the concentrations of intracellular metabolites in central carbon metabolism, nine amino acids, the purine nucleotides and redox cofactors. The general response to the transition from glucose to xylose was increased concentrations of amino acids and TCA-cycle intermediates, and decreased concentrations of sugar phosphates and redox cofactors. The two strains investigated had significantly different uptake rates of xylose which led to an enhanced response in the XI-strain. Despite the difference in xylose uptake rate, the adenylate energy charge remained high and stable around 0.8 in both strains. In contrast to the adenylate pool, large changes were observed in the guanylate pool. Conclusions The low uptake of xylose by the XI-strain led to several distinguished responses: depletion of key metabolites in glycolysis and NADPH

  17. Dynamic metabolomics differentiates between carbon and energy starvation in recombinant Saccharomyces cerevisiae fermenting xylose

    Science.gov (United States)

    2012-01-01

    Background The concerted effects of changes in gene expression due to changes in the environment are ultimately reflected in the metabolome. Dynamics of metabolite concentrations under a certain condition can therefore give a description of the cellular state with a high degree of functional information. We used this potential to evaluate the metabolic status of two recombinant strains of Saccharomyces cerevisiae during anaerobic batch fermentation of a glucose/xylose mixture. Two isogenic strains were studied, differing only in the pathways used for xylose assimilation: the oxidoreductive pathway with xylose reductase (XR) and xylitol dehydrogenase (XDH) or the isomerization pathway with xylose isomerase (XI). The isogenic relationship between the two strains ascertains that the observed responses are a result of the particular xylose pathway and not due to unknown changes in regulatory systems. An increased understanding of the physiological state of these strains is important for further development of efficient pentose-utilizing strains for bioethanol production. Results Using LC-MS/MS we determined the dynamics in the concentrations of intracellular metabolites in central carbon metabolism, nine amino acids, the purine nucleotides and redox cofactors. The general response to the transition from glucose to xylose was increased concentrations of amino acids and TCA-cycle intermediates, and decreased concentrations of sugar phosphates and redox cofactors. The two strains investigated had significantly different uptake rates of xylose which led to an enhanced response in the XI-strain. Despite the difference in xylose uptake rate, the adenylate energy charge remained high and stable around 0.8 in both strains. In contrast to the adenylate pool, large changes were observed in the guanylate pool. Conclusions The low uptake of xylose by the XI-strain led to several distinguished responses: depletion of key metabolites in glycolysis and NADPH, a reduced GTP/GDP ratio

  18. Transportes

    Directory of Open Access Journals (Sweden)

    Hidalgo Fernández-Cano, Amalio

    1960-01-01

    Full Text Available El movimiento de materiales dentro de la Factoría está atendido por tres principales medios de transporte, en consonancia con las características del material y de los desplazamientos. Así se han establecido: sistemas de cintas transportadoras, una red ferroviaria de ancho normal y una completa malla de caminos enlazando funcionalmente las instalaciones.

  19. Ethanol Production from Glucose and Xylose by Immobilized Zymomonas mobilis CP4(pZB5)

    Energy Technology Data Exchange (ETDEWEB)

    Blanco, M.; Davison, B.H.; Krishnan, M.S.; Nghiem, n.P.; Shattuck, C.K.

    1999-05-02

    Fermentation of glucose-xylose mixtures to ethanol was investigated in batch and continuous experiments using immobilized recombinant Zymomonas mobilis CP4(pZB5). This microorganism was immobilized by entrapment in k-carrageenan beads having a diameter of 1.5-2.5 mm. Batch experiments showed that the immobilized cells co-fermented glucose and xylose to ethanol and that the presence of glucose improved the xylose utilization rate. Batch fermentation of rice straw hydrolyzate containing 76 g/L glucose and 33.8 g/L xylose gave an ethanol concentration of 44.3 g/L after 24 hours, corresponding to a yeild of 0.46 g ethanol/g sugars. Comparable results were achieved with a synthetic sugar control. Continuous fermentation runs were performed in a laboratory scale fluidized-bed bioreactor (FBR). Glucose-xylose feed mixtures were run through the FBR at residence times of 2 to 4 hours. Glucose conversion to ethanol was maintained above 98% in all continuous runs. Xylose conversion to ethanol was highest at 91.5% for a feed containing 50 g/L glucose-13 g/L xylose at a dilution rate of 0.24 h-1. The xylose conversion to ethanol decreased with increasing feed xylose concentration, dilution rate and age of the immobilized cells. Volumetric ethanol productivities in the range of 6.5 to 15.3 g/L-h were obtained.

  20. Simultaneous glucose and xylose uptake by an acetone/butanol/ethanol producing laboratory Clostridium beijerinckii strain SE-2.

    Science.gov (United States)

    Zhang, Jie; Zhu, Wen; Xu, Haipeng; Li, Yan; Hua, Dongliang; Jin, Fuqiang; Gao, Mintian; Zhang, Xiaodong

    2016-04-01

    Most butanol-producing strains of Clostridium prefer glucose over xylose, leading to a slower butanol production from lignocellulose hydrolysates. It is therefore beneficial to find and use a strain that can simultaneously use both glucose and xylose. Clostridium beijerinckii SE-2 strain assimilated glucose and xylose simultaneously and produced ABE (acetone/butanol/ethanol). The classic diauxic growth behavior was not seen. Similar rates of sugar consumption (4.44 mM glucose h(-1) and 6.66 mM xylose h(-1)) were observed suggesting this strain could use either glucose or xylose as the substrate and it has a similar capability to degrade these two sugars. With different initial glucose:xylose ratios, glucose and xylose were consumed simultaneously at rates roughly proportional to their individual concentrations in the medium, leading to complete utilization of both sugars at the same time. ABE production profiles were similar on different substrates. Transcriptional studies on the effect of glucose and xylose supplementation, however, suggests a clear glucose inhibition on xylose metabolism-related genes is still present.

  1. Regolith Evolved Gas Analyzer

    Science.gov (United States)

    Hoffman, John H.; Hedgecock, Jud; Nienaber, Terry; Cooper, Bonnie; Allen, Carlton; Ming, Doug

    2000-01-01

    The Regolith Evolved Gas Analyzer (REGA) is a high-temperature furnace and mass spectrometer instrument for determining the mineralogical composition and reactivity of soil samples. REGA provides key mineralogical and reactivity data that is needed to understand the soil chemistry of an asteroid, which then aids in determining in-situ which materials should be selected for return to earth. REGA is capable of conducting a number of direct soil measurements that are unique to this instrument. These experimental measurements include: (1) Mass spectrum analysis of evolved gases from soil samples as they are heated from ambient temperature to 900 C; and (2) Identification of liberated chemicals, e.g., water, oxygen, sulfur, chlorine, and fluorine. REGA would be placed on the surface of a near earth asteroid. It is an autonomous instrument that is controlled from earth but does the analysis of regolith materials automatically. The REGA instrument consists of four primary components: (1) a flight-proven mass spectrometer, (2) a high-temperature furnace, (3) a soil handling system, and (4) a microcontroller. An external arm containing a scoop or drill gathers regolith samples. A sample is placed in the inlet orifice where the finest-grained particles are sifted into a metering volume and subsequently moved into a crucible. A movable arm then places the crucible in the furnace. The furnace is closed, thereby sealing the inner volume to collect the evolved gases for analysis. Owing to the very low g forces on an asteroid compared to Mars or the moon, the sample must be moved from inlet to crucible by mechanical means rather than by gravity. As the soil sample is heated through a programmed pattern, the gases evolved at each temperature are passed through a transfer tube to the mass spectrometer for analysis and identification. Return data from the instrument will lead to new insights and discoveries including: (1) Identification of the molecular masses of all of the gases

  2. Lactobacillus oligofermentans glucose, ribose and xylose transcriptomes show higher similarity between glucose and xylose catabolism-induced responses in the early exponential growth phase.

    Science.gov (United States)

    Andreevskaya, Margarita; Johansson, Per; Jääskeläinen, Elina; Rämö, Tanja; Ritari, Jarmo; Paulin, Lars; Björkroth, Johanna; Auvinen, Petri

    2016-08-03

    Lactobacillus oligofermentans has been mostly isolated from cold-stored packaged meat products in connection with their spoilage, but its precise role in meat spoilage is unknown. It belongs to the L. vaccinostercus group of obligate heterofermentative lactobacilli that generally ferment pentoses (e.g. xylose and ribose) more efficiently than hexoses (e.g. glucose). However, more efficient hexose utilization can be induced. The regulation mechanisms of the carbohydrate catabolism in such bacteria have been scarcely studied. To address this question, we provided the complete genome sequence of L. oligofermentans LMG 22743(T) and generated time course transcriptomes during its growth on glucose, ribose and xylose. The genome was manually annotated and its main functional features were examined. L. oligofermentans was confirmed to be able to efficiently utilize several hexoses and maltose, which is, presumably, induced by its repeated cultivation with glucose in vitro. Unexpectedly, in the beginning of the exponential growth phase, glucose- and xylose-induced transcriptome responses were more similar, whereas toward the end of the growth phase xylose and ribose transcriptomes became more alike. The promoter regions of genes simultaneously upregulated both on glucose and xylose in comparison with ribose (particularly, hexose and xylose utilization genes) were found to be enriched in the CcpA- binding site. Transcriptionally, no glucose-induced carbon catabolite repression was detected. The catabolism of glucose, which requires initial oxidation, led to significant overexpression of the NAD(P)H re-oxidation genes, the upstream regions of which were found to contain a motif, which was highly similar to a Rex repressor binding site. This paper presents the second complete genome and the first study of carbohydrate catabolism-dependent transcriptome response for a member of the L. vaccinostercus group. The transcriptomic changes detected in L. oligofermentans for growth

  3. Simultaneous utilization of glucose and xylose for lipid production by Trichosporon cutaneum

    Directory of Open Access Journals (Sweden)

    Jin Guojie

    2011-08-01

    Full Text Available Abstract Background Biochemical conversion of lignocellulose hydrolysates remains challenging, largely because most microbial processes have markedly reduced efficiency in the presence of both hexoses and pentoses. Thus, identification of microorganisms capable of efficient and simultaneous utilization of both glucose and xylose is pivotal to improving this process. Results In this study, we found that the oleaginous yeast strain Trichosporon cutaneum AS 2.571 assimilated glucose and xylose simultaneously, and accumulated intracellular lipid up to 59 wt% with a lipid coefficient up to 0.17 g/g sugar, upon cultivation on a 2:1 glucose/xylose mixture in a 3-liter stirred-tank bioreactor. In addition, no classic pattern of diauxic growth behavior was seen; the microbial cell mass increased during the whole culture process without any lag periods. In shake-flask cultures with different initial glucose:xylose ratios, glucose and xylose were consumed simultaneously at rates roughly proportional to their individual concentrations in the medium, leading to complete utilization of both sugars at the same time. Simultaneous utilization of glucose and xylose was also seen during fermentation of corn-stover hydrolysate with a lipid content and coefficient of 39.2% and 0.15 g/g sugar, respectively. The lipid produced had a fatty-acid compositional profile similar to those of conventional vegetable oil, indicating that it could have potential as a raw material for biodiesel production. Conclusion Efficient lipid production with simultaneous consumption of glucose and xylose was achieved in this study. This process provides an exciting opportunity to transform lignocellulosic materials into biofuel molecules, and should also encourage further study to elucidate this unique sugar-assimilation mechanism.

  4. Molecular simulation to investigate the cofactor specificity for pichia stipitis Xylose reductase.

    Science.gov (United States)

    Xia, Xiao-Le; Cong, Shan; Weng, Xiao-Rong; Chen, Jin-Hua; Wang, Jing-Fang; Chou, Kuo-Chen

    2013-11-01

    Xylose is one of the most abundant carbohydrates in nature, and widely used to produce bioethanol via fermentation in industry. Xylulose can produce two key enzymes: xylose reductase and xylitol dehydrogenase. Owing to the disparate cofactor specificities of xylose reductase and xylitol dehydrogenase, intracellular redox imbalance is detected during the xylose fermentation, resulting in low ethanol yields. To overcome this barrier, a common strategy is applied to artificially modify the cofactor specificity of xylose reductase. In this study, we utilized molecular simulation approaches to construct a 3D (three-dimensional) structural model for the NADP-dependent Pichia stipitis xylose reductase (PsXR). Based on the 3D model, the favourable binding modes for both cofactors NAD and NADP were obtained using the flexible docking procedure and molecular dynamics simulation. Structural analysis of the favourable binding modes showed that the cofactor binding site of PsXR was composed of 3 major components: a hydrophilic pocket, a hydrophobic pocket as well as a linker channel between the aforementioned two pockets. The hydrophilic pocket could recognize the nicotinamide moiety of the cofactors by hydrogen bonding networks, while the hydrophobic pocket functioned to position the adenine moiety of the cofactors by hydrophobic and Π-Π stacking interactions. The linker channel contained some key residues for ligand-binding; their mutation could have impact to the specificity of PsXR. Finally, it was found that any of the two single mutations, K21A and K270N, might reverse the cofactor specificity of PsXR from major NADP- to NADdependent, which was further confirmed by the additional experiments. Our findings may provide useful insights into the cofactor specificity of PsXR, stimulating new strategies for better designing xylose reductase and improving ethanol production in industry.

  5. Fine-tuning of NADH oxidase decreases byproduct accumulation in respiration deficient xylose metabolic Saccharomyces cerevisiae.

    Science.gov (United States)

    Hou, Jin; Suo, Fan; Wang, Chengqiang; Li, Xiaowei; Shen, Yu; Bao, Xiaoming

    2014-02-14

    Efficiently utilizing all available carbon from lignocellulosic feedstock presents a major barrier to the production of economically feasible biofuel. Previously, to enable xylose utilization, we introduced a cofactor-dependent xylose reductase (XR) and xylitol dehydrogenase (XDH) pathway, or a cofactor-independent xylose isomerase (XI) pathway, into Saccharomyces cerevisiae. The resulting strains metabolized xylose with high efficiency. However, in both pathway recombinant strains, the cofactor imbalance caused accumulation of the byproducts glycerol and/or xylitol and reduced the ethanol production efficiency. In this study, we introduced NADH oxidase from Lactococcus lactis into both XI and XR-XDH pathway recombinant strains. To reduce byproduct accumulation while maintaining xylose metabolism, we optimized the expression level of NADH oxidase by comparing its expression under the control of different promoters and plasmids. In recombinant XI strains, NADH oxidase was expressed at different levels, regulated by the GPD2 promoter or TEF1 promoter in the 2 μ plasmid. The expression under the control of GPD2 promoter decreased glycerol production by 84% and increased the ethanol yield and specific growth rate by 8% and 12%, respectively. In contrast, in the recombinant XR-XDH strains, such expression level was not efficient enough to decrease the byproduct accumulation. Therefore, higher NADH oxidase expression levels were tested. In the strain expressing NADH oxidase under the control of the TEF1 promoter in the centromeric plasmids, xylitol and glycerol production were reduced by 60% and 83%, respectively, without significantly affecting xylose consumption. By fine-tuning NADH oxidase expression, we decreased the glycerol or/and xylitol production in both recombinant XI and XR-XDH xylose-metabolizing yeast strains. The optimal NADH oxidase expression levels depend on metabolic pathways. Similar cofactor engineering strategies could maximize the production of

  6. Biohydrogen production from xylose at extreme thermophilic temperatures (70 degrees C) by mixed culture fermentation.

    Science.gov (United States)

    Kongjan, Prawit; Min, Booki; Angelidaki, Irini

    2009-03-01

    Biohydrogen production from xylose at extreme thermophilic temperatures (70 degrees C) was investigated in batch and continuous-mode operation. Biohydrogen was successfully produced from xylose by repeated batch cultivations with mixed culture received from a biohydrogen reactor treating household solid wastes at 70 degrees C. The highest hydrogen yield of 1.62+/-0.02 mol-H2/mol-xylose(consumed) was obtained at initial xylose concentration of 0.5 g/L with synthetic medium amended with 1g/L of yeast extract. Lower hydrogen yield was achieved at initial xylose concentration higher than 2g/L. Addition of yeast extract in the cultivation medium resulted in significant improvement of hydrogen yield. The main metabolic products during xylose fermentation were acetate, ethanol, and lactate. The specific growth rates were able to fit the experimental points relatively well with Haldane equation assuming substrate inhibition, and the following kinetic parameters were obtained: the maximum specific growth rate (mu(max)) was 0.17 h(-1), the half-saturation constant (K(s)) was 0.75g/L, and inhibition constant (K(i)) was 3.72 g/L of xylose. Intermittent N2 sparging could enhance hydrogen production when high hydrogen partial pressure (> 0.14 atm) was present in the headspace of the batch reactors. Biohydrogen could be successfully produced in continuously stirred reactor (CSTR) operated at 72-h hydraulic retention time (HRT) with 1g/L of xylose as substrate at 70 degrees C. The hydrogen production yield achieved in the CSTR was 1.36+/-0.03 mol-H2/mol-xylose(sonsumed), and the production rate was 62+/-2 ml/d x L(reactor). The hydrogen content in the methane-free mixed gas was approximately 31+/-1%, and the rest was carbon dioxide. The main intermediate by-products from the effluent were acetate, formate, and ethanol at 4.25+/-0.10, 3.01+/-0.11, and 2.59+/-0.16 mM, respectively.

  7. Comparison of xylose fermentation by two high-performance engineered strains of Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Xin Li

    2016-03-01

    Full Text Available Economical biofuel production from plant biomass requires the conversion of both cellulose and hemicellulose in the plant cell wall. The best industrial fermentation organism, the yeast Saccharomyces cerevisiae, has been developed to utilize xylose by heterologously expressing either a xylose reductase/xylitol dehydrogenase (XR/XDH pathway or a xylose isomerase (XI pathway. Although it has been proposed that the optimal means for fermenting xylose into biofuels would use XI instead of the XR/XDH pathway, no clear comparison of the best publicly-available yeast strains engineered to use XR/XDH or XI has been published. We therefore compared two of the best-performing engineered yeast strains in the public domain—one using the XR/XDH pathway and another using XI—in anaerobic xylose fermentations. We find that, regardless of conditions, the strain using XR/XDH has substantially higher productivity compared to the XI strain. By contrast, the XI strain has better yields in nearly all conditions tested.

  8. Deep eutectic solvent and inorganic salt pretreatment of lignocellulosic biomass for improving xylose recovery.

    Science.gov (United States)

    Loow, Yu-Loong; Wu, Ta Yeong; Yang, Ge Hoa; Ang, Lin Yang; New, Eng Kein; Siow, Lee Fong; Md Jahim, Jamaliah; Mohammad, Abdul Wahab; Teoh, Wen Hui

    2017-07-29

    Deep eutectic solvents (DESs) have received considerable attention in recent years due to their low cost, low toxicity, and biodegradable properties. In this study, a sequential pretreatment comprising of a DES (choline chloride:urea in a ratio of 1:2) and divalent inorganic salt (CuCl2) was evaluated, with the aim of recovering xylose from oil palm fronds (OPF). At a solid-to-liquid ratio of 1:10 (w/v), DES alone was ineffective in promoting xylose extraction from OPF. However, a combination of DES (120°C, 4h) and 0.4mol/L of CuCl2 (120°C, 30min) resulted in a pretreatment hydrolysate containing 14.76g/L of xylose, remarkably yielding 25% more xylose than the CuCl2-only pretreatment (11.87g/L). Characterization studies such as FE-SEM, BET, XRD, and FTIR confirmed the delignification of OPF when DES was implemented. Thus, the use of this integrated pretreatment system enabled xylose recoveries which were comparable with other traditional pretreatments. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Increased ethanol production by deletion of HAP4 in recombinant xylose-assimilating Saccharomyces cerevisiae.

    Science.gov (United States)

    Matsushika, Akinori; Hoshino, Tamotsu

    2015-12-01

    The Saccharomyces cerevisiae HAP4 gene encodes a transcription activator that plays a key role in controlling the expression of genes involved in mitochondrial respiration and reductive pathways. This work examines the effect of knockout of the HAP4 gene on aerobic ethanol production in a xylose-utilizing S. cerevisiae strain. A hap4-deleted recombinant yeast strain (B42-DHAP4) showed increased maximum concentration, production rate, and yield of ethanol compared with the reference strain MA-B42, irrespective of cultivation medium (glucose, xylose, or glucose/xylose mixtures). Notably, B42-DHAP4 was capable of producing ethanol from xylose as the sole carbon source under aerobic conditions, whereas no ethanol was produced by MA-B42. Moreover, the rate of ethanol production and ethanol yield (0.44 g/g) from the detoxified hydrolysate of wood chips was markedly improved in B42-DHAP4 compared to MA-B42. Thus, the results of this study support the view that deleting HAP4 in xylose-utilizing S. cerevisiae strains represents a useful strategy in ethanol production processes.

  10. Xylose isomerization with zeolites in a two-step alcohol-water process.

    Science.gov (United States)

    Paniagua, Marta; Saravanamurugan, Shunmugavel; Melian-Rodriguez, Mayra; Melero, Juan A; Riisager, Anders

    2015-03-01

    Isomerization of xylose to xylulose was efficiently catalyzed by large-pore zeolites in a two-step methanol-water process that enhanced the product yield significantly. The reaction pathway involves xylose isomerization to xylulose, which, in part, subsequently reacts with methanol to form methyl xyluloside (step 1) followed by hydrolysis after water addition to form additional xylulose (step 2). NMR spectroscopy studies performed with (13) C-labeled xylose confirmed the proposed reaction pathway. The most active catalyst examined was zeolite Y, which proved more active than zeolite beta, ZSM-5, and mordenite. The yield of xylulose obtained over H-USY (Si/Al=6) after 1 h of reaction at 100 °C was 39%. After water hydrolysis in the second reaction step, the yield increased to 47%. Results obtained from pyridine adsorption studies confirm that H-USY (6) is a catalyst that combines Brønsted and Lewis acid sites, and isomerizes xylose in alcohol media to form xylulose at low temperature. The applied zeolites are commercially available; do not contain any auxiliary tetravalent metals, for example, tin, titanium, or zirconium; isomerize xylose efficiently; are easy to regenerate; and are prone to recycling. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Comparison of xylose fermentation by two high-performance engineered strains ofSaccharomyces cerevisiae.

    Science.gov (United States)

    Li, Xin; Park, Annsea; Estrela, Raissa; Kim, Soo-Rin; Jin, Yong-Su; Cate, Jamie H D

    2016-03-01

    Economical biofuel production from plant biomass requires the conversion of both cellulose and hemicellulose in the plant cell wall. The best industrial fermentation organism, the yeast Saccharomyces cerevisiae, has been developed to utilize xylose by heterologously expressing either a xylose reductase/xylitol dehydrogenase (XR/XDH) pathway or a xylose isomerase (XI) pathway. Although it has been proposed that the optimal means for fermenting xylose into biofuels would use XI instead of the XR/XDH pathway, no clear comparison of the best publicly-available yeast strains engineered to use XR/XDH or XI has been published. We therefore compared two of the best-performing engineered yeast strains in the public domain-one using the XR/XDH pathway and another using XI-in anaerobic xylose fermentations. We find that, regardless of conditions, the strain using XR/XDH has substantially higher productivity compared to the XI strain. By contrast, the XI strain has better yields in nearly all conditions tested.

  12. Xylose from lignocellulosic waste in the production and industrial processing of pinneaple (Ananascomusus

    Directory of Open Access Journals (Sweden)

    Karla Ramírez Amador

    2016-03-01

    Full Text Available Lignocellulosicwaste from the pineapple production is a raw material useful for the xylose production by hydrolysis and it can be converted to xylitol. The objective of this work was to study the hydrolysis of pineapple peel with sulfuric acid at variable concentration (2-6%, reaction time (0-350 min and temperature at 98 ˚C. The concentration of xylose, glucose and degradation products as acetic acid and furfural was determined. Optimal conditions found for hydrolysis were 6% H2SO4 at 98 ˚C for 83 min which yield was 26,9 g xylose/L, 2,61 g glucose/L, 7,71 g acetic acid/L and 0,29 g furfural/L.

  13. NADPH-dependent D-aldose reductases and xylose fermentation in Fusarium oxysporum

    DEFF Research Database (Denmark)

    Panagiotou, Gianni; Christakopoulos, P.

    2004-01-01

    Two aldose (xylose) reductases (ARI and ARII) from Fusarium oxysporum were purified and characterized. The native ARI was a monomer with M-r 41000, pI 5.2 and showed a 52-fold preference for NADPH over NADH, while ARII was homodimeric with a subunit of M-r 37000, pI 3.6 and a 60-fold preference...... for NADPH over NADH. In this study, the influence of aeration and the response to the addition of electron acceptors on xylose fermentation by F. oxysporum were also studied. The batch cultivation of F. oxysporum on xylose was performed under aerobic, anaerobic and oxygen-limited conditions in stirred tank...

  14. Selective Preparation of Furfural from Xylose over Sulfonic Acid Functionalized Mesoporous Sba-15 Materials

    Directory of Open Access Journals (Sweden)

    Panpan Li

    2011-04-01

    Full Text Available Sulfonic acid functionalized mesoporous SBA-15 materials were prepared using the co-condensation and grafting methods, respectively, and their catalytic performance in the dehydration of xylose to furfural was examined. SBA-15-SO3H(C prepared by the co-condensation method showed 92–95% xylose conversion and 74% furfural selectivity, and 68–70% furfural yield under the given reaction conditions. The deactivation and regeneration of the SBA-15-SO3H(C catalyst for the dehydration of xylose was also investigated. The results indicate that the used and regeneration catalysts retained the SBA-15 mesoporous structure, and the S content of SBA-15-SO3H(C almost did not change. The deactivation of the catalysts is proposed to be associated with the accumulation of byproducts, which is caused by the loss reaction of furfural. After regeneration by H2O2, the catalytic activity of the catalyst almost recovered.

  15. Xylose Isomerization with Zeolites in a Two-Step Alcohol–Water Process

    DEFF Research Database (Denmark)

    Paniagua, Marta; Shunmugavel, Saravanamurugan; Melián Rodriguez, Mayra

    2015-01-01

    Isomerization of xylose to xylulose was efficiently catalyzed by large-pore zeolites in a two-step methanol–water process that enhanced the product yield significantly. The reaction pathway involves xylose isomerization to xylulose, which, in part, subsequently reacts with methanol to form methyl...... xyluloside (step 1) followed by hydrolysis after water addition to form additional xylulose (step 2). NMR spectroscopy studies performed with 13C-labeled xylose confirmed the proposed reaction pathway. The most active catalyst examined was zeolite Y, which proved more active than zeolite beta, ZSM-5......, and mordenite. The yield of xylulose obtained over H-USY (Si/Al=6) after 1 h of reaction at 1008C was 39%. After water hydrolysis in the second reaction step, the yield increased to 47%. Results obtained from pyridine adsorption studies confirm that H-USY (6) is a catalyst that combines Brønsted and Lewis acid...

  16. Production of 3-hydroxypropionic acid from glucose and xylose by metabolically engineered Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Kildegaard, Kanchana Rueksomtawin; Wang, Zheng; Chen, Yun

    2015-01-01

    biomass into the products of interest. We engineered Saccharomyces cerevisiae for production of 3-hydroxypropionic acid (3HP), a potential building block for acrylates, from glucose and xylose. We introduced the 3HP biosynthetic pathways via malonyl-CoA or β-alanine intermediates into a xylose...

  17. KINETICS OF GROWTH AND ETHANOL PRODUCTION ON DIFFERENT CARBON SUBSTRATES USING GENETICALLY ENGINEERED XYLOSE-FERMENTING YEAST

    Science.gov (United States)

    Saccharomyces cerevisiae 424A (LNH-ST) strain was used for fermentation of glucose and xylose. Growth kinetics and ethanol productivity were calculated for batch fermentation on media containing different combinations of glucose and xylose to give a final sugar concentra...

  18. Influence of genetic background of engineered xylose-fermenting industrial Saccharomyces cerevisiae strains for ethanol production from lignocellulosic hydrolysates

    Science.gov (United States)

    An industrial ethanol-producing Saccharomyces cerevisiae strain with genes needed for xylose-fermentation integrated into its genome was used to obtain haploids and diploid isogenic strains. The isogenic strains were more effective in metabolizing xylose than their parental strain (p < 0.05) and abl...

  19. Co-utilization of L-arabinose and D-xylose by laboratory and industrial Saccharomyces cerevisiae strains

    Directory of Open Access Journals (Sweden)

    Boles Eckhard

    2006-04-01

    Full Text Available Abstract Background Fermentation of lignocellulosic biomass is an attractive alternative for the production of bioethanol. Traditionally, the yeast Saccharomyces cerevisiae is used in industrial ethanol fermentations. However, S. cerevisiae is naturally not able to ferment the pentose sugars D-xylose and L-arabinose, which are present in high amounts in lignocellulosic raw materials. Results We describe the engineering of laboratory and industrial S. cerevisiae strains to co-ferment the pentose sugars D-xylose and L-arabinose. Introduction of a fungal xylose and a bacterial arabinose pathway resulted in strains able to grow on both pentose sugars. Introduction of a xylose pathway into an arabinose-fermenting laboratory strain resulted in nearly complete conversion of arabinose into arabitol due to the L-arabinose reductase activity of the xylose reductase. The industrial strain displayed lower arabitol yield and increased ethanol yield from xylose and arabinose. Conclusion Our work demonstrates simultaneous co-utilization of xylose and arabinose in recombinant strains of S. cerevisiae. In addition, the co-utilization of arabinose together with xylose significantly reduced formation of the by-product xylitol, which contributed to improved ethanol production.

  20. Genetic analysis of D-xylose metabolism by endophytic yeast strains of Rhodotorula graminis and Rhodotorula mucilaginosa

    Science.gov (United States)

    Xu, Ping; Bura, Renata; Doty, Sharon L.

    2011-01-01

    Two novel endophytic yeast strains, WP1 and PTD3, isolated from within the stems of poplar (Populus) trees, were genetically characterized with respect to their xylose metabolism genes. These two strains, belonging to the species Rhodotorula graminis and R. mucilaginosa, respectively, utilize both hexose and pentose sugars, including the common plant pentose sugar, D-xylose. The xylose reductase (XYL1) and xylitol dehydrogenase (XYL2) genes were cloned and characterized. The derived amino acid sequences of xylose reductase (XR) and xylose dehydrogenase (XDH) were 32%∼41% homologous to those of Pichia stipitis and Candida. spp., two species known to utilize xylose. The derived XR and XDH sequences of WP1 and PTD3 had higher homology (73% and 69% identity) with each other. WP1 and PTD3 were grown in single sugar and mixed sugar media to analyze the XYL1 and XYL2 gene regulation mechanisms. Our results revealed that for both strains, the gene expression is induced by D-xylose, and that in PTD3 the expression was not repressed by glucose in the presence of xylose. PMID:21931522

  1. Genetic analysis of D-xylose metabolism by endophytic yeast strains of Rhodotorula graminis and Rhodotorula mucilaginosa

    Directory of Open Access Journals (Sweden)

    Ping Xu

    2011-01-01

    Full Text Available Two novel endophytic yeast strains, WP1 and PTD3, isolated from within the stems of poplar (Populus trees, were genetically characterized with respect to their xylose metabolism genes. These two strains, belonging to the species Rhodotorula graminis and R. mucilaginosa, respectively, utilize both hexose and pentose sugars, including the common plant pentose sugar, D-xylose. The xylose reductase (XYL1 and xylitol dehydrogenase (XYL2 genes were cloned and characterized. The derived amino acid sequences of xylose reductase (XR and xylose dehydrogenase (XDH were 32%~41% homologous to those of Pichia stipitis and Candida. spp., two species known to utilize xylose. The derived XR and XDH sequences of WP1 and PTD3 had higher homology (73% and 69% identity with each other. WP1 and PTD3 were grown in single sugar and mixed sugar media to analyze the XYL1 and XYL2 gene regulation mechanisms. Our results revealed that for both strains, the gene expression is induced by D-xylose, and that in PTD3 the expression was not repressed by glucose in the presence of xylose.

  2. L-lactic acid production from D-xylose with Candida sonorensis expressing a heterologous lactate dehydrogenase encoding gene.

    Science.gov (United States)

    Koivuranta, Kari T; Ilmén, Marja; Wiebe, Marilyn G; Ruohonen, Laura; Suominen, Pirkko; Penttilä, Merja

    2014-08-08

    Bioplastics, like polylactic acid (PLA), are renewable alternatives for petroleum-based plastics. Lactic acid, the monomer of PLA, has traditionally been produced biotechnologically with bacteria. With genetic engineering, yeast have the potential to replace bacteria in biotechnological lactic acid production, with the benefits of being acid tolerant and having simple nutritional requirements. Lactate dehydrogenase genes have been introduced to various yeast to demonstrate this potential. Importantly, an industrial lactic acid producing process utilising yeast has already been implemented. Utilisation of D-xylose in addition to D-glucose in production of biochemicals such as lactic acid by microbial fermentation would be beneficial, as it would allow lignocellulosic raw materials to be utilised in the production processes. The yeast Candida sonorensis, which naturally metabolises D-xylose, was genetically modified to produce L-lactic acid from D-xylose by integrating the gene encoding L-lactic acid dehydrogenase (ldhL) from Lactobacillus helveticus into its genome. In microaerobic, CaCO3-buffered conditions a C. sonorensis ldhL transformant having two copies of the ldhL gene produced 31 g l-1 lactic acid from 50 g l-1 D-xylose free of ethanol.Anaerobic production of lactic acid from D-xylose was assessed after introducing an alternative pathway of D-xylose metabolism, i.e. by adding a xylose isomerase encoded by XYLA from Piromyces sp. alone or together with the xylulokinase encoding gene XKS1 from Saccharomyces cerevisiae. Strains were further modified by deletion of the endogenous xylose reductase encoding gene, alone or together with the xylitol dehydrogenase encoding gene. Strains of C. sonorensis expressing xylose isomerase produced L-lactic acid from D-xylose in anaerobic conditions. The highest anaerobic L-lactic acid production (8.5 g l-1) was observed in strains in which both the xylose reductase and xylitol dehydrogenase encoding genes had been

  3. Xylose from lignocellulosic waste in the production and industrial processing of pinneaple (Ananascomusus)

    OpenAIRE

    Ramírez Amador, Karla; Rojas Carrillo, Óscar; Alvarado Aguilar, Patricia; Vega-Baudrit, José

    2016-01-01

    Lignocellulosicwaste from the pineapple production is a raw material useful for the xylose production by hydrolysis and it can be converted to xylitol. The objective of this work was to study the hydrolysis of pineapple peel with sulfuric acid at variable concentration (2-6%), reaction time (0-350 min) and temperature at 98 ˚C. The concentration of xylose, glucose and degradation products as acetic acid and furfural was determined. Optimal conditions found for hydrolysis were 6% H2SO4 at 98 ˚...

  4. Increasing ethanol productivity during xylose fermentation by cell recycling of recombinant Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Roca, Christophe Francois Aime; Olsson, Lisbeth

    2003-01-01

    (-1). Consequently, the volumetric ethanol productivity increased ten-fold, from 0.5 g l(-1) h(-1) to 5.35 g l(-1) h(-1). By increasing the biomass concentration, the xylose consumption rate increased from 0.75 g xylose l(-1) h(-1) without recycling to 1.9 g l(-1) h(-1) with recycling. The specific...... ethanol productivity was in the range of 0.23-0.26 g g(-1) h(-1) with or without cell recycling, showing that an increased cell-mass concentration did not influence the efficiency of the yeast....

  5. Improved inhibitor tolerance in xylose-fermenting yeast Spathaspora passalidarum by mutagenesis and protoplast fusion

    DEFF Research Database (Denmark)

    Hou, Xiaoru; Yao, Shuo

    2012-01-01

    from fusion of the protoplasts of S. passalidarum M7 and a robust yeast, Saccharomyces cerevisiae ATCC 96581, were able to grow in 75% WSLQ and produce around 0.4 g ethanol/g consumed xylose. Among the selected hybrid strains, the hybrid FS22 showed the best fermentation capacity in 75% WSLQ...... final ethanol than the wild-type strain in a synthetic xylose medium containing 2 g/l furfural. However, this mutant was unable to grow in a medium containing 75% liquid fraction of pretreated wheat straw (WSLQ), in which furfural and many other inhibitors were present. Hybrid yeast strains, obtained...... to inhibitors from S. cerevisiae ATCC 96581....

  6. Fat: an evolving issue

    Directory of Open Access Journals (Sweden)

    John R. Speakman

    2012-09-01

    Work on obesity is evolving, and obesity is a consequence of our evolutionary history. In the space of 50 years, we have become an obese species. The reasons why can be addressed at a number of different levels. These include separating between whether the primary cause lies on the food intake or energy expenditure side of the energy balance equation, and determining how genetic and environmental effects contribute to weight variation between individuals. Opinion on whether increased food intake or decreased energy expenditure drives the obesity epidemic is still divided, but recent evidence favours the idea that food intake, rather than altered expenditure, is most important. There is more of a consensus that genetics explains most (probably around 65% of weight variation between individuals. Recent advances in genome-wide association studies have identified many polymorphisms that are linked to obesity, yet much of the genetic variance remains unexplained. Finding the causes of this unexplained variation will be an impetus of genetic and epigenetic research on obesity over the next decade. Many environmental factors – including gut microbiota, stress and endocrine disruptors – have been linked to the risk of developing obesity. A better understanding of gene-by-environment interactions will also be key to understanding obesity in the years to come.

  7. Evolving Concepts of Asthma

    Science.gov (United States)

    Ray, Anuradha; Wenzel, Sally E.

    2015-01-01

    Our understanding of asthma has evolved over time from a singular disease to a complex of various phenotypes, with varied natural histories, physiologies, and responses to treatment. Early therapies treated most patients with asthma similarly, with bronchodilators and corticosteroids, but these therapies had varying degrees of success. Similarly, despite initial studies that identified an underlying type 2 inflammation in the airways of patients with asthma, biologic therapies targeted toward these type 2 pathways were unsuccessful in all patients. These observations led to increased interest in phenotyping asthma. Clinical approaches, both biased and later unbiased/statistical approaches to large asthma patient cohorts, identified a variety of patient characteristics, but they also consistently identified the importance of age of onset of disease and the presence of eosinophils in determining clinically relevant phenotypes. These paralleled molecular approaches to phenotyping that developed an understanding that not all patients share a type 2 inflammatory pattern. Using biomarkers to select patients with type 2 inflammation, repeated trials of biologics directed toward type 2 cytokine pathways saw newfound success, confirming the importance of phenotyping in asthma. Further research is needed to clarify additional clinical and molecular phenotypes, validate predictive biomarkers, and identify new areas for possible interventions. PMID:26161792

  8. Evolving endoscopic surgery.

    Science.gov (United States)

    Sakai, Paulo; Faintuch, Joel

    2014-06-01

    Since the days of Albukasim in medieval Spain, natural orifices have been regarded not only as a rather repugnant source of bodily odors, fluids and excreta, but also as a convenient invitation to explore and treat the inner passages of the organism. However, surgical ingenuity needed to be matched by appropriate tools and devices. Lack of technologically advanced instrumentation was a strong deterrent during almost a millennium until recent decades when a quantum jump materialized. Endoscopic surgery is currently a vibrant and growing subspecialty, which successfully handles millions of patients every year. Additional opportunities lie ahead which might benefit millions more, however, requiring even more sophisticated apparatuses, particularly in the field of robotics, artificial intelligence, and tissue repair (surgical suturing). This is a particularly exciting and worthwhile challenge, namely of larger and safer endoscopic interventions, followed by seamless and scarless recovery. In synthesis, the future is widely open for those who use together intelligence and creativity to develop new prototypes, new accessories and new techniques. Yet there are many challenges in the path of endoscopic surgery. In this new era of robotic endoscopy, one will likely need a virtual simulator to train and assess the performance of younger doctors. More evidence will be essential in multiple evolving fields, particularly to elucidate whether more ambitious and complex pathways, such as intrathoracic and intraperitoneal surgery via natural orifice transluminal endoscopic surgery (NOTES), are superior or not to conventional techniques. © 2014 Journal of Gastroenterology and Hepatology Foundation and Wiley Publishing Asia Pty Ltd.

  9. Asymmetric evolving random networks

    Science.gov (United States)

    Coulomb, S.; Bauer, M.

    2003-10-01

    We generalize the Poissonian evolving random graph model of M. Bauer and D. Bernard (2003), to deal with arbitrary degree distributions. The motivation comes from biological networks, which are well-known to exhibit non Poissonian degree distributions. A node is added at each time step and is connected to the rest of the graph by oriented edges emerging from older nodes. This leads to a statistical asymmetry between incoming and outgoing edges. The law for the number of new edges at each time step is fixed but arbitrary. Thermodynamical behavior is expected when this law has a large time limit. Although (by construction) the incoming degree distributions depend on this law, this is not the case for most qualitative features concerning the size distribution of connected components, as long as the law has a finite variance. As the variance grows above 1/4, the average being < 1/2, a giant component emerges, which connects a finite fraction of the vertices. Below this threshold, the distribution of component sizes decreases algebraically with a continuously varying exponent. The transition is of infinite order, in sharp contrast with the case of static graphs. The local-in-time profiles for the components of finite size allow to give a refined description of the system.

  10. Evolving a photosynthetic organelle

    Directory of Open Access Journals (Sweden)

    Nakayama Takuro

    2012-04-01

    Full Text Available Abstract The evolution of plastids from cyanobacteria is believed to represent a singularity in the history of life. The enigmatic amoeba Paulinella and its 'recently' acquired photosynthetic inclusions provide a fascinating system through which to gain fresh insight into how endosymbionts become organelles. The plastids, or chloroplasts, of algae and plants evolved from cyanobacteria by endosymbiosis. This landmark event conferred on eukaryotes the benefits of photosynthesis - the conversion of solar energy into chemical energy - and in so doing had a huge impact on the course of evolution and the climate of Earth 1. From the present state of plastids, however, it is difficult to trace the evolutionary steps involved in this momentous development, because all modern-day plastids have fully integrated into their hosts. Paulinella chromatophora is a unicellular eukaryote that bears photosynthetic entities called chromatophores that are derived from cyanobacteria and has thus received much attention as a possible example of an organism in the early stages of organellogenesis. Recent studies have unlocked the genomic secrets of its chromatophore 23 and provided concrete evidence that the Paulinella chromatophore is a bona fide photosynthetic organelle 4. The question is how Paulinella can help us to understand the process by which an endosymbiont is converted into an organelle.

  11. Oxidative production of xylonic acid using xylose in distillation stillage of cellulosic ethanol fermentation broth by Gluconobacter oxydans.

    Science.gov (United States)

    Zhang, Hongsen; Han, Xushen; Wei, Chengxiang; Bao, Jie

    2017-01-01

    An oxidative production process of xylonic acid using xylose in distillation stillage of cellulosic ethanol fermentation broth was designed, experimentally investigated, and evaluated. Dry dilute acid pretreated and biodetoxified corn stover was simultaneously saccharified and fermented into 59.80g/L of ethanol (no xylose utilization). 65.39g/L of xylose was obtained in the distillation stillage without any concentrating step after ethanol was distillated. Then the xylose was completely converted into 66.42g/L of xylonic acid by Gluconobacter oxydans. The rigorous Aspen Plus modeling shows that the wastewater generation and energy consumption was significantly reduced comparing to the previous xylonic acid production process using xylose in pretreatment liquid. This study provided a practical process option for xylonic acid production from lignocellulose feedstock with significant reduction of wastewater and energy consumption. Copyright © 2016 Elsevier Ltd. All rights reserved.

  12. Production of D-arabitol from D-xylose by the oleaginous yeast Rhodosporidium toruloides IFO0880.

    Science.gov (United States)

    Jagtap, Sujit Sadashiv; Rao, Christopher V

    2017-11-11

    The sugar alcohol D-arabitol is one of the Department of Energy's top twelve bio-based building block chemicals. In this study, we found that the oleaginous yeast Rhodosporidium toruloides IFO0880 produces D-arabitol during growth on xylose in nitrogen-rich medium. Efficient xylose utilization was a prerequisite for extracellular D-arabitol production. During growth in complex media, R. toruloides produced 22 ± 2, 32 ± 2, and 49 ± 2 g/L D-arabitol from 70, 105, and 150 g/L xylose, respectively. In addition, we found that R. toruloides could potentially be used for the co-production of lipids and D-arabitol from xylose. These results demonstrate that R. toruloides can be used to produce multiple value-added chemicals from xylose.

  13. Engineered yeast with a CO2-fixation pathway to improve the bio-ethanol production from xylose-mixed sugars.

    Science.gov (United States)

    Li, Yun-Jie; Wang, Miao-Miao; Chen, Ya-Wei; Wang, Meng; Fan, Li-Hai; Tan, Tian-Wei

    2017-03-06

    Bio-ethanol production from lignocellulosic raw materials could serve as a sustainable potential for improving the supply of liquid fuels in face of the food-to-fuel competition and the growing energy demand. Xylose is the second abundant sugar of lignocelluloses hydrolysates, but its commercial-scale conversion to ethanol by fermentation is challenged by incomplete and inefficient utilization of xylose. Here, we use a coupled strategy of simultaneous maltose utilization and in-situ carbon dioxide (CO2) fixation to achieve efficient xylose fermentation by the engineered Saccharomyces cerevisiae. Our results showed that the introduction of CO2 as electron acceptor for nicotinamide adenine dinucleotide (NADH) oxidation increased the total ethanol productivity and yield at the expense of simultaneous maltose and xylose utilization. Our achievements present an innovative strategy using CO2 to drive and redistribute the central pathways of xylose to desirable products and demonstrate a possible breakthrough in product yield of sugars.

  14. Adaptive evolution of nontransgenic Escherichia coli KC01 for improved ethanol tolerance and homoethanol fermentation from xylose.

    Science.gov (United States)

    Wang, Yongze; Manow, Ryan; Finan, Christopher; Wang, Jinhua; Garza, Erin; Zhou, Shengde

    2011-09-01

    Due to its excellent capability to ferment five-carbon sugars, Escherichia coli has been considered one of the platform organisms to be engineered for production of cellulosic ethanol. Nevertheless, genetically engineered ethanologenic E. coli lacks the essential trait of alcohol tolerance. Development of ethanol tolerance is required for cost-effective ethanol fermentation. In this study, we improved alcohol tolerance of a nontransgenic E. coli KC01 (ldhA pflB ackA frdBC pdhR::pflBp6-aceEF-lpd) through adaptive evolution. During ~350 generations of adaptive evolution, a gradually increased concentration of ethanol was used as a selection pressure to enrich ethanol-tolerant mutants. The evolved mutant, E. coli SZ470, was able to grow anaerobically at 40 g l(-1) ethanol, a twofold improvement over parent KC01. When compared with KC01 for small-scale (500 ml) xylose (50 g l(-1)) fermentation, SZ470 achieved 67% higher cell mass, 48% faster volumetric ethanol productivity, and 50% shorter time to complete fermentation with ethanol titer of 23.5 g l(-1) and yield of 94%. These results demonstrate that an industry-oriented nontransgenic E. coli strain could be developed through incremental improvements of desired traits by a combination of molecular biology and traditional microbiology techniques.

  15. Deleting the para-nitrophenyl phosphatase (pNPPase), PHO13, in recombinant Saccharomyces cerevisiae improves growth and ethanol production on D-xylose

    Science.gov (United States)

    Jennifer Van Vleet; Thomas W. Jeffries; Lisbeth Olsson

    2008-01-01

    Overexpression of D-xylulokinase in Saccharomyces cerevisiae engineered for assimilation of xylose results in growth inhibition that is more pronounced at higher xylose concentrations. Mutants deficient in the para-nitrophenyl phosphatase, PHO13, resist growth inhibition on xylose. We studied this inhibition under aerobic growth conditions in well-controlled...

  16. Evolving PSTN to NGN

    Science.gov (United States)

    Wu, Liang T.

    2004-04-01

    The concept of Next Generation Network (NGN) was conceived around 1998 as an integrated solution to combine the quality and features of the PSTN with the low cost and routing flexibility of the Internet to provide a single infrastructure for the future public network. This carrier grade Internet solution calls for the creation of a consolidated, packet transport and switching infrastructure and the development of a flexible, open, software switch (softswitch) to handle voice telephony as well as multimedia services. Almost all the telecom equipment manufacturers as well as some Internet equipment vendors immediately subscribed to this vision and joined the race to create convergent products for the NGN market.

  17. The Influence of Sugar Cane Bagasse Type and Its Particle Size on Xylose Production and Xylose-to-Xylitol Bioconversion with the Yeast Debaryomyces hansenii.

    Science.gov (United States)

    Aghcheh, Razieh Karimi; Bonakdarpour, Babak; Ashtiani, Farzin Zokaee

    2016-11-01

    In the present study, the effect of the type of sugar cane bagasse (non-depithed or depithed) and its particle size on the production of xylose and its subsequent fermentation to xylitol by Debaryomyces hansenii CBS767 was investigated using a full factorial experimental design. It was found that the particle size range and whether bagasse was depithed or not had a significant effect on the concentration and yield of xylose in the resulting hemicellulose hydrolysate. Depithed bagasse resulted in higher xylose concentrations compared to non-depithed bagasse. The corresponding detoxified hemicellulose hydrolysates were used as fermentation media for the production of xylitol. The hemicellulose hydrolysate prepared from depithed bagasse also yielded meaningfully higher xylitol fermentation rates compared to non-depithed bagasse. However, in the case of non-depithed bagasse, the hemicellulose hydrolysate prepared from larger particle size range resulted in higher xylitol fermentation rates, whereas the effect in the case of non-depithed bagasse was not pronounced. Therefore, depithing of bagasse is an advantageous pretreatment when it is to be employed in bioconversion processes.

  18. NADH-linked aldose reductase : The key to anaerobic alcoholic fermentation of xylose by yeasts

    NARCIS (Netherlands)

    Bruinenberg, P.M.; De Bot, P.H.M.; Van Dijken, J.P.; Scheffers, W.A.

    1984-01-01

    The kinetics and enzymology of o-xylose utilization were studied in aerobic and anaerobic batch cultures of the facultatively fermentative yeasts Candida utilis, Pachysolen tannophilus, and Pichia stipitis. These yeasts did not produce ethanol under aerobic conditions. When shifted to anaerobiosis

  19. Furfural synthesis from D-xylose in the presence of sodium chloride : Microwave versus conventional heating

    NARCIS (Netherlands)

    Xiouras, C.; Radacsi, N.; Sturm, G.S.J.; Stefanidis, G.

    2016-01-01

    We investigate the existence of specific/nonthermal microwave effects for the dehydration reaction of xylose to furfural in the presence of NaCl. Such effects are reported for sugars dehydration reactions in several literature reports. To this end, we adopted three approaches that compare

  20. Production of 3-hydroxypropionic acid from glucose and xylose by metabolically engineered Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Kanchana R. Kildegaard

    2015-12-01

    Full Text Available Biomass, the most abundant carbon source on the planet, may in the future become the primary feedstock for production of fuels and chemicals, replacing fossil feedstocks. This will, however, require development of cell factories that can convert both C6 and C5 sugars present in lignocellulosic biomass into the products of interest. We engineered Saccharomyces cerevisiae for production of 3-hydroxypropionic acid (3HP, a potential building block for acrylates, from glucose and xylose. We introduced the 3HP biosynthetic pathways via malonyl-CoA or β-alanine intermediates into a xylose-consuming yeast. Using controlled fed-batch cultivation, we obtained 7.37±0.17 g 3HP L−1 in 120 hours with an overall yield of 29±1% Cmol 3HP Cmol−1 xylose. This study is the first demonstration of the potential of using S. cerevisiae for production of 3HP from the biomass sugar xylose.

  1. Fermentation of D-xylose and L-arabinose to ethanol by Erwinia chrysanthemi

    Energy Technology Data Exchange (ETDEWEB)

    Tolan, J.S.; Finn, R.K.

    1987-09-01

    Erwinia spp. are gram-negative facultative anaerobes within the family Enterobacteriacae which possess several desirable traits for the conversion of pentose sugars to ethanol, such as the ability to ferment a broad range of carbohydrates and the ease with which they can be genetically modified. Twenty-eight strains of Erwinia carotovora and E. chrysanthemi were screened for the ability to ferment D-xylose to ethanol. E. chrysanthemi B374 was chosen for further study on the basis of its superior (4%) ethanol tolerance. They have characterized the fermentation of D-xylose and L-arabinose by the wild type and mutants which bear plasmids containing the pyruvate decarboxylase gene from Zymomonas mobilis. Expression of the gene markedly increased the yields of ethanol (from 0.7 up to 1.45 mol/mol of xylose) and decreased the yields of formate, acetate, and lactate. However, the cells with pyruvate decarboxylase grew only one-fourth as fast as the wild type and tolerated only 2% ethanol. Alcohol tolerance was stimulated by the addition of yeast extract to the growth medium. Xylose catabolism was characterized by a high saturation constant K/sub s/ (4.5 mM).

  2. Creation of a synthetic xylose-inducible promoter for Saccharomyces cerevisiae

    Science.gov (United States)

    Saccharomyces cerevisiae is currently used to produce ethanol from glucose, but it cannot utilize five-carbon sugars contained in the hemicellulose component of biomass feedstocks. S. cerevisiae strains engineered for xylose fermentation have been made using constitutive promoters to express the req...

  3. Lactic acid production from xylose by engineered Saccharomyces cerevisiae without PDC or ADH deletion

    Science.gov (United States)

    Production of lactic acid from renewable sugars has received growing attention as lactic acid can be used for making renewable and bio-based plastics. However, most prior studies have focused on production of lactic acid from glucose despite cellulosic hydrolysates contain xylose as well as glucose....

  4. Comparative genomics of xylose-fermenting fungi for enhanced biofuel production

    Science.gov (United States)

    Dana J. Wolbach; Alan Kuo; Trey K. Sato; Katlyn M. Potts; Asaf A. Salamov; Kurt M. LaButti; Hui Sun; Alicia Clum; Jasmyn L. Pangilinan; Erika A. Lindquist; Susan Lucas; Alla Lapidus; Mingjie Jin; Christa Gunawan; Venkatesh Balan; Bruce E. Dale; Thomas W. Jeffries; Robert Zinkel; Kerrie W. Barry; Igor V. Grigoriev; Audrey P. Gasch

    2011-01-01

    Cellulosic biomass is an abundant and underused substrate for biofuel production. The inability of many microbes to metabolize the pentose sugars abundant within hemicellulose creates specific challenges for microbial biofuel production from cellulosic material. Although engineered strains of Saccharomyces cerevisiae can use the pentose xylose, the fermentative...

  5. Engineering of Saccharomyces cerevisiae for the production of fuel ethanol from xylose

    NARCIS (Netherlands)

    Kuijper, S.M.

    2006-01-01

    For various reasons mankind is looking for alternatives for fossil fuels. One of these alternatives is ethanol made from plant biomass. However, the plant material when broken down by hydrolysis into its sugar monomers contains a significant amount of xylose, a 5-carbon-sugar or pentose. Contrary to

  6. Analytical Validation of a New Enzymatic and Automatable Method for d-Xylose Measurement in Human Urine Samples

    Directory of Open Access Journals (Sweden)

    Israel Sánchez-Moreno

    2017-01-01

    Full Text Available Hypolactasia, or intestinal lactase deficiency, affects more than half of the world population. Currently, xylose quantification in urine after gaxilose oral administration for the noninvasive diagnosis of hypolactasia is performed with the hand-operated nonautomatable phloroglucinol reaction. This work demonstrates that a new enzymatic xylose quantification method, based on the activity of xylose dehydrogenase from Caulobacter crescentus, represents an excellent alternative to the manual phloroglucinol reaction. The new method is automatable and facilitates the use of the gaxilose test for hypolactasia diagnosis in the clinical practice. The analytical validation of the new technique was performed in three different autoanalyzers, using buffer or urine samples spiked with different xylose concentrations. For the comparison between the phloroglucinol and the enzymatic assays, 224 urine samples of patients to whom the gaxilose test had been prescribed were assayed by both methods. A mean bias of −16.08 mg of xylose was observed when comparing the results obtained by both techniques. After adjusting the cut-off of the enzymatic method to 19.18 mg of xylose, the Kappa coefficient was found to be 0.9531, indicating an excellent level of agreement between both analytical procedures. This new assay represents the first automatable enzymatic technique validated for xylose quantification in urine.

  7. Expression of protein engineered NADP{sup +}-dependent xylitol dehydrogenase increases ethanol production from xylose in recombinant Saccharomyces cerevisiae

    Energy Technology Data Exchange (ETDEWEB)

    Matsushika, Akinori; Inoue, Hiroyuki; Murakami, Katsuji; Takimura, Osamu; Sawayama, Shigeki [National Institute of Advanced Industrial Science and Technology, Hiroshima (Japan). Biomass Technology Research Center; Watanabe, Seiya; Kodaki, Tsutomu; Makino, Keisuke [Kyoto Univ. (Japan). Inst. of Advanced Energy

    2008-11-15

    A recombinant Saccharomyces cerevisiae strain transformed with xylose reductase (XR) and xylitol dehydrogenase (XDH) genes from Pichia stipitis has the ability to convert xylose to ethanol together with the unfavorable excretion of xylitol, which may be due to cofactor imbalance between NADPH-preferring XR and NAD{sup +}-dependent XDH. To reduce xylitol formation, we have already generated several XDH mutants with a reversal of coenzyme specificity toward NADP{sup +}. In this study, we constructed a set of recombinant S. cerevisiae strains with xylose-fermenting ability, including protein-engineered NADP{sup +}-dependent XDH-expressing strains. The most positive effect on xylose-to-ethanol fermentation was found by using a strain named MA-N5, constructed by chromosomal integration of the gene for NADP{sup +}-dependent XDH along with XR and endogenous xylulokinase genes. The MA-N5 strain had an increase in ethanol production and decrease in xylitol excretion compared with the reference strain expressing wild-type XDH when fermenting not only xylose but also mixed sugars containing glucose and xylose. Furthermore, the MA-N5 strain produced ethanol with a high yield of 0.49 g of ethanol/g of total consumed sugars in the nonsulfuric acid hydrolysate of wood chips. The results demonstrate that glucose and xylose present in the lignocellulosic hydrolysate can be efficiently fermented by this redox-engineered strain. (orig.)

  8. Breeding of a xylose-fermenting hybrid strain by mating genetically engineered haploid strains derived from industrial Saccharomyces cerevisiae.

    Science.gov (United States)

    Inoue, Hiroyuki; Hashimoto, Seitaro; Matsushika, Akinori; Watanabe, Seiya; Sawayama, Shigeki

    2014-12-01

    The industrial Saccharomyces cerevisiae IR-2 is a promising host strain to genetically engineer xylose-utilizing yeasts for ethanol fermentation from lignocellulosic hydrolysates. Two IR-2-based haploid strains were selected based upon the rate of xylulose fermentation, and hybrids were obtained by mating recombinant haploid strains harboring heterogeneous xylose dehydrogenase (XDH) (wild-type NAD(+)-dependent XDH or engineered NADP(+)-dependent XDH, ARSdR), xylose reductase (XR) and xylulose kinase (XK) genes. ARSdR in the hybrids selected for growth rates on yeast extract-peptone-dextrose (YPD) agar and YP-xylose agar plates typically had a higher activity than NAD(+)-dependent XDH. Furthermore, the xylose-fermenting performance of the hybrid strain SE12 with the same level of heterogeneous XDH activity was similar to that of a recombinant strain of IR-2 harboring a single set of genes, XR/ARSdR/XK. These results suggest not only that the recombinant haploid strains retain the appropriate genetic background of IR-2 for ethanol production from xylose but also that ARSdR is preferable for xylose fermentation.

  9. Expression of protein engineered NADP+-dependent xylitol dehydrogenase increases ethanol production from xylose in recombinant Saccharomyces cerevisiae.

    Science.gov (United States)

    Matsushika, Akinori; Watanabe, Seiya; Kodaki, Tsutomu; Makino, Keisuke; Inoue, Hiroyuki; Murakami, Katsuji; Takimura, Osamu; Sawayama, Shigeki

    2008-11-01

    A recombinant Saccharomyces cerevisiae strain transformed with xylose reductase (XR) and xylitol dehydrogenase (XDH) genes from Pichia stipitis has the ability to convert xylose to ethanol together with the unfavorable excretion of xylitol, which may be due to cofactor imbalance between NADPH-preferring XR and NAD(+)-dependent XDH. To reduce xylitol formation, we have already generated several XDH mutants with a reversal of coenzyme specificity toward NADP(+). In this study, we constructed a set of recombinant S. cerevisiae strains with xylose-fermenting ability, including protein-engineered NADP(+)-dependent XDH-expressing strains. The most positive effect on xylose-to-ethanol fermentation was found by using a strain named MA-N5, constructed by chromosomal integration of the gene for NADP(+)-dependent XDH along with XR and endogenous xylulokinase genes. The MA-N5 strain had an increase in ethanol production and decrease in xylitol excretion compared with the reference strain expressing wild-type XDH when fermenting not only xylose but also mixed sugars containing glucose and xylose. Furthermore, the MA-N5 strain produced ethanol with a high yield of 0.49 g of ethanol/g of total consumed sugars in the nonsulfuric acid hydrolysate of wood chips. The results demonstrate that glucose and xylose present in the lignocellulosic hydrolysate can be efficiently fermented by this redox-engineered strain.

  10. Isolation and characterization of a mutant recombinant Saccharomyces cerevisiae strain with high efficiency xylose utilization.

    Science.gov (United States)

    Tomitaka, Masataka; Taguchi, Hisataka; Fukuda, Kohsai; Akamatsu, Takashi; Kida, Kenji

    2013-12-01

    A recombinant xylose-utilizing Saccharomyces cerevisiae strain carrying one copy of heterologous XYL1 and XYL2 from Pichia stipitis and endogenous XKS1 under the control of the TDH3 promoter in the chromosomal DNA was constructed from the industrial haploid yeast strain NAM34-4C, which showed thermotolerance and acid tolerance. The recombinant S. cerevisiae strain SCB7 grew in minimal medium containing xylose as the sole carbon source, and its shortest generation time (G(short)) was 5 h. From this strain, four mutants showing rapid growth (G(short) = 2.5 h) in the minimal medium were isolated. The mutants carried four mutations that were classified into three linkage groups. Three mutations were dominant and one mutation was recessive to the wild type allele. The recessive mutation was in the PHO13 gene encoding para-nitrophenyl phosphatase. The other mutant genes were not linked to TAL1 gene encoding transaldolase. When the mutants and their parental strain were used for the batch fermentation in a complex medium at pH 4.0 containing 30 g/L xylose at 35 °C with shaking (60 rpm) and an initial cell density (Absorbance at 660 nm) of 1.0, all mutants showed efficient ethanol production and xylose consumption from the early stage of the fermentation culture. In two mutants, within 24 h, 4.8 g/L ethanol was produced, and the ethanol yield was 47%, which was 1.4 times higher than that achieved with the parental strain. The xylose concentration in the medium containing the mutant decreased linearly at a rate of 1 g/L/h until 24 h. Copyright © 2013 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  11. Glucose(xylose isomerase production by Streptomyces sp. CH7 grown on agricultural residues

    Directory of Open Access Journals (Sweden)

    Kankiya Chanitnun

    2012-09-01

    Full Text Available Streptomyces sp. CH7 was found to efficiently produce glucose(xylose isomerase when grown on either xylan or agricultural residues. This strain produced a glucose(xylose isomerase activity of roughly 1.8 U/mg of protein when it was grown in medium containing 1% xylose as a carbon source. Maximal enzymatic activities of about 5 and 3 U/mg were obtained when 1% xylan and 2.5% corn husks were used, respectively. The enzyme was purified from a mycelial extract to 16-fold purity with only two consecutive column chromatography steps using Macro-prep DEAE and Sephacryl-300, respectively. The approximate molecular weight of the purified enzyme is 170 kDa, and it has four identical subunits of 43.6 kDa as estimated by SDS-PAGE. Its Km values for glucose and xylose were found to be 258.96 and 82.77 mM, respectively, and its Vmax values are 32.42 and 63.64 μM/min/mg, respectively. The purified enzyme is optimally active at 85ºC and pH 7.0. It is stable at pH 5.5-8.5 and at temperatures up to 60ºC after 30 min. These findings indicate that glucose(xylose isomerase from Streptomyces sp. CH7 has the potential for industrial applications, especially for high-fructose syrup production and bioethanol fermentation from hemicellulosic hydrolysates by Saccharomyces cerevisiae.

  12. Natural selection promotes antigenic evolvability

    NARCIS (Netherlands)

    Graves, C.J.; Ros, V.I.D.; Stevenson, B.; Sniegowski, P.D.; Brisson, D.

    2013-01-01

    The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide

  13. Disgust: Evolved function and structure

    NARCIS (Netherlands)

    Tybur, J.M.; Lieberman, D.; Kurzban, R.; DeScioli, P.

    2013-01-01

    Interest in and research on disgust has surged over the past few decades. The field, however, still lacks a coherent theoretical framework for understanding the evolved function or functions of disgust. Here we present such a framework, emphasizing 2 levels of analysis: that of evolved function and

  14. Deleting the para-nitrophenyl phosphatase (pNPPase), PHO13, in recombinant Saccharomyces cerevisiae improves growth and ethanol production on D-xylose

    DEFF Research Database (Denmark)

    Van Vleet, Jennifer; Jeffries, T.W.; Olsson, Lisbeth

    2008-01-01

    Overexpression of D-xylulokinase in Saccharomyces cerevisiae engineered for assimilation of xylose results in growth inhibition that is more pronounced at higher xylose concentrations. Mutants deficient in the para-nitrophenyl phosphatase, PHO13, resist growth inhibition on xylose. We studied...... this inhibition under aerobic growth conditions in well-controlled bioreactors using engineered S. cerevisiae CEN.PK. Growth on glucose was not significantly affected in pho13 Delta mutants, but acetate production increased by 75%. Cell growth, ethanol production, and xylose consumption all increased markedly...... in pho13 Delta mutants. The specific growth rate and rate of specific xylose uptake were approximately 1.5 times higher in the deletion strain than in the parental strain when growing on glucose-xylose mixtures and up to 10-fold higher when growing on xylose alone. In addition to showing higher acetate...

  15. Evolving virtual creatures and catapults.

    Science.gov (United States)

    Chaumont, Nicolas; Egli, Richard; Adami, Christoph

    2007-01-01

    We present a system that can evolve the morphology and the controller of virtual walking and block-throwing creatures (catapults) using a genetic algorithm. The system is based on Sims' work, implemented as a flexible platform with an off-the-shelf dynamics engine. Experiments aimed at evolving Sims-type walkers resulted in the emergence of various realistic gaits while using fairly simple objective functions. Due to the flexibility of the system, drastically different morphologies and functions evolved with only minor modifications to the system and objective function. For example, various throwing techniques evolved when selecting for catapults that propel a block as far as possible. Among the strategies and morphologies evolved, we find the drop-kick strategy, as well as the systematic invention of the principle behind the wheel, when allowing mutations to the projectile.

  16. Improved production of homo-D-lactic acid via xylose fermentation by introduction of xylose assimilation genes and redirection of the phosphoketolase pathway to the pentose phosphate pathway in L-Lactate dehydrogenase gene-deficient Lactobacillus plantarum.

    Science.gov (United States)

    Okano, Kenji; Yoshida, Shogo; Yamada, Ryosuke; Tanaka, Tsutomu; Ogino, Chiaki; Fukuda, Hideki; Kondo, Akihiko

    2009-12-01

    The production of optically pure d-lactic acid via xylose fermentation was achieved by using a Lactobacillus plantarum NCIMB 8826 strain whose l-lactate dehydrogenase gene was deficient and whose phosphoketolase genes were replaced with a heterologous transketolase gene. After 60 h of fermentation, 41.2 g/liter of d-lactic acid was produced from 50 g/liter of xylose.

  17. Diversity and physiological characterization of D-xylose-fermenting yeasts isolated from the Brazilian Amazonian Forest.

    Directory of Open Access Journals (Sweden)

    Raquel M Cadete

    Full Text Available BACKGROUND: This study is the first to investigate the Brazilian Amazonian Forest to identify new D-xylose-fermenting yeasts that might potentially be used in the production of ethanol from sugarcane bagasse hemicellulosic hydrolysates. METHODOLOGY/PRINCIPAL FINDINGS: A total of 224 yeast strains were isolated from rotting wood samples collected in two Amazonian forest reserve sites. These samples were cultured in yeast nitrogen base (YNB-D-xylose or YNB-xylan media. Candida tropicalis, Asterotremella humicola, Candida boidinii and Debaryomyces hansenii were the most frequently isolated yeasts. Among D-xylose-fermenting yeasts, six strains of Spathaspora passalidarum, two of Scheffersomyces stipitis, and representatives of five new species were identified. The new species included Candida amazonensis of the Scheffersomyces clade and Spathaspora sp. 1, Spathaspora sp. 2, Spathaspora sp. 3, and Candida sp. 1 of the Spathaspora clade. In fermentation assays using D-xylose (50 g/L culture medium, S. passalidarum strains showed the highest ethanol yields (0.31 g/g to 0.37 g/g and productivities (0.62 g/L · h to 0.75 g/L · h. Candida amazonensis exhibited a virtually complete D-xylose consumption and the highest xylitol yields (0.55 g/g to 0.59 g/g, with concentrations up to 25.2 g/L. The new Spathaspora species produced ethanol and/or xylitol in different concentrations as the main fermentation products. In sugarcane bagasse hemicellulosic fermentation assays, S. stipitis UFMG-XMD-15.2 generated the highest ethanol yield (0.34 g/g and productivity (0.2 g/L · h, while the new species Spathaspora sp. 1 UFMG-XMD-16.2 and Spathaspora sp. 2 UFMG-XMD-23.2 were very good xylitol producers. CONCLUSIONS/SIGNIFICANCE: This study demonstrates the promise of using new D-xylose-fermenting yeast strains from the Brazilian Amazonian Forest for ethanol or xylitol production from sugarcane bagasse hemicellulosic hydrolysates.

  18. Analysis and prediction of the physiological effects of altered coenzyme specificity in xylose reductase and xylitol dehydrogenase during xylose fermentation by Saccharomyces cerevisiae.

    Science.gov (United States)

    Krahulec, Stefan; Klimacek, Mario; Nidetzky, Bernd

    2012-04-30

    An advanced strategy of Saccharomyces cerevisiae strain development for fermentation of xylose applies tailored enzymes in the process of metabolic engineering. The coenzyme specificities of the NADPH-preferring xylose reductase (XR) and the NAD⁺-dependent xylitol dehydrogenase (XDH) have been targeted in previous studies by protein design or evolution with the aim of improving the recycling of NADH or NADPH in their two-step pathway, converting xylose to xylulose. Yeast strains expressing variant pairs of XR and XDH that according to in vitro kinetic data were suggested to be much better matched in coenzyme usage than the corresponding pair of wild-type enzymes, exhibit widely varying capabilities for xylose fermentation. To achieve coherence between enzyme properties and the observed strain performance during fermentation, we explored the published kinetic parameters for wild-type and engineered forms of XR and XDH as possible predictors of xylitol by-product formation (Y(xylitol)) in yeast physiology. We found that the ratio of enzymatic reaction rates using NADP(H) and NAD(H) that was calculated by applying intracellular reactant concentrations to rate equations derived from bi-substrate kinetic analysis, succeeded in giving a statistically reliable forecast of the trend effect on Y(xylitol). Prediction based solely on catalytic efficiencies with or without binding affinities for NADP(H) and NAD(H) were not dependable, and we define a minimum demand on the enzyme kinetic characterization to be performed for this purpose. An immediate explanation is provided for the typically lower Y(xylitol) in the current strains harboring XR engineered for utilization of NADH as compared to strains harboring XDH engineered for utilization of NADP⁺. The known XDH enzymes all exhibit a relatively high K(m) for NADP⁺ so that physiological boundary conditions are somewhat unfavorable for xylitol oxidation by NADP⁺. A criterion of physiological fitness is developed for

  19. A selective and sensitive D-xylose electrochemical biosensor based on xylose dehydrogenase displayed on the surface of bacteria and multi-walled carbon nanotubes modified electrode.

    Science.gov (United States)

    Li, Liang; Liang, Bo; Shi, Jianguo; Li, Feng; Mascini, Marco; Liu, Aihua

    2012-03-15

    A novel Nafion/bacteria-displaying xylose dehydrogenase (XDH)/multi-walled carbon nanotubes (MWNTs) composite film-modified electrode was fabricated and applied for the sensitive and selective determination of d-xylose (INS 967), where the XDH-displayed bacteria (XDH-bacteria) was prepared using a newly identified ice nucleation protein from Pseudomonas borealis DL7 as an anchoring motif. The XDH-displayed bacteria can be used directly, eliminating further enzyme-extraction and purification, thus greatly improved the stability of the enzyme. The optimal conditions for the construction of biosensor were established: homogeneous Nafion-MWNTs composite dispersion (10 μL) was cast onto the inverted glassy carbon electrode, followed by casting 10-μL of XDH-bacteria aqueous solution to stand overnight to dry, then a 5-μL of Nafion solution (0.05 wt%) is syringed to the electrode surface. The bacteria-displaying XDH could catalyze the oxidization of xylose to xylonolactone with coenzyme NAD(+) in 0.1M PBS buffer (pH7.4), where NAD(+) (nicotinamide adenine dinucleotide) is reduced to NADH (the reduced form of nicotinamide adenine dinucleotide). The resultant NADH is further electrocatalytically oxidized by MWNTs on the electrode, resulting in an obvious oxidation peak around 0.50 V (vs. Ag/AgCl). In contrast, the bacteria-XDH-only modified electrode showed oxidation peak at higher potential of 0.7 V and less sensitivity. Therefore, the electrode/MWNTs/bacteria-XDH/Nafion exhibited good analytical performance such as long-term stability, a wide dynamic range of 0.6-100 μM and a low detection limit of 0.5 μM D-xylose (S/N=3). No interference was observed in the presence of 300-fold excess of other saccharides including D-glucose, D-fructose, D-maltose, D-galactose, D-mannose, D-sucrose, and D-cellbiose as well as 60-fold excess of L-arabinose. The proposed microbial biosensor is stable, specific, sensitive, reproducible, simple, rapid and cost-effective, which holds

  20. A dynamic flux balance model and bottleneck identification of glucose, xylose, xylulose co-fermentation in Saccharomyces cerevisiae

    Science.gov (United States)

    Economically viable production of lignocellulosic ethanol requires efficient conversion of feedstock sugars to ethanol. Saccharomyces cerevisiae cannot ferment xylose, the main five-carbon sugars in biomass, but can ferment xylulose, an enzymatically derived isomer. Xylulose fermentation is slow rel...

  1. When did oxygenic photosynthesis evolve?

    National Research Council Canada - National Science Library

    Roger Buick

    2008-01-01

    ...2.4 Ga ago, but when the photosynthetic oxygen production began is debatable. However, geological and geochemical evidence from older sedimentary rocks indicates that oxygenic photosynthesis evolved well before this oxygenation event...

  2. Marshal: Maintaining Evolving Models Project

    Data.gov (United States)

    National Aeronautics and Space Administration — SIFT proposes to design and develop the Marshal system, a mixed-initiative tool for maintaining task models over the course of evolving missions. Marshal-enabled...

  3. Natural selection promotes antigenic evolvability.

    Science.gov (United States)

    Graves, Christopher J; Ros, Vera I D; Stevenson, Brian; Sniegowski, Paul D; Brisson, Dustin

    2013-01-01

    The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed 'cassettes' that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios) and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish chronic infections.

  4. Natural selection promotes antigenic evolvability.

    Directory of Open Access Journals (Sweden)

    Christopher J Graves

    Full Text Available The hypothesis that evolvability - the capacity to evolve by natural selection - is itself the object of natural selection is highly intriguing but remains controversial due in large part to a paucity of direct experimental evidence. The antigenic variation mechanisms of microbial pathogens provide an experimentally tractable system to test whether natural selection has favored mechanisms that increase evolvability. Many antigenic variation systems consist of paralogous unexpressed 'cassettes' that recombine into an expression site to rapidly alter the expressed protein. Importantly, the magnitude of antigenic change is a function of the genetic diversity among the unexpressed cassettes. Thus, evidence that selection favors among-cassette diversity is direct evidence that natural selection promotes antigenic evolvability. We used the Lyme disease bacterium, Borrelia burgdorferi, as a model to test the prediction that natural selection favors amino acid diversity among unexpressed vls cassettes and thereby promotes evolvability in a primary surface antigen, VlsE. The hypothesis that diversity among vls cassettes is favored by natural selection was supported in each B. burgdorferi strain analyzed using both classical (dN/dS ratios and Bayesian population genetic analyses of genetic sequence data. This hypothesis was also supported by the conservation of highly mutable tandem-repeat structures across B. burgdorferi strains despite a near complete absence of sequence conservation. Diversification among vls cassettes due to natural selection and mutable repeat structures promotes long-term antigenic evolvability of VlsE. These findings provide a direct demonstration that molecular mechanisms that enhance evolvability of surface antigens are an evolutionary adaptation. The molecular evolutionary processes identified here can serve as a model for the evolution of antigenic evolvability in many pathogens which utilize similar strategies to establish

  5. Engineering and two-stage evolution of a lignocellulosic hydrolysate-tolerant Saccharomyces cerevisiae strain for anaerobic fermentation of xylose from AFEX pretreated corn stover.

    Science.gov (United States)

    Parreiras, Lucas S; Breuer, Rebecca J; Avanasi Narasimhan, Ragothaman; Higbee, Alan J; La Reau, Alex; Tremaine, Mary; Qin, Li; Willis, Laura B; Bice, Benjamin D; Bonfert, Brandi L; Pinhancos, Rebeca C; Balloon, Allison J; Uppugundla, Nirmal; Liu, Tongjun; Li, Chenlin; Tanjore, Deepti; Ong, Irene M; Li, Haibo; Pohlmann, Edward L; Serate, Jose; Withers, Sydnor T; Simmons, Blake A; Hodge, David B; Westphall, Michael S; Coon, Joshua J; Dale, Bruce E; Balan, Venkatesh; Keating, David H; Zhang, Yaoping; Landick, Robert; Gasch, Audrey P; Sato, Trey K

    2014-01-01

    The inability of the yeast Saccharomyces cerevisiae to ferment xylose effectively under anaerobic conditions is a major barrier to economical production of lignocellulosic biofuels. Although genetic approaches have enabled engineering of S. cerevisiae to convert xylose efficiently into ethanol in defined lab medium, few strains are able to ferment xylose from lignocellulosic hydrolysates in the absence of oxygen. This limited xylose conversion is believed to result from small molecules generated during biomass pretreatment and hydrolysis, which induce cellular stress and impair metabolism. Here, we describe the development of a xylose-fermenting S. cerevisiae strain with tolerance to a range of pretreated and hydrolyzed lignocellulose, including Ammonia Fiber Expansion (AFEX)-pretreated corn stover hydrolysate (ACSH). We genetically engineered a hydrolysate-resistant yeast strain with bacterial xylose isomerase and then applied two separate stages of aerobic and anaerobic directed evolution. The emergent S. cerevisiae strain rapidly converted xylose from lab medium and ACSH to ethanol under strict anaerobic conditions. Metabolomic, genetic and biochemical analyses suggested that a missense mutation in GRE3, which was acquired during the anaerobic evolution, contributed toward improved xylose conversion by reducing intracellular production of xylitol, an inhibitor of xylose isomerase. These results validate our combinatorial approach, which utilized phenotypic strain selection, rational engineering and directed evolution for the generation of a robust S. cerevisiae strain with the ability to ferment xylose anaerobically from ACSH.

  6. Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover

    Science.gov (United States)

    Parreiras, Lucas S.; Breuer, Rebecca J.; Avanasi Narasimhan, Ragothaman; Higbee, Alan J.; La Reau, Alex; Tremaine, Mary; Qin, Li; Willis, Laura B.; Bice, Benjamin D.; Bonfert, Brandi L.; Pinhancos, Rebeca C.; Balloon, Allison J.; Uppugundla, Nirmal; Liu, Tongjun; Li, Chenlin; Tanjore, Deepti; Ong, Irene M.; Li, Haibo; Pohlmann, Edward L.; Serate, Jose; Withers, Sydnor T.; Simmons, Blake A.; Hodge, David B.; Westphall, Michael S.; Coon, Joshua J.; Dale, Bruce E.; Balan, Venkatesh; Keating, David H.; Zhang, Yaoping; Landick, Robert; Gasch, Audrey P.; Sato, Trey K.

    2014-01-01

    The inability of the yeast Saccharomyces cerevisiae to ferment xylose effectively under anaerobic conditions is a major barrier to economical production of lignocellulosic biofuels. Although genetic approaches have enabled engineering of S. cerevisiae to convert xylose efficiently into ethanol in defined lab medium, few strains are able to ferment xylose from lignocellulosic hydrolysates in the absence of oxygen. This limited xylose conversion is believed to result from small molecules generated during biomass pretreatment and hydrolysis, which induce cellular stress and impair metabolism. Here, we describe the development of a xylose-fermenting S. cerevisiae strain with tolerance to a range of pretreated and hydrolyzed lignocellulose, including Ammonia Fiber Expansion (AFEX)-pretreated corn stover hydrolysate (ACSH). We genetically engineered a hydrolysate-resistant yeast strain with bacterial xylose isomerase and then applied two separate stages of aerobic and anaerobic directed evolution. The emergent S. cerevisiae strain rapidly converted xylose from lab medium and ACSH to ethanol under strict anaerobic conditions. Metabolomic, genetic and biochemical analyses suggested that a missense mutation in GRE3, which was acquired during the anaerobic evolution, contributed toward improved xylose conversion by reducing intracellular production of xylitol, an inhibitor of xylose isomerase. These results validate our combinatorial approach, which utilized phenotypic strain selection, rational engineering and directed evolution for the generation of a robust S. cerevisiae strain with the ability to ferment xylose anaerobically from ACSH. PMID:25222864

  7. Engineering and two-stage evolution of a lignocellulosic hydrolysate-tolerant Saccharomyces cerevisiae strain for anaerobic fermentation of xylose from AFEX pretreated corn stover.

    Directory of Open Access Journals (Sweden)

    Lucas S Parreiras

    Full Text Available The inability of the yeast Saccharomyces cerevisiae to ferment xylose effectively under anaerobic conditions is a major barrier to economical production of lignocellulosic biofuels. Although genetic approaches have enabled engineering of S. cerevisiae to convert xylose efficiently into ethanol in defined lab medium, few strains are able to ferment xylose from lignocellulosic hydrolysates in the absence of oxygen. This limited xylose conversion is believed to result from small molecules generated during biomass pretreatment and hydrolysis, which induce cellular stress and impair metabolism. Here, we describe the development of a xylose-fermenting S. cerevisiae strain with tolerance to a range of pretreated and hydrolyzed lignocellulose, including Ammonia Fiber Expansion (AFEX-pretreated corn stover hydrolysate (ACSH. We genetically engineered a hydrolysate-resistant yeast strain with bacterial xylose isomerase and then applied two separate stages of aerobic and anaerobic directed evolution. The emergent S. cerevisiae strain rapidly converted xylose from lab medium and ACSH to ethanol under strict anaerobic conditions. Metabolomic, genetic and biochemical analyses suggested that a missense mutation in GRE3, which was acquired during the anaerobic evolution, contributed toward improved xylose conversion by reducing intracellular production of xylitol, an inhibitor of xylose isomerase. These results validate our combinatorial approach, which utilized phenotypic strain selection, rational engineering and directed evolution for the generation of a robust S. cerevisiae strain with the ability to ferment xylose anaerobically from ACSH.

  8. The synthetic xylulose-1 phosphate pathway increases production of glycolic acid from xylose-rich sugar mixtures

    OpenAIRE

    Trichez, Débora; Cam, Yvan; Spina, Lucie; François, Jean-Marie

    2016-01-01

    Background: Glycolic acid (GA) is a two-carbon hydroxyacid with applications in the cosmetic, textile, and medical industry. Microbial GA production from all sugars can be achieved by engineering the natural glyoxylate shunt. The synthetic (D)-xylulose-1 phosphate (X1P) pathway provides a complementary route to produce GA from (D)-xylose. The simultaneous operation of the X1P and glyoxylate pathways increases the theoretical GA yield from xylose by 20 %, which may strongly improve GA producti...

  9. Effect of xylose and nutrients concentration on ethanol production by a newly isolated extreme thermophilic bacterium

    DEFF Research Database (Denmark)

    Tomás, Ana Faria; Karakashev, Dimitar Borisov; Angelidaki, Irini

    2011-01-01

    product under most of the conditions tested, including in media lacking vitamins, peptone and yeast extract. The results indicate that this new organism is a promising candidate for the development of a second generation bio-ethanol production process. © IWA Publishing 2011.......An extreme thermophilic ethanol-producing strain was isolated from an ethanol high-yielding mixed culture, originally isolated from a hydrogen producing reactor operated at 70 °C. Ethanol yields were assessed with increasing concentrations of xylose, up to 20 g/l. The ability of the strain to grow...... without nutrient addition (yeast extract, peptone and vitamins) was also assessed. The maximum ethanol yield achieved was 1.28 molethanol/ molxylose consumed (77% of the theoretical yield), at 2 g/l of initial xylose concentration. The isolate was able to grow and produce ethanol as the main fermentation...

  10. Metabolic engineering of Klebsiella oxytoca M5A1 for ethanol production from xylose and glucose

    Energy Technology Data Exchange (ETDEWEB)

    Ohta, Kazuyoshi; Beall, D.S.; Mejia, J.P.; Shanmugam, K.T.; Ingram, L.O. (Univ. of Florida, Gainesville (United States))

    1991-10-01

    The efficient diversion of pyruvate from normal fermentative pathways to ethanol production in Klebsiella oxytoca M5A1 requires the expression of Zymomanas mobilis genes encoding both pyruvate decarboxylase and alcohol dehydrogenase. Final ethanol concentrations obtained with the best recombinant, strain M5A1 (pLOI555), were in excess of 40 g/liter with an efficiency of 0.48 g of ethanol (xylose) and 0.50 g of ethanol (glucose) per g of sugar, as compared with a theoretical maximum of 0.51 of ethanol per g of sugar. The maximal volumetric productivity per hour for both sugars was 2.0 g/liter. This volumetric productivity with xylose is almost twice that previously obtained with ethanologenic Escherichia coli. Succinate was also produced as a minor product during fermentation.

  11. High performance separation of xylose and glucose by enzyme assisted nanofiltration

    DEFF Research Database (Denmark)

    Morthensen, Sofie Thage; Luo, Jianquan; Meyer, Anne S.

    2015-01-01

    to gluconic acid, 0.15M total feed concentration, pH 9.5, 25°C and 4bar), we achieved a xylose separation factor of 34 and a throughput of 18.7Lm−2h−1. In comparison, the separation factor was only 1.4 for solutions of xylose and glucose at the same process conditions, thus demonstrating the huge potential...... of the integrated system. Full conversion of glucose to gluconic acid assisted by glucose oxidase (GOD) could be achieved by coupling a parallel reaction catalyzed by catalase (CAT), where H2O2 (GOD-inhibitor formed in the first reaction) was decomposed to water and oxygen. GOD has a high oxygen...

  12. Dehydration of D-xylose to furfural using acid-functionalized MWCNTs catalysts

    Science.gov (United States)

    Termvidchakorn, Chompoopitch; Itthibenchapong, Vorranutch; Songtawee, Siripit; Chamnankid, Busaya; Namuangruk, Supawadee; Faungnawakij, Kajornsak; Charinpanitkul, Tawatchai; Khunchit, Radchadaporn; Hansupaluk, Nanthiya; Sano, Noriaki; Hinode, Hirofumi

    2017-09-01

    Acid-functionalized multi-wall carbon nanotubes (MWCNTs) catalysts were prepared by a wet chemical sonication with various acid solutions, i.e. H2SO4, H3PO4, HNO3, and HCl. Sulfonic groups and carboxyl groups were detected on MWCNTs with H2SO4 treatment (s-MWCNTs), while only carboxyl groups were presented from other acid treatments. The catalytic dehydration of D-xylose into furfural was evaluated using a batch reactor at 170 °C for 3 h under N2 pressure of 15 bar. The highest furfural selectivity was achieved around 57% by s-MWCNTs catalyst, suggesting a positive role of the sulfonic functionalized groups. The effect of Co species was related to their Lewis acid property resulting in the enhancement of xylose conversion with low selectivity to furfural product. Invited talk at 5th Thailand International Nanotechnology Conference (Nano Thailand-2016), 27-29 November 2016, Nakhon Ratchasima, Thailand.

  13. Conversion of Xylose to Furfuryl Alcohol and 2-Methylfuran in a Continuous Fixed-Bed Reactor.

    Science.gov (United States)

    Cui, Jinglei; Tan, Jingjing; Cui, Xiaojing; Zhu, Yulei; Deng, Tiansheng; Ding, Guoqiang; Li, Yongwang

    2016-06-08

    An efficient process was designed for the synthesis of furfuryl alcohol and 2-methylfuran from xylose using a continuous fixed-bed reactor over a catalyst combining Hβ zeolite and Cu/ZnO/Al2 O3 in γ-butyrolactone (GBL)/water as solvent. The cooperative effect of Hβ zeolite and GBL facilitated the dehydration of xylose and enhanced largely the furfural yield. The production of furfuryl alcohol and 2-methylfuran can be simply tuned by changing the hydrogenation temperature for furfural over the Cu/ZnO/Al2 O3 catalyst. The yield for furfuryl alcohol reached 87.2 % at 150 °C whereas a yield of 86.8 % was achieved for 2-methylfuran at 190 °C. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  14. Potential of xylose-fermented yeast isolated from sugarcane bagasse waste for xylitol production using hydrolysate as carbon source

    Directory of Open Access Journals (Sweden)

    Kusumawadee Thancharoen

    2016-10-01

    Full Text Available Xylitol is a high value sugar alcohol that is used as a sweetener. In the past years, the biological process of D-xylose from lignocellulosic material into xylitol has gained increasing interest as an alternative production method. In this study, sugarcane bagasse was used as raw material for xylitol production because of its high efficiency, reduced industrial cost, and high concentration of xylose. Pre-treatment of sugarcane bagasse with sulfuric acid was performed with various conditions. The results showed that the optimum condition was exhibited for 3.1% sulfuric acid at 126°C for 18 min producing 19 g/l xylose. Isolated yeasts from the sugarcane bagasse were selected and tested for xylitol ability from xylose. Results showed that Candida tropicalis KS 10-3 (from 72 isolates had the highest ability and produced 0.47 g xylitol/ g xylose in 96 hrs of cultivation containing 32.30 g/l xylose was used as the production medium.

  15. Metal Dependence of the Xylose Isomerase from Piromyces sp. E2 Explored by Activity Profiling and Protein Crystallography.

    Science.gov (United States)

    Lee, Misun; Rozeboom, Henriëtte J; de Waal, Paul P; de Jong, Rene M; Dudek, Hanna M; Janssen, Dick B

    2017-11-14

    Xylose isomerase from Piromyces sp. E2 (PirXI) can be used to equip Saccharomyces cerevisiae with the capacity to ferment xylose to ethanol. The biochemical properties and structure of the enzyme have not been described even though its metal content, catalytic parameters, and expression level are critical for rapid xylose utilization. We have isolated the enzyme after high-level expression in Escherichia coli, analyzed the metal dependence of its catalytic properties, and determined 12 crystal structures in the presence of different metals, substrates, and substrate analogues. The activity assays revealed that various bivalent metals can activate PirXI for xylose isomerization. Among these metals, Mn2+ is the most favorable for catalytic activity. Furthermore, the enzyme shows the highest affinity for Mn2+, which was established by measuring the activation constants (Kact) for different metals. Metal analysis of the purified enzyme showed that in vivo the enzyme binds a mixture of metals that is determined by metal availability as well as affinity, indicating that the native metal composition can influence activity. The crystal structures show the presence of an active site similar to that of other xylose isomerases, with a d-xylose binding site containing two tryptophans and a catalytic histidine, as well as two metal binding sites that are formed by carboxylate groups of conserved aspartates and glutamates. The binding positions and conformations of the metal-coordinating residues varied slightly for different metals, which is hypothesized to contribute to the observed metal dependence of the isomerase activity.

  16. Biohydrogen production from xylose at extreme thermophilic temperatures (70 degrees C) by mixed culture fermentation

    DEFF Research Database (Denmark)

    Kongjan, Prawit; Min, Booki; Angelidaki, Irini

    2009-01-01

    /L. Addition of yeast extract in the cultivation medium resulted in significant improvement of hydrogen yield. The main metabolic products during xylose fermentation were acetate, ethanol, and lactate. The specific growth rates were able to fit the experimental points relatively well with Haldane equation...... acetate, formate, and ethanol at 4.25 +/- 0.10, 3.01 +/- 0.11, and 2.59 +/- 0.16 mM, respectively....

  17. Cloning, expression, and characterization of a novel xylose reductase from Rhizopus oryzae.

    Science.gov (United States)

    Zhang, Min; Jiang, Shao-tong; Zheng, Zhi; Li, Xing-jiang; Luo, Shui-zhong; Wu, Xue-feng

    2015-07-01

    Rhizopus oryzae is valuable as a producer of organic acids via lignocellulose catalysis. R. oryzae metabolizes xylose, which is one component of lignocellulose hydrolysate. In this study, a novel NADPH-dependent xylose reductase gene from R. oryzae AS 3.819 (Roxr) was cloned and expressed in Pichia pastoris GS115. Homology alignment suggested that the 320-residue protein contained domains and active sites belonging to the aldo/keto reductase family. SDS-PAGE demonstrated that the recombinant xylose reductase has a molecular weight of approximately 37 kDa. The optimal catalytic pH and temperature of the purified recombinant protein were 5.8 and 50 °C, respectively. The recombinant protein was stable from pH 4.4 to 6.5 and at temperatures below 42 °C. The recombinant enzyme has bias for D-xylose and L-arabinose as substrates and NADPH as its coenzyme. Real-time quantitative reverse transcription PCR tests suggested that native Roxr expression is regulated by a carbon catabolite repression mechanism. Site-directed mutagenesis at two possible key sites involved in coenzyme binding, Thr(226)  → Glu(226) and Val(274)  → Asn(274), were performed, respectively. The coenzyme specificity constants of the resulted RoXR(T226E) and RoXR(V274N) for NADH increased 18.2-fold and 2.4-fold, which suggested possibility to improve the NADH preference of this enzyme through genetic modification. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  18. Xylose phosphorylation functions as a molecular switch to regulate proteoglycan biosynthesis.

    Science.gov (United States)

    Wen, Jianzhong; Xiao, Junyu; Rahdar, Meghdad; Choudhury, Biswa P; Cui, Jixin; Taylor, Gregory S; Esko, Jeffrey D; Dixon, Jack E

    2014-11-04

    Most eukaryotic cells elaborate several proteoglycans critical for transmitting biochemical signals into and between cells. However, the regulation of proteoglycan biosynthesis is not completely understood. We show that the atypical secretory kinase family with sequence similarity 20, member B (Fam20B) phosphorylates the initiating xylose residue in the proteoglycan tetrasaccharide linkage region, and that this event functions as a molecular switch to regulate subsequent glycosaminoglycan assembly. Proteoglycans from FAM20B knockout cells contain a truncated tetrasaccharide linkage region consisting of a disaccharide capped with sialic acid (Siaα2-3Galβ1-4Xylβ1) that cannot be further elongated. We also show that the activity of galactosyl transferase II (GalT-II, B3GalT6), a key enzyme in the biosynthesis of the tetrasaccharide linkage region, is dramatically increased by Fam20B-dependent xylose phosphorylation. Inactivating mutations in the GALT-II gene (B3GALT6) associated with Ehlers-Danlos syndrome cause proteoglycan maturation defects similar to FAM20B deletion. Collectively, our findings suggest that GalT-II function is impaired by loss of Fam20B-dependent xylose phosphorylation and reveal a previously unappreciated mechanism for regulation of proteoglycan biosynthesis.

  19. Xylose fermentation as a challenge for commercialization of lignocellulosic fuels and chemicals.

    Science.gov (United States)

    Sànchez Nogué, Violeta; Karhumaa, Kaisa

    2015-04-01

    Fuel ethanol production from lignocellulosic materials is at a level where commercial biofuel production is becoming a reality. The solubilization of the hemicellulose fraction in lignocellulosic-based feedstocks results in a large variety of sugar mixtures including xylose. However, allowing xylose fermentation in yeast that normally is used for fuel ethanol production requires genetic engineering. Moreover, the efficiency of lignocellulosic pretreatment, together with the release and generation of inhibitory compounds in this step, are some of the new challenges faced during second generation ethanol production. Successful advances in all these aspects will improve ethanol yield, productivity and titer, which will reduce the impact on capital and operating costs, leading to the consolidation of the fermentation of lignocellulosic biomass as an economically feasible option for the production of renewable fuels. Therefore the development of yeast strains capable of fermenting a wide variety of sugars in a highly inhibitory environment, while maintaining a high ethanol yield and production rate, is required. This review provides an overview of the current status in the use of xylose-engineered yeast strains and describes the remaining challenges to achieve an efficient deployment of lignocellulosic-based ethanol production.

  20. Efficient Hydrolysis of Rice Straw into Xylose and Glucose by a Two-step Process

    Directory of Open Access Journals (Sweden)

    YAN Lu-lu

    2016-07-01

    Full Text Available The hydrolysis of rice straw into xylose and glucose in dilute sulfuric acid aqueous solution was studied with a two-step process in batch autoclave reactor. The results showed that compared with the traditional one-step acid hydrolysis, both xylose and glucose could be produced in high yields from rice straw by using the two-step acid hydrolysis process. The effects of reaction temperature, reaction time, the amount of rice straw and acid concentration on the hydrolysis of rice straw were systematically studied, and showed that except initial rice straw loading amount, the other parameters had remarkable influence on the products distribution and yields. In the first-step of the hydrolysis process, a high xylose yield of 162.6 g·kg-1 was obtained at 140℃ after 120 min reaction time. When the solid residues from the first step were subjected to a second-step hydrolysis, a glucose yield as high as 216.5 g·kg-1 could be achieved at 180℃ after 120 min. This work provides a promising strategy for the efficient and value-added utilization of agricultural wastes such as rice straw.

  1. Iterative optimization of xylose catabolism in Saccharomyces cerevisiae using combinatorial expression tuning.

    Science.gov (United States)

    Latimer, Luke N; Dueber, John E

    2017-06-01

    A common challenge in metabolic engineering is rapidly identifying rate-controlling enzymes in heterologous pathways for subsequent production improvement. We demonstrate a workflow to address this challenge and apply it to improving xylose utilization in Saccharomyces cerevisiae. For eight reactions required for conversion of xylose to ethanol, we screened enzymes for functional expression in S. cerevisiae, followed by a combinatorial expression analysis to achieve pathway flux balancing and identification of limiting enzymatic activities. In the next round of strain engineering, we increased the copy number of these limiting enzymes and again tested the eight-enzyme combinatorial expression library in this new background. This workflow yielded a strain that has a ∼70% increase in biomass yield and ∼240% increase in xylose utilization. Finally, we chromosomally integrated the expression library. This library enriched for strains with multiple integrations of the pathway, which likely were the result of tandem integrations mediated by promoter homology. Biotechnol. Bioeng. 2017;114: 1301-1309. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  2. Employing a combinatorial expression approach to characterize xylose utilization in Saccharomyces cerevisiae.

    Science.gov (United States)

    Latimer, Luke N; Lee, Michael E; Medina-Cleghorn, Daniel; Kohnz, Rebecca A; Nomura, Daniel K; Dueber, John E

    2014-09-01

    Fermentation of xylose, a major constituent of lignocellulose, will be important for expanding sustainable biofuel production. We sought to better understand the effects of intrinsic (genotypic) and extrinsic (growth conditions) variables on optimal gene expression of the Scheffersomyces stipitis xylose utilization pathway in Saccharomyces cerevisiae by using a set of five promoters to simultaneously regulate each gene. Three-gene (xylose reductase, xylitol dehydrogenase (XDH), and xylulokinase) and eight-gene (expanded with non-oxidative pentose phosphate pathway enzymes and pyruvate kinase) promoter libraries were enriched under aerobic and anaerobic conditions or with a mutant XDH with altered cofactor usage. Through characterization of enriched strains, we observed (1) differences in promoter enrichment for the three-gene library depending on whether the pentose phosphate pathway genes were included during the aerobic enrichment; (2) the importance of selection conditions, where some aerobically-enriched strains underperform in anaerobic conditions compared to anaerobically-enriched strains; (3) improved growth rather than improved fermentation product yields for optimized strains carrying the mutant XDH compared to the wild-type XDH. Copyright © 2014 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

  3. Acid-catalysed xylose dehydration into furfural in the presence of kraft lignin.

    Science.gov (United States)

    Lamminpää, Kaisa; Ahola, Juha; Tanskanen, Juha

    2015-02-01

    In this study, the effects of kraft lignin (Indulin AT) on acid-catalysed xylose dehydration into furfural were studied in formic and sulphuric acids. The study was done using D-optimal design. Three variables in both acids were included in the design: time (20-80 min), temperature (160-180°C) and initial lignin concentration (0-20 g/l). The dependent variables were xylose conversion, furfural yield, furfural selectivity and pH change. The results showed that the xylose conversion and furfural yield decreased in sulphuric acid, while in formic acid the changes were minor. Additionally, it was showed that lignin has an acid-neutralising capacity, and the added lignin increased the pH of reactant solutions in both acids. The pH rise was considerably lower in formic acid than in sulphuric acid. However, the higher pH did not explain all the changes in conversion and yield, and thus lignin evidently inhibits the formation of furfural. Copyright © 2014 Elsevier Ltd. All rights reserved.

  4. Altering coenzyme specificity of Pichia stipitis xylose reductase by the semi-rational approach CASTing

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    Zhang Jingqing

    2007-11-01

    Full Text Available Abstract Background The NAD(PH-dependent Pichia stipitis xylose reductase (PsXR is one of the key enzymes for xylose fermentation, and has been cloned into the commonly used ethanol-producing yeast Saccharomyces cerevisiae. In order to eliminate the redox imbalance resulting from the preference of this enzyme toward NADPH, efforts have been made to alter the coenzyme specificity of PsXR by site-directed mutagenesis, with limited success. Given the industrial importance of PsXR, it is of interest to investigate further ways to create mutants of PsXR that prefers NADH rather than NADPH, by the alternative directed evolution approach. Results Based on a homology model of PsXR, six residues were predicted to interact with the adenine ribose of NAD(PH in PsXR and altered using a semi-rational mutagenesis approach (CASTing. Three rounds of saturation mutagenesis were carried to randomize these residues, and a microplate-based assay was applied in the screening. A best mutant 2-2C12, which carried four mutations K270S, N272P, S271G and R276F, was obtained. The mutant showed a preference toward NADH over NADPH by a factor of about 13-fold, or an improvement of about 42-fold, as measured by the ratio of the specificity constant kcat/Kmcoenzyme. Compared with the wild-type, the kcatNADH for the best mutant was only slightly lower, while the kcatNADPH decreased by a factor of about 10. Furthermore, the specific activity of 2-2C12 in the presence of NADH was 20.6 U·mg-1, which is highest among PsXR mutants reported. Conclusion A seemingly simplistic and yet very effective mutagenesis approach, CASTing, was applied successfully to alter the NAD(PH preference for Pichia stipitis xylose reductase, an important enzyme for xylose-fermenting yeast. The observed change in the NAD(PH preference for this enzyme seems to have resulted from the altered active site that is more unfavorable for NADPH than NADH in terms of both Km and kcat. There are potentials for

  5. Studies of Brønsted/Lewis Acid-Catalyzed Dehydration of Xylose to Furfural and Simultaneous Separation of Furfural by Pervaporation

    OpenAIRE

    Wang, Alex

    2017-01-01

    A major component of lignocellulosic biomass is hemicellulose, a polysaccharide composed of monomeric sugars, principally xylose. Xylose can be dehydrated, most often in aqueous solution, using Brønsted acid catalysts to form furfural, which can be further reacted to produce fuels, lubricants, polymers, solvents, and pharmaceutical precursors. Furfural production can also be enhanced by using Lewis acid catalysts, which promote the formation of xylulose, an isomer of xylose which more readily...

  6. The synthetic xylulose-1 phosphate pathway increases production of glycolic acid from xylose-rich sugar mixtures.

    Science.gov (United States)

    Alkim, Ceren; Trichez, Debora; Cam, Yvan; Spina, Lucie; François, Jean Marie; Walther, Thomas

    2016-01-01

    Glycolic acid (GA) is a two-carbon hydroxyacid with applications in the cosmetic, textile, and medical industry. Microbial GA production from all sugars can be achieved by engineering the natural glyoxylate shunt. The synthetic (d)-xylulose-1 phosphate (X1P) pathway provides a complementary route to produce GA from (d)-xylose. The simultaneous operation of the X1P and glyoxylate pathways increases the theoretical GA yield from xylose by 20 %, which may strongly improve GA production from hemicellulosic hydrolysates. We herein describe the construction of an E. coli strain that produces GA via the glyoxylate pathway at a yield of 0.31 , 0.29 , and 0.37 g/g from glucose, xylose, or a mixture of glucose and xylose (mass ratio: 33:66 %), respectively. When the X1P pathway operates in addition to the glyoxylate pathway, the GA yields on the three substrates are, respectively, 0.39 , 0.43 , and 0.47 g/g. Upon constitutive expression of the sugar permease GalP, the GA yield of the strain which simultaneously operates the glyoxylate and X1P pathways further increases to 0.63 g/g when growing on the glucose/xylose mixture. Under these conditions, the GA yield on the xylose fraction of the sugar mixture reaches 0.75 g/g, which is the highest yield reported to date. These results demonstrate that the synthetic X1P pathway has a very strong potential to improve GA production from xylose-rich hemicellulosic hydrolysates.

  7. New Protocol Based on UHPLC-MS/MS for Quantitation of Metabolites in Xylose-Fermenting Yeasts

    Science.gov (United States)

    Campos, Christiane Gonçalves; Veras, Henrique César Teixeira; de Aquino Ribeiro, José Antônio; Costa, Patrícia Pinto Kalil Gonçalves; Araújo, Katiúscia Pereira; Rodrigues, Clenilson Martins; de Almeida, João Ricardo Moreira; Abdelnur, Patrícia Verardi

    2017-12-01

    Xylose fermentation is a bottleneck in second-generation ethanol production. As such, a comprehensive understanding of xylose metabolism in naturally xylose-fermenting yeasts is essential for prospection and construction of recombinant yeast strains. The objective of the current study was to establish a reliable metabolomics protocol for quantification of key metabolites of xylose catabolism pathways in yeast, and to apply this protocol to Spathaspora arborariae. Ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS) was used to quantify metabolites, and afterwards, sample preparation was optimized to examine yeast intracellular metabolites. S. arborariae was cultivated using xylose as a carbon source under aerobic and oxygen-limited conditions. Ion pair chromatography (IPC) and hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) were shown to efficiently quantify 14 and 5 metabolites, respectively, in a more rapid chromatographic protocol than previously described. Thirteen and eleven metabolites were quantified in S. arborariae under aerobic and oxygen-limited conditions, respectively. This targeted metabolomics protocol is shown here to quantify a total of 19 metabolites, including sugars, phosphates, coenzymes, monosaccharides, and alcohols, from xylose catabolism pathways (glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle) in yeast. Furthermore, to our knowledge, this is the first time that intracellular metabolites have been quantified in S. arborariae after xylose consumption. The results indicated that fine control of oxygen levels during fermentation is necessary to optimize ethanol production by S. arborariae. The protocol presented here may be applied to other yeast species and could support yeast genetic engineering to improve second generation ethanol production. [Figure not available: see fulltext.

  8. New Protocol Based on UHPLC-MS/MS for Quantitation of Metabolites in Xylose-Fermenting Yeasts

    Science.gov (United States)

    Campos, Christiane Gonçalves; Veras, Henrique César Teixeira; de Aquino Ribeiro, José Antônio; Costa, Patrícia Pinto Kalil Gonçalves; Araújo, Katiúscia Pereira; Rodrigues, Clenilson Martins; de Almeida, João Ricardo Moreira; Abdelnur, Patrícia Verardi

    2017-09-01

    Xylose fermentation is a bottleneck in second-generation ethanol production. As such, a comprehensive understanding of xylose metabolism in naturally xylose-fermenting yeasts is essential for prospection and construction of recombinant yeast strains. The objective of the current study was to establish a reliable metabolomics protocol for quantification of key metabolites of xylose catabolism pathways in yeast, and to apply this protocol to Spathaspora arborariae. Ultra-high performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS) was used to quantify metabolites, and afterwards, sample preparation was optimized to examine yeast intracellular metabolites. S. arborariae was cultivated using xylose as a carbon source under aerobic and oxygen-limited conditions. Ion pair chromatography (IPC) and hydrophilic interaction liquid chromatography-tandem mass spectrometry (HILIC-MS/MS) were shown to efficiently quantify 14 and 5 metabolites, respectively, in a more rapid chromatographic protocol than previously described. Thirteen and eleven metabolites were quantified in S. arborariae under aerobic and oxygen-limited conditions, respectively. This targeted metabolomics protocol is shown here to quantify a total of 19 metabolites, including sugars, phosphates, coenzymes, monosaccharides, and alcohols, from xylose catabolism pathways (glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle) in yeast. Furthermore, to our knowledge, this is the first time that intracellular metabolites have been quantified in S. arborariae after xylose consumption. The results indicated that fine control of oxygen levels during fermentation is necessary to optimize ethanol production by S. arborariae. The protocol presented here may be applied to other yeast species and could support yeast genetic engineering to improve second generation ethanol production. [Figure not available: see fulltext.

  9. Separate hydrolysis and co-fermentation for improved xylose utilization in integrated ethanol production from wheat meal and wheat straw.

    Science.gov (United States)

    Erdei, Borbála; Frankó, Balázs; Galbe, Mats; Zacchi, Guido

    2012-03-12

    The commercialization of second-generation bioethanol has not been realized due to several factors, including poor biomass utilization and high production cost. It is generally accepted that the most important parameters in reducing the production cost are the ethanol yield and the ethanol concentration in the fermentation broth. Agricultural residues contain large amounts of hemicellulose, and the utilization of xylose is thus a plausible way to improve the concentration and yield of ethanol during fermentation. Most naturally occurring ethanol-fermenting microorganisms do not utilize xylose, but a genetically modified yeast strain, TMB3400, has the ability to co-ferment glucose and xylose. However, the xylose uptake rate is only enhanced when the glucose concentration is low. Separate hydrolysis and co-fermentation of steam-pretreated wheat straw (SPWS) combined with wheat-starch hydrolysate feed was performed in two separate processes. The average yield of ethanol and the xylose consumption reached 86% and 69%, respectively, when the hydrolysate of the enzymatically hydrolyzed (18.5% WIS) unwashed SPWS solid fraction and wheat-starch hydrolysate were fed to the fermentor after 1 h of fermentation of the SPWS liquid fraction. In the other configuration, fermentation of the SPWS hydrolysate (7.0% WIS), resulted in an average ethanol yield of 93% from fermentation based on glucose and xylose and complete xylose consumption when wheat-starch hydrolysate was included in the feed. Increased initial cell density in the fermentation (from 5 to 20 g/L) did not increase the ethanol yield, but improved and accelerated xylose consumption in both cases. Higher ethanol yield has been achieved in co-fermentation of xylose and glucose in SPWS hydrolysate when wheat-starch hydrolysate was used as feed, then in co-fermentation of the liquid fraction of SPWS fed with the mixed hydrolysates. Integration of first-generation and second-generation processes also increases the ethanol

  10. Separate hydrolysis and co-fermentation for improved xylose utilization in integrated ethanol production from wheat meal and wheat straw

    Directory of Open Access Journals (Sweden)

    Erdei Borbála

    2012-03-01

    Full Text Available Abstract Background The commercialization of second-generation bioethanol has not been realized due to several factors, including poor biomass utilization and high production cost. It is generally accepted that the most important parameters in reducing the production cost are the ethanol yield and the ethanol concentration in the fermentation broth. Agricultural residues contain large amounts of hemicellulose, and the utilization of xylose is thus a plausible way to improve the concentration and yield of ethanol during fermentation. Most naturally occurring ethanol-fermenting microorganisms do not utilize xylose, but a genetically modified yeast strain, TMB3400, has the ability to co-ferment glucose and xylose. However, the xylose uptake rate is only enhanced when the glucose concentration is low. Results Separate hydrolysis and co-fermentation of steam-pretreated wheat straw (SPWS combined with wheat-starch hydrolysate feed was performed in two separate processes. The average yield of ethanol and the xylose consumption reached 86% and 69%, respectively, when the hydrolysate of the enzymatically hydrolyzed (18.5% WIS unwashed SPWS solid fraction and wheat-starch hydrolysate were fed to the fermentor after 1 h of fermentation of the SPWS liquid fraction. In the other configuration, fermentation of the SPWS hydrolysate (7.0% WIS, resulted in an average ethanol yield of 93% from fermentation based on glucose and xylose and complete xylose consumption when wheat-starch hydrolysate was included in the feed. Increased initial cell density in the fermentation (from 5 to 20 g/L did not increase the ethanol yield, but improved and accelerated xylose consumption in both cases. Conclusions Higher ethanol yield has been achieved in co-fermentation of xylose and glucose in SPWS hydrolysate when wheat-starch hydrolysate was used as feed, then in co-fermentation of the liquid fraction of SPWS fed with the mixed hydrolysates. Integration of first-generation and

  11. Glucose and xylose co-fermentation of pretreated wheat straw using mutants of S. cerevisiae TMB3400.

    Science.gov (United States)

    Erdei, Borbála; Frankó, Balázs; Galbe, Mats; Zacchi, Guido

    2013-03-10

    Wheat straw was pretreated and fermented to ethanol. Two strains, which had been mutated from the genetically modified Saccharomyces cerevisiae TMB3400, KE6-12 and KE6-13i, have been used in this study and the results of performance were compared to that of the original strain. The glucose and xylose co-fermentation ability was investigated in batch fermentation of steam-pretreated wheat straw (SPWS) liquid (undiluted, and diluted 1.5 and 2 times). Both strains showed improved xylose uptake in diluted SPWS liquid, and increased ethanol yields compared with the original TMB3400 strain, although xylitol formation also increased slightly. In undiluted SPWS liquid, however, only KE6-13i performed better than the original strain regarding xylose utilization. Fed-batch fermentation of 1.5 and 2 times diluted liquid was performed by adding the glucose-rich hydrolysates from enzymatic hydrolysis of the solid fraction of SPWS at a constant feed rate after 5 h of fermentation, when the glucose had been depleted. The modified strains showed improved xylose conversion; however, the ethanol yield was not significantly improved due to increased glycerol production. Fed-batch fermentation resulted in faster xylose utilization than in the batch cases. Copyright © 2012 Elsevier B.V. All rights reserved.

  12. Effect of manganese ions on ethanol fermentation by xylose isomerase expressing Saccharomyces cerevisiae under acetic acid stress.

    Science.gov (United States)

    Ko, Ja Kyong; Um, Youngsoon; Lee, Sun-Mi

    2016-12-01

    The efficient fermentation of lignocellulosic hydrolysates in the presence of inhibitors is highly desirable for bioethanol production. Among the inhibitors, acetic acid released during the pretreatment of lignocellulose negatively affects the fermentation performance of biofuel producing organisms. In this study, we evaluated the inhibitory effects of acetic acid on glucose and xylose fermentation by a high performance engineered strain of xylose utilizing Saccharomyces cerevisiae, SXA-R2P-E, harboring a xylose isomerase based pathway. The presence of acetic acid severely decreased the xylose fermentation performance of this strain. However, the acetic acid stress was alleviated by metal ion supplementation resulting in a 52% increased ethanol production rate under 2g/L of acetic acid stress. This study shows the inhibitory effect of acetic acid on an engineered isomerase-based xylose utilizing strain and suggests a simple but effective method to improve the co-fermentation performance under acetic acid stress for efficient bioethanol production. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Inhibitor tolerance of a recombinant flocculating industrial Saccharomyces cerevisiae strain during glucose and xylose co-fermentation

    Directory of Open Access Journals (Sweden)

    Yun-Cheng Li

    Full Text Available ABSTRACT Lignocellulose-derived inhibitors have negative effects on the ethanol fermentation capacity of Saccharomyces cerevisiae. In this study, the effects of eight typical inhibitors, including weak acids, furans, and phenols, on glucose and xylose co-fermentation of the recombinant xylose-fermenting flocculating industrial S. cerevisiae strain NAPX37 were evaluated by batch fermentation. Inhibition on glucose fermentation, not that on xylose fermentation, correlated with delayed cell growth. The weak acids and the phenols showed additive effects. The effect of inhibitors on glucose fermentation was as follows (from strongest to weakest: vanillin > phenol > syringaldehyde > 5-HMF > furfural > levulinic acid > acetic acid > formic acid. The effect of inhibitors on xylose fermentation was as follows (from strongest to weakest: phenol > vanillin > syringaldehyde > furfural > 5-HMF > formic acid > levulinic acid > acetic acid. The NAPX37 strain showed substantial tolerance to typical inhibitors and showed good fermentation characteristics, when a medium with inhibitor cocktail or rape straw hydrolysate was used. This research provides important clues for inhibitors tolerance of recombinant industrial xylose-fermenting S. cerevisiae.

  14. Resiliently evolving supply-demand networks.

    Science.gov (United States)

    Rubido, Nicolás; Grebogi, Celso; Baptista, Murilo S

    2014-01-01

    The ability to design a transport network such that commodities are brought from suppliers to consumers in a steady, optimal, and stable way is of great importance for distribution systems nowadays. In this work, by using the circuit laws of Kirchhoff and Ohm, we provide the exact capacities of the edges that an optimal supply-demand network should have to operate stably under perturbations, i.e., without overloading. The perturbations we consider are the evolution of the connecting topology, the decentralization of hub sources or sinks, and the intermittence of supplier and consumer characteristics. We analyze these conditions and the impact of our results, both on the current United Kingdom power-grid structure and on numerically generated evolving archetypal network topologies.

  15. Fermentation of Xylose Causes Inefficient Metabolic State Due to Carbon/Energy Starvation and Reduced Glycolytic Flux in Recombinant Industrial Saccharomyces cerevisiae

    Science.gov (United States)

    Matsushika, Akinori; Nagashima, Atsushi; Goshima, Tetsuya; Hoshino, Tamotsu

    2013-01-01

    In the present study, comprehensive, quantitative metabolome analysis was carried out on the recombinant glucose/xylose-cofermenting S. cerevisiae strain MA-R4 during fermentation with different carbon sources, including glucose, xylose, or glucose/xylose mixtures. Capillary electrophoresis time-of-flight mass spectrometry was used to determine the intracellular pools of metabolites from the central carbon pathways, energy metabolism pathways, and the levels of twenty amino acids. When xylose instead of glucose was metabolized by MA-R4, glycolytic metabolites including 3- phosphoglycerate, 2- phosphoglycerate, phosphoenolpyruvate, and pyruvate were dramatically reduced, while conversely, most pentose phosphate pathway metabolites such as sedoheptulose 7- phosphate and ribulose 5-phosphate were greatly increased. These results suggest that the low metabolic activity of glycolysis and the pool of pentose phosphate pathway intermediates are potential limiting factors in xylose utilization. It was further demonstrated that during xylose fermentation, about half of the twenty amino acids declined, and the adenylate/guanylate energy charge was impacted due to markedly decreased adenosine triphosphate/adenosine monophosphate and guanosine triphosphate/guanosine monophosphate ratios, implying that the fermentation of xylose leads to an inefficient metabolic state where the biosynthetic capabilities and energy balance are severely impaired. In addition, fermentation with xylose alone drastically increased the level of citrate in the tricarboxylic acid cycle and increased the aromatic amino acids tryptophan and tyrosine, strongly supporting the view that carbon starvation was induced. Interestingly, fermentation with xylose alone also increased the synthesis of the polyamine spermidine and its precursor S-adenosylmethionine. Thus, differences in carbon substrates, including glucose and xylose in the fermentation medium, strongly influenced the dynamic metabolism of MA-R4

  16. The Evolving Resource Metadata Infrastructure

    Science.gov (United States)

    Biemesderfer, Chris

    The search and discovery mechanisms that will facilitate and simplify systematic research on the Internet depend on systematic classifications of resources, as well as on standardized access to such metadata. The principles and technologies that will make this possible are evolving in the work of the Internet Engineering Task Force and the digital library initiatives, among others. The desired outcome is a set of standards, tools, and practices that permits both cataloging and retrieval to be comprehensive and efficient.

  17. Production of ethylene glycol or glycolic acid from D-xylose in Saccharomyces cerevisiae.

    Science.gov (United States)

    Salusjärvi, Laura; Toivari, Mervi; Vehkomäki, Maija-Leena; Koivistoinen, Outi; Mojzita, Dominik; Niemelä, Klaus; Penttilä, Merja; Ruohonen, Laura

    2017-11-01

    The important platform chemicals ethylene glycol and glycolic acid were produced via the oxidative D-xylose pathway in the yeast Saccharomyces cerevisiae. The expression of genes encoding D-xylose dehydrogenase (XylB) and D-xylonate dehydratase (XylD) from Caulobacter crescentus and YagE or YjhH aldolase and aldehyde dehydrogenase AldA from Escherichia coli enabled glycolic acid production from D-xylose up to 150 mg/L. In strains expressing only xylB and xylD, 29 mg/L 2-keto-3-deoxyxylonic acid [(S)-4,5-dihydroxy-2-oxopentanoic acid] (2K3DXA) was produced and D-xylonic acid accumulated to ca. 9 g/L. A significant amount of D-xylonic acid (ca. 14%) was converted to 3-deoxypentonic acid (3DPA), and also, 3,4-dihydroxybutyric acid was formed. 2K3DXA was further converted to glycolaldehyde when genes encoding by either YagE or YjhH aldolase from E. coli were expressed. Reduction of glycolaldehyde to ethylene glycol by an endogenous aldo-keto reductase activity resulted further in accumulation of ethylene glycol of 14 mg/L. The possibility of simultaneous production of lactic and glycolic acids was evaluated by expression of gene encoding lactate dehydrogenase ldhL from Lactobacillus helveticus together with aldA. Interestingly, this increased the accumulation of glycolic acid to 1 g/L. The D-xylonate dehydratase activity in yeast was notably low, possibly due to inefficient Fe-S cluster synthesis in the yeast cytosol, and leading to D-xylonic acid accumulation. The dehydratase activity was significantly improved by targeting its expression to mitochondria or by altering the Fe-S cluster metabolism of the cells with FRA2 deletion.

  18. D-Xylose fermentation, xylitol production and xylanase activities by seven new species of Sugiyamaella.

    Science.gov (United States)

    Sena, Letícia M F; Morais, Camila G; Lopes, Mariana R; Santos, Renata O; Uetanabaro, Ana P T; Morais, Paula B; Vital, Marcos J S; de Morais, Marcos A; Lachance, Marc-André; Rosa, Carlos A

    2017-01-01

    Sixteen yeast isolates identified as belonging to the genus Sugiyamaella were studied in relation to D-xylose fermentation, xylitol production, and xylanase activities. The yeasts were recovered from rotting wood and sugarcane bagasse samples in different Brazilian regions. Sequence analyses of the internal transcribed spacer (ITS) region and the D1/D2 domains of large subunit rRNA gene showed that these isolates belong to seven new species. The species are described here as Sugiyamaella ayubii f.a., sp. nov. (UFMG-CM-Y607(T) = CBS 14108(T)), Sugiyamaella bahiana f.a., sp. nov. (UFMG-CM-Y304(T) = CBS 13474(T)), Sugiyamaella bonitensis f.a., sp. nov. (UFMG-CM-Y608(T) = CBS 14270(T)), Sugiyamaella carassensis f.a., sp. nov. (UFMG-CM-Y606(T) = CBS 14107(T)), Sugiyamaella ligni f.a., sp. nov. (UFMG-CM-Y295(T) = CBS 13482(T)), Sugiyamaella valenteae f.a., sp. nov. (UFMG-CM-Y609(T) = CBS 14109(T)) and Sugiyamaella xylolytica f.a., sp. nov. (UFMG-CM-Y348(T) = CBS 13493(T)). Strains of the described species S. boreocaroliniensis, S. lignohabitans, S. novakii and S. xylanicola, isolated from rotting wood of Brazilian ecosystems, were also compared for traits relevant to xylose metabolism. S. valenteae sp. nov., S. xylolytica sp. nov., S. bahiana sp. nov., S. bonitensis sp. nov., S. boreocarolinensis, S. lignohabitans and S. xylanicola were able to ferment D-xylose to ethanol. Xylitol production was observed for all Sugiyamaella species studied, except for S. ayubii sp. nov. All species studied showed xylanolytic activity, with S. xylanicola, S. lignohabitans and S. valenteae sp. nov. having the highest values. Our results suggest these Sugiyamaella species have good potential for biotechnological applications.

  19. Ranking in evolving complex networks

    Science.gov (United States)

    Liao, Hao; Mariani, Manuel Sebastian; Medo, Matúš; Zhang, Yi-Cheng; Zhou, Ming-Yang

    2017-05-01

    Complex networks have emerged as a simple yet powerful framework to represent and analyze a wide range of complex systems. The problem of ranking the nodes and the edges in complex networks is critical for a broad range of real-world problems because it affects how we access online information and products, how success and talent are evaluated in human activities, and how scarce resources are allocated by companies and policymakers, among others. This calls for a deep understanding of how existing ranking algorithms perform, and which are their possible biases that may impair their effectiveness. Many popular ranking algorithms (such as Google's PageRank) are static in nature and, as a consequence, they exhibit important shortcomings when applied to real networks that rapidly evolve in time. At the same time, recent advances in the understanding and modeling of evolving networks have enabled the development of a wide and diverse range of ranking algorithms that take the temporal dimension into account. The aim of this review is to survey the existing ranking algorithms, both static and time-aware, and their applications to evolving networks. We emphasize both the impact of network evolution on well-established static algorithms and the benefits from including the temporal dimension for tasks such as prediction of network traffic, prediction of future links, and identification of significant nodes.

  20. Metabolic engineering of ammonium assimilation in xylose-fermenting Saccharomyes cerevisiae improves ethanol production

    DEFF Research Database (Denmark)

    Roca, Christophe Francois Aime; Nielsen, Jens; Olsson, Lisbeth

    2003-01-01

    , and by over-expressing either GDH2, which encodes an NADH-dependent glutamate dehydrogenase, or GLT1 and GLN1, which encode the GS-GOGAT complex. Overexpression of GDH2 increased ethanol yield from 0.43 to 0.51 mol of carbon (Cmol) Cmol(-1), mainly by reducing xylitol excretion by 44%. Overexpression...... of the GS-GOGAT complex did not improve conversion of xylose to ethanol during batch cultivation, but it increased ethanol yield by 16% in carbon-limited continuous cultivation at a low dilution rate....

  1. Separate and Simultaneous enzymatic hydrolysis and fermentation of wheat hemicellulose with recombinant xylose utilizing Saccharomyces cerevisiae

    DEFF Research Database (Denmark)

    Olsson, Lisbeth; Sørensen, H. R.; Dam, B. P

    2006-01-01

    Fermentations with three different xylose-utilizing recombinant Saccharomyces cerevisiae strains (F12, CR4, and CB4) were performed using two different wheat hemicellulose substrates, unfermented starch free fibers, and an industrial ethanol fermentation residue, vinasse. With CR4 and F12...... ethanol concentrations were obtained with SSF. In general, the volumetric ethanol productivity was initially, highest in the SHF, but the overall volumetric ethanol productivity ended up being maximal in the SSF, at 0.013 and 0.010 g/Lh, with starch free fibers and vinasse, respectively....

  2. Effect of humic acids on electricity generation integrated with xylose degradation in microbial fuel cells

    DEFF Research Database (Denmark)

    Huang, Liping; Angelidaki, Irini

    2008-01-01

    Pentose and humic acids (HA) are the main components of hydrolysates, the liquid fraction produced during thermohydrolysis of lignocellulosic material. Electricity generation integrated with xylose (typical pentose) degradation as well as the effect of HA on electricity production in microbial fuel...... degradation and formation of more oxidized products (acetate and formate) as well as less reduced products (lactate and ethanol) compared to the controls. The reduced power generation in the presence of DMW was attributed to the presence of bacterial inhibitors such as phenolic compounds. Therefore, new...

  3. Process for assembly and transformation into Saccharomyces cerevisiae of a synthetic yeast artificial chromosome containing a multigene cassette to express enzymes that enhance xylose utilization designed for an automated pla

    Science.gov (United States)

    A yeast artificial chromosome (YAC) containing a multigene cassette for expression of enzymes that enhance xylose utilization (xylose isomerase [XI] and xylulokinase [XKS]) was constructed and transformed into Saccharomyces cerevisiae to demonstrate feasibility as a stable protein expression system ...

  4. Co-immobilization of glucose oxidase and xylose dehydrogenase displayed whole cell on multiwalled carbon nanotube nanocomposite films modified electrode for simultaneous voltammetric detection of D-glucose and D-xylose.

    Science.gov (United States)

    Li, Liang; Liang, Bo; Li, Feng; Shi, Jianguo; Mascini, Marco; Lang, Qiaolin; Liu, Aihua

    2013-04-15

    In this paper, we first report the construction of Nafion/glucose oxidase (GOD)/xylose dehydrogenase displayed bacteria (XDH-bacteria)/multiwalled carbon nanotubes (MWNTs) modified electrode for simultaneous voltammetric determination of D-glucose and D-xylose. The optimal conditions for the immobilized enzymes were established. Both enzymes retained their good stability and activities. In the mixture solution of D-glucose and D-xylose containing coenzyme NAD⁺ (the oxidized form of nicotinamide adenine dinucleotide), the Nafion/GOD/XDH-bacteria/MWNTs modified electrode exhibited quasi-reversible oxidation-reduction peak at -0.5 V (vs. saturated calomel electrode, SCE) originating from the catalytic oxidation of D-glucose, and oxidation peak at +0.55 V(vs. SCE) responding to the oxidation of NADH (the reduced form of nicotinamide adenine dinucleotide) by the carbon nanotubes, where NADH is the resultant product of coenzyme NAD⁺ involved in the catalysis of D-xylose by XDH-displayed bacteria. For the proposed biosensor, cathodic peak current at -0.5 V was linear with the concentration of D-glucose within the range of 0.25-6 mM with a low detection limit of 0.1 mM D-glucose (S/N=3), and the anodic peak current at +0.55 V was linear with the concentration of d-xylose in the range of 0.25∼4 mM with a low detection limit of 0.1 mM D-xylose (S/N=3). Further, D-xylose and D-glucose did not interfere with each other. 300-fold excess saccharides including D-maltose, D-galactose, D-mannose, D-sucrose, D-fructose, D-cellobiose, and 60-fold excess L-arabinose, and common interfering substances (100-fold excess ascorbic acid, dopamine, uric acid) as well as 300-fold excess D-xylitol did not affect the detection of D-glucose and D-xylose (both 1 mM). Therefore, the proposed biosensor is stable, specific, reproducible, simple, rapid and cost-effective, which holds great potential in real applications. Copyright © 2012 Elsevier B.V. All rights reserved.

  5. Real-time NMR monitoring of intermediates and labile products of the bifunctional enzyme UDP-apiose/UDP-xylose synthase.

    Science.gov (United States)

    Guyett, Paul; Glushka, John; Gu, Xiaogang; Bar-Peled, Maor

    2009-06-12

    The conversion of UDP-alpha-d-glucuronic acid to UDP-alpha-d-xylose and UDP-alpha-d-apiose by a bifunctional potato enzyme UDP-apiose/UDP-xylose synthase was studied using real-time nuclear magnetic resonance (NMR) spectroscopy. UDP-alpha-d-glucuronic acid is converted via the intermediate uridine 5'-beta-l-threo-pentapyranosyl-4''-ulose diphosphate to UDP-alpha-d-apiose and simultaneously to UDP-alpha-d-xylose. The UDP-alpha-d-apiose that is formed is unstable and is converted to alpha-d-apio-furanosyl-1,2-cyclic phosphate and UMP. High-resolution real-time NMR spectroscopy is a powerful tool for the direct and quantitative characterization of previously undetected transient and labile components formed during a complex enzyme-catalyzed reaction.

  6. Utilization of biodiesel-derived glycerol or xylose for increased growth and lipid production by indigenous microalgae.

    Science.gov (United States)

    Leite, Gustavo B; Paranjape, Kiran; Abdelaziz, Ahmed E M; Hallenbeck, Patrick C

    2015-05-01

    Microalgae are a promising alternative for sustainable biofuel production, but production yields and costs present a significant bottleneck. Here, the use of glycerol and xylose to boost the lipid yield was evaluated using ten strains from the Université de Montréal collection of microalgae. This report shows that some microalgal strains are capable of mixotrophic and heterotrophic growth on xylose, the major carbon source found in wastewater streams from pulp and paper industries, with an increase in growth rate of 2.8-fold in comparison to photoautotrophic growth, reaching up to μ=1.1/d. On glycerol, growth rates reached as high as μ=1.52/d. Lipid productivity increased up to 370% on glycerol and 180% on xylose for the strain LB1H10, showing the suitability of this strain for further development of biofuels production through mixotrophic cultivation. Copyright © 2014 Elsevier Ltd. All rights reserved.

  7. Metabolic characterization and transformation of the non-dairy Lactococcus lactis strain KF147, for production of ethanol from xylose

    DEFF Research Database (Denmark)

    Petersen, Kia Vest; Liu, Jianming; Chen, Jun

    2017-01-01

    over-expression of phosphoketolase increased the flux through the phosphoketolase pathway. In general, significant amounts of the mixed-acid products, including lactate, formate, acetate and ethanol, were formed irrespective of xylose concentrations. To demonstrate the potential of KF147 for converting......The non-dairy lactic acid bacterium Lactococcus lactis KF147 can utilize xylose as the sole energy source. To assess whether KF147 could serve as a platform organism for converting second generation sugars into useful chemicals, we characterized growth and product formation for KF147 when grown...... the arcA gene encoding the arginine deiminase. The fermentation product profile suggested two routes for xylose degradation, the phosphoketolase pathway and the pentose phosphate pathway. Inactivation of the phosphoketolase pathway redirected the entire flux through the pentose phosphate pathway whereas...

  8. Point mutation of the xylose reductase (XR) gene reduces xylitol accumulation and increases citric acid production in Aspergillus carbonarius.

    Science.gov (United States)

    Weyda, István; Lübeck, Mette; Ahring, Birgitte K; Lübeck, Peter S

    2014-04-01

    Aspergillus carbonarius accumulates xylitol when it grows on D-xylose. In fungi, D-xylose is reduced to xylitol by the NAD(P)H-dependent xylose reductase (XR). Xylitol is then further oxidized by the NAD(+)-dependent xylitol dehydrogenase (XDH). The cofactor impairment between the XR and XDH can lead to the accumulation of xylitol under oxygen-limiting conditions. Most of the XRs are NADPH dependent and contain a conserved Ile-Pro-Lys-Ser motif. The only known naturally occurring NADH-dependent XR (from Candida parapsilosis) carries an arginine residue instead of the lysine in this motif. In order to overcome xylitol accumulation in A. carbonarius a Lys-274 to Arg point mutation was introduced into the XR with the aim of changing the specificity toward NADH. The effect of the genetic engineering was examined in fermentation for citric acid production and xylitol accumulation by using D-xylose as the sole carbon source. Fermentation with the mutant strain showed a 2.8-fold reduction in xylitol accumulation and 4.5-fold increase in citric acid production compared to the wild-type strain. The fact that the mutant strain shows decreased xylitol levels is assumed to be associated with the capability of the mutated XR to use the NADH generated by the XDH, thus preventing the inhibition of XDH by the high levels of NADH and ensuring the flux of xylose through the pathway. This work shows that enhanced production of citric acid can be achieved using xylose as the sole carbon source by reducing accumulation of other by-products, such as xylitol.

  9. Evolved Expendable Launch Vehicle (EELV)

    Science.gov (United States)

    2015-12-15

    transitioning to a long-term sustained competitive environment and fully implement the National Space Transportation Policy direction: to increase the U.S...commercial space transportation industry robustness and cost effectiveness; foster innovation-driven entrepreneurship and international...Command Quantity to Sustain : 0 Unit of Measure: Years Service Life per Unit: 31.00 Years Fiscal Years in Service: FY 2000 - FY 2030 Sustainment

  10. Enzymatic Xylose Release from Pretreated Corn Bran Arabinoxylan: Differential Effects of Deacetylation and Deferuloylation on Insoluble and Soluble Substrate Fractions

    DEFF Research Database (Denmark)

    Agger, Jane; Viksø-Nielsen, Ander; Meyer, Anne S.

    2010-01-01

    In the present work enzymatic hydrolysis of arabinoxylan from pretreated corn bran (190 °C, 10 min) was evaluated by measuring the release of xylose and arabinose after treatment with a designed minimal mixture of monocomponent enzymes consisting of α-l-arabinofuranosidases, an endoxylanase......, and a β-xylosidase. The pretreatment divided the corn bran material 50:50 into soluble and insoluble fractions having A:X ratios of 0.66 and 0.40, respectively. Addition of acetyl xylan esterase to the monocomponent enzyme mixture almost doubled the xylose release from the insoluble substrate fraction...

  11. The evolvability of programmable hardware

    Science.gov (United States)

    Raman, Karthik; Wagner, Andreas

    2011-01-01

    In biological systems, individual phenotypes are typically adopted by multiple genotypes. Examples include protein structure phenotypes, where each structure can be adopted by a myriad individual amino acid sequence genotypes. These genotypes form vast connected ‘neutral networks’ in genotype space. The size of such neutral networks endows biological systems not only with robustness to genetic change, but also with the ability to evolve a vast number of novel phenotypes that occur near any one neutral network. Whether technological systems can be designed to have similar properties is poorly understood. Here we ask this question for a class of programmable electronic circuits that compute digital logic functions. The functional flexibility of such circuits is important in many applications, including applications of evolutionary principles to circuit design. The functions they compute are at the heart of all digital computation. We explore a vast space of 1045 logic circuits (‘genotypes’) and 1019 logic functions (‘phenotypes’). We demonstrate that circuits that compute the same logic function are connected in large neutral networks that span circuit space. Their robustness or fault-tolerance varies very widely. The vicinity of each neutral network contains circuits with a broad range of novel functions. Two circuits computing different functions can usually be converted into one another via few changes in their architecture. These observations show that properties important for the evolvability of biological systems exist in a commercially important class of electronic circuitry. They also point to generic ways to generate fault-tolerant, adaptable and evolvable electronic circuitry. PMID:20534598

  12. The 'E' factor -- evolving endodontics.

    Science.gov (United States)

    Hunter, M J

    2013-03-01

    Endodontics is a constantly developing field, with new instruments, preparation techniques and sealants competing with trusted and traditional approaches to tooth restoration. Thus general dental practitioners must question and understand the significance of these developments before adopting new practices. In view of this, the aim of this article, and the associated presentation at the 2013 British Dental Conference & Exhibition, is to provide an overview of endodontic methods and constantly evolving best practice. The presentation will review current preparation techniques, comparing rotary versus reciprocation, and question current trends in restoration of the endodontically treated tooth.

  13. Effects of microwave heating on porous structure of regenerated powdered activated carbon used in xylose.

    Science.gov (United States)

    Li, Wei; Wang, Xinying; Peng, Jinhui

    2014-01-01

    The regeneration of spent powdered activated carbons used in xylose decolourization by microwave heating was investigated. Effects of microwave power and microwave heating time on the adsorption capacity of regenerated activated carbons were evaluated. The optimum conditions obtained are as follows: microwave power 800W; microwave heating time 30min. Regenerated activated carbon in this work has high adsorption capacities for the amount of methylene blue of 16 cm3/0.1 g and the iodine number of 1000.06mg/g. The specific surface areas of fresh commercial activated carbon, spent carbon and regenerated activated carbon were calculated according to the Brunauer, Emmett and Teller method, and the pore-size distributions of these carbons were characterized by non-local density functional theory (NLDFT). The results show that the specific surface area and the total pore volume of regenerated activated carbon are 1064 m2/g and 1.181 mL/g, respectively, indicating the feasibility of regeneration of spent powdered activated carbon used in xylose decolourization by microwave heating. The results of surface fractal dimensions also confirm the results of isotherms and NLDFT.

  14. Consecutively Preparing D-Xylose, Organosolv Lignin, and Amorphous Ultrafine Silica from Rice Husk

    Science.gov (United States)

    Zhang, Hongxi; Ding, Xuefeng; Wang, Zichen; Zhao, Xu

    2014-01-01

    Rice husk is an abundant agricultural by-product reaching the output of 80 million tons annually in the world. The most common treatment method of rice husk is burning or burying, which caused serious air pollution and resource waste. In order to solve this problem, a new method is proposed to comprehensively utilize the rice husk in this paper. Firstly, the D-xylose was prepared from the semicellulose via dilute acid hydrolysis. Secondly, the lignin was separated via organic solvent pulping from the residue. Finally, the amorphous ultrafine silica was prepared via pyrolysis of the residue produced in the second process. In this way, the three main contents of rice husk (semicellulose, lignin, and silica) are consecutively converted to three fine chemicals, without solid waste produced. The yields of D-xylose and organosolv lignin reach 58.2% and 58.5%, respectively. The purity and specific surface of amorphous ultrafine silica reach 99.92% and 225.20 m2/g. PMID:25140120

  15. Synthesis and microarray-assisted binding studies of core xylose and fucose containing N-glycans.

    Science.gov (United States)

    Brzezicka, Katarzyna; Echeverria, Begoña; Serna, Sonia; van Diepen, Angela; Hokke, Cornelis H; Reichardt, Niels-Christian

    2015-05-15

    The synthesis of a collection of 33 xylosylated and core-fucosylated N-glycans found only in nonmammalian organisms such as plants and parasitic helminths has been achieved by employing a highly convergent chemo-enzymatic approach. The influence of these core modifications on the interaction with plant lectins, with the human lectin DC-SIGN (Dendritic Cell-Specific Intercellular adhesion molecule-3-Grabbing Nonintegrin), and with serum antibodies from schistosome-infected individuals was studied. Core xylosylation markedly reduced or completely abolished binding to several mannose-binding plant lectins and to DC-SIGN, a C-type lectin receptor present on antigen presenting cells. Employing the synthetic collection of core-fucosylated and core-xylosylated N-glycans in the context of a larger glycan array including structures lacking these core modifications, we were able to dissect core xylose and core fucose specific antiglycan antibody responses in S. mansoni infection sera, and we observed clear and immunologically relevant differences between children and adult groups infected with this parasite. The work presented here suggests that, quite similar to bisecting N-acetylglucosamine, core xylose distorts the conformation of the unsubstituted glycan, with important implications for the immunogenicity and protein binding properties of complex N-glycans.

  16. Metabolic engineering and classical selection of the methylotrophic thermotolerant yeast Hansenula polymorpha for improvement of high-temperature xylose alcoholic fermentation.

    Science.gov (United States)

    Kurylenko, Olena O; Ruchala, Justyna; Hryniv, Orest B; Abbas, Charles A; Dmytruk, Kostyantyn V; Sibirny, Andriy A

    2014-08-20

    The methylotrophic yeast, Hansenula polymorpha is an industrially important microorganism, and belongs to the best studied yeast species with well-developed tools for molecular research. The complete genome sequence of the strain NCYC495 of H. polymorpha is publicly available. Some of the well-studied strains of H. polymorpha are known to ferment glucose, cellobiose and xylose to ethanol at elevated temperature (45 - 50°C) with ethanol yield from xylose significantly lower than that from glucose and cellobiose. Increased yield of ethanol from xylose was demonstrated following directed metabolic changes but, still the final ethanol concentration achieved is well below what is considered feasible for economic recovery by distillation. In this work, we describe the construction of strains of H. polymorpha with increased ethanol production from xylose using an ethanol-non-utilizing strain (2EthOH-) as the host. The transformants derived from 2EthOH- overexpressing modified xylose reductase (XYL1m) and native xylitol dehydrogenase (XYL2) were isolated. These transformants produced 1.5-fold more ethanol from xylose than the original host strain. The additional overexpression of XYL3 gene coding for xylulokinase, resulted in further 2.3-fold improvement in ethanol production with no measurable xylitol formed during xylose fermentation. The best ethanol producing strain obtained by metabolic engineering approaches was subjected to selection for resistance to the known inhibitor of glycolysis, the anticancer drug 3-bromopyruvate. The best mutant selected had an ethanol yield of 0.3 g/g xylose and produced up to 9.8 g of ethanol/l during xylose alcoholic fermentation at 45°C without correction for ethanol evaporation. Our results indicate that xylose conversion to ethanol at elevated temperature can be significantly improved in H. polymorpha by combining methods of metabolic engineering and classical selection.

  17. Functional expression in Lactobacillus plantarum of xylP encoding the isoprimeverose transporter of Lactobacillus pentosus

    NARCIS (Netherlands)

    Chaillou, S.; Postma, P.W.; Pouwels, P.H.

    1998-01-01

    The xylP gene of Lactobacillus pentosus, the first gene of the xylPQR operon, was recently found to be involved in isoprimeverose metabolism. By expression of xylP on a multicopy plasmid in Lactobacillus plantarum 80, a strain which lacks active isoprimeverose and D-xylose transport activities, it

  18. Fed-batch SSCF using steam-exploded wheat straw at high dry matter consistencies and a xylose-fermenting Saccharomyces cerevisiae strain: effect of laccase supplementation.

    Science.gov (United States)

    Moreno, Antonio D; Tomás-Pejó, Elia; Ibarra, David; Ballesteros, Mercedes; Olsson, Lisbeth

    2013-11-13

    Lignocellulosic bioethanol is expected to play an important role in fossil fuel replacement in the short term. Process integration, improvements in water economy, and increased ethanol titers are key considerations for cost-effective large-scale production. The use of whole steam-pretreated slurries under high dry matter (DM) conditions and conversion of all fermentable sugars offer promising alternatives to achieve these goals. Wheat straw slurry obtained from steam explosion showed high concentrations of degradation compounds, hindering the fermentation performance of the evolved xylose-recombinant Saccharomyces cerevisiae KE6-12 strain. Fermentability tests using the liquid fraction showed a higher number of colony-forming units (CFU) and higher xylose consumption rates when treating the medium with laccase. During batch simultaneous saccharification and co-fermentation (SSCF) processes, cell growth was totally inhibited at 12% DM (w/v) in untreated slurries. However, under these conditions laccase treatment prior to addition of yeast reduced the total phenolic content of the slurry and enabled the fermentation. During this process, an ethanol concentration of 19 g/L was obtained, corresponding to an ethanol yield of 39% of the theoretical yield. By changing the operation from batch mode to fed-batch mode, the concentration of inhibitors at the start of the process was reduced and 8 g/L of ethanol were obtained in untreated slurries with a final consistency of 16% DM (w/v). When fed-batch SSCF medium was supplemented with laccase 33 hours after yeast inoculation, no effect on ethanol yield or cell viability was found compared to untreated fermentations. However, if the laccase supplementation (21 hours after yeast inoculation) took place before the first addition of substrate (at 25 hours), improved cell viability and an increased ethanol titer of up to 32 g/L (51% of the theoretical) were found. Laccase treatment in SSCF processes reduces the inhibitory effect

  19. Primordial evolvability: Impasses and challenges.

    Science.gov (United States)

    Vasas, Vera; Fernando, Chrisantha; Szilágyi, András; Zachár, István; Santos, Mauro; Szathmáry, Eörs

    2015-09-21

    While it is generally agreed that some kind of replicating non-living compounds were the precursors of life, there is much debate over their possible chemical nature. Metabolism-first approaches propose that mutually catalytic sets of simple organic molecules could be capable of self-replication and rudimentary chemical evolution. In particular, the graded autocatalysis replication domain (GARD) model, depicting assemblies of amphiphilic molecules, has received considerable interest. The system propagates compositional information across generations and is suggested to be a target of natural selection. However, evolutionary simulations indicate that the system lacks selectability (i.e. selection has negligible effect on the equilibrium concentrations). We elaborate on the lessons learnt from the example of the GARD model and, more widely, on the issue of evolvability, and discuss the implications for similar metabolism-first scenarios. We found that simple incorporation-type chemistry based on non-covalent bonds, as assumed in GARD, is unlikely to result in alternative autocatalytic cycles when catalytic interactions are randomly distributed. An even more serious problem stems from the lognormal distribution of catalytic factors, causing inherent kinetic instability of such loops, due to the dominance of efficiently catalyzed components that fail to return catalytic aid. Accordingly, the dynamics of the GARD model is dominated by strongly catalytic, but not auto-catalytic, molecules. Without effective autocatalysis, stable hereditary propagation is not possible. Many repetitions and different scaling of the model come to no rescue. Despite all attempts to show the contrary, the GARD model is not evolvable, in contrast to reflexively autocatalytic networks, complemented by rare uncatalyzed reactions and compartmentation. The latter networks, resting on the creation and breakage of chemical bonds, can generate novel ('mutant') autocatalytic loops from a given set of

  20. Peripartum hysterectomy: an evolving picture.

    LENUS (Irish Health Repository)

    Turner, Michael J

    2012-02-01

    Peripartum hysterectomy (PH) is one of the obstetric catastrophes. Evidence is emerging that the role of PH in modern obstetrics is evolving. Improving management of postpartum hemorrhage and newer surgical techniques should decrease PH for uterine atony. Rising levels of repeat elective cesarean deliveries should decrease PH following uterine scar rupture in labor. Increasing cesarean rates, however, have led to an increase in the number of PHs for morbidly adherent placenta. In the case of uterine atony or rupture where PH is required, a subtotal PH is often sufficient. In the case of pathological placental localization involving the cervix, however, a total hysterectomy is required. Furthermore, the involvement of other pelvic structures may prospectively make the diagnosis difficult and the surgery challenging. If resources permit, PH for pathological placental localization merits a multidisciplinary approach. Despite advances in clinical practice, it is likely that peripartum hysterectomy will be more challenging for obstetricians in the future.

  1. Draft genome sequence of the D-Xylose-Fermenting yeast Spathaspora xylofermentans UFMG-HMD23.3

    Science.gov (United States)

    Here, we report the draft genome sequence of the yeast Spathaspora xylofermentans UFMG-HMD23.3 (CBMAI 1427=CBS 12681), a D-xylose fermenting yeast isolated from the Amazonian forest. The genome consists of 298 contigs, with a total size of 15.1 Mb, including the mitochondrial genome, and 5,948 predi...

  2. Conformational changes and ligand recognition of Escherichia coli D-xylose binding protein revealed

    DEFF Research Database (Denmark)

    Sooriyaarachchi, Sanjeewani; Ubhayasekera, Wimal; Park, Chankyu

    2010-01-01

    . The open liganded structure shows that xylose binds first to the C-terminal domain, with only very small conformational changes resulting. After a 34° closing motion, additional interactions are formed with the N-terminal domain; changes in this domain are larger and serve to make the structure more...

  3. Biosynthesis of D-xylulose 5-phosphate from D-xylose and polyphosphate through a minimized two-enzyme cascade.

    Science.gov (United States)

    Kim, Jae-Eung; Zhang, Y-H Percival

    2016-02-01

    Sugar phosphates cannot be produced easily by microbial fermentation because negatively-charged compounds cannot be secreted across intact cell membrane. D-xylulose 5-phosphate (Xu5P), a very expensive sugar phosphate, was synthesized from D-xylose and polyphosphate catalyzed by enzyme cascades in one pot. The synthetic enzymatic pathway comprised of xylose isomerase and xylulokinase was designed to produce Xu5P, along with a third enzyme, polyphosphate kinase, responsible for in site ATP regeneration. Due to the promiscuous activity of the ATP-based xylulokinase from a hyperthermophilic bacterium Thermotoga maritima on polyphosphate, the number of enzymes in the pathway was minimized to two without polyphosphate kinase. The reactions catalyzed by the two-enzyme and three-enzyme pathways were compared for Xu5P production, and the reaction conditions were optimized by examining effects of reaction temperature, enzyme ratio and substrate concentration. The optimized two-enzyme system produced 32 mM Xu5P from 50 mM xylose and polyphosphate after 36 h at 45°C. Biosynthesis of less costly Xu5P from D-xylose and polyphosphate could be highly feasible via this minimized two-enzyme pathway. © 2015 Wiley Periodicals, Inc.

  4. Separation of xylose and glucose using an integrated membrane system for enzymatic cofactor regeneration and downstream purification

    DEFF Research Database (Denmark)

    Morthensen, Sofie Thage; Sigurdardóttir, Sigyn Björk; Meyer, Anne S.

    2017-01-01

    Mixtures of xylose, glucose and pyruvate were fed to a membrane bioreactor equipped with a charged NF membrane (NTR 7450). Value-added products were obtained in the reactor via enzymatic cofactor-dependent catalysis of glucose to gluconic acid and pyruvate to lactic acid, respectively. The initial...

  5. Response surface methodology (RSM) to evaluate moisture effects on corn stover in recovering xylose by DEO hydrolysis

    Science.gov (United States)

    Rita C.L.B. Rodrigues; William R. Kenealy; Diane Dietrich; Thomas W. Jeffries

    2012-01-01

    Response surface methodology (RSM), based on a 22 full factorial design, evaluated the moisture effects in recovering xylose by diethyloxalate (DEO) hydrolysis. Experiments were carried out in laboratory reactors (10 mL glass ampoules) containing corn stover (0.5 g) properly ground. The ampoules were kept at 160 °C for 90 min. Both DEO...

  6. Effects of pH and substrate concentrations on dark fermentative biohydrogen production from xylose by extreme thermophilic mixed culture.

    Science.gov (United States)

    Qiu, Chunsheng; Shi, Puyu; Xiao, Shumin; Sun, Liping

    2017-01-01

    Biohydrogen is considered as one of the most promising energy alternatives considering the climate and energy crisis. The dark fermentative hydrogen production from xylose at extreme thermophilic condition (70 °C) using mixed culture was conducted in this study. The effects of initial pH values (ranged from 5.0 to 10.0) and substrate concentrations (ranged from 2.5 to 15.0 g/L) on the hydrogen production, substrate degradation and metabolite distributions were investigated using batch-mode operations. Results showed that initial substrate pH values in the neutral region (6.0-7.0) were beneficial for hydrogen production. The fermentation at initial pH 7.0 and 7.5 g/L xylose reached an optimal hydrogen yield of 1.29 mol-H2/mol-xyloseconsumed. Ethanol, butyrate, and propionate were the major liquid metabolites. The xylose biodegradation efficiency of the mixed culture decreased sharply at high initial culture pH values. The increase of xylose concentration resulted in the accumulation of propionate and an obvious decrease in the final pH value, as well as a low hydrogen yield. Polymerase chain reaction-denaturing gradient gel electrophoresis analysis indicated that hydrogen producing bacteria were enriched by repeated culture under extreme thermophilic conditions. Also, the mixed culture was dominated with bacterial species related to Clostridium and Thermoanaerobacterium.

  7. High production of fumaric acid from xylose by newly selected strain Rhizopus arrhizus RH 7-13-9#.

    Science.gov (United States)

    Liu, Huan; Wang, Weinan; Deng, Li; Wang, Fang; Tan, Tianwei

    2015-06-01

    Fumaric acid, as an important material for polymerization, is highly expected to be produced by fermentation of lignocellulosic biomass which is composed of cellulose, hemicellulose and lignin. Xylose as the main component of hemicellulose cannot be efficiently utilized by most of the common fermentation. In this study, a new strain Rhizopus arrhizus RH 7-13-9# was selected from the R. arrhizus RH 7-13 through a novel convenient and efficient selection method. Efficient production of fumaric acid (45.31 g/L) from xylose was achieved by the new strain, and the volumetric productivity was still 0.472 g/L h. Moreover, the conversion of xylose reached 73% which is close to the theoretic yield (77%). The production of fumaric acid was increased approximate by 172%, compared with the initial strain counterpart. These results indicated that xylose, as the main component of hemicellulose, has a promising application for the production of fumaric acid on an industrial-scale. Copyright © 2015 Elsevier Ltd. All rights reserved.

  8. Genetically engineered Escherichia coli FBR5: Part I. Comparison of high cell density bioreactors for enhanced ethanol production from xylose

    Science.gov (United States)

    Five reactor systems (free cell batch, free cell continuous, entrapped cell immobilized, adsorbed cell packed bed, and cell recycle membrane reactors) were compared for ethanol production from xylose employing Escherichia coli FBR5. In the free cell batch and free cell continuous reactors (continuo...

  9. Extreme evolved solar systems (EESS)

    Science.gov (United States)

    Gaensicke, Boris

    2017-08-01

    In just 20 years, we went from not knowing if the solar system is a fluke of Nature to realising that it is totally normal for stars to have planets. More remarkably, it is now clear that planet formation is a robust process, as rich multi-planet systems are found around stars more massive and less massive than the Sun. More recently, planetary systems have been identified in increasingly complex architectures, including circumbinary planets, wide binaries with planets orbiting one or both stellar components, and planets in triple stellar systems.We have also learned that many planetary systems will survive the evolution of their host stars into the white dwarf phase. Small bodies are scattered by unseen planets into the gravitational field of the white dwarfs, tidally disrupt, form dust discs, and eventually accrete onto the white dwarf, where they can be spectroscopically detected. HST/COS has played a critical role in the study these evolved planetary systems, demonstrating that overall the bulk composition of the debris is rocky and resembles in composition the inner the solar system, including evidence for water-rich planetesimals. Past observations of planetary systems at white dwarfs have focused on single stars with main-sequence progenitors of 1.5 to 2.5Msun. Here we propose to take the study of evolved planetary systems into the extremes of parameter ranges to answer questions such as: * How efficient is planet formation around 4-10Msun stars? * What are the metallicities of the progenitors of debris-accreting white dwarfs?* What is the fate of circumbinary planets?* Can star-planet interactions generate magnetic fields in the white dwarf host?

  10. Reduced Immunogenicity of Arabidopsis hgl1 Mutant N-Glycans Caused by Altered Accessibility of Xylose and core Fucose Epitopes*

    Science.gov (United States)

    Kaulfürst-Soboll, Heidi; Rips, Stephan; Koiwa, Hisashi; Kajiura, Hiroyuki; Fujiyama, Kazuhito; von Schaewen, Antje

    2011-01-01

    Arabidopsis N-glycosylation mutants with enhanced salt sensitivity show reduced immunoreactivity of complex N-glycans. Among them, hybrid glycosylation 1 (hgl1) alleles lacking Golgi α-mannosidase II are unique, because their glycoprotein N-glycans are hardly labeled by anti-complex glycan antibodies, even though they carry β1,2-xylose and α1,3-fucose epitopes. To dissect the contribution of xylose and core fucose residues to plant stress responses and immunogenic potential, we prepared Arabidopsis hgl1 xylT double and hgl1 fucTa fucTb triple mutants by crossing previously established T-DNA insertion lines and verified them by mass spectrometry analyses. Root growth assays revealed that hgl1 fucTa fucTb but not hgl1 xylT plants are more salt-sensitive than hgl1, hinting at the importance of core fucose modification and masking of xylose residues. Detailed immunoblot analyses with anti-β1,2-xylose and anti-α1,3-fucose rabbit immunoglobulin G antibodies as well as cross-reactive carbohydrate determinant-specific human immunoglobulin E antibodies (present in sera of allergy patients) showed that xylose-specific reactivity of hgl1 N-glycans is indeed reduced. Based on three-dimensional modeling of plant N-glycans, we propose that xylose residues are tilted by 30° because of untrimmed mannoses in hgl1 mutants. Glycosidase treatments of protein extracts restored immunoreactivity of hgl1 N-glycans supporting these models. Furthermore, among allergy patient sera, untrimmed mannoses persisting on the α1,6-arm of hgl1 N-glycans were inhibitory to immunoreaction with core fucoses to various degrees. In summary, incompletely trimmed glycoprotein N-glycans conformationally prevent xylose and, to lesser extent, core fucose accessibility. Thus, in addition to N-acetylglucosaminyltransferase I, Golgi α-mannosidase II emerges as a so far unrecognized target for lowering the immunogenic potential of plant-derived glycoproteins. PMID:21478158

  11. Reduced immunogenicity of Arabidopsis hgl1 mutant N-glycans caused by altered accessibility of xylose and core fucose epitopes.

    Science.gov (United States)

    Kaulfürst-Soboll, Heidi; Rips, Stephan; Koiwa, Hisashi; Kajiura, Hiroyuki; Fujiyama, Kazuhito; von Schaewen, Antje

    2011-07-01

    Arabidopsis N-glycosylation mutants with enhanced salt sensitivity show reduced immunoreactivity of complex N-glycans. Among them, hybrid glycosylation 1 (hgl1) alleles lacking Golgi α-mannosidase II are unique, because their glycoprotein N-glycans are hardly labeled by anti-complex glycan antibodies, even though they carry β1,2-xylose and α1,3-fucose epitopes. To dissect the contribution of xylose and core fucose residues to plant stress responses and immunogenic potential, we prepared Arabidopsis hgl1 xylT double and hgl1 fucTa fucTb triple mutants by crossing previously established T-DNA insertion lines and verified them by mass spectrometry analyses. Root growth assays revealed that hgl1 fucTa fucTb but not hgl1 xylT plants are more salt-sensitive than hgl1, hinting at the importance of core fucose modification and masking of xylose residues. Detailed immunoblot analyses with anti-β1,2-xylose and anti-α1,3-fucose rabbit immunoglobulin G antibodies as well as cross-reactive carbohydrate determinant-specific human immunoglobulin E antibodies (present in sera of allergy patients) showed that xylose-specific reactivity of hgl1 N-glycans is indeed reduced. Based on three-dimensional modeling of plant N-glycans, we propose that xylose residues are tilted by 30° because of untrimmed mannoses in hgl1 mutants. Glycosidase treatments of protein extracts restored immunoreactivity of hgl1 N-glycans supporting these models. Furthermore, among allergy patient sera, untrimmed mannoses persisting on the α1,6-arm of hgl1 N-glycans were inhibitory to immunoreaction with core fucoses to various degrees. In summary, incompletely trimmed glycoprotein N-glycans conformationally prevent xylose and, to lesser extent, core fucose accessibility. Thus, in addition to N-acetylglucosaminyltransferase I, Golgi α-mannosidase II emerges as a so far unrecognized target for lowering the immunogenic potential of plant-derived glycoproteins.

  12. Evaluation of fermentation kinetics of acid-treated corn cob hydrolysate for xylose fermentation in the presence of acetic acid by Pichia stipitis.

    Science.gov (United States)

    Kashid, Mohan; Ghosalkar, Anand

    2017-08-01

    The efficient utilization of lignocellulosic biomass for ethanol production depends on the fermentability of the biomass hydrolysate obtained after pretreatment. In this work we evaluated the kinetics of ethanol production from xylose using Pichia stipitis in acid-treated corn cob hydrolysate. Acetic acid is one of the main inhibitors in corn cob hydrolysate that negatively impacts kinetics of xylose fermentation by P. stipitis. Unstructured kinetic model has been formulated that describes cell mass growth and ethanol production as a function of xylose, oxygen, ethanol, and acetic acid concentration. Kinetic parameters were estimated under different operating conditions affecting xylose fermentation. This is the first report on kinetics of xylose fermentation by P. stipitis which includes inhibition of acetic acid on growth and product formation. In the presence of acetic acid in the hydrolysate, the model accurately predicted reduction in maximum specific growth rate (from 0.23 to 0.15 h -1 ) and increase in ethanol yield per unit biomass (from 3 to 6.2 gg -1 ), which was also observed during experimental trials. Presence of acetic acid in the fermentation led to significant reduction in the cell growth rate, reduction in xylose consumption and ethanol production rate. The developed model accurately described physiological state of P. stipitis during corn cob hydrolysate fermentation. Proposed model can be used to predict the influence of xylose, ethanol, oxygen, and acetic acid concentration on cell growth and ethanol productivity in industrial fermentation.

  13. Improved ethanol production from xylose in the presence of acetic acid by the overexpression of the HAA1 gene in Saccharomyces cerevisiae.

    Science.gov (United States)

    Sakihama, Yuri; Hasunuma, Tomohisa; Kondo, Akihiko

    2015-03-01

    The hydrolysis of lignocellulosic biomass liberates sugars, primarily glucose and xylose, which are subsequently converted to ethanol by microbial fermentation. The rapid and efficient fermentation of xylose by recombinant Saccharomyces cerevisiae strains is limited by weak acids generated during biomass pretreatment processes. In particular, acetic acid negatively affects cell growth, xylose fermentation rate, and ethanol production. The ability of S. cerevisiae to efficiently utilize xylose in the presence of acetic acid is an essential requirement for the cost-effective production of ethanol from lignocellulosic hydrolysates. Here, an acetic acid-responsive transcriptional activator, HAA1, was overexpressed in a recombinant xylose-fermenting S. cerevisiae strain to yield BY4741X/HAA1. This strain exhibited improved cell growth and ethanol production from xylose under aerobic and oxygen limited conditions, respectively, in the presence of acetic acid. The HAA1p regulon enhanced transcript levels in BY4741X/HAA1. The disruption of PHO13, a p-nitrophenylphosphatase gene, in BY4741X/HAA1 led to further improvement in both yeast growth and the ability to ferment xylose, indicating that HAA1 overexpression and PHO13 deletion act by different mechanisms to enhance ethanol production. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

  14. Presence of glucose, xylose, and glycerol fermenting bacteria in the deep biosphere of the former Homestake gold mine, South Dakota

    Directory of Open Access Journals (Sweden)

    Gurdeep eRastogi

    2013-02-01

    Full Text Available Eight fermentative bacterial strains were isolated from mixed enrichment cultures of a composite soil sample collected at 1.34 km depth from the former Homestake gold mine in Lead, SD, USA. Phylogenetic analysis of their 16S rRNA gene sequences revealed that these isolates were affiliated with the phylum Firmicutes belonging to genera Bacillus and Clostridium. Batch fermentation studies demonstrated that isolates had the ability to ferment glucose, xylose, or glycerol to industrially valuable products such as ethanol and 1,3-propanediol (PDO.Batch fermentation studies on selected seven bacterial strains demonstrated that these have the ability to ferment glucose, xylose, or glycerol to industrially valuable products such as ethanol and 1,3-propanediol (PDO. Ethanol was detected as the major fermentation end product in glucose-fermenting cultures at pH 10 with yields of 0.206 - 0.304 g of ethanol/g of glucose. While a xylose-fermenting strain yielded 0.189 g of ethanol/g of xylose and 0.585 g of acetic acid/g of xylose at the end of fermentation. At pH 7, glycerol-fermenting isolates produced PDO (0.323 - 0.458 g of PDO/g of glycerol and ethanol (0.284 - 0.350 g of ethanol/g of glycerol as major end products while acetic acid and succinic acid were identified as minor by-products in fermentation broths. These results suggest that the deep biosphere of the former Homestake gold mine harbors bacterial strains which could be used in bio-based production of ethanol and PDO.

  15. The effect of Pleurotus ostreatus arabinofuranosidase and its evolved variant in lignocellulosic biomasses conversion.

    Science.gov (United States)

    Marcolongo, Loredana; Ionata, Elena; La Cara, Francesco; Amore, Antonella; Giacobbe, Simona; Pepe, Olimpia; Faraco, Vincenza

    2014-11-01

    The fungal arabinofuranosidase from Pleurotus ostreatus PoAbf recombinantly expressed in Pichia pastoris rPoAbf and its evolved variant rPoAbf F435Y/Y446F were tested for their effectiveness to enhance the enzymatic saccharification of three lignocellulosic biomasses, namely Arundo donax, corn cobs and brewer's spent grains (BSG), after chemical or chemical-physical pretreatment. All the raw materials were subjected to an alkaline pretreatment by soaking in aqueous ammonia solution whilst the biomass from A. donax was also pretreated by steam explosion. The capability of the wild-type and mutant rPoAbf to increase the fermentable sugars recovery was assessed by using these enzymes in combination with different (hemi)cellulolytic activities. These enzymatic mixtures were either entirely of commercial origin or contained the cellulase from Streptomyces sp. G12 CelStrep recombinantly expressed in Escherichia coli in substitution to the commercial counterparts. The addition of the arabinofuranosidases from P. ostreatus improved the hydrolytic efficiency of the commercial enzymatic cocktails on all the pretreated biomasses. The best results were obtained using the rPoAbf evolved variant and are represented by increases of the xylose recovery up to 56.4%. These data clearly highlight the important role of the accessory hemicellulolytic activities to optimize the xylan bioconversion yields. Copyright © 2014 Elsevier Inc. All rights reserved.

  16. Discovery of mycangia and the associated xylose-fermenting yeasts in stag beetles (Coleoptera: Lucanidae)

    Science.gov (United States)

    Tanahashi, Masahiko; Kubota, Kôhei; Matsushita, Norihisa; Togashi, Katsumi

    2010-03-01

    Most wood-feeding insects need an association with microbes to utilize wood as food, and some have special organs to store and convey the microbes. We report here the discovery of the microbe-storage organ (mycangium) in stag beetles (Coleoptera: Lucanidae), which develop in decayed wood. The mycangium, which was discovered in the abdomen, is present in all adult females of 22 lucanid species examined in this study, but absent in adult males. By contrast, adult insects of both sexes of selected Passalidae, Geotrupidae, and Scarabaeidae, which are related to Lucanidae, lacked mycangia similar to those of the lucanid species. Yeast-like microbes were isolated from the mycangium of five lucanid species. DNA sequence analyses indicate that the microbes are closely related to the xylose-fermenting yeasts Pichia stipitis, Pichia segobiensis, or Pichia sp. known from the gut of a passalid species.

  17. Alcoholic fermentation of xylose by immobilized Pichia stipitis in a fixed-bed pulsed bioreactor

    Energy Technology Data Exchange (ETDEWEB)

    Sanroman, A.; Chamy, R.; Nunez, M.J.; Lema, J.M. (Santiago de Compostela Univ. (Spain). Dept. of Chemical Engineering)

    1994-01-01

    To enhance the productivity of the fermentation of xylose by Pichia stipitis, it is important to use bioreactors that (a) allow a high concentration of yeast (this can be achieved by using immobilised yeasts), (b) reduce the diffusional limitations resulting from dead volume (due mainly to the supplied and produced gas), and (c) diminish the effect of inhibition by ethanol. The process of immobilising P. stipitis in [kappa]-carrageenan was amended through the subsequent treatment of the bioparticles with a hardening agent (Al[sup 3+]). The variables examined were the cellular mass/gel mass ratio, the concentration of the hardening solution, and the contact time between the bioparticles and the hardening agent. (author)

  18. Galacturonic Acid Inhibits the Growth of Saccharomyces cerevisiae on Galactose, Xylose, and Arabinose

    Science.gov (United States)

    Huisjes, Eline H.; de Hulster, Erik; van Dam, Jan C.; Pronk, Jack T.

    2012-01-01

    The efficient fermentation of mixed substrates is essential for the microbial conversion of second-generation feedstocks, including pectin-rich waste streams such as citrus peel and sugar beet pulp. Galacturonic acid is a major constituent of hydrolysates of these pectin-rich materials. The yeast Saccharomyces cerevisiae, the main producer of bioethanol, cannot use this sugar acid. The impact of galacturonic acid on alcoholic fermentation by S. cerevisiae was investigated with anaerobic batch cultures grown on mixtures of glucose and galactose at various galacturonic acid concentrations and on a mixture of glucose, xylose, and arabinose. In cultures grown at pH 5.0, which is well above the pKa value of galacturonic acid (3.51), the addition of 10 g · liter−1 galacturonic acid did not affect galactose fermentation kinetics and growth. In cultures grown at pH 3.5, the addition of 10 g · liter−1 galacturonic acid did not significantly affect glucose consumption. However, at this lower pH, galacturonic acid completely inhibited growth on galactose and reduced galactose consumption rates by 87%. Additionally, it was shown that galacturonic acid strongly inhibits the fermentation of xylose and arabinose by the engineered pentose-fermenting S. cerevisiae strain IMS0010. The data indicate that inhibition occurs when nondissociated galacturonic acid is present extracellularly and corroborate the hypothesis that a combination of a decreased substrate uptake rate due to competitive inhibition on Gal2p, an increased energy requirement to maintain cellular homeostasis, and/or an accumulation of galacturonic acid 1-phosphate contributes to the inhibition. The role of galacturonic acid as an inhibitor of sugar fermentation should be considered in the design of yeast fermentation processes based on pectin-rich feedstocks. PMID:22582063

  19. CERN internal communication is evolving

    CERN Multimedia

    2016-01-01

    CERN news will now be regularly updated on the CERN People page (see here).      Dear readers, All over the world, communication is becoming increasingly instantaneous, with news published in real time on websites and social networks. In order to keep pace with these changes, CERN's internal communication is evolving too. From now on, you will be informed of what’s happening at CERN more often via the “CERN people” page, which will frequently be updated with news. The Bulletin is following this trend too: twice a month, we will compile the most important articles published on the CERN site, with a brand-new layout. You will receive an e-mail every two weeks as soon as this new form of the Bulletin is available. If you have interesting news or stories to share, tell us about them through the form at: https://communications.web.cern.ch/got-story-cern-website​. You can also find out about news from CERN in real time...

  20. Data for rapid ethanol production at elevated temperatures by engineered thermotolerant Kluyveromyces marxianus via the NADP(H-preferring xylose reductase–xylitol dehydrogenase pathway

    Directory of Open Access Journals (Sweden)

    Biao Zhang

    2015-12-01

    Full Text Available A thermo-tolerant NADP(H-preferring xylose pathway was constructed in Kluyveromyces marxianus for ethanol production with xylose at elevated temperatures (Zhang et al., 2015 [25]. Ethanol production yield and efficiency was enhanced by pathway engineering in the engineered strains. The constructed strain, YZJ088, has the ability to co-ferment glucose and xylose for ethanol and xylitol production, which is a critical step toward enabling economic biofuel production from lignocellulosic biomass. This study contains the fermentation results of strains using the metabolic pathway engineering procedure. The ethanol-producing abilities of various yeast strains under various conditions were compared, and strain YZJ088 showed the highest production and fastest productivity at elevated temperatures. The YZJ088 xylose fermentation results indicate that it fermented well with xylose at either low or high inoculum size. When fermented with an initial cell concentration of OD600=15 at 37 °C, YZJ088 consumed 200 g/L xylose and produced 60.07 g/L ethanol; when the initial cell concentration was OD600=1 at 37 °C, YZJ088 consumed 98.96 g/L xylose and produced 33.55 g/L ethanol with a productivity of 0.47 g/L/h. When fermented with 100 g/L xylose at 42 °C, YZJ088 produced 30.99 g/L ethanol with a productivity of 0.65 g/L/h, which was higher than that produced at 37 °C.

  1. Reduction of furan derivatives by overexpressing NADH-dependent Adh1 improves ethanol fermentation using xylose as sole carbon source with Saccharomyces cerevisiae harboring XR-XDH pathway.

    Science.gov (United States)

    Ishii, Jun; Yoshimura, Kazuya; Hasunuma, Tomohisa; Kondo, Akihiko

    2013-03-01

    Several alcohol dehydrogenase (ADH)-related genes have been identified as enzymes for reducing levels of toxic compounds, such as, furfural and/or 5-hydroxymethylfurfural (5-HMF), in hydrolysates of pretreated lignocelluloses. To date, overexpression of these ADH genes in yeast cells have aided ethanol production from glucose or glucose/xylose mixture in the presence of furfural or 5-HMF. However, the effects of these ADH isozymes on ethanol production from xylose as a sole carbon source remain uncertain. We showed that overexpression of mutant NADH-dependent ADH1 derived from TMB3000 strain in the recombinant Saccharomyces cerevisiae, into which xylose reductase (XR) and xylitol dehydrogenase (XDH) pathway of Pichia stipitis has been introduced, improved ethanol production from xylose as a sole carbon source in the presence of 5-HMF. Enhanced furan-reducing activity is able to regenerate NAD(+) to relieve redox imbalance, resulting in increased ethanol yield arising from decreased xylitol accumulation. In addition, we found that overexpression of wild-type ADH1 prevented the more severe inhibitory effects of furfural in xylose fermentation as well as overexpression of TMB3000-derived mutant. After 120 h of fermentation, the recombinant strains overexpressing wild-type and mutant ADH1 completely consumed 50 g/L xylose in the presence of 40 mM furfural and most efficiently produced ethanol (15.70 g/L and 15.24 g/L) when compared with any other test conditions. This is the first report describing the improvement of ethanol production from xylose as the sole carbon source in the presence of furan derivatives with xylose-utilizing recombinant yeast strains via the overexpression of ADH-related genes.

  2. Effects of acid impregnated steam explosion process on xylose recovery and enzymatic conversion of cellulose in corncob.

    Science.gov (United States)

    Fan, Xiaoguang; Cheng, Gang; Zhang, Hongjia; Li, Menghua; Wang, Shizeng; Yuan, Qipeng

    2014-12-19

    Corncob residue is a cellulose-rich byproduct obtained from industrial xylose production via dilute acid hydrolysis processes. Enzymatic hydrolysis of cellulose in acid hydrolysis residue of corncob (AHRC) is often less efficient without further pretreatment. In this work, the process characteristics of acid impregnated steam explosion were studied in conjunction with a dilute acid process, and their effects on physiochemical changes and enzymatic saccharification of corncob residue were compared. With the acid impregnated steam explosion process, both higher xylose recovery and higher cellulose conversion were obtained. The maximum conversion of cellulose in acid impregnated steam explosion residue of corncob (ASERC) reached 85.3%, which was 1.6 times higher than that of AHRC. Biomass compositional analysis showed similar cellulose and lignin content in ASERC and AHRC. XRD analysis demonstrated comparable crystallinity of ASERC and AHRC. The improved enzymatic hydrolysis efficiency was attributed to higher porosity in ASERC, measured by mercury porosimetry. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. The intra- and extracellular proteome of Aspergillus niger growing on defined medium with xylose or maltose as carbon substrate

    Science.gov (United States)

    2010-01-01

    Background The filamentous fungus Aspergillus niger is well-known as a producer of primary metabolites and extracellular proteins. For example, glucoamylase is the most efficiently secreted protein of Aspergillus niger, thus the homologous glucoamylase (glaA) promoter as well as the glaA signal sequence are widely used for heterologous protein production. Xylose is known to strongly repress glaA expression while maltose is a potent inducer of glaA promoter controlled genes. For a more profound understanding of A. niger physiology, a comprehensive analysis of the intra- and extracellular proteome of Aspergillus niger AB1.13 growing on defined medium with xylose or maltose as carbon substrate was carried out using 2-D gel electrophoresis/Maldi-ToF and nano-HPLC MS/MS. Results The intracellular proteome of A. niger growing either on xylose or maltose in well-aerated controlled bioreactor cultures revealed striking similarities. In both cultures the most abundant intracellular protein was the TCA cycle enzyme malate-dehydrogenase. Moreover, the glycolytic enzymes fructose-bis-phosphate aldolase and glyceraldehyde-3-phosphate-dehydrogenase and the flavohemoglobin FhbA were identified as major proteins in both cultures. On the other hand, enzymes involved in the removal of reactive oxygen species, such as superoxide dismutase and peroxiredoxin, were present at elevated levels in the culture growing on maltose but only in minor amounts in the xylose culture. The composition of the extracellular proteome differed considerably depending on the carbon substrate. In the secretome of the xylose-grown culture, a variety of plant cell wall degrading enzymes were identified, mostly under the control of the xylanolytic transcriptional activator XlnR, with xylanase B and ferulic acid esterase as the most abundant ones. The secretome of the maltose-grown culture did not contain xylanolytic enzymes, instead high levels of catalases were found and glucoamylase (multiple spots) was

  4. Overexpression, crystallization and preliminary X-ray crystallographic analysis of a putative xylose isomerase from Bacteroides thetaiotaomicron.

    Science.gov (United States)

    Cho, Jea-Won; Han, Byeong-Gu; Park, Sang Youn; Kim, Seung Jun; Kim, Myoung-Dong; Lee, Byung Il

    2013-10-01

    Bacteroides thetaiotaomicron BT0793, a putative xylose isomerase, was overexpressed in Escherichia coli, purified and crystallized using polyethylene glycol monomethyl ether 550 as the precipitant. X-ray diffraction data were collected to 2.10 Å resolution at 100 K using synchrotron X-rays. The crystal was found to belong to space group P1, with unit-cell parameters a=96.3, b=101.7, c=108.3 Å, α=82.8, β=68.2, γ=83.0°. The asymmetric unit contained eight subunits of xylose isomerase with a crystal volume per protein weight (VM) of 2.38 Å3 Da(-1) and a solvent content of 48.3%.

  5. Spathaspora arborariae sp. nov., a d-xylose-fermenting yeast species isolated from rotting wood in Brazil.

    Science.gov (United States)

    Cadete, Raquel M; Santos, Renata O; Melo, Monaliza A; Mouro, Adriane; Gonçalves, Davi L; Stambuk, Boris U; Gomes, Fátima C O; Lachance, Marc-André; Rosa, Carlos A

    2009-12-01

    Four strains of a new yeast species were isolated from rotting wood from two sites in an Atlantic Rain Forest and a Cerrado ecosystem in Brazil. The analysis of the sequences of the D1/D2 domains of the large-subunit rRNA gene showed that this species belongs to the Spathaspora clade. The new species ferments D-xylose efficiently and is related to Candida jeffriesii and Spathaspora passalidarum, both of which also ferment D-xylose. Similar to S. passalidarum, the new species produces unconjugated asci with a single greatly elongated ascospore with curved ends. The type strain of Spathaspora arborariae sp. nov. is UFMG-HM19.1A(T) (=CBS11463(T)=NRRL Y-48658(T)).

  6. The level of glucose-6-phosphate dehydrogenase activity strongly influences xylose fermentation and inhibitor sensitivity in recombinant Saccharomyces cerevisiae strains

    DEFF Research Database (Denmark)

    Jeppsson, M.; Johansson, B.; Jensen, Peter Ruhdal

    2003-01-01

    than the strain with wild-type G6PDH-activity, which suggested that the availability of intracellular NADPH correlated with tolerance towards lignocellulose-derived inhibitors. Low G6PDH-activity strains were also more sensitive to H2O2 than the control strain TMB3001....... production levels of G6PDH on xylose fermentation. We used a synthetic promoter library and the copper-regulated CUP1 promoter to generate G6PDH-activities between 0% and 179% of the wildtype level. G6PDH-activities of 1% and 6% of the wild-type level resulted in 2.8- and 5.1-fold increase in specific xylose...

  7. The intra- and extracellular proteome of Aspergillus niger growing on defined medium with xylose or maltose as carbon substrate

    Directory of Open Access Journals (Sweden)

    Wissing Josef

    2010-04-01

    Full Text Available Abstract Background The filamentous fungus Aspergillus niger is well-known as a producer of primary metabolites and extracellular proteins. For example, glucoamylase is the most efficiently secreted protein of Aspergillus niger, thus the homologous glucoamylase (glaA promoter as well as the glaA signal sequence are widely used for heterologous protein production. Xylose is known to strongly repress glaA expression while maltose is a potent inducer of glaA promoter controlled genes. For a more profound understanding of A. niger physiology, a comprehensive analysis of the intra- and extracellular proteome of Aspergillus niger AB1.13 growing on defined medium with xylose or maltose as carbon substrate was carried out using 2-D gel electrophoresis/Maldi-ToF and nano-HPLC MS/MS. Results The intracellular proteome of A. niger growing either on xylose or maltose in well-aerated controlled bioreactor cultures revealed striking similarities. In both cultures the most abundant intracellular protein was the TCA cycle enzyme malate-dehydrogenase. Moreover, the glycolytic enzymes fructose-bis-phosphate aldolase and glyceraldehyde-3-phosphate-dehydrogenase and the flavohemoglobin FhbA were identified as major proteins in both cultures. On the other hand, enzymes involved in the removal of reactive oxygen species, such as superoxide dismutase and peroxiredoxin, were present at elevated levels in the culture growing on maltose but only in minor amounts in the xylose culture. The composition of the extracellular proteome differed considerably depending on the carbon substrate. In the secretome of the xylose-grown culture, a variety of plant cell wall degrading enzymes were identified, mostly under the control of the xylanolytic transcriptional activator XlnR, with xylanase B and ferulic acid esterase as the most abundant ones. The secretome of the maltose-grown culture did not contain xylanolytic enzymes, instead high levels of catalases were found and

  8. Coutilization of D-Glucose, D-Xylose, and L-Arabinose in Saccharomyces cerevisiae by Coexpressing the Metabolic Pathways and Evolutionary Engineering

    Directory of Open Access Journals (Sweden)

    Chengqiang Wang

    2017-01-01

    Full Text Available Efficient and cost-effective fuel ethanol production from lignocellulosic materials requires simultaneous cofermentation of all hydrolyzed sugars, mainly including D-glucose, D-xylose, and L-arabinose. Saccharomyces cerevisiae is a traditional D-glucose fermenting strain and could utilize D-xylose and L-arabinose after introducing the initial metabolic pathways. The efficiency and simultaneous coutilization of the two pentoses and D-glucose for ethanol production in S. cerevisiae still need to be optimized. Previously, we constructed an L-arabinose-utilizing S. cerevisiae BSW3AP. In this study, we further introduced the XI and XR-XDH metabolic pathways of D-xylose into BSW3AP to obtain D-glucose, D-xylose, and L-arabinose cofermenting strain. Benefits of evolutionary engineering: the resulting strain BSW4XA3 displayed a simultaneous coutilization of D-xylose and L-arabinose with similar consumption rates, and the D-glucose metabolic capacity was not decreased. After 120 h of fermentation on mixed D-glucose, D-xylose, and L-arabinose, BSW4XA3 consumed 24% more amounts of pentoses and the ethanol yield of mixed sugars was increased by 30% than that of BSW3AP. The resulting strain BSW4XA3 was a useful chassis for further enhancing the coutilization efficiency of mixed sugars for bioethanol production.

  9. A novel method to prepare L-Arabinose from xylose mother liquor by yeast-mediated biopurification

    Directory of Open Access Journals (Sweden)

    Lin Shuangjun

    2011-06-01

    Full Text Available Abstract Background L-arabinose is an important intermediate for anti-virus drug synthesis and has also been used in food additives for diets-controlling in recent years. Commercial production of L-arabinose is a complex progress consisting of acid hydrolysis of gum arabic, followed by multiple procedures of purification, thus making high production cost. Therefore, there is a biotechnological and commercial interest in the development of new cost-effective and high-performance methods for obtaining high purity grade L-arabinose. Results An alternative, economical method for purifying L-arabinose from xylose mother liquor was developed in this study. After screening 306 yeast strains, a strain of Pichia anomala Y161 was selected as it could effectively metabolize other sugars but not L-arabinose. Fermentation in a medium containing xylose mother liquor permitted enrichment of L-arabinose by a significant depletion of other sugars. Biochemical analysis of this yeast strain confirmed that its poor capacity for utilizing L-arabinose was due to low activities of the enzymes required for the metabolism of this sugar. Response surface methodology was employed for optimization the fermentation conditions in shake flask cultures. The optimum conditions were: 75 h fermentation time, at 32.5°C, in a medium containing 21% (v/v xylose mother liquor. Under these conditions, the highest purity of L-arabinose reached was 86.1% of total sugar, facilitating recovery of white crystalline L-arabinose from the fermentation medium by simple methods. Conclusion Yeast-mediated biopurification provides a dynamic method to prepare high purity of L-arabinose from the feedstock solution xylose mother liqour, with cost-effective and high-performance properties.

  10. Co-utilization of L-arabinose and D-xylose by laboratory and industrial Saccharomyces cerevisiae strains

    OpenAIRE

    Boles Eckhard; Hahn-Hägerdal Bärbel; Wiedemann Beate; Karhumaa Kaisa; Gorwa-Grauslund Marie-F

    2006-01-01

    Abstract Background Fermentation of lignocellulosic biomass is an attractive alternative for the production of bioethanol. Traditionally, the yeast Saccharomyces cerevisiae is used in industrial ethanol fermentations. However, S. cerevisiae is naturally not able to ferment the pentose sugars D-xylose and L-arabinose, which are present in high amounts in lignocellulosic raw materials. Results We describe the engineering of laboratory and industrial S. cerevisiae strains to co-ferment the pento...

  11. Direct ethanol production from glucose, xylose and sugarcane bagasse by the corn endophytic fungi Fusarium verticillioides and Acremonium zeae.

    Science.gov (United States)

    de Almeida, Maíra N; Guimarães, Valéria M; Falkoski, Daniel L; Visser, Evan M; Siqueira, Germano A; Milagres, Adriane M F; de Rezende, Sebastião T

    2013-10-10

    Production of ethanol with two corn endophytic fungi, Fusarium verticillioides and Acremonium zeae, was studied. The yield of ethanol from glucose, xylose and a mixture of both sugars were 0.47, 0.46 and 0.50g/g ethanol/sugar for F. verticillioides and 0.37, 0.39 and 0.48g/g ethanol/sugar for A. zeae. Both fungi were able to co-ferment glucose and xylose. Ethanol production from 40g/L of pre-treated sugarcane bagasse was 4.6 and 3.9g/L for F. verticillioides and A. zeae, respectively, yielding 0.31g/g of ethanol per consumed sugar. Both fungi studied were capable of co-fermenting glucose and xylose at high yields. Moreover, they were able to produce ethanol directly from lignocellulosic biomass, demonstrating to be suitable microorganisms for consolidated bioprocessing. Copyright © 2013 Elsevier B.V. All rights reserved.

  12. Effects of Inhibitors on the Transcriptional Profiling of Gluconobater oxydans NL71 Genes after Biooxidation of Xylose into Xylonate

    Directory of Open Access Journals (Sweden)

    Yong Xu

    2017-04-01

    Full Text Available D-Xylonic acid belongs to the top 30 biomass-based platform chemicals and represents a promising application of xylose. Until today, Gluconobacter oxydans NL71 is the most efficient microbe capable of fermenting xylose into xylonate. However, its growth is seriously inhibited when concentrated lignocellulosic hydrolysates are used as substrates due to the presence of various degraded compounds formed during biomass pretreatment. Three critical lignocellulosic inhibitors were thereby identified, i.e., formic acid, furfural, and 4-hydroxybenzaldehyde. As microbe fermentation is mostly regulated at the genome level, four groups of cell transcriptomes were obtained for a comparative investigation by RNA sequencing of a control sample with samples treated separately with the above-mentioned inhibitors. The digital gene expression profiles screened 572, 714 genes, and 408 DEGs was obtained by the comparisons among four transcriptomes. A number of genes related to the different functional groups showed characteristic expression patterns induced by three inhibitors, in which 19 genes were further tested and confirmed by qRT-PCR. We extrapolated many differentially expressed genes that could explain the cellular responses to the inhibitory effects. We provide results that enable the scientific community to better define the molecular processes involved in the microbes' responses to lignocellulosic inhibitors during the cellular biooxidation of xylose into xylonic acid.

  13. Shotgun proteomic monitoring of Clostridium acetobutylicum during stationary phase of butanol fermentation using xylose and comparison with the exponential phase

    Energy Technology Data Exchange (ETDEWEB)

    Sivagnanam, Kumaran [McGill University, Montreal, Quebec; Raghavan, Vijaya G. S. [McGill University, Montreal, Quebec; Shah, Manesh B [ORNL; Hettich, Robert {Bob} L [ORNL; Verberkmoes, Nathan C [ORNL; Lefsrud, Mark G [McGill University, Montreal, Quebec

    2012-01-01

    Economically viable production of solvents through acetone butanol ethanol (ABE) fermentation requires a detailed understanding of Clostridium acetobutylicum. This study focuses on the proteomic profiling of C. acetobutylicum ATCC 824 from the stationary phase of ABE fermentation using xylose and compares with the exponential growth by shotgun proteomics approach. Comparative proteomic analysis revealed 22.9% of the C. acetobutylicum genome and 18.6% was found to be common in both exponential and stationary phases. The proteomic profile of C. acetobutylicum changed during the ABE fermentation such that 17 proteins were significantly differentially expressed between the two phases. Specifically, the expression of five proteins namely, CAC2873, CAP0164, CAP0165, CAC3298, and CAC1742 involved in the solvent production pathway were found to be significantly lower in the stationary phase compared to the exponential growth. Similarly, the expression of fucose isomerase (CAC2610), xylulose kinase (CAC2612), and a putative uncharacterized protein (CAC2611) involved in the xylose utilization pathway were also significantly lower in the stationary phase. These findings provide an insight into the metabolic behavior of C. acetobutylicum between different phases of ABE fermentation using xylose.

  14. Catalytic conversion of xylose and corn stalk into furfural over carbon solid acid catalyst in γ-valerolactone.

    Science.gov (United States)

    Zhang, Tingwei; Li, Wenzhi; Xu, Zhiping; Liu, Qiyu; Ma, Qiaozhi; Jameel, Hasan; Chang, Hou-min; Ma, Longlong

    2016-06-01

    A novel carbon solid acid catalyst was synthesized by the sulfonation of carbonaceous material which was prepared by carbonization of sucrose using 4-BDS as a sulfonating agent. TEM, N2 adsorption-desorption, elemental analysis, XPS and FT-IR were used to characterize the catalyst. Then, the catalyst was applied for the conversion of xylose and corn stalk into furfural in GVL. The influence of the reaction time, temperature and dosage of catalyst on xylose dehydration were also investigated. The Brønsted acid catalyst exhibited high activity in the dehydration of xylose, with a high furfural yield of 78.5% at 170°C in 30min. What's more, a 60.6% furfural yield from corn stalk was achieved in 100min at 200°C. The recyclability of the sulfonated carbon catalyst was perfect, and it could be reused for 5times without the loss of furfural yields. Copyright © 2016 Elsevier Ltd. All rights reserved.

  15. Engineering of ethanolic E. coli with the Vitreoscilla hemoglobin gene enhances ethanol production from both glucose and xylose.

    Science.gov (United States)

    Sanny, Tony; Arnaldos, Marina; Kunkel, Stephanie A; Pagilla, Krishna R; Stark, Benjamin C

    2010-11-01

    Escherichia coli strain FBR5, which has been engineered to direct fermentation of sugars to ethanol, was further engineered, using three different constructs, to contain and express the Vitreoscilla hemoglobin gene (vgb). The three resulting strains expressed Vitreoscilla hemoglobin (VHb) at various levels, and the production of ethanol was inversely proportional to the VHb level. High levels of VHb were correlated with an inhibition of ethanol production; however, the strain (TS3) with the lowest VHb expression (approximately the normal induced level in Vitreoscilla) produced, under microaerobic conditions in shake flasks, more ethanol than the parental strain (FBR5) with glucose, xylose, or corn stover hydrolysate as the predominant carbon source. Ethanol production was dependent on growth conditions, but increases were as high as 30%, 119%, and 59% for glucose, xylose, and corn stover hydrolysate, respectively. Only in the case of glucose, however, was the theoretical yield of ethanol by TS3 greater than that achieved by others with FBR5 grown under more closely controlled conditions. TS3 had no advantage over FBR5 regarding ethanol production from arabinose. In 2 L fermentors, TS3 produced about 10% and 15% more ethanol than FBR5 for growth on glucose and xylose, respectively. The results suggest that engineering of microorganisms with vgb/VHb could be of significant use in enhancing biological production of ethanol.

  16. DNA evolved to minimize frameshift mutations

    OpenAIRE

    Agoni, Valentina

    2013-01-01

    Point mutations can surely be dangerous but what is worst than to lose the reading frame?! Does DNA evolved a strategy to try to limit frameshift mutations?! Here we investigate if DNA sequences effectively evolved a system to minimize frameshift mutations analyzing the transcripts of proteins with high molecular weights.

  17. Xylose Migration During Tandem Mass Spectrometry of N-Linked Glycans

    Science.gov (United States)

    Hecht, Elizabeth S.; Loziuk, Philip L.; Muddiman, David C.

    2017-04-01

    Understanding the rearrangement of gas-phase ions via tandem mass spectrometry is critical to improving manual and automated interpretation of complex datasets. N-glycan analysis may be carried out under collision induced (CID) or higher energy collision dissociation (HCD), which favors cleavage at the glycosidic bond. However, fucose migration has been observed in tandem MS, leading to the formation of new bonds over four saccharide units away. In the following work, we report the second instance of saccharide migration ever to occur for N-glycans. Using horseradish peroxidase as a standard, the beta-1,2 xylose was observed to migrate from a hexose to a glucosamine residue on the (Xyl)Man3GlcNac2 glycan. This investigation was followed up in a complex N-linked glycan mixture derived from stem differentiating xylem tissue, and the rearranged product ion was observed for 75% of the glycans. Rearrangement was not favored in isomeric glycans with a core or antennae fucose and unobserved in glycans predicted to have a permanent core-fucose modification. As the first empirical observation of this rearrangement, this work warrants dissemination so it may be searched in de novo sequencing glycan workflows.

  18. Rapid differentiation of Candida dubliniensis from Candida albicans by early D-xylose assimilation.

    Science.gov (United States)

    Ellepola, A N B; Khan, Z U

    2012-01-01

    To determine if D-xylose (XYL) and/or α-methyl-D-glucoside (MDG) assimilation can be used reliably as a rapid test to differentiate Candida dubliniensis from Candida albicans at an earlier time point such as 2 h after inoculation. Thirty isolates of C. albicans and C. dubliniensis recovered from anatomical sites and clinical specimens were used. Isolates were inoculated into the API 20C AUX yeast identification system, and incubated at 30°C. XYL and MDG assimilations were read at 2-hour intervals beginning 2 h after the initial inoculation and up to 24 h of incubation; thereafter, results were read after 48 and 72 h. Twenty-nine (97%) C. albicans isolates had assimilated XYL at 16 h and, by 24 h, all isolates were positive for XYL assimilation. None of the C. dubliniensis isolates assimilated XYL. The MDG assimilation revealed that 24, 40, 92 and 100% of C. albicans isolates became positive after 16, 24, 48 and 72 h of incubation, respectively, whereas only 3% of C. dubliniensis isolates assimilated MDG after 72 h. The findings showed that it is possible to rapidly differentiate C. albicans from C. dubliniensis isolates using the API 20C AUX carbohydrate assimilation kits after 16 h of incubation at 30°C based on the XYL assimilation. Copyright © 2012 S. Karger AG, Basel.

  19. Production of medium-chain-length polyhydroxyalkanoates by sequential feeding of xylose and octanoic acid in engineered Pseudomonas putida KT2440

    Directory of Open Access Journals (Sweden)

    Le Meur Sylvaine

    2012-08-01

    Full Text Available Abstract Background Pseudomonas putida KT2440 is able to synthesize large amounts of medium-chain-length polyhydroxyalkanoates (mcl-PHAs. To reduce the substrate cost, which represents nearly 50% of the total PHA production cost, xylose, a hemicellulose derivate, was tested as the growth carbon source in an engineered P. putida KT2440 strain. Results The genes encoding xylose isomerase (XylA and xylulokinase (XylB from Escherichia coli W3110 were introduced into P. putida KT2440. The recombinant KT2440 exhibited a XylA activity of 1.47 U and a XylB activity of 0.97 U when grown on a defined medium supplemented with xylose. The cells reached a maximum specific growth rate of 0.24 h-1 and a final cell dry weight (CDW of 2.5 g L-1 with a maximal yield of 0.5 g CDW g-1 xylose. Since no mcl-PHA was accumulated from xylose, mcl-PHA production can be controlled by the addition of fatty acids leading to tailor-made PHA compositions. Sequential feeding strategy was applied using xylose as the growth substrate and octanoic acid as the precursor for mcl-PHA production. In this way, up to 20% w w-1 of mcl-PHA was obtained. A yield of 0.37 g mcl-PHA per g octanoic acid was achieved under the employed conditions. Conclusions Sequential feeding of relatively cheap carbohydrates and expensive fatty acids is a practical way to achieve more cost-effective mcl-PHA production. This study is the first reported attempt to produce mcl-PHA by using xylose as the growth substrate. Further process optimizations to achieve higher cell density and higher productivity of mcl-PHA should be investigated. These scientific exercises will undoubtedly contribute to the economic feasibility of mcl-PHA production from renewable feedstock.

  20. Conversion of an inactive xylose isomerase into a functional enzyme by co-expression of GroEL-GroES chaperonins in Saccharomyces cerevisiae.

    Science.gov (United States)

    Temer, Beatriz; Dos Santos, Leandro Vieira; Negri, Victor Augusti; Galhardo, Juliana Pimentel; Magalhães, Pedro Henrique Mello; José, Juliana; Marschalk, Cidnei; Corrêa, Thamy Lívia Ribeiro; Carazzolle, Marcelo Falsarella; Pereira, Gonçalo Amarante Guimarães

    2017-09-09

    Second-generation ethanol production is a clean bioenergy source with potential to mitigate fossil fuel emissions. The engineering of Saccharomyces cerevisiae for xylose utilization is an essential step towards the production of this biofuel. Though xylose isomerase (XI) is the key enzyme for xylose conversion, almost half of the XI genes are not functional when expressed in S. cerevisiae. To date, protein misfolding is the most plausible hypothesis to explain this phenomenon. This study demonstrated that XI from the bacterium Propionibacterium acidipropionici becomes functional in S. cerevisiae when co-expressed with GroEL-GroES chaperonin complex from Escherichia coli. The developed strain BTY34, harboring the chaperonin complex, is able to efficiently convert xylose to ethanol with a yield of 0.44 g ethanol/g xylose. Furthermore, the BTY34 strain presents a xylose consumption rate similar to those observed for strains carrying the widely used XI from the fungus Orpinomyces sp. In addition, the tetrameric XI structure from P. acidipropionici showed an elevated number of hydrophobic amino acid residues on the surface of protein when compared to XI commonly expressed in S. cerevisiae. Based on our results, we elaborate an extensive discussion concerning the uncertainties that surround heterologous expression of xylose isomerases in S. cerevisiae. Probably, a correct folding promoted by GroEL-GroES could solve some issues regarding a limited or absent XI activity in S. cerevisiae. The strains developed in this work have promising industrial characteristics, and the designed strategy could be an interesting approach to overcome the non-functionality of bacterial protein expression in yeasts.

  1. WSC-07: Evolving the Web Services Challenge

    NARCIS (Netherlands)

    Blake, M. Brian; Cheung, William K.W.; Jaeger, Michael C.; Wombacher, Andreas

    Service-oriented architecture (SOA) is an evolving architectural paradigm where businesses can expose their capabilities as modular, network-accessible software services. By decomposing capabilities into modular services, organizations can share their offerings at multiple levels of granularity

  2. Satcom access in the evolved packet core

    NARCIS (Netherlands)

    Cano, M.D.; Norp, A.H.J.; Popova, M.P.

    2012-01-01

    Satellite communications (Satcom) networks are increasingly integrating with terrestrial communications networks, namely Next Generation Networks (NGN). In the area of NGN the Evolved Packet Core (EPC) is a new network architecture that can support multiple access technologies. When Satcom is

  3. Acquisition: Acquisition of the Evolved SEASPARROW Missile

    National Research Council Canada - National Science Library

    2002-01-01

    .... The Evolved SEASPARROW Missile, a Navy Acquisition Category II program, is an improved version of the RIM-7P SEASPARROW missile that will intercept high-speed maneuvering, anti-ship cruise missiles...

  4. Cyberspace Operations: Influence Upon Evolving War Theory

    Science.gov (United States)

    2011-03-18

    St ra te gy R es ea rc h Pr oj ec t CYBERSPACE OPERATIONS: INFLUENCE UPON EVOLVING WAR THEORY BY COLONEL KRISTIN BAKER United States...DATES COVERED (From - To) 4. TITLE AND SUBTITLE Cyberspace Operations: Influence Upon Evolving War Theory 5a. CONTRACT NUMBER... Leadership 8. PERFORMING ORGANIZATION REPORT NUMBER 9. SPONSORING / MONITORING AGENCY NAME(S) AND ADDRESS(ES) 10. SPONSOR/MONITOR’S ACRONYM(S

  5. Evolving effective incremental SAT solvers with GP

    OpenAIRE

    Bader, Mohamed; Poli, R.

    2008-01-01

    Hyper-Heuristics could simply be defined as heuristics to choose other heuristics, and it is a way of combining existing heuristics to generate new ones. In a Hyper-Heuristic framework, the framework is used for evolving effective incremental (Inc*) solvers for SAT. We test the evolved heuristics (IncHH) against other known local search heuristics on a variety of benchmark SAT problems.

  6. Co-fermentation of a mixture of glucose and xylose to fumaric acid by Rhizopus arrhizus RH 7-13-9.

    Science.gov (United States)

    Liu, Huan; Hu, Huirong; Jin, Yuhan; Yue, Xuemin; Deng, Li; Wang, Fang; Tan, Tianwei

    2017-06-01

    Lignocellulose is the most abundant biomass, composed of cellulose, hemicellulose and lignin. It can be converted into glucose and xylose, which could be utilized as carbon source to produce fumaric acid. But glucose and xylose were commonly used separately to produce fumaric acid, while the co-fermentation of glucose and xylose process was not studied so far. In this work, the co-fermentation process was researched through a new strain R. arrhizus RH 7-13-9# isolated from high concentration xylose. It was firstly proven to utilize glucose efficiently and 37.52g/L fumaric acid was obtained from 80g/L glucose. Furthermore, the effect of different ratios of glucose/xylose and carbon/nitrogen in the co-fermentation process was investigated and the best ratios were 75/25 (w/w) and 800/1 (w/w), where the yield of fumaric acid reached 46.78g/L. Copyright © 2017 Elsevier Ltd. All rights reserved.

  7. Evolvability Search: Directly Selecting for Evolvability in order to Study and Produce It

    DEFF Research Database (Denmark)

    Mengistu, Henok; Lehman, Joel Anthony; Clune, Jeff

    2016-01-01

    One hallmark of natural organisms is their significant evolvability, i.e.,their increased potential for further evolution. However, reproducing such evolvability in artificial evolution remains a challenge, which both reduces the performance of evolutionary algorithms and inhibits the study...... of evolvable digital phenotypes. Although some types of selection in evolutionary computation indirectly encourage evolvability, one unexplored possibility is to directly select for evolvability. To do so, we estimate an individual's future potential for diversity by calculating the behavioral diversity of its...... immediate offspring, and select organisms with increased offspring variation. While the technique is computationally expensive, we hypothesized that direct selection would better encourage evolvability than indirect methods. Experiments in two evolutionary robotics domains confirm this hypothesis: in both...

  8. Uridine 5'-diphosphate-xylose: anthocyanidin 3-O-glucose-xylosyltransferase from petals of Matthiola incana R.Br.

    Science.gov (United States)

    Teusch, M

    1986-12-01

    Petals of genetically defined lines of Matthiola incana R.Br. contain a glycosyltransferase which catalyzes the transfer of the xylosyl moiety of uridine 5'-diphosphate-xylose to the glucose of cyanidin 3-glucoside. The enzyme also uses 3-glucosides of pelargonidin and delphinidin, cyanidin 3-(p-coumaroyl)-glucoside and 3-(caffeoyl)-glucoside as substrates. The xylosyltransferase exhibits a pH optimum of 6.5. The enzyme activity depends on the stage of bud and flower development. Accumulation of cyanidin 3-glucoside during flower development is correlated with xylosyltransferase activity.

  9. Evolved atmospheric entry corridor with safety factor

    Science.gov (United States)

    Liang, Zixuan; Ren, Zhang; Li, Qingdong

    2018-02-01

    Atmospheric entry corridors are established in previous research based on the equilibrium glide condition which assumes the flight-path angle to be zero. To get a better understanding of the highly constrained entry flight, an evolved entry corridor that considers the exact flight-path angle is developed in this study. Firstly, the conventional corridor in the altitude vs. velocity plane is extended into a three-dimensional one in the space of altitude, velocity, and flight-path angle. The three-dimensional corridor is generated by a series of constraint boxes. Then, based on a simple mapping method, an evolved two-dimensional entry corridor with safety factor is obtained. The safety factor is defined to describe the flexibility of the flight-path angle for a state within the corridor. Finally, the evolved entry corridor is simulated for the Space Shuttle and the Common Aero Vehicle (CAV) to demonstrate the effectiveness of the corridor generation approach. Compared with the conventional corridor, the evolved corridor is much wider and provides additional information. Therefore, the evolved corridor would benefit more to the entry trajectory design and analysis.

  10. Dehydration of D-xylose over SiO{sub 2}-Al{sub 2}O{sub 3} catalyst: Perspective on the pathways for condensed products

    Energy Technology Data Exchange (ETDEWEB)

    You, Su Jin; Park, Eun Duck; Park, Myung-June [Ajou University, Suwon (Korea, Republic of)

    2016-03-15

    This work addresses the kinetic mechanism for the dehydration of D-xylose over the SiO{sub 2}-Al{sub 2}O{sub 3} solid catalyst, where the formation of condensed products is included in addition to the production of furfural and its decomposition. The kinetic modeling and parametric sensitivity show that the isomerization of D-xylose takes place in the early stages of the reaction, followed by the dehydration of isomers. Accordingly, the homogeneous polymerization of isomers is found to be dominant. The developed model is used to evaluate the effects of operating conditions on the catalytic performance; high temperature and D-xylose concentration guarantee high furfural yield.

  11. Antigliadin antibody, D-xylose, and cellobiose/mannitol permeability tests as indicators of mucosal damage in children with coeliac disease.

    Science.gov (United States)

    Troncone, R; Starita, A; Coletta, S; Mayer, M; Greco, L

    1992-08-01

    A dual sugar (cellobiose/mannitol) permeability test using an iso-osmolar solution was performed, to compare its ability to predict small-bowel mucosal damage in children affected by coeliac disease with the determination of serum levels of D-xylose and antigliadin antibody. Eighty-three children (67 on gluten-containing diet and 16 on gluten-free diet) were investigated. The D-xylose and the serum antigliadin antibody test predicted accurately 70% and 78% of the small-bowel biopsy results, respectively, whereas the cellobiose-mannitol permeability test predicted 93%. These data confirm the superiority of the permeability test over the D-xylose test, although the former cannot be advocated as a substitute for jejunal biopsy. Our results suggest a complementary use of the permeability test and the antigliadin antibody measurement as screening tests for coeliac disease before applying more invasive procedures.

  12. Interactively Evolving Compositional Sound Synthesis Networks

    DEFF Research Database (Denmark)

    Jónsson, Björn Þór; Hoover, Amy K.; Risi, Sebastian

    2015-01-01

    While the success of electronic music often relies on the uniqueness and quality of selected timbres, many musicians struggle with complicated and expensive equipment and techniques to create their desired sounds. Instead, this paper presents a technique for producing novel timbres that are evolved......, CPPNs can theoretically compute any function and can build on those present in traditional synthesizers (e.g. square, sawtooth, triangle, and sine waves functions) to produce completely novel timbres. Evolved with NeuroEvolution of Augmenting Topologies (NEAT), the aim of this paper is to explore...... the space of potential sounds that can be generated through such compositional sound synthesis networks (CSSNs). To study the effect of evolution on subjective appreciation, participants in a listener study ranked evolved timbres by personal preference, resulting in preferences skewed toward the first...

  13. Quantifying evolvability in small biological networks

    Energy Technology Data Exchange (ETDEWEB)

    Nemenman, Ilya [Los Alamos National Laboratory; Mugler, Andrew [COLUMBIA UNIV; Ziv, Etay [COLUMBIA UNIV; Wiggins, Chris H [COLUMBIA UNIV

    2008-01-01

    The authors introduce a quantitative measure of the capacity of a small biological network to evolve. The measure is applied to a stochastic description of the experimental setup of Guet et al. (Science 2002, 296, pp. 1466), treating chemical inducers as functional inputs to biochemical networks and the expression of a reporter gene as the functional output. The authors take an information-theoretic approach, allowing the system to set parameters that optimise signal processing ability, thus enumerating each network's highest-fidelity functions. All networks studied are highly evolvable by the measure, meaning that change in function has little dependence on change in parameters. Moreover, each network's functions are connected by paths in the parameter space along which information is not significantly lowered, meaning a network may continuously change its functionality without completely losing it along the way. This property further underscores the evolvability of the networks.

  14. Process for Assembly and Transformation into Saccharomyces cerevisiae of a Synthetic Yeast Artificial Chromosome Containing a Multigene Cassette to Express Enzymes That Enhance Xylose Utilization Designed for an Automated Platform.

    Science.gov (United States)

    Hughes, Stephen R; Cox, Elby J; Bang, Sookie S; Pinkelman, Rebecca J; López-Núñez, Juan Carlos; Saha, Badal C; Qureshi, Nasib; Gibbons, William R; Fry, Michelle R; Moser, Bryan R; Bischoff, Kenneth M; Liu, Siqing; Sterner, David E; Butt, Tauseef R; Riedmuller, Steven B; Jones, Marjorie A; Riaño-Herrera, Néstor M

    2015-12-01

    A yeast artificial chromosome (YAC) containing a multigene cassette for expression of enzymes that enhance xylose utilization (xylose isomerase [XI] and xylulokinase [XKS]) was constructed and transformed into Saccharomyces cerevisiae to demonstrate feasibility as a stable protein expression system in yeast and to design an assembly process suitable for an automated platform. Expression of XI and XKS from the YAC was confirmed by Western blot and PCR analyses. The recombinant and wild-type strains showed similar growth on plates containing hexose sugars, but only recombinant grew on D-xylose and L-arabinose plates. In glucose fermentation, doubling time (4.6 h) and ethanol yield (0.44 g ethanol/g glucose) of recombinant were comparable to wild type (4.9 h and 0.44 g/g). In whole-corn hydrolysate, ethanol yield (0.55 g ethanol/g [glucose + xylose]) and xylose utilization (38%) for recombinant were higher than for wild type (0.47 g/g and 12%). In hydrolysate from spent coffee grounds, yield was 0.46 g ethanol/g (glucose + xylose), and xylose utilization was 93% for recombinant. These results indicate introducing a YAC expressing XI and XKS enhanced xylose utilization without affecting integrity of the host strain, and the process provides a potential platform for automated synthesis of a YAC for expression of multiple optimized genes to improve yeast strains. © 2015 Society for Laboratory Automation and Screening.

  15. Anaerobic poly-3-D-hydroxybutyrate production from xylose in recombinant Saccharomyces cerevisiae using a NADH-dependent acetoacetyl-CoA reductase.

    Science.gov (United States)

    de Las Heras, Alejandro Muñoz; Portugal-Nunes, Diogo J; Rizza, Nathasha; Sandström, Anders G; Gorwa-Grauslund, Marie F

    2016-11-18

    Poly-3-D-hydroxybutyrate (PHB) that is a promising precursor for bioplastic with similar physical properties as polypropylene, is naturally produced by several bacterial species. The bacterial pathway is comprised of the three enzymes β-ketothiolase, acetoacetyl-CoA reductase (AAR) and PHB synthase, which all together convert acetyl-CoA into PHB. Heterologous expression of the pathway genes from Cupriavidus necator has enabled PHB production in the yeast Saccharomyces cerevisiae from glucose as well as from xylose, after introduction of the fungal xylose utilization pathway from Scheffersomyces stipitis including xylose reductase (XR) and xylitol dehydrogenase (XDH). However PHB titers are still low. In this study the acetoacetyl-CoA reductase gene from C. necator (CnAAR), a NADPH-dependent enzyme, was replaced by the NADH-dependent AAR gene from Allochromatium vinosum (AvAAR) in recombinant xylose-utilizing S. cerevisiae and PHB production was compared. A. vinosum AAR was found to be active in S. cerevisiae and able to use both NADH and NADPH as cofactors. This resulted in improved PHB titers in S. cerevisiae when xylose was used as sole carbon source (5-fold in aerobic conditions and 8.4-fold under oxygen limited conditions) and PHB yields (4-fold in aerobic conditions and up to 5.6-fold under oxygen limited conditions). Moreover, the best strain was able to accumulate up to 14% of PHB per cell dry weight under fully anaerobic conditions. This study reports a novel approach for boosting PHB accumulation in S. cerevisiae by replacement of the commonly used AAR from C. necator with the NADH-dependent alternative from A. vinosum. Additionally, to the best of our knowledge, it is the first demonstration of anaerobic PHB synthesis from xylose.

  16. Evolution of evolvability in gene regulatory networks.

    Directory of Open Access Journals (Sweden)

    Anton Crombach

    Full Text Available Gene regulatory networks are perhaps the most important organizational level in the cell where signals from the cell state and the outside environment are integrated in terms of activation and inhibition of genes. For the last decade, the study of such networks has been fueled by large-scale experiments and renewed attention from the theoretical field. Different models have been proposed to, for instance, investigate expression dynamics, explain the network topology we observe in bacteria and yeast, and for the analysis of evolvability and robustness of such networks. Yet how these gene regulatory networks evolve and become evolvable remains an open question. An individual-oriented evolutionary model is used to shed light on this matter. Each individual has a genome from which its gene regulatory network is derived. Mutations, such as gene duplications and deletions, alter the genome, while the resulting network determines the gene expression pattern and hence fitness. With this protocol we let a population of individuals evolve under Darwinian selection in an environment that changes through time. Our work demonstrates that long-term evolution of complex gene regulatory networks in a changing environment can lead to a striking increase in the efficiency of generating beneficial mutations. We show that the population evolves towards genotype-phenotype mappings that allow for an orchestrated network-wide change in the gene expression pattern, requiring only a few specific gene indels. The genes involved are hubs of the networks, or directly influencing the hubs. Moreover, throughout the evolutionary trajectory the networks maintain their mutational robustness. In other words, evolution in an alternating environment leads to a network that is sensitive to a small class of beneficial mutations, while the majority of mutations remain neutral: an example of evolution of evolvability.

  17. How the first biopolymers could have evolved.

    Science.gov (United States)

    Abkevich, V I; Gutin, A M; Shakhnovich, E I

    1996-01-01

    In this work, we discuss a possible origin of the first biopolymers with stable unique structures. We suggest that at the prebiotic stage of evolution, long organic polymers had to be compact to avoid hydrolysis and had to be soluble and thus must not be exceedingly hydrophobic. We present an algorithm that generates such sequences for model proteins. The evolved sequences turn out to have a stable unique structure, into which they quickly fold. This result illustrates the idea that the unique three-dimensional native structures of first biopolymers could have evolved as a side effect of nonspecific physicochemical factors acting at the prebiotic stage of evolution. PMID:8570645

  18. Evolving Intelligent Systems Methodology and Applications

    CERN Document Server

    Angelov, Plamen; Kasabov, Nik

    2010-01-01

    From theory to techniques, the first all-in-one resource for EIS. There is a clear demand in advanced process industries, defense, and Internet and communication (VoIP) applications for intelligent yet adaptive/evolving systems. Evolving Intelligent Systems is the first self- contained volume that covers this newly established concept in its entirety, from a systematic methodology to case studies to industrial applications. Featuring chapters written by leading world experts, it addresses the progress, trends, and major achievements in this emerging research field, with a strong emphasis on th

  19. Engineering a synthetic anaerobic respiration for reduction of xylose to xylitol using NADH output of glucose catabolism by Escherichia coli AI21.

    Science.gov (United States)

    Iverson, Andrew; Garza, Erin; Manow, Ryan; Wang, Jinhua; Gao, Yuanyuan; Grayburn, Scott; Zhou, Shengde

    2016-04-16

    Anaerobic rather than aerobic fermentation is preferred for conversion of biomass derived sugars to high value redox-neutral and reduced commodities. This will likely result in a higher yield of substrate to product conversion and decrease production cost since substrate often accounts for a significant portion of the overall cost. To this goal, metabolic pathway engineering has been used to optimize substrate carbon flow to target products. This approach works well for the production of redox neutral products such as lactic acid from redox neutral sugars using the reducing power NADH (nicotinamide adenine dinucleotide, reduced) generated from glycolysis (2 NADH per glucose equivalent). Nevertheless, greater than two NADH per glucose catabolized is needed for the production of reduced products (such as xylitol) from redox neutral sugars by anaerobic fermentation. The Escherichia coli strain AI05 (ΔfrdBC ΔldhA ΔackA Δ(focA-pflB) ΔadhE ΔptsG ΔpdhR::pflBp 6-(aceEF-lpd)), previously engineered for reduction of xylose to xylitol using reducing power (NADH equivalent) of glucose catabolism, was further engineered by 1) deleting xylAB operon (encoding for xylose isomerase and xylulokinase) to prevent xylose from entering the pentose phosphate pathway; 2) anaerobically expressing the sdhCDAB-sucABCD operon (encoding for succinate dehydrogenase, α-ketoglutarate dehydrogenase and succinyl-CoA synthetase) to enable an anaerobically functional tricarboxcylic acid cycle with a theoretical 10 NAD(P)H equivalent per glucose catabolized. These reducing equivalents can be oxidized by synthetic respiration via xylose reduction, producing xylitol. The resulting strain, AI21 (pAI02), achieved a 96 % xylose to xylitol conversion, with a yield of 6 xylitol per glucose catabolized (molar yield of xylitol per glucose consumed (YRPG) = 6). This represents a 33 % improvement in xylose to xylitol conversion, and a 63 % increase in xylitol yield per glucose catabolized over

  20. Physiological effects of over-expressing compartment-specific components of the protein folding machinery in xylose-fermenting Saccharomyces cerevisiae.

    Science.gov (United States)

    Bergdahl, Basti; Gorwa-Grauslund, Marie F; van Niel, Ed W J

    2014-04-23

    Efficient utilization of both glucose and xylose is necessary for a competitive ethanol production from lignocellulosic materials. Although many advances have been made in the development of xylose-fermenting strains of Saccharomyces cerevisiae, the productivity remains much lower compared to glucose. Previous transcriptional analyses of recombinant xylose-fermenting strains have mainly focused on central carbon metabolism. Very little attention has been given to other fundamental cellular processes such as the folding of proteins. Analysis of previously measured transcript levels in a recombinant XR/XDH-strain showed a wide down-regulation of genes targeted by the unfolded protein response during xylose fermentation. Under anaerobic conditions the folding of proteins is directly connected with fumarate metabolism and requires two essential enzymes: FADH2-dependent fumarate reductase (FR) and Ero1p. In this study we tested whether these enzymes impair the protein folding process causing the very slow growth of recombinant yeast strains on xylose under anaerobic conditions. Four strains over-expressing the cytosolic (FRD1) or mitochondrial (OSM1) FR genes and ERO1 in different combinations were constructed. The growth and fermentation performance was evaluated in defined medium as well as in a complex medium containing glucose and xylose. Over-expression of FRD1, alone or in combination with ERO1, did not have any significant effect on xylose fermentation in any medium used. Over-expression of OSM1, on the other hand, led to a diversion of carbon from glycerol to acetate and a decrease in growth rate by 39% in defined medium and by 25% in complex medium. Combined over-expression of OSM1 and ERO1 led to the same diversion of carbon from glycerol to acetate and had a stronger detrimental effect on the growth in complex medium. Increasing the activities of the FR enzymes and Ero1p is not sufficient to increase the anaerobic growth on xylose. So additional components of

  1. Optimizing the enzymatic synthesis of beta-D-galactopyranosyl-D-xyloses for their use in the evaluation of lactase activity in vivo.

    Science.gov (United States)

    Hermida, Carmen; Corrales, Guillermo; Cañada, Francisco J; Aragón, Juan J; Fernández-Mayoralas, Alfonso

    2007-07-15

    Disaccharides 2-O-, 3-O-, and 4-O-beta-D-galactopyranosyl-D-xyloses (2, 3, and 1, respectively) were obtained by beta-galactosidase-catalyzed reactions for their use in the evaluation of intestinal lactase activity in vivo. Their administration to suckling rats followed by determination of the derived D-xylose in the urine and measurement of lactase activity in intestinal homogenates showed 1 to be the most suitable disaccharide for a potential test of the deficiency of intestinal lactase. The synthesis of 1 was further studied by evaluating the effect of different variables on the yield and regioselectivity of the enzymatic galactosylation, and the purification process was optimized.

  2. Preface: evolving rotifers, evolving science: Proceedings of the XIV International Rotifer Symposium

    Czech Academy of Sciences Publication Activity Database

    Devetter, Miloslav; Fontaneto, D.; Jersabek, Ch.D.; Welch, D.B.M.; May, L.; Walsh, E.J.

    2017-01-01

    Roč. 796, č. 1 (2017), s. 1-6 ISSN 0018-8158 Institutional support: RVO:60077344 Keywords : evolving rotifers * 14th International Rotifer Symposium * evolving science Subject RIV: EG - Zoology OBOR OECD: Zoology Impact factor: 2.056, year: 2016

  3. Dipeptide transporters in Fusarium graminearum

    DEFF Research Database (Denmark)

    Droce, Aida; Giese, Henriette; Søndergaard, Teis

    Fungi have evolved different transport mechanisms in order to utilize both inorganic and organic nitrogen sources because nitrogen availability often is one of the limiting factors in pathogenic processes. In this study we have characterized four di/tripeptide transporters in the necrotrophic plant...

  4. Continuous alcoholic fermentation of glucose/xylose mixtures by co-immobilized Saccharomyces cerevisiae and Candida shehatae.

    Science.gov (United States)

    Lebeau, T; Jouenne, T; Junter, G A

    1998-09-01

    Viable Saccharomyces cerevisiae and Candida shehatae cells were co-immobilized in a composite agar layer/microporous membrane structure. This immobilized-cell structure was placed in a vertical position between the two halves of a double-chambered, stainless-steel bioreactor of original design and applied to the continuous alcoholic fermentation of a mixture of glucose (35 g dm-3) and xylose (15 g dm-3). Various dilution rates and initial cell loadings of the gel layer were tested. Simultaneous consumption of the two sugars was always observed. The best fermentation performance was obtained at low dilution rate (0.02 h-1) with an excess of C. shehatae over S. cerevisiae in the initial cell loading of the gel (5.0 mg dry weight and 0.65 mg dry weight cm-3 gel respectively): 100% of glucose and 73% of xylose were consumed with an ethanol yield coefficient of 0.48 g g total sugars-1. In these conditions, however, the ethanol production rate per unit volume of gel remained low (0.37 g h-1 dm-3). Viable cell counts in gel samples after incubation highlighted significant heterogeneities in the spatial distribution of the two yeast species in both the vertical and the transverse directions. In particular, the overall cell number decreased from the bottom to the top of the agar sheet, which may explain the low ethanol productivity relative to the total gel volume.

  5. Effect of autohydrolysis and enzymatic treatment on oil palm (Elaeis guineensis Jacq.) frond fibres for xylose and xylooligosaccharides production.

    Science.gov (United States)

    Sabiha-Hanim, Saleh; Noor, Mohd Azemi Mohd; Rosma, Ahmad

    2011-01-01

    Oil palm (Elaeis guineensis Jacq.) is one of the most important commercial crops for the production of palm oil, which generates 10.88 tons of oil palm fronds per hectare of plantation as a by-product. In this study, oil palm frond fibres were subjected to an autohydrolysis treatment using an autoclave, operated at 121 °C for 20-80 min, to facilitate the separation of hemicelluloses. The hemicellulose-rich solution (autohydrolysate) was subjected to further hydrolysis with 4-16 U of mixed Trichoderma viride endo-(1,4)-β-xylanases (EC 3.2.1.8) per 100 mg of autohydrolysate. Autoclaving of palm fronds at 121°C for 60 min (a severity factor of 2.40) recovered 75% of the solid residue, containing 57.9% cellulose and 18% Klason lignin, and an autohydrolysate containing 14.94% hemicellulose, with a fractionation efficiency of 49.20%. Subsequent enzymatic hydrolysis of the autohydrolysate with 8 U of endoxylanase at 40 °C for 24 h produced a solution containing 17.5% xylooligosaccharides and 25.6% xylose. The results clearly indicate the potential utilization of oil palm frond, an abundantly available lignocellulosic biomass for the production of xylose and xylooligosaccharides which can serve as functional food ingredients. Copyright © 2010 Elsevier Ltd. All rights reserved.

  6. Co-consumption of glucose and xylose for organic acid production by Aspergillus carbonarius cultivated in wheat straw hydrolysate.

    Science.gov (United States)

    Yang, Lei; Lübeck, Mette; Souroullas, Konstantinos; Lübeck, Peter S

    2016-04-01

    Aspergillus carbonarius exhibits excellent abilities to utilize a wide range of carbon sources and to produce various organic acids. In this study, wheat straw hydrolysate containing high concentrations of glucose and xylose was used for organic acid production by A. carbonarius. The results indicated that A. carbonarius efficiently co-consumed glucose and xylose and produced various types of organic acids in hydrolysate adjusted to pH 7. The inhibitor tolerance of A. carbonarius to the hydrolysate at different pH values was investigated and compared using spores and recycled mycelia. This comparison showed a slight difference in the inhibitor tolerance of the spores and the recycled mycelia based on their growth patterns. Moreover, the wild-type and a glucose oxidase deficient (Δgox) mutant were compared for their abilities to produce organic acids using the hydrolysate and a defined medium. The two strains showed a different pattern of organic acid production in the hydrolysate where the Δgox mutant produced more oxalic acid but less citric acid than the wild-type, which was different from the results obtained in the defined medium This study demonstrates the feasibility of using lignocellulosic biomass for the organic acid production by A. carbonarius.

  7. Spathaspora piracicabensis f. a., sp. nov., a D-xylose-fermenting yeast species isolated from rotting wood in Brazil.

    Science.gov (United States)

    Varize, Camila S; Cadete, Raquel M; Lopes, Lucas D; Christofoleti-Furlan, Renata M; Lachance, Marc-André; Rosa, Carlos A; Basso, Luiz C

    2017-11-09

    Two strains of a novel yeast species were isolated from rotting wood of an ornamental tree (purple quaresmeira, Tibouchina granulosa, Melastomataceae) in an Atlantic Rainforest area in Brazil. Analysis of the sequences of the internal transcribed spacer (ITS-5.8S) region and the D1/D2 domains of the large subunit rRNA gene showed that this species belongs to the Spathaspora clade, and is phylogenetically related to Spathaspora brasiliensis, Candida materiae and Sp. girioi. The novel species ferments D-xylose, producing ethanol, with amounts between 3.37 and 3.48 g L(-1) ethanol from 2% D-xylose. Ascospores were not observed from this new species. The name Spathaspora piracicabensis f. a., sp. nov. is proposed to accommodate these isolates. The type strain is UFMG-CM-Y5867(T) (= CBS 15054(T) = ESALQ-I54(T)). The MycoBank number is MB 822,320.

  8. Functional properties of chitosan-xylose Maillard reaction products and their application to semi-dried noodle.

    Science.gov (United States)

    Zhu, Ke-Xue; Li, Jie; Li, Man; Guo, Xiao-Na; Peng, Wei; Zhou, Hui-Ming

    2013-02-15

    The objective of this research was to evaluate the antimicrobial, antioxidant and darkening inhibitory activities of Maillard reaction products (MRPs) prepared from chitosan and xylose, and their effects on the preservation and quality of semi-dried noodles. The development of brown color and UV absorbance changes indicated the proceeding of Maillard reaction. The antimicrobial activity, reducing power, DPPH radical scavenging activity, copper-chelating activity and PPO inhibitory effects of chitosan-xylose conjugates increased with the reaction. Addition of MRPs could improve the textural and cooking quality of semi-dried noodles. Incorporation of 0.35% MRPs (6 h) into semi-dried noodle resulted in an extension of shelf life for more than 7 days than the control noodles (at room temperature). The discoloration caused by the addition of MRPs was limited, and MRPs could inhibit darkening of the noodle effectively. Results suggested that the MRPs could be used as a novel promising preservative for semi-dried noodles. Copyright © 2012 Elsevier Ltd. All rights reserved.

  9. Zinc, magnesium, and calcium ion supplementation confers tolerance to acetic acid stress in industrial Saccharomyces cerevisiae utilizing xylose.

    Science.gov (United States)

    Ismail, Ku Syahidah Ku; Sakamoto, Takatoshi; Hasunuma, Tomohisa; Zhao, Xin-Qing; Kondo, Akihiko

    2014-12-01

    Lignocellulosic biomass is a potential substrate for ethanol production. However, pretreatment of lignocellulosic materials produces inhibitory compounds such as acetic acid, which negatively affect ethanol production by Saccharomyces cerevisiae. Supplementation of the medium with three metal ions (Zn(2+) , Mg(2+) , and Ca(2+) ) increased the tolerance of S. cerevisiae toward acetic acid compared to the absence of the ions. Ethanol production from xylose was most improved (by 34%) when the medium was supplemented with 2 mM Ca(2+) , followed by supplementation with 3.5 mM Mg(2+) (29% improvement), and 180 μM Zn(2+) (26% improvement). Higher ethanol production was linked to high cell viability in the presence of metal ions. Comparative transcriptomics between the supplemented cultures and the control suggested that improved cell viability resulted from the induction of genes controlling the cell wall and membrane. Only one gene, FIT2, was found to be up-regulated in common between the three metal ions. Also up-regulation of HXT1 and TKL1 might enhance xylose consumption in the presence of acetic acid. Thus, the addition of ionic nutrients is a simple and cost-effective method to improve the acetic acid tolerance of S. cerevisiae. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Thermal and Evolved-Gas Analyzer Illustration

    Science.gov (United States)

    2008-01-01

    This is a computer-aided drawing of the Thermal and Evolved-Gas Analyzer, or TEGA, on NASA's Phoenix Mars Lander. The Phoenix Mission is led by the University of Arizona, Tucson, on behalf of NASA. Project management of the mission is by NASA's Jet Propulsion Laboratory, Pasadena, Calif. Spacecraft development is by Lockheed Martin Space Systems, Denver.

  11. Apollo 16 Evolved Lithology Sodic Ferrogabbro

    Science.gov (United States)

    Zeigler, Ryan; Jolliff, B. L.; Korotev, R. L.

    2014-01-01

    Evolved lunar igneous lithologies, often referred to as the alkali suite, are a minor but important component of the lunar crust. These evolved samples are incompatible-element rich samples, and are, not surprisingly, most common in the Apollo sites in (or near) the incompatible-element rich region of the Moon known as the Procellarum KREEP Terrane (PKT). The most commonly occurring lithologies are granites (A12, A14, A15, A17), monzogabbro (A14, A15), alkali anorthosites (A12, A14), and KREEP basalts (A15, A17). The Feldspathic Highlands Terrane is not entirely devoid of evolved lithologies, and rare clasts of alkali gabbronorite and sodic ferrogabbro (SFG) have been identified in Apollo 16 station 11 breccias 67915 and 67016. Curiously, nearly all pristine evolved lithologies have been found as small clasts or soil particles, exceptions being KREEP basalts 15382/6 and granitic sample 12013 (which is itself a breccia). Here we reexamine the petrography and geochemistry of two SFG-like particles found in a survey of Apollo 16 2-4 mm particles from the Cayley Plains 62283,7-15 and 62243,10-3 (hereafter 7-15 and 10-3 respectively). We will compare these to previously reported SFG samples, including recent analyses on the type specimen of SFG from lunar breccia 67915.

  12. Recombinant Ralstonia eutropha engineered to utilize xylose and its use for the production of poly(3-hydroxybutyrate) from sunflower stalk hydrolysate solution.

    Science.gov (United States)

    Kim, Hee Su; Oh, Young Hoon; Jang, Young-Ah; Kang, Kyoung Hee; David, Yokimiko; Yu, Ju Hyun; Song, Bong Keun; Choi, Jong-il; Chang, Yong Keun; Joo, Jeong Chan; Park, Si Jae

    2016-06-03

    Lignocellulosic raw materials have extensively been examined for the production of bio-based fuels, chemicals, and polymers using microbial platforms. Since xylose is one of the major components of the hydrolyzed lignocelluloses, it is being considered a promising substrate in lignocelluloses based fermentation process. Ralstonia eutropha, one of the most powerful and natural producers of polyhydroxyalkanoates (PHAs), has extensively been examined for the production of bio-based chemicals, fuels, and polymers. However, to the best of our knowledge, lignocellulosic feedstock has not been employed for R. eutropha probably due to its narrow spectrum of substrate utilization. Thus, R. eutropha engineered to utilize xylose should be useful in the development of microbial process for bio-based products from lignocellulosic feedstock. Recombinant R. eutropha NCIMB11599 expressing the E. coli xylAB genes encoding xylose isomerase and xylulokinase respectively, was constructed and examined for the synthesis of poly(3-hydroxybutyrate) [P(3HB)] using xylose as a sole carbon source. It could produce 2.31 g/L of P(3HB) with a P(3HB) content of 30.95 wt% when it was cultured in a nitrogen limited chemically defined medium containing 20.18 g/L of xylose in a batch fermentation. Also, recombinant R. eutropha NCIMB11599 expressing the E. coli xylAB genes produced 5.71 g/L of P(3HB) with a P(3HB) content of 78.11 wt% from a mixture of 10.05 g/L of glucose and 10.91 g/L of xylose in the same culture condition. The P(3HB) concentration and content could be increased to 8.79 g/L and 88.69 wt%, respectively, when it was cultured in the medium containing 16.74 g/L of glucose and 6.15 g/L of xylose. Further examination of recombinant R. eutropha NCIMB11599 expressing the E. coli xylAB genes by fed-batch fermentation resulted in the production of 33.70 g/L of P(3HB) in 108 h with a P(3HB) content of 79.02 wt%. The concentration of xylose could be maintained as high as 6 g/L, which is

  13. Evolving networks-Using past structure to predict the future

    Science.gov (United States)

    Shang, Ke-ke; Yan, Wei-sheng; Small, Michael

    2016-08-01

    Many previous studies on link prediction have focused on using common neighbors to predict the existence of links between pairs of nodes. More broadly, research into the structural properties of evolving temporal networks and temporal link prediction methods have recently attracted increasing attention. In this study, for the first time, we examine the use of links between a pair of nodes to predict their common neighbors and analyze the relationship between the weight and the structure in static networks, evolving networks, and in the corresponding randomized networks. We propose both new unweighted and weighted prediction methods and use six kinds of real networks to test our algorithms. In unweighted networks, we find that if a pair of nodes connect to each other in the current network, they will have a higher probability to connect common nodes both in the current and the future networks-and the probability will decrease with the increase of the number of neighbors. Furthermore, we find that the original networks have their particular structure and statistical characteristics which benefit link prediction. In weighted networks, the prediction algorithm performance of networks which are dominated by human factors decrease with the decrease of weight and are in general better in static networks. Furthermore, we find that geographical position and link weight both have significant influence on the transport network. Moreover, the evolving financial network has the lowest predictability. In addition, we find that the structure of non-social networks has more robustness than social networks. The structure of engineering networks has both best predictability and also robustness.

  14. Monitoring Rhodotorula glutinis CCMI 145 physiological response and oil production growing on xylose and glucose using multi-parameter flow cytometry.

    Science.gov (United States)

    da Silva, Teresa Lopes; Feijão, Daniela; Roseiro, José Carlos; Reis, Alberto

    2011-02-01

    Flow cytometry was used to monitor the lipid content, viability and intrinsic light scatter properties of Rhodotorula glutinis CCMI 145 cells growing on batch cultures using xylose and glucose as carbon sources. The highest lipid content was observed for cells grown on glucose, at the end of the exponential phase (17.8% w/w). The proportion of cells stained with PI attaining 77% at the end of the glucose growth. Cells growing on xylose produced a maximum lipid content of 10.6% (w/w), at the stationary phase. An increase in the proportion of cells stained with PI was observed, reaching 29% at the end of xylose growth. Changes in the side and forward light scatter detected during the yeast batch cultures supported that R. glutinis cells grown on glucose experienced harsher conditions, resulting in a high level of cytoplasmic membrane damage, which did not occur when R. glutinis cells grew on xylose. Copyright © 2010 Elsevier Ltd. All rights reserved.

  15. Molecular cloning and functional expression in Lactobacillus plantarum 80 of xylT, encoding the D-xylose-H+ symporter of Lactobacillus brevis

    NARCIS (Netherlands)

    Chaillou, S.; Bor, Y.-C.; Batt, C.A.; Postma, P.W.; Pouwels, P.H.

    1998-01-01

    A 3-kb region, located downstream of the Lactobacillus brevis xylA gene (encoding D-xylose isomerase), was cloned in Escherichia coli TG1. The sequence revealed two open reading frames which could code for the D-xylulose kinase gene (xylB) and another gene (xylT) encoding a protein of 457 amino

  16. Diagnosis of bacterial overgrowth of the small intestine. Comparison of the 14C-D-xylose breath test and jejunal cultures in 60 patients

    DEFF Research Database (Denmark)

    Rumessen, J J; Gudmand-Høyer, E; Bachmann, E

    1985-01-01

    Sixty consecutive patients suspected of having bacterial overgrowth of the small intestine (BOG) had aerobic and anaerobic bacterial cultures made of fasting upper jejunal fluid and also a 14C-D-xylose breath test (XBT). Culture-proven BOG was present in 23 patients. In another 15 patients...

  17. Differential RNA-seq, Multi-Network Analysis and Metabolic Regulation Analysis of Kluyveromyces marxianus Reveals a Compartmentalised Response to Xylose.

    Directory of Open Access Journals (Sweden)

    Du Toit W P Schabort

    Full Text Available We investigated the transcriptomic response of a new strain of the yeast Kluyveromyces marxianus, in glucose and xylose media using RNA-seq. The data were explored in a number of innovative ways using a variety of networks types, pathway maps, enrichment statistics, reporter metabolites and a flux simulation model, revealing different aspects of the genome-scale response in an integrative systems biology manner. The importance of the subcellular localisation in the transcriptomic response is emphasised here, revealing new insights. As was previously reported by others using a rich medium, we show that peroxisomal fatty acid catabolism was dramatically up-regulated in a defined xylose mineral medium without fatty acids, along with mechanisms to activate fatty acids and transfer products of β-oxidation to the mitochondria. Notably, we observed a strong up-regulation of the 2-methylcitrate pathway, supporting capacity for odd-chain fatty acid catabolism. Next we asked which pathways would respond to the additional requirement for NADPH for xylose utilisation, and rationalised the unexpected results using simulations with Flux Balance Analysis. On a fundamental level, we investigated the contribution of the hierarchical and metabolic regulation levels to the regulation of metabolic fluxes. Metabolic regulation analysis suggested that genetic level regulation plays a major role in regulating metabolic fluxes in adaptation to xylose, even for the high capacity reactions, which is unexpected. In addition, isozyme switching may play an important role in re-routing of metabolic fluxes in subcellular compartments in K. marxianus.

  18. Furfural Production from d-Xylose and Xylan by Using Stable Nafion NR50 and NaCl in a Microwave-Assisted Biphasic Reaction

    National Research Council Canada - National Science Library

    Le Guenic, Sarah; Gergela, David; Ceballos, Claire; Delbecq, Frederic; Len, Christophe

    2016-01-01

    ...) biphasic system under microwave irradiation. Heated up between 170 and 190 °C in the presence of Nafion NR50 and NaCl, d-xylose, l-arabinose and xylan gave furfural with maximum yields of 80%, 42% and 55%, respectively...

  19. A one-pot synthesis of 1,6,9,13-tetraoxadispiro(4.2.4.2)tetradecane by hydrodeoxygenation of xylose using a palladium catalyst

    Science.gov (United States)

    In an effort to expand the number of biobased chemicals available from sugars, xylose has been converted to 1,6,9,13-tetraoxadispiro(4.2.4.2)tetradecane in a one-pot reaction using palladium supported on silica-alumina as the catalyst. The title compound is produced in 35-40% yield under 7 MPa H2 pr...

  20. Membrane separation of enzyme-converted biomass compounds: Recovery of xylose and production of gluconic acid as a value-added product

    DEFF Research Database (Denmark)

    Morthensen, Sofie Thage; Zeuner, Birgitte; Meyer, Anne S.

    2018-01-01

    The purpose of the present study was to assess the efficiency of enzyme-assisted nanofiltration for separation of xylose from glucose present in genuine biorefinery liquors obtained from hydrothermal pretreatment of wheat straw, corn stover and Miscanthus stalks. Glucose oxidase and catalase were...

  1. Genome sequence and physiological analysis of Yamadazyma laniorum f.a. sp. nov. and a reevaluation of the apocryphal xylose fermentation of its sister species, Candida tenuis

    Science.gov (United States)

    Xylose fermentation is a rare trait that is immensely important to the cellulosic biofuel industry, and Candida tenuis is one of the few yeasts that has been reported with this trait. Here we report the isolation of two strains representing a candidate sister species to C. tenuis. Integrated analysi...

  2. Multi-stage Continuous Culture Fermentation of Glucose-Xylose Mixtures to Fuel Ethanol using Genetically Engineered Saccharomyces cerevisiae 424A

    Science.gov (United States)

    Multi-stage continuous (chemostat) culture fermentation (MCCF) with variable fermentor volumes was carried out to study utilizing glucose and xylose for ethanol production by means of mixed sugar fermentation (MSF). Variable fermentor volumes were used to enable enhanced sugar u...

  3. Beta(1,2)-xylose and alpha(1,3)-fucose residues have a strong contribution in IgE binding to plant glycoallergens

    NARCIS (Netherlands)

    van Ree, R.; Cabanes-Macheteau, M.; Akkerdaas, J.; Milazzo, J. P.; Loutelier-Bourhis, C.; Rayon, C.; Villalba, M.; Koppelman, S.; Aalberse, R.; Rodriguez, R.; Faye, L.; Lerouge, P.

    2000-01-01

    Primary structures of the N-glycans of two major pollen allergens (Lol p 11 and Ole e 1) and a major peanut allergen (Ara h 1) were determined. Ole e 1 and Ara h 1 carried high mannose and complex N-glycans, whereas Lol p 11 carried only the complex. The complex structures all had a beta(1,2)-xylose

  4. A novel mechanism and kinetic model to explain enhanced xylose yields from dilute sulfuric acid compared to hydrothermal pretreatment of corn stover.

    Science.gov (United States)

    Shen, Jiacheng; Wyman, Charles E

    2011-10-01

    Pretreatment of corn stover in 0.5% sulfuric acid at 160 °C for 40 min realized a maximum monomeric plus oligomeric xylose yield of 93.1% compared to a maximum of only 71.5% for hydrothermal (no added mineral acid) pretreatment at 180 °C for 30 min. To explain differences in dilute acid and hydrothermal yields, a fast reacting xylan fraction (0.0889) was assumed to be able to directly form monomeric xylose while a slow reacting portion (0.9111) must first form oligomers during hydrothermal pretreatment. Two reactions to oligomers were proposed: reversible from fast reacting xylan and irreversible from slow reacting xylan. A kinetic model and its analytical solution simulated xylan removal data well for dilute acid and hydrothermal pretreatment of corn stover. These results suggested that autocatalytic reactions from xylan to furfural in hydrothermal pretreatment were controlled by oligomeric xylose decomposition, while acid-catalytic reactions in dilute acid pretreatment were controlled by monomeric xylose decomposition. Copyright © 2011. Published by Elsevier Ltd.

  5. Evolving wormhole geometries within nonlinear electrodynamics

    Energy Technology Data Exchange (ETDEWEB)

    Arellano, Aaron V B [Facultad de Ciencias, Universidad Autonoma del Estado de Mexico, El Cerrillo, Piedras Blancas, CP 50200, Toluca (Mexico); Lobo, Francisco S N [Centro de Astronomia e Astrofisica da Universidade de Lisboa, Campo Grande, Ed C8 1749-016 Lisbon (Portugal)

    2006-10-21

    In this work, we explore the possibility of evolving (2 + 1) and (3 + 1)-dimensional wormhole spacetimes, conformally related to the respective static geometries, within the context of nonlinear electrodynamics. For (3 + 1)-dimensional spacetime, it is found that the Einstein field equation imposes a contracting wormhole solution and the obedience of the weak energy condition. Nevertheless, in the presence of an electric field, the latter presents a singularity at the throat; however, for a pure magnetic field the solution is regular. For (2 + 1)-dimensional case, it is also found that the physical fields are singular at the throat. Thus, taking into account the principle of finiteness, which states that a satisfactory theory should avoid physical quantities becoming infinite, one may rule out evolving (3 + 1)-dimensional wormhole solutions, in the presence of an electric field, and (2 + 1)-dimensional case coupled to nonlinear electrodynamics.

  6. Continual Learning through Evolvable Neural Turing Machines

    DEFF Research Database (Denmark)

    Lüders, Benno; Schläger, Mikkel; Risi, Sebastian

    2016-01-01

    Continual learning, i.e. the ability to sequentially learn tasks without catastrophic forgetting of previously learned ones, is an important open challenge in machine learning. In this paper we take a step in this direction by showing that the recently proposed Evolving Neural Turing Machine (ENT......) approach is able to perform one-shot learning in a reinforcement learning task without catastrophic forgetting of previously stored associations.......Continual learning, i.e. the ability to sequentially learn tasks without catastrophic forgetting of previously learned ones, is an important open challenge in machine learning. In this paper we take a step in this direction by showing that the recently proposed Evolving Neural Turing Machine (ENTM...

  7. Designing Garments to Evolve Over Time

    DEFF Research Database (Denmark)

    Riisberg, Vibeke; Grose, Lynda

    2017-01-01

    This paper proposes a REDO of the current fashion paradigm by investigating how garments might be designed to evolve over time. The purpose is to discuss ways of expanding the traditional role of the designer to include temporal dimensions of creating, producing and using clothes and to suggest a...... to a REDO of design education, to further research and the future fashion and textile industry.......This paper proposes a REDO of the current fashion paradigm by investigating how garments might be designed to evolve over time. The purpose is to discuss ways of expanding the traditional role of the designer to include temporal dimensions of creating, producing and using clothes and to suggest...... a range of potential fashion futures that decouple from declining resources. In the first part literature on 'Past and Present' historical and current aspects of sustainability in fashion and textiles are presented. In the second part, three exploratory case studies are described: Two projects by students...

  8. Antibody therapeutics - the evolving patent landscape.

    Science.gov (United States)

    Petering, Jenny; McManamny, Patrick; Honeyman, Jane

    2011-09-01

    The antibody patent landscape has evolved dramatically over the past 30 years, particularly in areas of technology relating to antibody modification to reduce immunogenicity in humans or improve antibody function. In some cases antibody techniques that were developed in the 1980s are still the subject of patent protection in the United States or Canada. Copyright © 2011 Elsevier B.V. All rights reserved.

  9. The evolving epidemiology of inflammatory bowel disease.

    LENUS (Irish Health Repository)

    Shanahan, Fergus

    2009-07-01

    Epidemiologic studies in inflammatory bowel disease (IBD) include assessments of disease burden and evolving patterns of disease presentation. Although it is hoped that sound epidemiologic studies provide aetiological clues, traditional risk factor-based epidemiology has provided limited insights into either Crohn\\'s disease or ulcerative colitis etiopathogenesis. In this update, we will summarize how the changing epidemiology of IBD associated with modernization can be reconciled with current concepts of disease mechanisms and will discuss studies of clinically significant comorbidity in IBD.

  10. Directional Communication in Evolved Multiagent Teams

    Science.gov (United States)

    2013-06-10

    networks. Artificial Life, 15(2):185– 212, 2009. [23] K. O. Stanley and R. Miikkulainen. Evolving neural networks through augmenting topologies ...paper. 2.2 Neuroevolution of Augmenting Topologies The HyperNEAT approach is itself an extension of the original NEAT (Neu- roevolution of Augmenting ...Gauci and K. O. Stanley. Autonomous evolution of topographic regu- larities in artificial neural networks. Neural Computation, 22(7):1860–1898, 2010

  11. The Evolving Leadership Path of Visual Analytics

    Energy Technology Data Exchange (ETDEWEB)

    Kluse, Michael; Peurrung, Anthony J.; Gracio, Deborah K.

    2012-01-02

    This is a requested book chapter for an internationally authored book on visual analytics and related fields, coordianted by a UK university and to be published by Springer in 2012. This chapter is an overview of the leadship strategies that PNNL's Jim Thomas and other stakeholders used to establish visual analytics as a field, and how those strategies may evolve in the future.

  12. Raeder paratrigeminal neuralgia evolving to hemicrania continua.

    Science.gov (United States)

    Porzukowiak, Tina Renae

    2015-04-01

    Raeder paratrigeminal neuralgia is most commonly characterized as deep, boring, nonpulsatile, severe, unilateral facial and head pain in the distribution of the V1 area combined with ipsilateral oculosympathetic palsy and autonomic symptoms. Raeder paratrigeminal neuralgia evolving into hemicrania continua, a rare primary, chronic headache syndrome characterized by unilateral pain and response to indomethacin, has rarely been documented. The purpose of this case report is to contribute to the medical literature a single case of Raeder paratrigeminal neuralgia presenting as multiple cranial nerve palsies that evolved into hemicrania continua that was successfully treated with onabotulinumtoxinA. A 52-year-old white woman presented to the emergency department with the complaint of severe, aching, constant eye pain radiating to the V1 area for 1 week with associated ptosis and photophobia of the left eye. Ocular examination revealed involvement of cranial nerves II, III, V, and VI. Additional symptoms included ipsilateral lacrimation, eyelid edema, and rhinorrhea. Extensive medical work-up showed normal results. Raeder paratrigeminal neuralgia was diagnosed with multiple cranial nerve involvement; the headache component became chronic with periodic exacerbations of autonomic symptoms evolving to a diagnosis of hemicrania continua. The patient was intolerant to traditional indomethacin treatment, and the headache was successfully treated with onabotulinumtoxinA injections. Recognition of ipsilateral signs such as miosis, ptosis, hydrosis, eyelid edema, hyperemia, rhinorrhea, or nasal congestion is useful in the differential diagnosis of painful ophthalmoplegia, particularly in the diagnosis of Raeder paratrigeminal neuralgia and hemicrania continua. This case study illustrates a rare presentation of Raeder paratrigeminal neuralgia evolving into hemicrania continua presenting as a painful ophthalmoplegia with multiple cranial nerve involvement. The example supports the

  13. Evolvability of Amyloidogenic Proteins in Human Brain

    Science.gov (United States)

    Hashimoto, Makoto; Ho, Gilbert; Sugama, Shuei; Takamatsu, Yoshiki; Shimizu, Yuka; Takenouchi, Takato; Waragai, Masaaki; Masliah, Eliezer

    2018-01-01

     Currently, the physiological roles of amyloidogenic proteins (APs) in human brain, such as amyloid-β and α-synuclein, are elusive. Given that many APs arose by gene duplication and have been resistant against the pressures of natural selection, APs may be associated with some functions that are advantageous for survival of offspring. Nonetheless, evolvability is the sole physiological quality of APs that has been characterized in microorganisms such as yeast. Since yeast and human brain may share similar strategies in coping with diverse range of critical environmental stresses, the objective of this paper was to discuss the potential role of evolvability of APs in aging-associated neurodegenerative disorders, including Alzheimer’s disease and Parkinson’s disease. Given the heterogeneity of APs in terms of structure and cytotoxicity, it is argued that APs might be involved in preconditioning against diverse stresses in human brain. It is further speculated that these stress-related APs, most likely protofibrillar forms, might be transmitted to offspring via the germline, conferring preconditioning against forthcoming stresses. Thus, APs might represent a vehicle for the inheritance of the acquired characteristics against environmental stresses. Curiously, such a characteristic of APs is reminiscent of Charles Darwin’s ‘gemmules’, imagined molecules of heritability described in his pangenesis theory. We propose that evolvability might be a physiological function of APs during the reproductive stage and neurodegenerative diseases could be a by-product effect manifested later in aging. Collectively, our evolvability hypothesis may play a complementary role in the pathophysiology of APs with the conventional amyloid cascade hypothesis. PMID:29439348

  14. Simultaneous Decolorization and Biohydrogen Production from Xylose by Klebsiella oxytoca GS-4-08 in the Presence of Azo Dyes with Sulfonate and Carboxyl Groups.

    Science.gov (United States)

    Yu, Lei; Cao, Ming-Yue; Wang, Peng-Tao; Wang, Shi; Yue, Ying-Rong; Yuan, Wen-Duo; Qiao, Wei-Chuan; Wang, Fei; Song, Xin

    2017-05-15

    Biohydrogen production from the pulp and paper effluent containing rich lignocellulosic material could be achieved by the fermentation process. Xylose, an important hemicellulose hydrolysis product, is used less efficiently as a substrate for biohydrogen production. Moreover, azo dyes are usually added to fabricate anticounterfeiting paper, which further increases the complexity of wastewater. This study reports that xylose could serve as the sole carbon source for a pure culture of Klebsiella oxytoca GS-4-08 to achieve simultaneous decolorization and biohydrogen production. With 2 g liter-1 of xylose as the substrate, a maximum xylose utilization rate (URxyl) and a hydrogen molar yield (HMY) of 93.99% and 0.259 mol of H2 mol of xylose-1, respectively, were obtained. Biohydrogen kinetics and electron equivalent (e- equiv) balance calculations indicated that methyl red (MR) penetrates and intracellularly inhibits both the pentose phosphate pathway and pyruvate fermentation pathway, while methyl orange (MO) acted independently of the glycolysis and biohydrogen pathway. The data demonstrate that biohydrogen pathways in the presence of azo dyes with sulfonate and carboxyl groups were different, but the azo dyes could be completely reduced during the biohydrogen production period in the presence of MO or MR. The feasibility of hydrogen production from industrial pulp and paper effluent by the strain if the xylose is sufficient was also proved and was not affected by toxic substances which usually exist in such wastewater, except for chlorophenol. This study offers a promising energy-recycling strategy for treating pulp and paper wastewaters, especially for those containing azo dyes.IMPORTANCE The pulp and paper industry is a major industry in many developing countries, and the global market of pulp and paper wastewater treatment is expected to increase by 60% between 2012 and 2020. Such wastewater contains large amounts of refractory contaminants, such as lignin, whose

  15. High-order evolving surface finite element method for parabolic problems on evolving surfaces

    OpenAIRE

    Kovács, Balázs

    2016-01-01

    High-order spatial discretisations and full discretisations of parabolic partial differential equations on evolving surfaces are studied. We prove convergence of the high-order evolving surface finite element method, by showing high-order versions of geometric approximation errors and perturbation error estimates and by the careful error analysis of a modified Ritz map. Furthermore, convergence of full discretisations using backward difference formulae and implicit Runge-Kutta methods are als...

  16. Comparison of Gavage, Water Bottle, and a High-Moisture Diet Bolus as Dosing Methods for Quantitative D-xylose Administration to B6D2F1 (Mus musculus) Mice

    Science.gov (United States)

    Zimmer, J. Paul; Lewis, Sherry M.; Moyer, Jerry L.

    1993-01-01

    Gavage, water bottle, and diet incorporation are 3 dosing methods used orally to administer test compounds to rodents. These 3 methods were compared in mice to determine which represented the most quantitative delivery system. For dietary incorporation, a high-moisture bolus form of NIH-31 rodent meal was developed using hydroxypropyl methylcellulose as an autoclave-stable binding agent. A high-moisture bolus were selected to increase the acceptability of the dosed diet and to promote quantitative consumption through reduced wastage. The test compound used was D-xylose, a pentose sugar that may be quantitatively detected, colorimetrically, in urine following oral dosing. Six male and 6 female B6D2FI mice were placed in metabolism cages and dosed with a known quantity of D-xylose by each of the 3 methods. Urine was collected before and after each method of administration and analysed for total D-xylose; the per cent recovery was based upon the amount of D-xylose consumed. Quantitative consumption was apparently greatest for water bottle dosing with an average recovery of 56.0% of the original D-xylose dose. High-moisture bolus incorporation ranked second with 50.0% D-xylose recovery, and gavage was third with 41.0% D-xylose recovery.

  17. Increased enzymatic hydrolysis of sugarcane bagasse by a novel glucose- and xylose-stimulated β-glucosidase from Anoxybacillus flavithermus subsp. yunnanensis E13T.

    Science.gov (United States)

    Liu, Yang; Li, Rui; Wang, Jing; Zhang, Xiaohan; Jia, Rong; Gao, Yi; Peng, Hui

    2017-03-16

    β-Glucosidase is claimed as a key enzyme in cellulose hydrolysis. The cellulosic fibers are usually entrapped with hemicelluloses containing xylose. So there is ongoing interest in searching for glucose- and xylose-stimulated β-glucosidases to increase the efficiency of hydrolysis of cellulosic biomass. A thermostable β-glucosidase gene (Bglp) was cloned from Anoxybacillus flavithermus subsp. yunnanensis E13T and characterized. Optimal enzyme activity was observed at 60 °C and pH 7.0. Bglp was relatively stable at 60 °C with a 10-h half-life. The kinetic parameters V max and K m for p-nitrophenyl-β-D-glucopyranoside (pNPG) were 771 ± 39 μmol/min/mg and 0.29 ± 0.01 mM, respectively. The activity of Bglp is dramatically stimulated by glucose or xylose at concentrations up to 1.4 M. After Bglp was added to Celluclast® 1.5 L, the conversion of sugarcane bagasse was 48.4 ± 0.8%, which was much higher than of Celluclast® 1.5 L alone. Furthermore, Bglp showed obvious advantages in the hydrolysis when initial concentrations of glucose and xylose are high. The supplementation of BglP significantly enhanced the glucose yield from sugarcane bagasse, especially in the presence of high concentrations of glucose or xylose. Bglp should be a promising candidate for industrial applications.

  18. Hypernetwork generation for multi-modal transportation system modeling.

    Science.gov (United States)

    2013-04-01

    The transportation debate has evolved in recent decades to include ideas such as sustainability and livability alongside mobility and safety. Definitional complexities aside, there is no doubt that this evolution has created a national transportation...

  19. A new method of utilizing rice husk: consecutively preparing D-xylose, organosolv lignin, ethanol and amorphous superfine silica.

    Science.gov (United States)

    Zhang, Hongxi; Ding, Xuefeng; Chen, Xue; Ma, Yuejia; Wang, Zichen; Zhao, Xu

    2015-06-30

    Rice husk is an abundant agricultural by-product with the annual output of 120 and 40 million tons in the world and China, respectively. The common disposal method of rice husk in China has caused the pollution. This manuscript deals with a new method of comprehensively utilizing rice husk, by which hazardous materials are avoided to release. 100.3, 219.4, 50.1 and 170.5 g of D-xylose, organosolv lignin, ethanol and superfine silica are consecutively prepared from 1000 g of rice husk. This new method is helpful to resolving the problem of pollution and waste aroused by rice husk. Copyright © 2015 Elsevier B.V. All rights reserved.

  20. Hydrogenation of xylose to xylitol on sponge nickel catalyst: a study of the process and catalyst deactivation kinetics

    Directory of Open Access Journals (Sweden)

    Mikkola J.-P.

    2003-01-01

    Full Text Available The kinetics of hydrogenation of xylose to xylitol on a sponge nickel catalyst (commonly referred to as Raney Ni catalyst and of catalyst deactivation were studied. Plausible explanations for the decrease in catalytic activity by means of surface studies, nitrogen adsorption and thermogravimetric analyses of the fresh and spent catalysts are presented. The kinetic parameters of the process were estimated by the use of a semi-competitive model, which allows full competition between the organic species and the hydrogen atoms for the adsorption sites on the catalyst surface (competitive case. In the model, a competitiveness factor (alpha is introduced to take into account that even after complete coverage of the surface by the organic species, interstitial sites remain for the adsorption of the hydrogen atoms.

  1. Continuous alcoholic fermentation of glucose/xylose mixtures by co-immobilized saccharomyces cerevisiae and candida shehatae

    Energy Technology Data Exchange (ETDEWEB)

    Lebeau, T.; Jouenne, T.; Junter, G.A. [Equipe de Technologie Microbienne, CNRS/Univ. de Rouen, 76 Bois Guillaume (France)

    1998-12-31

    Viable Saccharomyces cerevisiae and Candida shehatae cells were co-immobilized in a composite agar layer/microporous membrane structure. This immobilized-cell structure was placed in a vertical position between the two halves of a double-chambered, stainless-steel bioreactor of original design and applied to the continuous alcoholic fermentation of a mixture of glucose (35 g dm{sup -3}) and xylose (15 g dm{sup -3}). Various dilution rates and initial cell loadings of the gel layer were tested. Simultaneous consumption of the two sugars was always observed. The best fermentation performance was obtained at low dilution rate (0.02 h{sup -1}) with an excess of C. shehatae over S. cerevisiae in the initial cell loading of the gel (5.0 mg dry weight and 0.65 mg dry weight cm{sup -3} gel respectively): 100% of glucose and 73% of xylose were consumed with an ethanol yield coefficient of 0.48 g g total sugars{sup -1}. In these conditions, however, the ethanol production rate per unit volume of gel remained low (0.37 g h{sup -1} dm{sup -3}). Viable cell counts in gel samples after incubation highlighted significant heterogeneities in the spatial distribution of the two yeast species in both the vertical and the transverse directions. In particular, the overall cell number decreased from the bottom to the top of the agar sheet, which may explain the low ethanol productivity relative to the total gel volume. (orig.)

  2. Biohydrogen production from xylose by fresh and digested activated sludge at 37, 55 and 70 °C.

    Science.gov (United States)

    Dessì, Paolo; Lakaniemi, Aino-Maija; Lens, Piet N L

    2017-05-15

    Two heat-treated inocula, fresh and digested activated sludge from the same municipal wastewater treatment plant, were compared for their H2 production via dark fermentation at mesophilic (37 °C), thermophilic (55 °C) and hyperthermophilic (70 °C) conditions using xylose as the substrate. At both 37 and 55 °C, the fresh activated sludge yielded more H2 than the digested sludge, whereas at 70 °C, neither of the inocula produced H2 effectively. A maximum yield of 1.85 mol H2 per mol of xylose consumed was obtained at 55 °C. H2 production was linked to acetate and butyrate production, and there was a linear correlation (R2 = 0.96) between the butyrate and H2 yield for the fresh activated sludge inoculum at 55 °C. Approximately 2.4 mol H2 per mol of butyrate produced were obtained against a theoretical maximum of 2.0, suggesting that H2 was produced via the acetate pathway prior to switching to the butyrate pathway due to the increased H2 partial pressure. Clostridia sp. were the prevalent species at both 37 and 55 °C, irrespectively of the inoculum type. Although the two inocula originated from the same plant, different thermophilic microorganisms were detected at 55 °C. Thermoanaerobacter sp., detected only in the fresh activated sludge cultures, may have contributed to the high H2 yield obtained with such an inoculum. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Ethanol production from paper sludge by simultaneous saccharification and co-fermentation using recombinant xylose-fermenting microorganisms.

    Science.gov (United States)

    Zhang, Jiayi; Lynd, Lee R

    2010-10-01

    Simultaneous saccharification and co-fermentation (SSCF) of waste paper sludge to ethanol was investigated using two recombinant xylose-fermenting microbes: Zymomonas mobilis 8b and Saccharomyces cerevisiae RWB222. S. cerevisiae RWB222 produced over 40 g/L ethanol with a yield of 0.39 g ethanol/g carbohydrate on paper sludge at 37 degrees C, while similar titers and yields were achieved by Z. mobilis 8b at 30 degrees C. Both S. cerevisiae RWB222 and Z. mobilis 8b exhibited decreasing cell viability at 37 degrees C when producing over 40 g/L ethanol. A high ethanol concentration can account for S. cerevisiae RWB222 viability loss, but ethanol concentration was not the only factor influencing Z. mobilis 8b viability loss at 37 degrees C. Over 3 g/L residual glucose was observed at the end of paper sludge SSCF by Z. mobilis 8b, and a statistical analysis revealed that a high calcium concentration originating from paper sludge, a high ethanol concentration, and a high temperature were the key interactive factors resulting in glucose accumulation. The highest ethanol yields were achieved by SSCF of paper sludge with S. cerevisiae RWB222 at 37 degrees C and Z. mobilis 8b at 30 degrees C. With good sugar consumption at 37 degrees C, S. cerevisiae RWB222 was able to gain an improvement in the polysaccharide to sugar yield compared to that at 30 degrees C, whereas Z. mobilis 8b at 30 degrees C had a lower polysaccharide to sugar yield, but a higher sugar to ethanol yield than S. cerevisiae. Both organisms under optimal conditions achieved a 19% higher overall conversion of paper sludge to ethanol than the non-xylose utilizing S. cerevisiae D5A at its optimal process temperature of 37 degrees C.

  4. Influence of solid loading on D-xylose production through dilute sulphuric acid hydrolysis of olive stones

    Directory of Open Access Journals (Sweden)

    Cuevas, M.

    2015-09-01

    Full Text Available The selective hydrolysis of hemicellulose from olive stones was attempted in order to achieve a maximum D-xylose yield. For this aim, batch hydrolysis was conducted under different operating conditions of temperature, acid concentration and solid loading. Firstly, distilled water, sulphuric acid and nitric acid were assessed as hydrolytic agents at different temperatures (200, 205, 210 and 220 °C and at a fixed acid concentration (0.025 M. Sulphuric acid and 200 °C were selected for the subsequent dilute acid hydrolysis optimization based on the obtained D-xylose yields. The combined influence of solid loading (from 29.3 to 170.7 g olive stones into 300 mL acid solution and sulphuric acid concentration (0.006–0.034 M on the release of D-xylose was then estimated by response surface methodology. According to a statistical analysis, both parameters had significant interaction effects on D-xylose production. The results illustrated that the higher the solid loading, the higher the required acid concentration. The decrease in the solid/liquid ratio in the reactor had a positive effect on D-xylose extraction and on the amount of acid used. The optimum solid loading and sulphuric acid concentration were determined to be 50 g (solid/liquid ratio 1/6 and 0.016 M, respectively. Under these conditions, the predicted D-xylose yield (expressed as g of sugar per 100 g of dry matter fed was 20.4 (87.2% of maximum attainable.Se ha desarrollado una hidrólisis selectiva de la fracción hemicelulósica del hueso de aceituna con el fin de obtener el máximo rendimiento de D-xilosa. Para ello las hidrólisis se llevaron a cabo en un reactor discontinuo a distintas condiciones de temperatura, concentración de ácido y carga de sólidos. En primer lugar se evaluó la capacidad hidrolítica del agua destilada y de los ácidos nítrico y sulfúrico a distintas temperaturas (200, 205, 210 y 220°C manteniendo fija la concentración de ácido (0,025 M. A partir de

  5. Evolvability Is an Evolved Ability: The Coding Concept as the Arch-Unit of Natural Selection.

    Science.gov (United States)

    Janković, Srdja; Ćirković, Milan M

    2016-03-01

    Physical processes that characterize living matter are qualitatively distinct in that they involve encoding and transfer of specific types of information. Such information plays an active part in the control of events that are ultimately linked to the capacity of the system to persist and multiply. This algorithmicity of life is a key prerequisite for its Darwinian evolution, driven by natural selection acting upon stochastically arising variations of the encoded information. The concept of evolvability attempts to define the total capacity of a system to evolve new encoded traits under appropriate conditions, i.e., the accessible section of total morphological space. Since this is dependent on previously evolved regulatory networks that govern information flow in the system, evolvability itself may be regarded as an evolved ability. The way information is physically written, read and modified in living cells (the "coding concept") has not changed substantially during the whole history of the Earth's biosphere. This biosphere, be it alone or one of many, is, accordingly, itself a product of natural selection, since the overall evolvability conferred by its coding concept (nucleic acids as information carriers with the "rulebook of meanings" provided by codons, as well as all the subsystems that regulate various conditional information-reading modes) certainly played a key role in enabling this biosphere to survive up to the present, through alterations of planetary conditions, including at least five catastrophic events linked to major mass extinctions. We submit that, whatever the actual prebiotic physical and chemical processes may have been on our home planet, or may, in principle, occur at some time and place in the Universe, a particular coding concept, with its respective potential to give rise to a biosphere, or class of biospheres, of a certain evolvability, may itself be regarded as a unit (indeed the arch-unit) of natural selection.

  6. Survivability is more fundamental than evolvability.

    Directory of Open Access Journals (Sweden)

    Michael E Palmer

    Full Text Available For a lineage to survive over long time periods, it must sometimes change. This has given rise to the term evolvability, meaning the tendency to produce adaptive variation. One lineage may be superior to another in terms of its current standing variation, or it may tend to produce more adaptive variation. However, evolutionary outcomes depend on more than standing variation and produced adaptive variation: deleterious variation also matters. Evolvability, as most commonly interpreted, is not predictive of evolutionary outcomes. Here, we define a predictive measure of the evolutionary success of a lineage that we call the k-survivability, defined as the probability that the lineage avoids extinction for k generations. We estimate the k-survivability using multiple experimental replicates. Because we measure evolutionary outcomes, the initial standing variation, the full spectrum of generated variation, and the heritability of that variation are all incorporated. Survivability also accounts for the decreased joint likelihood of extinction of sub-lineages when they 1 disperse in space, or 2 diversify in lifestyle. We illustrate measurement of survivability with in silico models, and suggest that it may also be measured in vivo using multiple longitudinal replicates. The k-survivability is a metric that enables the quantitative study of, for example, the evolution of 1 mutation rates, 2 dispersal mechanisms, 3 the genotype-phenotype map, and 4 sexual reproduction, in temporally and spatially fluctuating environments. Although these disparate phenomena evolve by well-understood microevolutionary rules, they are also subject to the macroevolutionary constraint of long-term survivability.

  7. Present weather and climate: evolving conditions

    Science.gov (United States)

    Hoerling, Martin P; Dettinger, Michael; Wolter, Klaus; Lukas, Jeff; Eischeid, Jon K.; Nemani, Rama; Liebmann, Brant; Kunkel, Kenneth E.

    2013-01-01

    This chapter assesses weather and climate variability and trends in the Southwest, using observed climate and paleoclimate records. It analyzes the last 100 years of climate variability in comparison to the last 1,000 years, and links the important features of evolving climate conditions to river flow variability in four of the region’s major drainage basins. The chapter closes with an assessment of the monitoring and scientific research needed to increase confidence in understanding when climate episodes, events, and phenomena are attributable to human-caused climate change.

  8. f( R) gravity solutions for evolving wormholes

    Science.gov (United States)

    Bhattacharya, Subhra; Chakraborty, Subenoy

    2017-08-01

    The scalar-tensor f( R) theory of gravity is considered in the framework of a simple inhomogeneous space-time model. In this research we use the reconstruction technique to look for possible evolving wormhole solutions within viable f( R) gravity formalism. These f( R) models are then constrained so that they are consistent with existing experimental data. Energy conditions related to the matter threading the wormhole are analyzed graphically and are in general found to obey the null energy conditions (NEC) in regions around the throat, while in the limit f(R)=R, NEC can be violated at large in regions around the throat.

  9. Information theory, evolutionary innovations and evolvability.

    Science.gov (United States)

    Wagner, Andreas

    2017-12-05

    How difficult is it to 'discover' an evolutionary adaptation or innovation? I here suggest that information theory, in combination with high-throughput DNA sequencing, can help answer this question by quantifying a new phenotype's information content. I apply this framework to compute the phenotypic information associated with novel gene regulation and with the ability to use novel carbon sources. The framework can also help quantify how DNA duplications affect evolvability, estimate the complexity of phenotypes and clarify the meaning of 'progress' in Darwinian evolution.This article is part of the themed issue 'Process and pattern in innovations from cells to societies'. © 2017 The Author(s).

  10. Evolving Random Forest for Preference Learning

    DEFF Research Database (Denmark)

    Abou-Zleikha, Mohamed; Shaker, Noor

    2015-01-01

    This paper introduces a novel approach for pairwise preference learning through a combination of an evolutionary method and random forest. Grammatical evolution is used to describe the structure of the trees in the Random Forest (RF) and to handle the process of evolution. Evolved random forests ...... obtained for predicting pairwise self-reports of users for the three emotional states engagement, frustration and challenge show very promising results that are comparable and in some cases superior to those obtained from state-of-the-art methods....

  11. Oil and gas impacts on transportation.

    Science.gov (United States)

    2015-01-01

    Colorados oil and gas industry is continually evolving, and there have been considerable changes in drilling techniques and geographic focus since the 2010 CDOT research study on Energy Development and the Transportation System. This research stud...

  12. Improved xylose metabolism by a CYC8 mutant of Saccharomyces cerevisiae

    NARCIS (Netherlands)

    Nijland, Jeroen G; Shin, Hyun Yong; Boender, Leonie G M; de Waal, Paul P; Klaassen, Paul; Driessen, Arnold J M

    Engineering Saccharomyces cerevisiae for the utilization of pentose sugars is an important goal for the production of second-generation bioethanol and biochemicals. However, S. cerevisiae lacks specific pentose transporters and, in the presence of glucose, pentoses enter the cell inefficiently via

  13. Netgram: Visualizing Communities in Evolving Networks.

    Directory of Open Access Journals (Sweden)

    Raghvendra Mall

    Full Text Available Real-world complex networks are dynamic in nature and change over time. The change is usually observed in the interactions within the network over time. Complex networks exhibit community like structures. A key feature of the dynamics of complex networks is the evolution of communities over time. Several methods have been proposed to detect and track the evolution of these groups over time. However, there is no generic tool which visualizes all the aspects of group evolution in dynamic networks including birth, death, splitting, merging, expansion, shrinkage and continuation of groups. In this paper, we propose Netgram: a tool for visualizing evolution of communities in time-evolving graphs. Netgram maintains evolution of communities over 2 consecutive time-stamps in tables which are used to create a query database using the sql outer-join operation. It uses a line-based visualization technique which adheres to certain design principles and aesthetic guidelines. Netgram uses a greedy solution to order the initial community information provided by the evolutionary clustering technique such that we have fewer line cross-overs in the visualization. This makes it easier to track the progress of individual communities in time evolving graphs. Netgram is a generic toolkit which can be used with any evolutionary community detection algorithm as illustrated in our experiments. We use Netgram for visualization of topic evolution in the NIPS conference over a period of 11 years and observe the emergence and merging of several disciplines in the field of information processing systems.

  14. Evolving MEMS Resonator Designs for Fabrication

    Science.gov (United States)

    Hornby, Gregory S.; Kraus, William F.; Lohn, Jason D.

    2008-01-01

    Because of their small size and high reliability, microelectromechanical (MEMS) devices have the potential to revolution many areas of engineering. As with conventionally-sized engineering design, there is likely to be a demand for the automated design of MEMS devices. This paper describes our current status as we progress toward our ultimate goal of using an evolutionary algorithm and a generative representation to produce designs of a MEMS device and successfully demonstrate its transfer to an actual chip. To produce designs that are likely to transfer to reality, we present two ways to modify evaluation of designs. The first is to add location noise, differences between the actual dimensions of the design and the design blueprint, which is a technique we have used for our work in evolving antennas and robots. The second method is to add prestress to model the warping that occurs during the extreme heat of fabrication. In future we expect to fabricate and test some MEMS resonators that are evolved in this way.

  15. Netgram: Visualizing Communities in Evolving Networks

    Science.gov (United States)

    Mall, Raghvendra; Langone, Rocco; Suykens, Johan A. K.

    2015-01-01

    Real-world complex networks are dynamic in nature and change over time. The change is usually observed in the interactions within the network over time. Complex networks exhibit community like structures. A key feature of the dynamics of complex networks is the evolution of communities over time. Several methods have been proposed to detect and track the evolution of these groups over time. However, there is no generic tool which visualizes all the aspects of group evolution in dynamic networks including birth, death, splitting, merging, expansion, shrinkage and continuation of groups. In this paper, we propose Netgram: a tool for visualizing evolution of communities in time-evolving graphs. Netgram maintains evolution of communities over 2 consecutive time-stamps in tables which are used to create a query database using the sql outer-join operation. It uses a line-based visualization technique which adheres to certain design principles and aesthetic guidelines. Netgram uses a greedy solution to order the initial community information provided by the evolutionary clustering technique such that we have fewer line cross-overs in the visualization. This makes it easier to track the progress of individual communities in time evolving graphs. Netgram is a generic toolkit which can be used with any evolutionary community detection algorithm as illustrated in our experiments. We use Netgram for visualization of topic evolution in the NIPS conference over a period of 11 years and observe the emergence and merging of several disciplines in the field of information processing systems. PMID:26356538

  16. BOOK REVIEW: OPENING SCIENCE, THE EVOLVING GUIDE ...

    Science.gov (United States)

    The way we get our funding, collaborate, do our research, and get the word out has evolved over hundreds of years but we can imagine a more open science world, largely facilitated by the internet. The movement towards this more open way of doing and presenting science is coming, and it is not taking hundreds of years. If you are interested in these trends, and would like to find out more about where this is all headed and what it means to you, consider downloding Opening Science, edited by Sönke Bartling and Sascha Friesike, subtitled The Evolving Guide on How the Internet is Changing Research, Collaboration, and Scholarly Publishing. In 26 chapters by various authors from a range of disciplines the book explores the developing world of open science, starting from the first scientific revolution and bringing us to the next scientific revolution, sometimes referred to as “Science 2.0”. Some of the articles deal with the impact of the changing landscape of how science is done, looking at the impact of open science on Academia, or journal publishing, or medical research. Many of the articles look at the uses, pitfalls, and impact of specific tools, like microblogging (think Twitter), social networking, and reference management. There is lots of discussion and definition of terms you might use or misuse like “altmetrics” and “impact factor”. Science will probably never be completely open, and Twitter will probably never replace the journal article,

  17. The influence of Aspergillus niger transcription factors AraR and XlnR in the gene expression during growth in D-xylose, L-arabinose and steam-exploded sugarcane bagasse.

    Science.gov (United States)

    de Souza, Wagner Rodrigo; Maitan-Alfenas, Gabriela Piccolo; de Gouvêa, Paula Fagundes; Brown, Neil Andrew; Savoldi, Marcela; Battaglia, Evy; Goldman, Maria Helena S; de Vries, Ronald P; Goldman, Gustavo Henrique

    2013-11-01

    The interest in the conversion of plant biomass to renewable fuels such as bioethanol has led to an increased investigation into the processes regulating biomass saccharification. The filamentous fungus Aspergillus niger is an important microorganism capable of producing a wide variety of plant biomass degrading enzymes. In A. niger the transcriptional activator XlnR and its close homolog, AraR, controls the main (hemi-)cellulolytic system responsible for plant polysaccharide degradation. Sugarcane is used worldwide as a feedstock for sugar and ethanol production, while the lignocellulosic residual bagasse can be used in different industrial applications, including ethanol production. The use of pentose sugars from hemicelluloses represents an opportunity to further increase production efficiencies. In the present study, we describe a global gene expression analysis of A. niger XlnR- and AraR-deficient mutant strains, grown on a D-xylose/L-arabinose monosaccharide mixture and steam-exploded sugarcane bagasse. Different gene sets of CAZy enzymes and sugar transporters were shown to be individually or dually regulated by XlnR and AraR, with XlnR appearing to be the major regulator on complex polysaccharides. Our study contributes to understanding of the complex regulatory mechanisms responsible for plant polysaccharide-degrading gene expression, and opens new possibilities for the engineering of fungi able to produce more efficient enzymatic cocktails to be used in biofuel production. Copyright © 2013 Elsevier Inc. All rights reserved.

  18. PENGARUH Ph, KADAR XILOSA DAN KADAR GLUKOSA TERHADAP PRODUKSI XYLITOL OLEH Candida shehatae WAY 08 [The Influence of Intial Xylose and Glucose Consentration on Xylitol production by Candida shehatae WAY 08

    Directory of Open Access Journals (Sweden)

    Wisnu Adi Yulianto 1

    2001-08-01

    Full Text Available The objectiviea of this research were to determine the optimum culture conditions of initial pH, xylose and glucose concentration for xylitol production by Candida shehatae WAY 08. The initial pH was altered whitin the range of 4-7, the xylose concentration from 5020%, and the glucose (cosubstrate from 0-4%. The fermentation was performed at 30°C in 500 ml erlenmeyer flaks placed in a shaker incubator at 250 rpm for 7d. biomas concentration war determined by oven method. Xylose, glucose and xylitol concentrations were determined by HPCL.the result incated that the highest xylitol volumetric productivity of Candida shehatae WAY 08 was 0,314 g/I/h at the initial pH of 5 in medium containing 150 g/I xylose. Addition of glucose into media inhibited the xylitol production, but in creased the xylitol yield.

  19. Evolvability as a Quality Attribute of Software Architectures

    NARCIS (Netherlands)

    Ciraci, S.; van den Broek, P.M.; Duchien, Laurence; D'Hondt, Maja; Mens, Tom

    We review the definition of evolvability as it appears on the literature. In particular, the concept of software evolvability is compared with other system quality attributes, such as adaptability, maintainability and modifiability.

  20. Escherichia coli kgtP encodes an alpha-ketoglutarate transporter.

    OpenAIRE

    Seol, W; Shatkin, A J

    1991-01-01

    The witA gene located between pss and rrnG on the Escherichia coli chromosome encodes a 432-amino acid protein. It is homologous to a human hepatoma glucose transporter and to E. coli membrane proteins that transport citrate (CitA), arabinose (AraE), and xylose (XylE), and, like these carrier proteins, WitA also contains 12 highly hydrophobic putative membrane-spanning regions. Gene disruption mutants constructed in two E. coli strains grew slowly or not at all, depending on genetic backgroun...

  1. Tracking correlated, simultaneously evolving target populations, II

    Science.gov (United States)

    Mahler, Ronald

    2017-05-01

    This paper is the sixth in a series aimed at weakening the independence assumptions that are typically presumed in multitarget tracking. Earlier papers investigated Bayes …lters that propagate the correlations between two evolving multitarget systems. Last year at this conference we attempted to derive PHD …lter-type approximations that account for both spatial correlation and cardinality correlation (i.e., correlation between the target numbers of the two systems). Unfortunately, this approach required heuristic models of both clutter and target appearance in order to incorporate both spatial and cardinality correlation. This paper describes a fully rigorous approach- provided, however, that spatial correlation between the two populations is ignored and only their cardinality correlations are taken into account. We derive the time-update and measurement-update equations for a CPHD …lter describing the evolution of such correlated multitarget populations.

  2. A local-world evolving hypernetwork model

    Science.gov (United States)

    Yang, Guang-Yong; Liu, Jian-Guo

    2014-01-01

    Complex hypernetworks are ubiquitous in the real system. It is very important to investigate the evolution mechanisms. In this paper, we present a local-world evolving hypernetwork model by taking into account the hyperedge growth and local-world hyperedge preferential attachment mechanisms. At each time step, a newly added hyperedge encircles a new coming node and a number of nodes from a randomly selected local world. The number of the selected nodes from the local world obeys the uniform distribution and its mean value is m. The analytical and simulation results show that the hyperdegree approximately obeys the power-law form and the exponent of hyperdegree distribution is γ = 2 + 1/m. Furthermore, we numerically investigate the node degree, hyperedge degree, clustering coefficient, as well as the average distance, and find that the hypernetwork model shares the scale-free and small-world properties, which shed some light for deeply understanding the evolution mechanism of the real systems.

  3. The Evolving Theory of Evolutionary Radiations.

    Science.gov (United States)

    Simões, M; Breitkreuz, L; Alvarado, M; Baca, S; Cooper, J C; Heins, L; Herzog, K; Lieberman, B S

    2016-01-01

    Evolutionary radiations have intrigued biologists for more than 100 years, and our understanding of the patterns and processes associated with these radiations continues to grow and evolve. Recently it has been recognized that there are many different types of evolutionary radiation beyond the well-studied adaptive radiations. We focus here on multifarious types of evolutionary radiations, paying special attention to the abiotic factors that might trigger diversification in clades. We integrate concepts such as exaptation, species selection, coevolution, and the turnover-pulse hypothesis (TPH) into the theoretical framework of evolutionary radiations. We also discuss other phenomena that are related to, but distinct from, evolutionary radiations that have relevance for evolutionary biology. Copyright © 2015 Elsevier Ltd. All rights reserved.

  4. Epidemic spreading on evolving signed networks

    CERN Document Server

    Saeedian, M; Jafari, G R; Kertesz, J

    2016-01-01

    Most studies of disease spreading consider the underlying social network as obtained without the contagion, though epidemic influences peoples willingness to contact others: A friendly contact may be turned to unfriendly to avoid infection. We study the susceptible-infected (SI) disease spreading model on signed networks, in which each edge is associated with a positive or negative sign representing the friendly or unfriendly relation between its end nodes. In a signed network, according to Heiders theory, edge signs evolve such that finally a state of structural balance is achieved, corresponding to no frustration in physics terms. However, the danger of infection affects the evolution of its edge signs. To describe the coupled problem of the sign evolution and disease spreading, we generalize the notion of structural balance by taking into account the state of the nodes. We introduce an energy function and carry out Monte-Carlo simulations on complete networks to test the energy landscape, where we find loc...

  5. Finch: A System for Evolving Java (Bytecode)

    Science.gov (United States)

    Orlov, Michael; Sipper, Moshe

    The established approach in genetic programming (GP) involves the definition of functions and terminals appropriate to the problem at hand, after which evolution of expressions using these definitions takes place. We have recently developed a system, dubbed FINCH (Fertile Darwinian Bytecode Harvester), to evolutionarily improve actual, extant software, which was not intentionally written for the purpose of serving as a GP representation in particular, nor for evolution in general. This is in contrast to existing work that uses restricted subsets of the Java bytecode instruction set as a representation language for individuals in genetic programming. The ability to evolve Java programs will hopefully lead to a valuable new tool in the software engineer's toolkit.

  6. Obtaining partial purified xylose reductase from Candida guilliermondii Obtenção de xilose redutase de Candida guilliermondii parcialmente purificada

    Directory of Open Access Journals (Sweden)

    Ester Junko Tomotani

    2009-09-01

    Full Text Available The enzymatic bioconversion of xylose into xylitol by xylose reductase (XR is an alternative for chemical and microbiological processes. The partial purified XR was obtained by using the following three procedures: an agarose column, a membrane reactor or an Amicon Ultra-15 50K Centrifugal Filter device at yields of 40%, 7% and 67%, respectively.A bioconversão enzimática da xilose em xilitol pela xilose redutase (XR é uma alternativa para as vias química e microbiológica. Avaliouse a purificação parcial da XR, utilizando os três seguintes procedimentos: uma coluna de agarose, um reator com membrana ou tubos de ultracentrifugação Amicon Ultra-15 50K, com rendimento de 40%, 7% ou 67%, respectivamente.

  7. Untersuchung des Xylose- und Arabinose-Stoffwechsels in Clostridium acetobutylicum ATCC 824 und Clostridium saccharobutylicum NCP 262.

    OpenAIRE

    Lesiak, Justyna Maria

    2015-01-01

    Xylulose kinase (xylB) and arabinose kinase (araK) mutants of Clostridium acetobutylicum and C. saccharobutylicum were investigated and compared to wild type strains, regarding their abilities to metabolize xylose, arabinose and glucose. To create mutants in C. saccharobutylicum, an effective triparental mating system for DNA transfer was developed, and additionally restrictase mutants were constructed and characterized. Furthermore, growth and gene expression of C. acetobutylicum in continuo...

  8. Unearthing the ecology of soil microorganisms using a high resolution DNA-SIP approach to explore cellulose and xylose metabolism in soil

    Directory of Open Access Journals (Sweden)

    Charles ePepe-Ranney

    2016-05-01

    Full Text Available We explored microbial contributions to decomposition using a sophisticated approach to DNA Stable Isotope Probing (SIP. Our experiment evaluated the dynamics and ecological characteristics of functionally defined microbial groups that metabolize labile and structural C in soils. We added to soil a complex amendment representing plant derived organic matter substituted with either 13C-xylose or 13C-cellulose to represent labile and structural C pools derived from abundant components of plant biomass. We found evidence for 13C-incorporation into DNA from 13C-xylose and 13C-cellulose in 49 and 63 operational taxonomic units (OTUs, respectively. The types of microorganisms that assimilated 13C in the 13C-xylose treatment changed over time being predominantly Firmicutes at day 1 followed by Bacteroidetes at day 3 and then Actinobacteria at day 7. These 13C-labeling dynamics suggest labile C traveled through different trophic levels. In contrast, microorganisms generally metabolized cellulose-C after 14 days and did not change to the same extent in phylogenetic composition over time. Microorganisms that metabolized cellulose-C belonged to poorly characterized but cosmopolitan soil lineages including Verrucomicrobia, Chloroflexi and Planctomycetes.

  9. Inverse metabolic engineering based on transient acclimation of yeast improves acid-containing xylose fermentation and tolerance to formic and acetic acids.

    Science.gov (United States)

    Hasunuma, Tomohisa; Sakamoto, Takatoshi; Kondo, Akihiko

    2016-01-01

    Improving the production of ethanol from xylose is an important goal in metabolic engineering of Saccharomyces cerevisiae. Furthermore, S. cerevisiae must produce ethanol in the presence of weak acids (formate and acetate) generated during pre-treatment of lignocellulosic biomass. In this study, weak acid-containing xylose fermentation was significantly improved using cells that were acclimated to the weak acids during pre-cultivation. Transcriptome analyses showed that levels of transcripts for transcriptional/translational machinery-related genes (RTC3 and ANB1) were enhanced by formate and acetate acclimation. Recombinant yeast strains overexpressing RTC3 and ANB1 demonstrated improved ethanol production from xylose in the presence of the weak acids, along with improved tolerance to the acids. Novel metabolic engineering strategy based on the combination of short-term acclimation and system-wide analysis was developed, which can develop stress-tolerant strains in a short period of time, although conventional evolutionary engineering approach has required long periods of time to isolate inhibitor-adapted strains.

  10. Ethanol production from glucose and xylose obtained from steam exploded water-extracted olive tree pruning using phosphoric acid as catalyst.

    Science.gov (United States)

    Negro, M J; Alvarez, C; Ballesteros, I; Romero, I; Ballesteros, M; Castro, E; Manzanares, P; Moya, M; Oliva, J M

    2014-02-01

    In this work, the effect of phosphoric acid (1% w/w) in steam explosion pretreatment of water extracted olive tree pruning at 175°C and 195°C was evaluated. The objective is to produce ethanol from all sugars (mainly glucose and xylose) contained in the pretreated material. The water insoluble fraction obtained after pretreatment was used as substrate in a simultaneous saccharification and fermentation (SSF) process by a commercial strain of Saccharomyces cerevisiae. The liquid fraction, containing mainly xylose, was detoxified by alkali and ion-exchange resin and then fermented by the xylose fermenting yeast Scheffersomyces stipitis. Ethanol yields reached in a SSF process were close to 80% when using 15% (w/w) substrate consistency and about 70% of theoretical when using prehydrolysates detoxified by ion-exchange resins. Considering sugars recovery and ethanol yields about 160g of ethanol from kg of water extracted olive tree pruning could be obtained. Copyright © 2013 Elsevier Ltd. All rights reserved.

  11. Enterococcus faecium QU 50: a novel thermophilic lactic acid bacterium for high-yield l-lactic acid production from xylose.

    Science.gov (United States)

    Abdel-Rahman, Mohamed Ali; Tashiro, Yukihiro; Zendo, Takeshi; Sakai, Kenji; Sonomoto, Kenji

    2015-01-01

    Production of optically pure lactic acid from lignocellulosic material for commercial purposes is hampered by several difficulties, including heterofermentation of pentose sugars and high energy consumption by mesophilic lactic acid bacteria. Here, we report a novel lactic acid bacterium, strain QU 50, that has the potential to produce optically pure l-lactic acid (≥99.2%) in a homofermentative manner from xylose under thermophilic conditions. Strain QU 50 was isolated from Egyptian fertile soil and identified as Enterococcus faecium QU 50 by analyzing its sugar fermentation pattern and 16S rRNA gene sequence. Enterococcus faecium QU 50 fermented xylose efficiently to produce lactic acid over wide pH (6.0-10.0) and temperature ranges (30-52°C), with a pH of 6.5 and temperature of 50°C being optimal. To our knowledge, this is the first report of homofermentative lactic acid production from xylose by a thermophilic lactic acid bacterium. © FEMS 2014. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  12. Variation in the degree of D-xylose substitution in water-extractable European durum wheat (Triticum durum desf.) semolina arabinoxylans.

    Science.gov (United States)

    Roels, S P; Collado, M; Loosveld, A M; Grobet, P J; Delcour, J A

    1999-05-01

    Durum wheat (Triticum durum Desf.) semolina water-extractable arabinoxylan (TWEAX) (yield 0.28%, arabinose-to-xylose ratio (A/X) 0. 62) was fractionated by a stepwise increase in ethanol concentration (up to 65%). The A/X ratios of the resulting fractions varied between 0.42 and 0.80. With increasing ethanol concentrations, increasing A/X ratios went hand in hand with a relative increase of low molecular weight compounds, indicating that high molecular weight compounds with a low A/X ratio are preferentially precipitated from alcohol/water mixtures. (1)H NMR showed that, whereas in TWEAX the levels of unsubstituted xyloses (X(0)), monosubstituted (X(1)), and disubstituted (X(2)) xyloses were 63.1%, 11.8%, and 25.1%, respectively, fractions that precipitated with increasing ethanol concentrations had decreasing levels of X(0). Simultaneously, the level of X(1) decreased equally until it leveled of at ca. 10%. Concomitantly, the level of X(2) increased. The levels of X(0), X(1), and X(2) varied between 69.7% and 53.4%, 18.2% and 10.7%, and 12.2% and 35.9%, respectively.

  13. Development of an industrial medium for economical 2,3-butanediol production through co-fermentation of glucose and xylose by Klebsiella oxytoca.

    Science.gov (United States)

    Ji, Xiao-Jun; Huang, He; Du, Jun; Zhu, Jian-Guo; Ren, Lu-Jing; Li, Shuang; Nie, Zhi-Kui

    2009-11-01

    An industrial medium containing urea as a sole nitrogen source, low levels of corn steep liquor and mineral salts as nutrition factors to retain high 2,3-butanediol production through co-fermentation of glucose and xylose (2:1, wt/wt) by Klebsiella oxytoca was developed. Urea and corn steep liquor were identified as the most significant factors by the two-level Plackett-Burman design. Steepest ascent experiments were applied to approach the optimal region of the two factors and a central composite design was employed to determine their optimal levels. Under the optimal medium, the yield of 2,3-butanediol plus acetoin relative to glucose and xylose was up to 0.428 g/g, which was 85.6% of theoretical value. The cheap nitrogen source and nutrition factors combining the co-fermentation process using lignocellulose derived glucose and xylose as the carbon source in the developed medium would be a potential solution to improve the economics of microbial 2,3-butanediol production.

  14. The evolving energy budget of accretionary wedges

    Science.gov (United States)

    McBeck, Jessica; Cooke, Michele; Maillot, Bertrand; Souloumiac, Pauline

    2017-04-01

    The energy budget of evolving accretionary systems reveals how deformational processes partition energy as faults slip, topography uplifts, and layer-parallel shortening produces distributed off-fault deformation. The energy budget provides a quantitative framework for evaluating the energetic contribution or consumption of diverse deformation mechanisms. We investigate energy partitioning in evolving accretionary prisms by synthesizing data from physical sand accretion experiments and numerical accretion simulations. We incorporate incremental strain fields and cumulative force measurements from two suites of experiments to design numerical simulations that represent accretionary wedges with stronger and weaker detachment faults. One suite of the physical experiments includes a basal glass bead layer and the other does not. Two physical experiments within each suite implement different boundary conditions (stable base versus moving base configuration). Synthesizing observations from the differing base configurations reduces the influence of sidewall friction because the force vector produced by sidewall friction points in opposite directions depending on whether the base is fixed or moving. With the numerical simulations, we calculate the energy budget at two stages of accretion: at the maximum force preceding the development of the first thrust pair, and at the minimum force following the development of the pair. To identify the appropriate combination of material and fault properties to apply in the simulations, we systematically vary the Young's modulus and the fault static and dynamic friction coefficients in numerical accretion simulations, and identify the set of parameters that minimizes the misfit between the normal force measured on the physical backwall and the numerically simulated force. Following this derivation of the appropriate material and fault properties, we calculate the components of the work budget in the numerical simulations and in the

  15. On the Critical Role of Divergent Selection in Evolvability

    Directory of Open Access Journals (Sweden)

    Joel Lehman

    2016-08-01

    Full Text Available An ambitious goal in evolutionary robotics is to evolve increasingly complex robotic behaviors with minimal human design effort. Reaching this goal requires evolutionary algorithms that can unlock from genetic encodings their latent potential for evolvability. One issue clouding this goal is conceptual confusion about evolvability, which often obscures the aspects of evolvability that are important or desirable. The danger from such confusion is that it may establish unrealistic goals for evolvability that prove unproductive in practice. An important issue separate from conceptual confusion is the common misalignment between selection and evolvability in evolutionary robotics. While more expressive encodings can represent higher-level adaptations (e.g. sexual reproduction or developmental systems that increase long-term evolutionary potential (i.e. evolvability, realizing such potential requires gradients of fitness and evolvability to align. In other words, selection is often a critical factor limiting increasing evolvability. Thus, drawing from a series of recent papers, this article seeks to both (1 clarify and focus the ways in which the term evolvability is used within artificial evolution, and (2 argue for the importance of one type of selection, i.e. divergent selection, for enabling evolvability. The main argument is that there is a fundamental connection between divergent selection and evolvability (on both the individual and population level that does not hold for typical goal-oriented selection. The conclusion is that selection pressure plays a critical role in realizing the potential for evolvability, and that divergent selection in particular provides a principled mechanism for encouraging evolvability in artificial evolution.

  16. How does cognition evolve? Phylogenetic comparative psychology

    Science.gov (United States)

    Matthews, Luke J.; Hare, Brian A.; Nunn, Charles L.; Anderson, Rindy C.; Aureli, Filippo; Brannon, Elizabeth M.; Call, Josep; Drea, Christine M.; Emery, Nathan J.; Haun, Daniel B. M.; Herrmann, Esther; Jacobs, Lucia F.; Platt, Michael L.; Rosati, Alexandra G.; Sandel, Aaron A.; Schroepfer, Kara K.; Seed, Amanda M.; Tan, Jingzhi; van Schaik, Carel P.; Wobber, Victoria

    2014-01-01

    Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution. PMID:21927850

  17. Approximating centrality in evolving graphs: toward sublinearity

    Science.gov (United States)

    Priest, Benjamin W.; Cybenko, George

    2017-05-01

    The identification of important nodes is a ubiquitous problem in the analysis of social networks. Centrality indices (such as degree centrality, closeness centrality, betweenness centrality, PageRank, and others) are used across many domains to accomplish this task. However, the computation of such indices is expensive on large graphs. Moreover, evolving graphs are becoming increasingly important in many applications. It is therefore desirable to develop on-line algorithms that can approximate centrality measures using memory sublinear in the size of the graph. We discuss the challenges facing the semi-streaming computation of many centrality indices. In particular, we apply recent advances in the streaming and sketching literature to provide a preliminary streaming approximation algorithm for degree centrality utilizing CountSketch and a multi-pass semi-streaming approximation algorithm for closeness centrality leveraging a spanner obtained through iteratively sketching the vertex-edge adjacency matrix. We also discuss possible ways forward for approximating betweenness centrality, as well as spectral measures of centrality. We provide a preliminary result using sketched low-rank approximations to approximate the output of the HITS algorithm.

  18. How does cognition evolve? Phylogenetic comparative psychology.

    Science.gov (United States)

    MacLean, Evan L; Matthews, Luke J; Hare, Brian A; Nunn, Charles L; Anderson, Rindy C; Aureli, Filippo; Brannon, Elizabeth M; Call, Josep; Drea, Christine M; Emery, Nathan J; Haun, Daniel B M; Herrmann, Esther; Jacobs, Lucia F; Platt, Michael L; Rosati, Alexandra G; Sandel, Aaron A; Schroepfer, Kara K; Seed, Amanda M; Tan, Jingzhi; van Schaik, Carel P; Wobber, Victoria

    2012-03-01

    Now more than ever animal studies have the potential to test hypotheses regarding how cognition evolves. Comparative psychologists have developed new techniques to probe the cognitive mechanisms underlying animal behavior, and they have become increasingly skillful at adapting methodologies to test multiple species. Meanwhile, evolutionary biologists have generated quantitative approaches to investigate the phylogenetic distribution and function of phenotypic traits, including cognition. In particular, phylogenetic methods can quantitatively (1) test whether specific cognitive abilities are correlated with life history (e.g., lifespan), morphology (e.g., brain size), or socio-ecological variables (e.g., social system), (2) measure how strongly phylogenetic relatedness predicts the distribution of cognitive skills across species, and (3) estimate the ancestral state of a given cognitive trait using measures of cognitive performance from extant species. Phylogenetic methods can also be used to guide the selection of species comparisons that offer the strongest tests of a priori predictions of cognitive evolutionary hypotheses (i.e., phylogenetic targeting). Here, we explain how an integration of comparative psychology and evolutionary biology will answer a host of questions regarding the phylogenetic distribution and history of cognitive traits, as well as the evolutionary processes that drove their evolution.

  19. On the Discovery of Evolving Truth.

    Science.gov (United States)

    Li, Yaliang; Li, Qi; Gao, Jing; Su, Lu; Zhao, Bo; Fan, Wei; Han, Jiawei

    2015-08-01

    In the era of big data, information regarding the same objects can be collected from increasingly more sources. Unfortunately, there usually exist conflicts among the information coming from different sources. To tackle this challenge, truth discovery, i.e., to integrate multi-source noisy information by estimating the reliability of each source, has emerged as a hot topic. In many real world applications, however, the information may come sequentially, and as a consequence, the truth of objects as well as the reliability of sources may be dynamically evolving. Existing truth discovery methods, unfortunately, cannot handle such scenarios. To address this problem, we investigate the temporal relations among both object truths and source reliability, and propose an incremental truth discovery framework that can dynamically update object truths and source weights upon the arrival of new data. Theoretical analysis is provided to show that the proposed method is guaranteed to converge at a fast rate. The experiments on three real world applications and a set of synthetic data demonstrate the advantages of the proposed method over state-of-the-art truth discovery methods.

  20. Sexual regret: evidence for evolved sex differences.

    Science.gov (United States)

    Galperin, Andrew; Haselton, Martie G; Frederick, David A; Poore, Joshua; von Hippel, William; Buss, David M; Gonzaga, Gian C

    2013-10-01

    Regret and anticipated regret enhance decision quality by helping people avoid making and repeating mistakes. Some of people's most intense regrets concern sexual decisions. We hypothesized evolved sex differences in women's and men's experiences of sexual regret. Because of women's higher obligatory costs of reproduction throughout evolutionary history, we hypothesized that sexual actions, particularly those involving casual sex, would be regretted more intensely by women than by men. In contrast, because missed sexual opportunities historically carried higher reproductive fitness costs for men than for women, we hypothesized that poorly chosen sexual inactions would be regretted more by men than by women. Across three studies (Ns = 200, 395, and 24,230), we tested these hypotheses using free responses, written scenarios, detailed checklists, and Internet sampling to achieve participant diversity, including diversity in sexual orientation. Across all data sources, results supported predicted psychological sex differences and these differences were localized in casual sex contexts. These findings are consistent with the notion that the psychology of sexual regret was shaped by recurrent sex differences in selection pressures operating over deep time.

  1. Extracting evolving pathologies via spectral clustering.

    Science.gov (United States)

    Bernardis, Elena; Pohl, Kilian M; Davatzikos, Christos

    2013-01-01

    A bottleneck in the analysis of longitudinal MR scans with white matter brain lesions is the temporally consistent segmentation of the pathology. We identify pathologies in 3D+t(ime) within a spectral graph clustering framework. Our clustering approach simultaneously segments and tracks the evolving lesions by identifying characteristic image patterns at each time-point and voxel correspondences across time-points. For each 3D image, our method constructs a graph where weights between nodes capture the likeliness of two voxels belonging to the same region. Based on these weights, we then establish rough correspondences between graph nodes at different time-points along estimated pathology evolution directions. We combine the graphs by aligning the weights to a reference time-point, thus integrating temporal information across the 3D images, and formulate the 3D+t segmentation problem as a binary partitioning of this graph. The resulting segmentation is very robust to local intensity fluctuations and yields better results than segmentations generated for each time-point.

  2. Functional Topology of Evolving Urban Drainage Networks

    Science.gov (United States)

    Yang, Soohyun; Paik, Kyungrock; McGrath, Gavan S.; Urich, Christian; Krueger, Elisabeth; Kumar, Praveen; Rao, P. Suresh C.

    2017-11-01

    We investigated the scaling and topology of engineered urban drainage networks (UDNs) in two cities, and further examined UDN evolution over decades. UDN scaling was analyzed using two power law scaling characteristics widely employed for river networks: (1) Hack's law of length (L)-area (A) [L∝Ah] and (2) exceedance probability distribution of upstream contributing area (δ) [P>(A≥δ>)˜aδ-ɛ]. For the smallest UDNs ((A≥δ>) plots for river networks are abruptly truncated, those for UDNs display exponential tempering [P>(A≥δ>)=aδ-ɛexp⁡>(-cδ>)]. The tempering parameter c decreases as the UDNs grow, implying that the distribution evolves in time to resemble those for river networks. However, the power law exponent ɛ for large UDNs tends to be greater than the range reported for river networks. Differences in generative processes and engineering design constraints contribute to observed differences in the evolution of UDNs and river networks, including subnet heterogeneity and nonrandom branching.

  3. The Evolving Classification of Pulmonary Hypertension.

    Science.gov (United States)

    Foshat, Michelle; Boroumand, Nahal

    2017-05-01

    - An explosion of information on pulmonary hypertension has occurred during the past few decades. The perception of this disease has shifted from purely clinical to incorporate new knowledge of the underlying pathology. This transfer has occurred in light of advancements in pathophysiology, histology, and molecular medical diagnostics. - To update readers about the evolving understanding of the etiology and pathogenesis of pulmonary hypertension and to demonstrate how pathology has shaped the current classification. - Information presented at the 5 World Symposia on pulmonary hypertension held since 1973, with the last meeting occurring in 2013, was used in this review. - Pulmonary hypertension represents a heterogeneous group of disorders that are differentiated based on differences in clinical, hemodynamic, and histopathologic features. Early concepts of pulmonary hypertension were largely influenced by pharmacotherapy, hemodynamic function, and clinical presentation of the disease. The initial nomenclature for pulmonary hypertension segregated the clinical classifications from pathologic subtypes. Major restructuring of this disease classification occurred between the first and second symposia, which was the first to unite clinical and pathologic information in the categorization scheme. Additional changes were introduced in subsequent meetings, particularly between the third and fourth World Symposia meetings, when additional pathophysiologic information was gained. Discoveries in molecular diagnostics significantly progressed the understanding of idiopathic pulmonary arterial hypertension. Continued advancements in imaging modalities, mechanistic pathogenicity, and molecular biomarkers will enable physicians to define pulmonary hypertension phenotypes based on the pathobiology and allow for treatment customization.

  4. Evolving application of biomimetic nanostructured hydroxyapatite

    Directory of Open Access Journals (Sweden)

    Norberto Roveri

    2010-11-01

    Full Text Available Norberto Roveri, Michele IafiscoLaboratory of Environmental and Biological Structural Chemistry (LEBSC, Dipartimento di Chimica ‘G. Ciamician’, Alma Mater Studiorum, Università di Bologna, Bologna, ItalyAbstract: By mimicking Nature, we can design and synthesize inorganic smart materials that are reactive to biological tissues. These smart materials can be utilized to design innovative third-generation biomaterials, which are able to not only optimize their interaction with biological tissues and environment, but also mimic biogenic materials in their functionalities. The biomedical applications involve increasing the biomimetic levels from chemical composition, structural organization, morphology, mechanical behavior, nanostructure, and bulk and surface chemical–physical properties until the surface becomes bioreactive and stimulates cellular materials. The chemical–physical characteristics of biogenic hydroxyapatites from bone and tooth have been described, in order to point out the elective sides, which are important to reproduce the design of a new biomimetic synthetic hydroxyapatite. This review outlines the evolving applications of biomimetic synthetic calcium phosphates, details the main characteristics of bone and tooth, where the calcium phosphates are present, and discusses the chemical–physical characteristics of biomimetic calcium phosphates, methods of synthesizing them, and some of their biomedical applications.Keywords: hydroxyapatite, nanocrystals, biomimetism, biomaterials, drug delivery, remineralization

  5. Evolving application of biomimetic nanostructured hydroxyapatite.

    Science.gov (United States)

    Roveri, Norberto; Iafisco, Michele

    2010-11-09

    By mimicking Nature, we can design and synthesize inorganic smart materials that are reactive to biological tissues. These smart materials can be utilized to design innovative third-generation biomaterials, which are able to not only optimize their interaction with biological tissues and environment, but also mimic biogenic materials in their functionalities. The biomedical applications involve increasing the biomimetic levels from chemical composition, structural organization, morphology, mechanical behavior, nanostructure, and bulk and surface chemical-physical properties until the surface becomes bioreactive and stimulates cellular materials. The chemical-physical characteristics of biogenic hydroxyapatites from bone and tooth have been described, in order to point out the elective sides, which are important to reproduce the design of a new biomimetic synthetic hydroxyapatite. This review outlines the evolving applications of biomimetic synthetic calcium phosphates, details the main characteristics of bone and tooth, where the calcium phosphates are present, and discusses the chemical-physical characteristics of biomimetic calcium phosphates, methods of synthesizing them, and some of their biomedical applications.

  6. Epidemic spreading on evolving signed networks

    Science.gov (United States)

    Saeedian, M.; Azimi-Tafreshi, N.; Jafari, G. R.; Kertesz, J.

    2017-02-01

    Most studies of disease spreading consider the underlying social network as obtained without the contagion, though epidemic influences people's willingness to contact others: A "friendly" contact may be turned to "unfriendly" to avoid infection. We study the susceptible-infected disease-spreading model on signed networks, in which each edge is associated with a positive or negative sign representing the friendly or unfriendly relation between its end nodes. In a signed network, according to Heider's theory, edge signs evolve such that finally a state of structural balance is achieved, corresponding to no frustration in physics terms. However, the danger of infection affects the evolution of its edge signs. To describe the coupled problem of the sign evolution and disease spreading, we generalize the notion of structural balance by taking into account the state of the nodes. We introduce an energy function and carry out Monte Carlo simulations on complete networks to test the energy landscape, where we find local minima corresponding to the so-called jammed states. We study the effect of the ratio of initial friendly to unfriendly connections on the propagation of disease. The steady state can be balanced or a jammed state such that a coexistence occurs between susceptible and infected nodes in the system.

  7. Orbital Decay in Binaries with Evolved Stars

    Science.gov (United States)

    Sun, Meng; Arras, Phil; Weinberg, Nevin N.; Troup, Nicholas; Majewski, Steven R.

    2018-01-01

    Two mechanisms are often invoked to explain tidal friction in binary systems. The ``dynamical tide” is the resonant excitation of internal gravity waves by the tide, and their subsequent damping by nonlinear fluid processes or thermal diffusion. The ``equilibrium tide” refers to non-resonant excitation of fluid motion in the star’s convection zone, with damping by interaction with the turbulent eddies. There have been numerous studies of these processes in main sequence stars, but less so on the subgiant and red giant branches. Motivated by the newly discovered close binary systems in the Apache Point Observatory Galactic Evolution Experiment (APOGEE-1), we have performed calculations of both the dynamical and equilibrium tide processes for stars over a range of mass as the star’s cease core hydrogen burning and evolve to shell burning. Even for stars which had a radiative core on the main sequence, the dynamical tide may have very large amplitude in the newly radiative core in post-main sequence, giving rise to wave breaking. The resulting large dynamical tide dissipation rate is compared to the equilibrium tide, and the range of secondary masses and orbital periods over which rapid orbital decay may occur will be discussed, as well as applications to close APOGEE binaries.

  8. UKAEA'S evolving contract philosophy

    Energy Technology Data Exchange (ETDEWEB)

    Nicol, R. D. [UK Atomic Energy Authority, UKAEA, Harwell, Oxfordshire (United Kingdom)

    2003-07-01

    The United Kingdom Atomic Energy Authority (UKAEA) has gone through fundamental change over the last ten years. At the heart of this change has been UKAEA's relationship with the contracting and supply market. This paper describes the way in which UKAEA actively developed the market to support the decommissioning programme, and how the approach to contracting has evolved as external pressures and demands have changed. UKAEA's pro-active approach to industry has greatly assisted the development of a healthy, competitive market for services supporting decommissioning in the UK. There have been difficult changes and many challenges along the way, and some retrenchment was necessary to meet regulatory requirements. Nevertheless, UKAEA has sustained a high level of competition - now measured in terms of competed spend as a proportion of competable spend - with annual out-turns consistently over 80%. The prime responsibility for market development will pass to the new Nuclear Decommissioning Authority (NDA) in 2005, as the owner, on behalf of the Government, of the UK's civil nuclear liabilities. The preparatory work for the NDA indicates that the principles established by UKAEA will be carried forward. (author)

  9. An evolving model of online bipartite networks

    Science.gov (United States)

    Zhang, Chu-Xu; Zhang, Zi-Ke; Liu, Chuang

    2013-12-01

    Understanding the structure and evolution of online bipartite networks is a significant task since they play a crucial role in various e-commerce services nowadays. Recently, various attempts have been tried to propose different models, resulting in either power-law or exponential degree distributions. However, many empirical results show that the user degree distribution actually follows a shifted power-law distribution, the so-called Mandelbrot’s law, which cannot be fully described by previous models. In this paper, we propose an evolving model, considering two different user behaviors: random and preferential attachment. Extensive empirical results on two real bipartite networks, Delicious and CiteULike, show that the theoretical model can well characterize the structure of real networks for both user and object degree distributions. In addition, we introduce a structural parameter p, to demonstrate that the hybrid user behavior leads to the shifted power-law degree distribution, and the region of power-law tail will increase with the increment of p. The proposed model might shed some lights in understanding the underlying laws governing the structure of real online bipartite networks.

  10. Effects of furfural and acetic acid on growth and lipid production from glucose and xylose by Rhodotorula glutinis

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Guochang; French, William Todd; Hernandez, Rafael; Alley, Earl; Paraschivescu, Maria [Dave C. Swalm School of Chemical Engineering, Mississippi State University, P.O. Box 9595, Mississippi State, MS 39762 (United States)

    2011-01-15

    Microbial conversion of lignocellulosic sugars to triacylglycerols (a biodiesel or renewable diesel feedstock) was investigated using the oleaginous yeast Rhodotorula glutinis (ATCC 15125). In the shake flask experiments, R. glutinis was first grown in a nitrogen-rich medium utilizing an artificial acid hydrolysate of lignocellulosic biomass switchgrass as the sole carbon and energy source. Once the culture had reached the stationary phase, the cells were harvested and transferred to a fresh nitrogen-free media containing artificial acid hydrolysate sugars for lipid accumulation. Analysis of the data collected showed that the yeast were able to grow in the medium containing artificial acid hydrolysate sugars as the carbon and energy source. The net specific Growth rate(s) indicated that the presence of acetic acid and furfural in the artificial acid hydrolysate inhibited the growth of R. glutinis on glucose, but not the growth on xylose. The lipid accumulated in the cells, determined by gravimetrical method, increased from initial 4.3%-39.0% of dry cell mass weight. The major fatty acids of the accumulated lipids were palmitic acid, stearic acid, oleic acid, linoleic acid and {gamma}-linoleic acid. These results indicate that it is feasible to convert the sugars in acid hydrolysate of lignocellulosic biomass to triacylglycerols using R. glutinis. (author)

  11. Spathaspora boniae sp. nov., a D-xylose-fermenting species in the Candida albicans/Lodderomyces clade.

    Science.gov (United States)

    Morais, Camila G; Batista, Thiago M; Kominek, Jacek; Borelli, Beatriz M; Furtado, Carolina; Moreira, Rennan G; Franco, Gloria R; Rosa, Luiz H; Fonseca, César; Hittinger, Chris T; Lachance, Marc-André; Rosa, Carlos A

    2017-10-01

    Two yeast isolates producing asci-containing elongate ascospores with curved ends typical of the genus Spathaspora were isolated from rotting wood samples collected in an Atlantic rainforest ecosystem in Brazil. Phylogenetic analysis of the LSU rRNA gene D1/D2 domain sequences demonstrated that the strains represent a new species and placed it next to Candida blackwellae, in a clade that also contains Candida albicans and Candida dubliniensis. Other sequences of the ribosomal gene cluster supported same placementin the same clade, and a phylogenomic analysis placed this new species in an early emerging position relative to the larger C. albicans/Lodderomyces clade. One interpretation is that the genus Spathaspora is, in fact, paraphyletic. In conformity with this view, we propose the novel species Spathaspora boniae sp. nov. to accommodate the isolates. The type strain of Spathaspora boniae sp. nov. is UFMG-CM-Y306(T) (=CBS 13262(T)). The MycoBank number is MB 821297. A detailed analysis of xylose metabolism was conducted for the new species.

  12. Simultaneous saccharification and co-fermentation for improving the xylose utilization of steam exploded corn stover at high solid loading.

    Science.gov (United States)

    Liu, Zhi-Hua; Chen, Hong-Zhang

    2016-02-01

    Simultaneous saccharification and co-fermentation (SSCF) of steam exploded corn stover (SECS) was investigated at 5-25% solid loadings compared with other conversion processes. SECS was washed with a 15-fold excess of deionized water to remove inhibitors of hydrolysis and fermentation. The concentration, yield, and productivity of ethanol was 34.3g/L, 90.0%, 2.61g/L/h in the co-fermentation of 60g/L glucose and 10g/L xylose by Saccharomyces cerevisiae IPE003. Ethanol concentration and productivity increased with increasing solid loading while ethanol yield decreased in all conversion processes of SECS. Glucan and xylan conversion was 82.0% and 82.1% in SSCF at 20% solid loading, respectively, while the concentration, yield and productivity of ethanol was 60.8g/L, 75.3% and 0.63g/L/h. The feeding strategy of SECS addition within 24h improved the SSCF performance. Therefore, SSCF increased ethanol productivity and was an effective conversion process for ethanol production at high solid loading. Copyright © 2015 Elsevier Ltd. All rights reserved.

  13. Study the performance of photogalvanic cells for solar energy conversion and storage: Rose Bengal-D-Xylose-NaLS system

    Energy Technology Data Exchange (ETDEWEB)

    Gangotri, K.M. [Department of Chemistry, Jai Narain Vyas University, Jodhpur, Rajasthan 342 033 (India); Bhimwal, Mahesh Kumar [Solar Energy Laboratory, Department of Chemistry, Jai Narain Vyas University, Jodhpur, Rajasthan 342 033 (India)

    2010-07-15

    The Rose Bengal is used as photosensitizer with D-Xylose as reductant and sodium lauryl sulphate (NaLS) as surfactant for the enhancement of the conversion efficiency and storage capacity of photogalvanic cell for its commercial viability. The observed value of the photogeneration of photopotential was 885.0 mV and photocurrent was 460.0 {mu}A whereas maximum power of the cell was 407.10 {mu}W. The observed power at power point was 158.72 {mu}W and the conversion efficiency was 1.52%. The fill factor 0.3151 was experimentally determined at the power point of the cell. The rate of initial generation of photocurrent was 63.88 {mu}A min{sup -1}. The photogalvanic cell so developed can work for 145.0 min in dark on irradiation for 165.0 min, i.e. the storage capacity of the photogalvanic cell is 87.87%. A simple mechanism for the photogeneration of photocurrent has also been proposed. (author)

  14. Functional analysis of candidate ABC transporter proteins for sitosterol transport

    DEFF Research Database (Denmark)

    Albrecht, C; Elliott, J I; Sardini, A

    2002-01-01

    Two ATP-binding cassette (ABC) proteins, ABCG5 and ABCG8, have recently been associated with the accumulation of dietary cholesterol in the sterol storage disease sitosterolemia. These two 'half-transporters' are assumed to dimerize to form the complete sitosterol transporter which reduces...... the absorption of sitosterol and related molecules in the intestine by pumping them back into the lumen. Although mutations altering ABCG5 and ABCG8 are found in affected patients, no functional demonstration of sitosterol transport has been achieved. In this study, we investigated whether other ABC transporters......-specific ABC transporters have acquired specificity to exclude sitosterol and related sterols like cholesterol presumably because the abundance of cholesterol in the membrane would interfere with their action; in consequence, specific transporters have evolved to handle these sterols....

  15. Quantum mechanics in an evolving Hilbert space

    Science.gov (United States)

    Artacho, Emilio; O'Regan, David D.

    2017-03-01

    Many basis sets for electronic structure calculations evolve with varying external parameters, such as moving atoms in dynamic simulations, giving rise to extra derivative terms in the dynamical equations. Here we revisit these derivatives in the context of differential geometry, thereby obtaining a more transparent formalization, and a geometrical perspective for better understanding the resulting equations. The effect of the evolution of the basis set within the spanned Hilbert space separates explicitly from the effect of the turning of the space itself when moving in parameter space, as the tangent space turns when moving in a curved space. New insights are obtained using familiar concepts in that context such as the Riemann curvature. The differential geometry is not strictly that for curved spaces as in general relativity, a more adequate mathematical framework being provided by fiber bundles. The language used here, however, will be restricted to tensors and basic quantum mechanics. The local gauge implied by a smoothly varying basis set readily connects with Berry's formalism for geometric phases. Generalized expressions for the Berry connection and curvature are obtained for a parameter-dependent occupied Hilbert space spanned by nonorthogonal Wannier functions. The formalism is applicable to basis sets made of atomic-like orbitals and also more adaptative moving basis functions (such as in methods using Wannier functions as intermediate or support bases), but should also apply to other situations in which nonorthogonal functions or related projectors should arise. The formalism is applied to the time-dependent quantum evolution of electrons for moving atoms. The geometric insights provided here allow us to propose new finite-difference time integrators, and also better understand those already proposed.

  16. The evolving role of tiotropium in asthma

    Directory of Open Access Journals (Sweden)

    McIvor ER

    2017-08-01

    Full Text Available Emma R McIvor,1 R Andrew McIvor2 1Queen’s University, Belfast, UK; 2Department of Medicine, McMaster University, Firestone Institute for Respiratory Health, Hamilton, Ontario, Canada Abstract: Tiotropium is a long-acting muscarinic antagonist (LAMA that exerts its bronchodilatory effect by blocking endogenous acetylcholine receptors in the airways. Its safety and efficacy are well established for the treatment of COPD, and it is now being recognized for its role in improving lung function and control in asthma. This review discusses the evolving role of tiotropium delivered by the Respimat® in patients across the range of asthma severities and ages, and provides an overview of safety and efficacy data. Tiotropium is the only LAMA currently approved for the treatment of asthma, and evidence from a large-scale clinical trial program, including several Phase III studies in adults, has demonstrated that tiotropium improves lung function and asthma control, with a safety profile comparable with that of placebo. Clinical trials in adolescent patients (aged 12–17 years have also shown improvements in lung function and trends toward improved asthma control. Of note, the efficacy and safety profiles are consistent regardless of baseline characteristics and phenotype. Given the large and growing body of evidence, it is likely that as clinical experience with tiotropium increases, this treatment may possibly emerge as the key choice for add-on therapy to inhaled corticosteroids/long-acting β2-agonists, and in patients who do not tolerate long-acting bronchodilators or other medications, in the future. Keywords: tiotropium, anticholinergics, asthma, efficacy

  17. Emergent spacetime in stochastically evolving dimensions

    Energy Technology Data Exchange (ETDEWEB)

    Afshordi, Niayesh [Perimeter Institute for Theoretical Physics, 31 Caroline St. N., Waterloo, ON, N2L 2Y5 (Canada); Department of Physics and Astronomy, University of Waterloo, Waterloo, ON, N2L 3G1 (Canada); HEPCOS, Department of Physics, SUNY at Buffalo, Buffalo, NY 14260-1500 (United States); Stojkovic, Dejan, E-mail: ds77@buffalo.edu [Perimeter Institute for Theoretical Physics, 31 Caroline St. N., Waterloo, ON, N2L 2Y5 (Canada); HEPCOS, Department of Physics, SUNY at Buffalo, Buffalo, NY 14260-1500 (United States)

    2014-12-12

    Changing the dimensionality of the space–time at the smallest and largest distances has manifold theoretical advantages. If the space is lower dimensional in the high energy regime, then there are no ultraviolet divergencies in field theories, it is possible to quantize gravity, and the theory of matter plus gravity is free of divergencies or renormalizable. If the space is higher dimensional at cosmological scales, then some cosmological problems (including the cosmological constant problem) can be attacked from a completely new perspective. In this paper, we construct an explicit model of “evolving dimensions” in which the dimensions open up as the temperature of the universe drops. We adopt the string theory framework in which the dimensions are fields that live on the string worldsheet, and add temperature dependent mass terms for them. At the Big Bang, all the dimensions are very heavy and are not excited. As the universe cools down, dimensions open up one by one. Thus, the dimensionality of the space we live in depends on the energy or temperature that we are probing. In particular, we provide a kinematic Brandenberger–Vafa argument for how a discrete causal set, and eventually a continuum (3+1)-dim spacetime along with Einstein gravity emerges in the Infrared from the worldsheet action. The (3+1)-dim Planck mass and the string scale become directly related, without any compactification. Amongst other predictions, we argue that LHC might be blind to new physics even if it comes at the TeV scale. In contrast, cosmic ray experiments, especially those that can register the very beginning of the shower, and collisions with high multiplicity and density of particles, might be sensitive to the dimensional cross-over.

  18. Emergent spacetime in stochastically evolving dimensions

    Science.gov (United States)

    Afshordi, Niayesh; Stojkovic, Dejan

    2014-12-01

    Changing the dimensionality of the space-time at the smallest and largest distances has manifold theoretical advantages. If the space is lower dimensional in the high energy regime, then there are no ultraviolet divergencies in field theories, it is possible to quantize gravity, and the theory of matter plus gravity is free of divergencies or renormalizable. If the space is higher dimensional at cosmological scales, then some cosmological problems (including the cosmological constant problem) can be attacked from a completely new perspective. In this paper, we construct an explicit model of ;evolving dimensions; in which the dimensions open up as the temperature of the universe drops. We adopt the string theory framework in which the dimensions are fields that live on the string worldsheet, and add temperature dependent mass terms for them. At the Big Bang, all the dimensions are very heavy and are not excited. As the universe cools down, dimensions open up one by one. Thus, the dimensionality of the space we live in depends on the energy or temperature that we are probing. In particular, we provide a kinematic Brandenberger-Vafa argument for how a discrete causal set, and eventually a continuum (3 + 1)-dim spacetime along with Einstein gravity emerges in the Infrared from the worldsheet action. The (3 + 1)-dim Planck mass and the string scale become directly related, without any compactification. Amongst other predictions, we argue that LHC might be blind to new physics even if it comes at the TeV scale. In contrast, cosmic ray experiments, especially those that can register the very beginning of the shower, and collisions with high multiplicity and density of particles, might be sensitive to the dimensional cross-over.

  19. Emergent spacetime in stochastically evolving dimensions

    Directory of Open Access Journals (Sweden)

    Niayesh Afshordi

    2014-12-01

    Full Text Available Changing the dimensionality of the space–time at the smallest and largest distances has manifold theoretical advantages. If the space is lower dimensional in the high energy regime, then there are no ultraviolet divergencies in field theories, it is possible to quantize gravity, and the theory of matter plus gravity is free of divergencies or renormalizable. If the space is higher dimensional at cosmological scales, then some cosmological problems (including the cosmological constant problem can be attacked from a completely new perspective. In this paper, we construct an explicit model of “evolving dimensions” in which the dimensions open up as the temperature of the universe drops. We adopt the string theory framework in which the dimensions are fields that live on the string worldsheet, and add temperature dependent mass terms for them. At the Big Bang, all the dimensions are very heavy and are not excited. As the universe cools down, dimensions open up one by one. Thus, the dimensionality of the space we live in depends on the energy or temperature that we are probing. In particular, we provide a kinematic Brandenberger–Vafa argument for how a discrete causal set, and eventually a continuum (3+1-dim spacetime along with Einstein gravity emerges in the Infrared from the worldsheet action. The (3+1-dim Planck mass and the string scale become directly related, without any compactification. Amongst other predictions, we argue that LHC might be blind to new physics even if it comes at the TeV scale. In contrast, cosmic ray experiments, especially those that can register the very beginning of the shower, and collisions with high multiplicity and density of particles, might be sensitive to the dimensional cross-over.

  20. Evolvable Cryogenics (ECRYO) Pressure Transducer Calibration Test

    Science.gov (United States)

    Diaz, Carlos E., Jr.

    2015-01-01

    This paper provides a summary of the findings of recent activities conducted by Marshall Space Flight Center's (MSFC) In-Space Propulsion Branch and MSFC's Metrology and Calibration Lab to assess the performance of current "state of the art" pressure transducers for use in long duration storage and transfer of cryogenic propellants. A brief historical narrative in this paper describes the Evolvable Cryogenics program and the relevance of these activities to the program. This paper also provides a review of three separate test activities performed throughout this effort, including: (1) the calibration of several pressure transducer designs in a liquid nitrogen cryogenic environmental chamber, (2) the calibration of a pressure transducer in a liquid helium Dewar, and (3) the calibration of several pressure transducers at temperatures ranging from 20 to 70 degrees Kelvin (K) using a "cryostat" environmental chamber. These three separate test activities allowed for study of the sensors along a temperature range from 4 to 300 K. The combined data shows that both the slope and intercept of the sensor's calibration curve vary as a function of temperature. This homogeneous function is contrary to the linearly decreasing relationship assumed at the start of this investigation. Consequently, the data demonstrates the need for lookup tables to change the slope and intercept used by any data acquisition system. This ultimately would allow for more accurate pressure measurements at the desired temperature range. This paper concludes with a review of a request for information (RFI) survey conducted amongst different suppliers to determine the availability of current "state of the art" flight-qualified pressure transducers. The survey identifies requirements that are most difficult for the suppliers to meet, most notably the capability to validate the sensor's performance at temperatures below 70 K.

  1. Key role of lipid management in nitrogen and aroma metabolism in an evolved wine yeast strain.

    Science.gov (United States)

    Rollero, Stéphanie; Mouret, Jean-Roch; Sanchez, Isabelle; Camarasa, Carole; Ortiz-Julien, Anne; Sablayrolles, Jean-Marie; Dequin, Sylvie

    2016-02-09

    Fermentative aromas play a key role in the organoleptic profile of young wines. Their production depends both on yeast strain and fermentation conditions. A present-day trend in the wine industry consists in developing new strains with aromatic properties using adaptive evolution approaches. An evolved strain, Affinity™ ECA5, overproducing esters, was recently obtained. In this study, dynamics of nitrogen consumption and of the fermentative aroma synthesis of the evolved and its ancestral strains were compared and coupled with a transcriptomic analysis approach to better understand the metabolic reshaping of Affinity™ ECA5. Nitrogen assimilation was different between the two strains, particularly amino acids transported by carriers regulated by nitrogen catabolite repression. We also observed differences in the kinetics of fermentative aroma production, especially in the bioconversion of higher alcohols into acetate esters. Finally, transcriptomic data showed that the enhanced bioconversion into acetate esters by the evolved strain was associated with the repression of genes involved in sterol biosynthesis rather than an enhanced expression of ATF1 and ATF2 (genes coding for the enzymes responsible for the synthesis of acetate esters from higher alcohols). An integrated approach to yeast metabolism-combining transcriptomic analyses and online monitoring data-showed differences between the two strains at different levels. Differences in nitrogen source consumption were observed suggesting modifications of NCR in the evolved strain. Moreover, the evolved strain showed a different way of managing the lipid source, which notably affected the production of acetate esters, likely because of a greater availability of acetyl-CoA for the evolved strain.

  2. Engaging Undergraduate Students in Transportation Studies through Simulating Transportation for Realistic Engineering Education and Training (STREET)

    OpenAIRE

    Chen-Fu Liao; David Levinson; Henry Liu

    2008-01-01

    The practice of transportation engineering and planning has evolved substantially over the past several decades. A new paradigm for transportation engineering education is required to better engage students and deliver knowledge. Simulation tools have been used by transportation professionals to evaluate and analyze the potential impact of design or control strategy changes. Conveying complex transportation concepts can be effectively achieved by exploring them through simulation. Simulation ...

  3. Orthogonally Evolved AI to Improve Difficulty Adjustment in Video Games

    DEFF Research Database (Denmark)

    Hintze, Arend; Olson, Randal; Lehman, Joel Anthony

    2016-01-01

    (i.e. agents subject to fewer generations of evolution) make for easier opponents, while highly-evolved agents are more challenging to overcome. In this publication we test a new approach for difficulty adjustment in games: orthogonally evolved AI, where the player receives support from collaborating...... opponents. Furthermore, human interaction can modulate (and be informed by) the performance and behavior of collaborating agents. In this way, orthogonally evolved AI both facilitates smoother difficulty adjustment and enables new game experiences....

  4. Evolving R Coronae Borealis Stars with MESA

    Science.gov (United States)

    Clayton, Geoffrey C.; Lauer, Amber; Chatzopoulos, Emmanouil; Frank, Juhan

    2018-01-01

    being a WD. Solving the mystery of how the RCB stars evolve will lead to a better understanding of other important types of stellar merger events such as Type Ia SNe.

  5. Protein coalitions in a core mammalian biochemical network linked by rapidly evolving proteins

    Directory of Open Access Journals (Sweden)

    Tsoka Sophia

    2011-05-01

    Full Text Available Abstract Background Cellular ATP levels are generated by glucose-stimulated mitochondrial metabolism and determine metabolic responses, such as glucose-stimulated insulin secretion (GSIS from the β-cells of pancreatic islets. We describe an analysis of the evolutionary processes affecting the core enzymes involved in glucose-stimulated insulin secretion in mammals. The proteins involved in this system belong to ancient enzymatic pathways: glycolysis, the TCA cycle and oxidative phosphorylation. Results We identify two sets of proteins, or protein coalitions, in this group of 77 enzymes with distinct evolutionary patterns. Members of the glycolysis, TCA cycle, metabolite transport, pyruvate and NADH shuttles have low rates of protein sequence evolution, as inferred from a human-mouse comparison, and relatively high rates of evolutionary gene duplication. Respiratory chain and glutathione pathway proteins evolve faster, exhibiting lower rates of gene duplication. A small number of proteins in the system evolve significantly faster than co-pathway members and may serve as rapidly evolving adapters, linking groups of co-evolving genes. Conclusions Our results provide insights into the evolution of the involved proteins. We find evidence for two coalitions of proteins and the role of co-adaptation in protein evolution is identified and could be used in future research within a functional context.

  6. Preparing for Mars: The Evolvable Mars Campaign 'Proving Ground' Approach

    Science.gov (United States)

    Bobskill, Marianne R.; Lupisella, Mark L.; Mueller, Rob P.; Sibille, Laurent; Vangen, Scott; Williams-Byrd, Julie

    2015-01-01

    provide the foundation required to enable a variety of possible destinations and missions consistent with the Evolvable Mars Campaign.. The International Space Station will be used to the greatest extent possible for exploration capability and technology development. Beyond this, NASA is evaluating a number of options for Proving Ground missions. An "Asteroid Redirect Mission" will demonstrate needed capabilities (e.g., Solar Electric Propulsion) and transportation systems for the crew (i.e., Space Launch System and Orion) and for cargo (i.e., Asteroid Redirect Vehicle). The Mars 2020 mission and follow-on robotic precursor missions will gather Mars surface environment information and will mature technologies. NASA is considering emplacing a small pressurized module in cis-lunar space to support crewed operations of increasing duration and to serve as a platform for critical exploration capabilities testing (e.g., radiation mitigation; extended duration deep space habitation). In addition, "opportunistic mission operations" could demonstrate capabilities not on the Mars critical path that may, nonetheless, enhance exploration operations (e.g., teleoperations, crew assisted Mars sample return). The Proving Ground may also include "pathfinder" missions to test and demonstrate specific capabilities at Mars (e.g., entry, descent, and landing). This paper describes the (1) process used to conduct an architecture-driven technology development assessment, (2) exploration mission critical and supporting capabilities, and (3) approach for addressing test and demonstration opportunities encompassing the spectrum of flight elements and destinations consistent with the Evolvable Mars Campaign.

  7. Soft interfaces: complex, dynamic, reacting and evolving

    Science.gov (United States)

    Squires, Todd

    2015-03-01

    ``Dirac'' plasmons are self-sustained carrier density oscillations that occur in a doped graphene sheet. These collective modes have recently attracted enormous experimental and theoretical interest for their potential use in plasmonics. In this talk I will discuss the two most important figures of merit of ``graphene plasmonics,'' namely the ratio between the Dirac plasmon wavelength and the illumination wavelength, and the Dirac plasmon damping rate. I will emphasize the subtle difference between plasmon lifetime and Drude transport scattering time. I will then present a theoretical framework that enables fully microscopic calculations of Dirac plasmon damping rates due to electron-electron, electron-impurity, and electron-phonon collisions. Finally, I will conclude by discussing how our theoretical predictions compare with recent accurate measurements in high-quality graphene sheets encapsulated in boron nitride. Work done in collaboration with A. Principi, M. Carrega, G. Vignale, A. Woessner, M.B. Lundeberg, Y. Gao, P. Alonso-González, K. Watanabe, T. Taniguchi, J. Hone, R. Hillenbrand, and F.H.L. Koppens. ``Dirac'' plasmons are self-sustained carrier density oscillations that occur in a doped graphene sheet. These collective modes have recently attracted enormous experimental and theoretical interest for their potential use in plasmonics. In this talk I will discuss the two most important figures of merit of ``graphene plasmonics,'' namely the ratio between the Dirac plasmon wavelength and the illumination wavelength, and the Dirac plasmon damping rate. I will emphasize the subtle difference between plasmon lifetime and Drude transport scattering time. I will then present a theoretical framework that enables fully microscopic calculations of Dirac plasmon damping rates due to electron-electron, electron-impurity, and electron-phonon collisions. Finally, I will conclude by discussing how our theoretical predictions compare with recent accurate measurements in

  8. Ethanol production from xylose with the yeast Pichia stipitis and simultaneous product recovery by gas stripping using a gas-lift loop fermentor with attached side-arm (GLSA).

    Science.gov (United States)

    Domínguez, J M; Cao, N; Gong, C S; Tsao, G T

    2000-02-05

    The bioconversion of xylose into ethanol with the yeast Pichia stipitis CBS 5773 is inhibited when 20 g/L of ethanol are present in the fermentation broth. In order to avoid this limitation, the fermentation was carried out with simultaneous recovery of product by CO(2) stripping. The fermentation was also improved by attaching a side-arm to the main body of a classical gas-lift loop fermentor. This side-arm increases the liquid circulation, mass transfer, and gas distribution, reducing the amount of oxygen in the inlet gas necessary to perform the fermentation of xylose under microaerobic conditions (K(L)a approximately 16 h(-1)). The continuous stripping of ethanol from the fermentation broth in this new bioreactor system allowed the consumption of higher xylose concentrations than using Erlenmeyer shaker flasks, improved significantly the process productivity and provided a clean ethanol solution by using an ice-cooled condenser system. Finally, a fed-batch fermentation was carried out with a K(L)a = 15.8 h(-1). Starting with 248.2 g of xylose, 237.6 g of xylose was consumed to produce 88.1 g of ethanol which represents 72.6% of the theoretical yield (47.2 g/L of ethanol was recovered in the condenser, while 9.6 g/L remained in the fermentation broth). Copyright 2000 John Wiley & Sons, Inc.

  9. Ethanol production from xylose with the yeast Pichia stipitis and simultaneous product recovery by gas stripping using a gas-lift loop fermentor with attached side-arm (GLSA)

    Energy Technology Data Exchange (ETDEWEB)

    Dominguez, J.M.; Cao, N.; Gong, C.S.; Tsao, G.T.

    2000-02-05

    The bioconversion of xylose into ethanol with the yeast Pichia stipitis CBS 5773 is inhibited when 20 g/L of ethanol are present in the fermentation broth. In order to avoid this limitation, the fermentation was carried out with simultaneous recovery of product by CO{sub 2} stripping. The fermentation was also improved by attaching a side-arm to the main body of a classical gas-lift loop fermentor. This side-arm increases the liquid circulation, mass transfer, and gas distribution, reducing the amount of oxygen in the inlet gas necessary to perform the fermentation of xylose under microaerobic conditions (K{sub L}a{approx_equal} 16 h{sup {minus}1}). The continuous stripping of ethanol from the fermentation broth in this new bioreactor system allowed the consumption of higher xylose concentrations than using Erlenmeyer shaker flasks, improved significantly the process productivity and provided a clean ethanol solution by using an ice-cooled condenser system. Finally, a fed-batch fermentation was carried out with a K{sub L}a = 15.8 h{sup {minus}1}. Starting with 248.2 g of xylose, 237.6 g of xylose was consumed to produce 88.1 g of ethanol which represents 72.6% of the theoretical yield.

  10. Radiation Transport

    Energy Technology Data Exchange (ETDEWEB)

    Urbatsch, Todd James [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

    2015-06-15

    We present an overview of radiation transport, covering terminology, blackbody raditation, opacities, Boltzmann transport theory, approximations to the transport equation. Next we introduce several transport methods. We present a section on Caseology, observing transport boundary layers. We briefly broach topics of software development, including verification and validation, and we close with a section on high energy-density experiments that highlight and support radiation transport.

  11. It is hard to predict the future: the evolving nature of threats and vulnerabilities.

    Science.gov (United States)

    Ackerman, G A

    2006-04-01

    This paper describes the evolving nature of threats and vulnerabilities associated with biological disasters with animal origins, and introduces some of the pitfalls and opportunities associated with anticipating future threats. Evolving threats and vulnerabilities include continued deforestation and encroachment on virgin habitats, the effects of globalisation on trade and transportation, the increased interdependence and social vulnerability of modern society, the commingling of intensive agriculture and traditional farming methods, the periodic appearance of pandemics and epizootics, and indications that numerous human actors are displaying an increasing interest in and capability of using biological agents as weapons. These developments must be viewed in the context of various impediments to accurately gauging future threats, such as the appearance of new elements that depart from current trends and the inherent difficulty in anticipating human, and especially terrorist, behaviour. The paper concludes with some broad recommendations for structuring a policy response to the threat in an environment of uncertainty about the future.

  12. Loops and autonomy promote evolvability of ecosystem networks.

    Science.gov (United States)

    Luo, Jianxi

    2014-09-29

    The structure of ecological networks, in particular food webs, determines their ability to evolve further, i.e. evolvability. The knowledge about how food web evolvability is determined by the structures of diverse ecological networks can guide human interventions purposefully to either promote or limit evolvability of ecosystems. However, the focus of prior food web studies was on stability and robustness; little is known regarding the impact of ecological network structures on their evolvability. To correlate ecosystem structure and evolvability, we adopt the NK model originally from evolutionary biology to generate and assess the ruggedness of fitness landscapes of a wide spectrum of model food webs with gradual variation in the amount of feeding loops and link density. The variation in network structures is controlled by linkage rewiring. Our results show that more feeding loops and lower trophic link density, i.e. higher autonomy of species, of food webs increase the potential for the ecosystem to generate heritable variations with improved fitness. Our findings allow the prediction of the evolvability of actual food webs according to their network structures, and provide guidance to enhancing or controlling the evolvability of specific ecosystems.

  13. Protein structural modularity and robustness are associated with evolvability.

    Science.gov (United States)

    Rorick, Mary M; Wagner, Günter P

    2011-01-01

    Theory suggests that biological modularity and robustness allow for maintenance of fitness under mutational change, and when this change is adaptive, for evolvability. Empirical demonstrations that these traits promote evolvability in nature remain scant however. This is in part because modularity, robustness, and evolvability are difficult to define and measure in real biological systems. Here, we address whether structural modularity and/or robustness confer evolvability at the level of proteins by looking for associations between indices of protein structural modularity, structural robustness, and evolvability. We propose a novel index for protein structural modularity: the number of regular secondary structure elements (helices and strands) divided by the number of residues in the structure. We index protein evolvability as the proportion of sites with evidence of being under positive selection multiplied by the average rate of adaptive evolution at these sites, and we measure this as an average over a phylogeny of 25 mammalian species. We use contact density as an index of protein designability, and thus, structural robustness. We find that protein evolvability is positively associated with structural modularity as well as structural robustness and that the effect of structural modularity on evolvability is independent of the structural robustness index. We interpret these associations to be the result of reduced constraints on amino acid substitutions in highly modular and robust protein structures, which results in faster adaptation through natural selection.

  14. Adaptation of Escherichia coli to glucose promotes evolvability in lactose.

    Science.gov (United States)

    Phillips, Kelly N; Castillo, Gerardo; Wünsche, Andrea; Cooper, Tim F

    2016-02-01

    The selective history of a population can influence its subsequent evolution, an effect known as historical contingency. We previously observed that five of six replicate populations that were evolved in a glucose-limited environment for 2000 generations, then switched to lactose for 1000 generations, had higher fitness increases in lactose than populations started directly from the ancestor. To test if selection in glucose systematically increased lactose evolvability, we started 12 replay populations--six from a population subsample and six from a single randomly selected clone--from each of the six glucose-evolved founder populations. These replay populations and 18 ancestral populations were evolved for 1000 generations in a lactose-limited environment. We found that replay populations were initially slightly less fit in lactose than the ancestor, but were more evolvable, in that they increased in fitness at a faster rate and to higher levels. This result indicates that evolution in the glucose environment resulted in genetic changes that increased the potential of genotypes to adapt to lactose. Genome sequencing identified four genes--iclR, nadR, spoT, and rbs--that were mutated in most glucose-evolved clones and are candidates for mediating increased evolvability. Our results demonstrate that short-term selective costs during selection in one environment can lead to changes in evolvability that confer longer term benefits. © 2016 The Author(s). Evolution © 2016 The Society for the Study of Evolution.

  15. Man o' War Mutation in UDP-α-D-Xylose Synthase Favors the Abortive Catalytic Cycle and Uncovers a Latent Potential for Hexamer Formation

    Energy Technology Data Exchange (ETDEWEB)

    Walsh, Jr., Richard M.; Polizzi, Samuel J.; Kadirvelraj, Renuka; Howard, Wesley W.; Wood, Zachary A. [Georgia

    2015-03-17

    The man o’ war (mow) phenotype in zebrafish is characterized by severe craniofacial defects due to a missense mutation in UDP-α-D-xylose synthase (UXS), an essential enzyme in proteoglycan biosynthesis. The mow mutation is located in the UXS dimer interface ~16 Å away from the active site, suggesting an indirect effect on the enzyme mechanism. We have examined the structural and catalytic consequences of the mow mutation (R236H) in the soluble fragment of human UXS (hUXS), which shares 93% sequence identity with the zebrafish enzyme. In solution, hUXS dimers undergo a concentration-dependent association to form a tetramer. Sedimentation velocity studies show that the R236H substitution induces the formation of a new hexameric species. Using two new crystal structures of the hexamer, we show that R236H and R236A substitutions cause a local unfolding of the active site that allows for a rotation of the dimer interface necessary to form the hexamer. The disordered active sites in the R236H and R236A mutant constructs displace Y231, the essential acid/base catalyst in the UXS reaction mechanism. The loss of Y231 favors an abortive catalytic cycle in which the reaction intermediate, UDP-α-D-4-keto-xylose, is not reduced to the final product, UDP-α-D-xylose. Surprisingly, the mow-induced hexamer is almost identical to the hexamers formed by the deeply divergent UXS homologues from Staphylococcus aureus and Helicobacter pylori (21% and 16% sequence identity, respectively). The persistence of a latent hexamer-building interface in the human enzyme suggests that the ancestral UXS may have been a hexamer.

  16. Man o' war mutation in UDP-α-D-xylose synthase favors the abortive catalytic cycle and uncovers a latent potential for hexamer formation.

    Science.gov (United States)

    Walsh, Richard M; Polizzi, Samuel J; Kadirvelraj, Renuka; Howard, Wesley W; Wood, Zachary A

    2015-01-27

    The man o' war (mow) phenotype in zebrafish is characterized by severe craniofacial defects due to a missense mutation in UDP-α-d-xylose synthase (UXS), an essential enzyme in proteoglycan biosynthesis. The mow mutation is located in the UXS dimer interface ∼16 Å away from the active site, suggesting an indirect effect on the enzyme mechanism. We have examined the structural and catalytic consequences of the mow mutation (R236H) in the soluble fragment of human UXS (hUXS), which shares 93% sequence identity with the zebrafish enzyme. In solution, hUXS dimers undergo a concentration-dependent association to form a tetramer. Sedimentation velocity studies show that the R236H substitution induces the formation of a new hexameric species. Using two new crystal structures of the hexamer, we show that R236H and R236A substitutions cause a local unfolding of the active site that allows for a rotation of the dimer interface necessary to form the hexamer. The disordered active sites in the R236H and R236A mutant constructs displace Y231, the essential acid/base catalyst in the UXS reaction mechanism. The loss of Y231 favors an abortive catalytic cycle in which the reaction intermediate, UDP-α-d-4-keto-xylose, is not reduced to the final product, UDP-α-d-xylose. Surprisingly, the mow-induced hexamer is almost identical to the hexamers formed by the deeply divergent UXS homologues from Staphylococcus aureus and Helicobacter pylori (21% and 16% sequence identity, respectively). The persistence of a latent hexamer-building interface in the human enzyme suggests that the ancestral UXS may have been a hexamer.

  17. Establishment of a tobacco BY2 cell line devoid of plant-specific xylose and fucose as a platform for the production of biotherapeutic proteins.

    Science.gov (United States)

    Hanania, Uri; Ariel, Tami; Tekoah, Yoram; Fux, Liat; Sheva, Maor; Gubbay, Yehuda; Weiss, Mara; Oz, Dina; Azulay, Yaniv; Turbovski, Albina; Forster, Yehava; Shaaltiel, Yoseph

    2017-09-01

    Plant-produced glycoproteins contain N-linked glycans with plant-specific residues of β(1,2)-xylose and core α(1,3)-fucose, which do not exist in mammalian-derived proteins. Although our experience with two enzymes that are used for enzyme replacement therapy does not indicate that the plant sugar residues have deleterious effects, we made a conscious decision to eliminate these moieties from plant-expressed proteins. We knocked out the β(1,2)-xylosyltranferase (XylT) and the α(1,3)-fucosyltransferase (FucT) genes, using CRISPR/Cas9 genome editing, in Nicotiana tabacum L. cv Bright Yellow 2 (BY2) cell suspension. In total, we knocked out 14 loci. The knocked-out lines were stable, viable and exhibited a typical BY2 growing rate. Glycan analysis of the endogenous proteins of these lines exhibited N-linked glycans lacking β(1,2)-xylose and/or α(1,3)-fucose. The knocked-out lines were further transformed successfully with recombinant DNaseI. The expression level and the activity of the recombinant protein were similar to that of the protein produced in the wild-type BY2 cells. The recombinant DNaseI was shown to be totally free from any xylose and/or fucose residues. The glyco-engineered BY2 lines provide a valuable platform for producing potent biopharmaceutical products. Furthermore, these results demonstrate the power of the CRISPR/Cas9 technology for multiplex gene editing in BY2 cells. © 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

  18. aguA, the Gene Encoding an Extracellular α-Glucuronidase from Aspergillus tubingensis, Is Specifically Induced on Xylose and Not on Glucuronic Acid

    Science.gov (United States)

    de Vries, Ronald P.; Poulsen, Charlotte H.; Madrid, Susan; Visser, Jaap

    1998-01-01

    An extracellular α-glucuronidase was purified and characterized from a commercial Aspergillus preparation and from culture filtrate of Aspergillus tubingensis. The enzyme has a molecular mass of 107 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and 112 kDa as determined by mass spectrometry, has a determined pI just below 5.2, and is stable at pH 6.0 for prolonged times. The pH optimum for the enzyme is between 4.5 and 6.0, and the temperature optimum is 70°C. The α-glucuronidase is active mainly on small substituted xylo-oligomers but is also able to release a small amount of 4-O-methylglucuronic acid from birchwood xylan. The enzyme acts synergistically with endoxylanases and β-xylosidase in the hydrolysis of xylan. The enzyme is N glycosylated and contains 14 putative N-glycosylation sites. The gene encoding this α-glucuronidase (aguA) was cloned from A. tubingensis. It consists of an open reading frame of 2,523 bp and contains no introns. The gene codes for a protein of 841 amino acids, containing a eukaryotic signal sequence of 20 amino acids. The mature protein has a predicted molecular mass of 91,790 Da and a calculated pI of 5.13. Multiple copies of the gene were introduced in A. tubingensis, and expression was studied in a highly overproducing transformant. The aguA gene was expressed on xylose, xylobiose, and xylan, similarly to genes encoding endoxylanases, suggesting a coordinate regulation of expression of xylanases and α-glucuronidase. Glucuronic acid did not induce the expression of aguA and also did not modulate the expression on xylose. Addition of glucose prevented expression of aguA on xylan but only reduced the expression on xylose. PMID:9440512

  19. aguA, the gene encoding an extracellular alpha-glucuronidase from Aspergillus tubingensis, is specifically induced on xylose and not on glucuronic acid.

    Science.gov (United States)

    de Vries, R P; Poulsen, C H; Madrid, S; Visser, J

    1998-01-01

    An extracellular alpha-glucuronidase was purified and characterized from a commercial Aspergillus preparation and from culture filtrate of Aspergillus tubingensis. The enzyme has a molecular mass of 107 kDa as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and 112 kDa as determined by mass spectrometry, has a determined pI just below 5.2, and is stable at pH 6.0 for prolonged times. The pH optimum for the enzyme is between 4.5 and 6.0, and the temperature optimum is 70 degrees C. The alpha-glucuronidase is active mainly on small substituted xylo-oligomers but is also able to release a small amount of 4-O-methylglucuronic acid from birchwood xylan. The enzyme acts synergistically with endoxylanases and beta-xylosidase in the hydrolysis of xylan. The enzyme is N glycosylated and contains 14 putative N-glycosylation sites. The gene encoding this alpha-glucuronidase (aguA) was cloned from A. tubingensis. It consists of an open reading frame of 2,523 bp and contains no introns. The gene codes for a protein of 841 amino acids, containing a eukaryotic signal sequence of 20 amino acids. The mature protein has a predicted molecular mass of 91,790 Da and a calculated pI of 5.13. Multiple copies of the gene were introduced in A. tubingensis, and expression was studied in a highly overproducing transformant. The aguA gene was expressed on xylose, xylobiose, and xylan, similarly to genes encoding endoxylanases, suggesting a coordinate regulation of expression of xylanases and alpha-glucuronidase. Glucuronic acid did not induce the expression of aguA and also did not modulate the expression on xylose. Addition of glucose prevented expression of aguA on xylan but only reduced the expression on xylose.

  20. High level expression of a novel family 3 neutral β-xylosidase from Humicola insolens Y1 with high tolerance to D-xylose.

    Directory of Open Access Journals (Sweden)

    Wei Xia

    Full Text Available A novel β-xylosidase gene of glycosyl hydrolase (GH family 3, xyl3A, was identified from the thermophilic fungus Humicola insolens Y1, which is an innocuous and non-toxic fungus that produces a wide variety of GHs. The cDNA of xyl3A, 2334 bp in length, encodes a 777-residue polypeptide containing a putative signal peptide of 19 residues. The gene fragment without the signal peptide-coding sequence was cloned and overexpressed in Pichia pastoris GS115 at a high level of 100 mg/L in 1-L Erlenmeyer flasks without fermentation optimization. Recombinant Xyl3A showed both β-xylosidase and α-arabinfuranosidase activities, but had no hydrolysis capacity towards polysaccharides. It was optimally active at pH 6.0 and 60°C with a specific activity of 11.6 U/mg. It exhibited good stability over pH 4.0-9.0 (incubated at 37°C for 1 h and at temperatures of 60°C and below, retaining over 80% maximum activity. The enzyme had stronger tolerance to xylose than most fungal GH3 β-xylosidases with a high Ki value of 29 mM, which makes Xyl3A more efficient to produce xylose in fermentation process. Sequential combination of Xyl3A following endoxylanase Xyn11A of the same microbial source showed significant synergistic effects on the degradation of various xylans and deconstructed xylo-oligosaccharides to xylose with high efficiency. Moreover, using pNPX as both the donor and acceptor, Xyl3A exhibited a transxylosylation activity to synthesize pNPX2. All these favorable properties suggest that Xyl3A has good potential applications in the bioconversion of hemicelluloses to biofuels.

  1. Reptation-induced coalescence of tunnels and cavities in Escherichia Coli XylE transporter conformers accounts for facilitated diffusion.

    Science.gov (United States)

    Cunningham, Philip; Naftalin, Richard J

    2014-11-01

    Structural changes and xylose docking to eight conformers of Escherichia Coli XylE, a xylose transporter similar to mammalian passive glucose transporters GLUTs, have been examined. Xylose docks to inward and outward facing conformers at a high affinity central site (K(i) 4-20 µM), previously identified by crystallography and additionally consistently docks to lower affinity sites in the external and internal vestibules (K(i) 12-50 µM). All these sites lie within intramolecular tunnels and cavities. Several local regions in the central transmembrane zone have large positional divergences of both skeleton carbon Cα positions and side chains. One such in TM 10 is the destabilizing sequence G388-P389-V390-C391 with an average RMSD (4.5 ± 0.4 Å). Interchange between conformer poses results in coalescence of tunnels with adjacent cavities, thereby producing a transitory channel spanning the entire transporter. A fully open channel exists in one inward-facing apo-conformer, (PDB 4ja4c) as demonstrated by several different tunnel-finding algorithms. The conformer interchanges produce a gated network within a branched central channel that permits staged ligand diffusion across the transporter during the open gate periods. Simulation of this model demonstrates that small-scale conformational changes required for sequentially opening gate with frequencies in the ns-μs time domain accommodate diffusive ligand flow between adjacent sites with association-dissociation rates in the μs-ms domain without imposing delays. This current model helps to unify the apparently opposing concepts of alternate access and multisite models of ligand transport.

  2. Monosaccharide transport into hemocytes of a sipunculan worm Themiste dyscrita

    Energy Technology Data Exchange (ETDEWEB)

    Ingermann, R.L.; Hall, R.E.; Bissonnette, J.M.; Terwilliger, R.C.

    1985-07-01

    The hemerythrin-containing blood cells, or hemocytes, of the sipunculan worm Themiste dyscrita were found to have a stereospecific and nonconcentrative monosaccharide transport system. The transport system transferred both D-glucose and 3-O-methyl-D-glucose (3-OMG), and transport into cells by this system was rapid, reaching 50% equilibrium in approximately 20 s at 10 degrees C with an initial concentration gradient of 0.1 mM; the contribution to total uptake by simple diffusion was very small. 3-OMG uptake showed saturation kinetics with a low half-saturation constant (Km less than or equal to 0.1 mM). The uptake of labeled 3-OMG by the hemocytes was strongly inhibited by unlabeled 3-OMG, 2-deoxy-D-glucose, alpha- and beta-D-glucose, D-galactose, and D-mannose. It was moderately inhibited by D-xylose, only slightly by alpha-methyl-D-glucoside and D-fructose, and uninhibited by sucrose, L-glucose, or D-sorbitol. Phloretin was more potent than phloridzin in blocking entry of 3-OMG. Cytochalasin B did not bind tightly to the T. dyscrita transporter and was not a potent inhibitor of transport; it half-maximally inhibited 3-OMG transport at 0.1 mM. Therefore, despite some differences the data suggest functional similarities in the mechanism of monosaccharide transport into blood cells of mammals and this invertebrate.

  3. Fostering transport and logistics research in the Benelux countries

    NARCIS (Netherlands)

    Witlox, Frank; Dullaert, Wout; Jourquin, Bart

    Promoting high quality research and education in the field of transport, within its region, is the main goal of the Benelux Interuniversity Association of Transport Economists - BIVEC-GIBET for short. Founded in 1978, the Association has evolved from a small group of transport economists into a

  4. Chlorine solubility in evolved alkaline magmas

    Directory of Open Access Journals (Sweden)

    M. R. Carroll

    2005-06-01

    Full Text Available Experimental studies of Cl solubility in trachytic to phonolitic melts provide insights into the capacity of alkaline magmas to transport Cl from depth to the earth?s surface and atmosphere, and information on Cl solubility variations with pressure, temperature and melt or fluid composition is crucial for understanding the reasons for variations in Cl emissions at active volcanoes. This paper provides a brief review of Cl solubility experiments conducted on a range of trachytic to phonolitic melt compositions. Depending on the experimental conditions the melts studied were in equilibrium with either a Cl-bearing aqueous fluid or a subcritical assemblage of low- Cl aqueous fluid + Cl-rich brine. The nature of the fluid phase(s was identified by examination of fluid inclusions present in run product glasses and the fluid bulk composition was calculated by mass balance. Chlorine concentrations in the glass increase with increasing Cl molality in the fluid phase until a plateau in Cl concentration is reached when melt coexists with aqueous fluid + brine. With fluids of similar Cl molality, higher Cl concentrations are observed in peralkaline phonolitic melts compared with peraluminous phonolitic melts; overall the Cl concentrations observed in phonolitic and trachytic melts are approximately twice those found in calcalkaline rhyolitic melts under similar conditions. The observed negative pressure dependence of Cl solubility implies that Cl contents of melts may actually increase during magma decompression if the magma coexists with aqueous fluid and Cl-rich brine (assuming melt-vapor equilibrium is maintained. The high Cl contents (approaching 1 wt% Cl observed in some melts/glasses from the Vesuvius and Campi Flegrei areas suggest saturation with a Cl-rich brine prior to eruption.

  5. Xylitol production from waste xylose mother liquor containing miscellaneous sugars and inhibitors: one-pot biotransformation by Candida tropicalis and recombinant Bacillus subtilis.

    Science.gov (United States)

    Wang, Hengwei; Li, Lijuan; Zhang, Lebin; An, Jin; Cheng, Hairong; Deng, Zixin

    2016-05-16

    The process of industrial xylitol production is a massive source of organic pollutants, such as waste xylose mother liquor (WXML), a viscous reddish-brown liquid. Currently, WXML is difficult to reuse due to its miscellaneous low-cost sugars, high content of inhibitors and complex composition. WXML, as an organic pollutant of hemicellulosic hydrolysates, accumulates and has become an issue of industrial concern in China. Previous studies have focused only on the catalysis of xylose in the hydrolysates into xylitol using one strain, without considering the removal of other miscellaneous sugars, thus creating an obstacle to subsequent large-scale purification. In the present study, we aimed to develop a simple one-pot biotransformation to produce high-purity xylitol from WXML to improve its economic value. In the present study, we developed a procedure to produce xylitol from WXML, which combines detoxification, biotransformation and removal of by-product sugars (purification) in one bioreactor using two complementary strains, Candida tropicalis X828 and Bacillus subtilis Bs12. At the first stage of micro-aerobic biotransformation, the yeast cells were allowed to grow and metabolized glucose and the inhibitors furfural and hydroxymethyl furfural (HMF), and converted xylose into xylitol. At the second stage of aerobic biotransformation, B. subtilis Bs12 was activated and depleted the by-product sugars. The one-pot process was successfully scaled up from shake flasks to 5, 150 L and 30 m(3) bioreactors. Approximately 95 g/L of pure xylitol could be obtained from the medium containing 400 g/L of WXML at a yield of 0.75 g/g xylose consumed, and the by-product sugars glucose, L-arabinose and galactose were depleted simultaneously. Our results demonstrate that the one-pot procedure is a viable option for the industrial application of WXML to produce value-added chemicals. The integration of complementary strains in the biotransformation of hemicellulosic hydrolysates is

  6. Towards a Microbial Production of Fatty Acids as Precursors of Biokerosene from Glucose and Xylose Vers une production microbienne d’acides gras en vue de l’application biokérosène à partir de glucose et xylose

    Directory of Open Access Journals (Sweden)

    Babau M.

    2013-09-01

    Full Text Available The aviation industry considers the development of sustainable biofuels as one of the biggest challenges of the next ten years. The aim is to lower the environmental impact of the steadily increasing use of fossil fuels on climate change, yielding greater energy independence and fuel security. Thus, the development of a new route for the production of lipids from renewable non-food resources is now being promoted with the recent ASTM certification of hydrotreated oils. Our study focuses on the potential of growth of the oleaginous yeast Rhodotorula glutinis using glucose and xylose which can come from renewable lignocellulosic substrates and of lipid accumulation using glucose as substrate. Experiments were carried out in fed-batch mode which allowed feed flux management. Carbon fluxes were controlled with modifying xylose/glucose ratios to quantify metabolism in optimal growth condition. Besides, the management of carbon and nitrogen fluxes allowed characterizing lipid accumulation. Thus, it has been shown that the yeast Rhodotorula glutinis can simultaneously consume glucose and xylose. When the ratio xylose/glucose increased, the growth rate and the carbon conversion yield into biomass decreased: it was of 0.36 h-1 and 0.64 Cmol x*.Cmol glu-1 for pure glucose, it was of 0.15 h-1 and 0.56 Cmol.Cmol-1 for 10% xylose and it was of 0.037 h-1 and 0.18 Cmol.Cmol-1 for pure xylose. The necessity to maintain residual growth and to manage carbon fluxes to optimize lipid accumulation performance was revealed. Lipid accumulation on glucose engendered a final biomass concentration of 150 gCDW.L-1, microbial production (72% of lipids and maximal productivity over 1.48 glip.L-1.h-1. The culture temperature is an important parameter to modulate the lipid profile. The results were encouraging. Lipid accumulation using lignocellulosic feedstock was shown to be a highly promising route. Le développement de filières de production de molécules

  7. NASA's Space Launch System: An Evolving Capability for Exploration An Evolving Capability for Exploration

    Science.gov (United States)

    Creech, Stephen D.; Crumbly, Christopher M.; Robinson, Kimerly F.

    2016-01-01

    A foundational capability for international human deep-space exploration, NASA's Space Launch System (SLS) vehicle represents a new spaceflight infrastructure asset, creating opportunities for mission profiles and space systems that cannot currently be executed. While the primary purpose of SLS, which is making rapid progress towards initial launch readiness in two years, will be to support NASA's Journey to Mars, discussions are already well underway regarding other potential utilization of the vehicle's unique capabilities. In its initial Block 1 configuration, capable of launching 70 metric tons (t) to low Earth orbit (LEO), SLS is capable of propelling the Orion crew vehicle to cislunar space, while also delivering small CubeSat-class spacecraft to deep-space destinations. With the addition of a more powerful upper stage, the Block 1B configuration of SLS will be able to deliver 105 t to LEO and enable more ambitious human missions into the proving ground of space. This configuration offers opportunities for launching co-manifested payloads with the Orion crew vehicle, and a class of secondary payloads, larger than today's CubeSats. Further upgrades to the vehicle, including advanced boosters, will evolve its performance to 130 t in its Block 2 configuration. Both Block 1B and Block 2 also offer the capability to carry 8.4- or 10-m payload fairings, larger than any contemporary launch vehicle. With unmatched mass-lift capability, payload volume, and C3, SLS not only enables spacecraft or mission designs currently impossible with contemporary EELVs, it also offers enhancing benefits, such as reduced risk, operational costs and/or complexity, shorter transit time to destination or launching large systems either monolithically or in fewer components. This paper will discuss both the performance and capabilities of Space Launch System as it evolves, and the current state of SLS utilization planning.

  8. Towards Co-evolution of Membrane Transport and Metabolism

    Science.gov (United States)

    Wei, Chenyu; Pohorille, Andrzej

    2014-01-01

    Protocellular boundaries were inextricably connected to the metabolism they encapsulated: to be inheritable, early metabolism must have led to an increased rate of growth and division of vesicles and, similarly, transport through vesicle boundaries must have supported the evolution of metabolism. Even though explaining how this coupling emerged and evolved in the absence of the complex machinery of modern cells is one of the key issues in studies on the origin of life, little is known about the biochemical and biophysical processes that might have been involved. This gap in our knowledge is a major impediment in efforts to construct scenarios for the origin of life and laboratory models of protocells. A combination of experimental and computational studies carried out by us and our collaborators is aimed at helping to close this gap. Properties of membranes might have contributed to the selection of RNA as an early biopolymer. A kinetic mechanism was proposed (Sacerdote & Szostak, 2005) in which ribose was supplied more quickly than other aldopentoses to primordial cells for preferential incorporation of ribonucleotides into nucleic acids. This proposal is based on a finding that ribose permeates membranes an order of magnitude faster than its diastereomers, arabinose and xylose. Our computer simulations, which yield permeation rates in excellent agreement with experiment, and kinetic modeling explain this phenomenon in terms of inter- and intramolecular interactions involving exocyclic hydroxyl groups attached to carbon atoms of the pyranose ring (Wei and Pohorille, 2009). They also constrain scenarios for the formation of the earliest nucleic acids (Wei and Pohorille, 2013). In one scenario, sugars permeate protocellular walls and subsequently are used to synthesize nucleic acids inside protocells. As long as this process proceeds at the rate faster than 6x10(exp -3)/s, ribose derivatives will be available for synthesis easier than their diastereomers. If

  9. Sustainable Transportation

    DEFF Research Database (Denmark)

    Hall, Ralph P.; Gudmundsson, Henrik; Marsden, Greg

    2014-01-01

    that relate to the construction and maintenance of transportation infrastructure and the operation or use of the different transportation modes. The concept of sustainable transportation emerged in response to these concerns as part of the broader notion of sustainable development. Given the transportation...

  10. Risk-Based Prioritization of Research for Aviation Security Using Logic-Evolved Decision Analysis

    Science.gov (United States)

    Eisenhawer, S. W.; Bott, T. F.; Sorokach, M. R.; Jones, F. P.; Foggia, J. R.

    2004-01-01

    The National Aeronautics and Space Administration is developing advanced technologies to reduce terrorist risk for the air transportation system. Decision support tools are needed to help allocate assets to the most promising research. An approach to rank ordering technologies (using logic-evolved decision analysis), with risk reduction as the metric, is presented. The development of a spanning set of scenarios using a logic-gate tree is described. Baseline risk for these scenarios is evaluated with an approximate reasoning model. Illustrative risk and risk reduction results are presented.

  11. Self-Evolvable Systems Machine Learning in Social Media

    CERN Document Server

    Iordache, Octavian

    2012-01-01

    This monograph presents key method to successfully manage the growing  complexity of systems  where conventional engineering and scientific methodologies and technologies based on learning and adaptability come to their limits and new ways are nowadays required. The transition from adaptable to evolvable and finally to self-evolvable systems is highlighted, self-properties such as self-organization, self-configuration, and self-repairing are introduced and challenges and limitations of the self-evolvable engineering systems are evaluated.

  12. High-level intracellular expression of heterologous proteins in Brevibacillus choshinensis SP3 under the control of a xylose inducible promoter

    Directory of Open Access Journals (Sweden)

    D’Urzo Nunzia

    2013-02-01

    Full Text Available Abstract Background In past years research has focused on the development of alternative Gram positive bacterial expression systems to produce industrially relevant proteins. Brevibacillus choshinensis is an easy to handle non-sporulating bacterium, lacking extracellular proteases, that has been already shown to provide a high level of recombinant protein expression. One major drawback, limiting the applicability of the Brevibacillus expression system, is the absence of expression vectors based on inducible promoters. Here we used the PxylA inducible promoter, commonly employed in other Bacillae expression systems, in Brevibacillus. Results Using GFP, α-amylase and TcdA-GT as model proteins, high level of intracellular protein expression (up to 250 mg/L for the GFP was achieved in Brevibacillus, using the pHis1522 vector carrying the B. megaterium xylose-inducible promoter (PxylA. The GFP expression yields were more than 25 fold higher than those reported for B. megaterium carrying the same vector. All the tested proteins show significant increment in their expression levels (2-10 folds than those obtained using the available plasmids based on the P2 constitutive promoter. Conclusion Combining the components of two different commercially available Gram positive expression systems, such as Brevibacillus (from Takara Bio and B. megaterium (from Mobitec, we demonstrate that vectors based on the B. megaterium PxylA xylose inducible promoter can be successfully used to induce high level of intracellular expression of heterologous proteins in Brevibacillus.

  13. A metabolic-based approach to improve xylose utilization for fumaric acid production from acid pretreated wheat bran by Rhizopus oryzae.

    Science.gov (United States)

    Wang, Guanyi; Huang, Di; Li, Yong; Wen, Jianping; Jia, Xiaoqiang

    2015-03-01

    In this work, wheat bran (WB) was utilized as feedstock to synthesize fumaric acid by Rhizopus oryzae. Firstly, the pretreatment process of WB by dilute sulfuric acid hydrolysis undertaken at 100°C for 30min offered the best performance for fumaric acid production. Subsequently, through optimizing the seed culture medium, a suitable morphology (0.55mm pellets diameter) of R. oryzae was obtained. Furthermore, a metabolic-based approach was developed to profile the differences of intracellular metabolites concentration of R. oryzae between xylose (the abundant sugar in wheat bran hydrolysate (WBH)) and glucose metabolism. The xylitol, sedoheptulose 7-phosphate, ribulose 5-phosphate, glucose 6-phosphate, proline and serine were responsible for fumaric acid biosynthesis limitation in xylose fermentation. Consequently, regulation strategies were proposed, leading to a 149% increase in titer (up to 15.4g/L). Finally, by combinatorial regulation strategies the highest production was 20.2g/L from WBH, 477% higher than that of initial medium. Copyright © 2014 Elsevier Ltd. All rights reserved.

  14. Production of d-psicose from d-glucose by co-expression of d-psicose 3-epimerase and xylose isomerase.

    Science.gov (United States)

    Chen, Xiaoyan; Wang, Wen; Xu, Jingliang; Yuan, Zhenhong; Yuan, Tao; Zhang, Yu; Liang, Cuiyi; He, Minchao; Guo, Ying

    2017-10-01

    d-Psicose has been drawing increasing attention in recent years because of its medical and health applications. The production of d-psicose from d-glucose requires the co-expression and synergistic action of xylose isomerase and d-psicose 3-epimerase. To co-express these genes, vector pET-28a(+)-dual containing two T7 promoters and RBS sites and an Multiple Cloning Sites was constructed using the Escherichia coli expression plasmid pET-28a(+). The xylose isomerase gene from E. coli MG1665 and the d-psicose 3-epimerase gene from Agrobacterium tumefaciens CGMCC 1.1488 were cloned and co-expressed in E. coli BL21(DE3). After 24h incubation with the dual enzyme system at 40°C, the sugar conversion ratio from d-glucose to d-psicose reached 10%. The optimal conditions were 50°C, pH 7.5 with Co2+ and Mg2+. The d-psicose yields from sugarcane bagasse and microalgae hydrolysate were 1.42 and 1.69g/L, respectively. Copyright © 2017 Elsevier Inc. All rights reserved.

  15. Functional architecture of MFS D-glucose transporters.

    Science.gov (United States)

    Madej, M Gregor; Sun, Linfeng; Yan, Nieng; Kaback, H Ronald

    2014-02-18

    The Major Facilitator Superfamily (MFS) is a diverse group of secondary transporters with over 10,000 members, found in all kingdoms of life, including Homo sapiens. One objective of determining crystallographic models of the bacterial representatives is identification and physical localization of residues important for catalysis in transporters with medical relevance. The recently solved crystallographic models of the D-xylose permease XylE from Escherichia coli and GlcP from Staphylococcus epidermidus, homologs of the human D-glucose transporters, the GLUTs (SLC2), provide information about the structure of these transporters. The goal of this work is to examine general concepts derived from the bacterial XylE, GlcP, and other MFS transporters for their relevance to the GLUTs by comparing conservation of functionally critical residues. An energy landscape for symport and uniport is presented. Furthermore, the substrate selectivity of XylE is compared with GLUT1 and GLUT5, as well as a XylE mutant that transports D-glucose.

  16. A Loose Relationship: Incomplete H+/Sugar Coupling in the MFS Sugar Transporter GlcP.

    Science.gov (United States)

    Bazzone, Andre; Zabadne, Annas J; Salisowski, Anastasia; Madej, M Gregor; Fendler, Klaus

    2017-12-19

    The glucose transporter from Staphylococcus epidermidis, GlcPSe, is a homolog of the human GLUT sugar transporters of the major facilitator superfamily. Together with the xylose transporter from Escherichia coli, XylEEc, the other prominent prokaryotic GLUT homolog, GlcPSe, is equipped with a conserved proton-binding site arguing for an electrogenic transport mode. However, the electrophysiological analysis of GlcPSe presented here reveals important differences between the two GLUT homologs. GlcPSe, unlike XylEEc, does not perform steady-state electrogenic transport at symmetrical pH conditions. Furthermore, when a pH gradient is applied, partially uncoupled transport modes can be generated. In contrast to other bacterial sugar transporters analyzed so far, in GlcPSe sugar binding, translocation and release are also accomplished by the deprotonated transporter. Based on these experimental results, we conclude that coupling of sugar and H+ transport is incomplete in GlcPSe. To verify the viability of the observed partially coupled GlcPSe transport modes, we propose a universal eight-state kinetic model in which any degree of coupling is realized and H+/sugar symport represents only a specific instance. Furthermore, using sequence comparison with strictly coupled XylEEc and similar sugar transporters, we identify an additional charged residue that may be essential for effective H+/sugar symport. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  17. Identification of Important Amino Acids in Gal2p for Improving the L-arabinose Transport and Metabolism in Saccharomyces cerevisiae

    Directory of Open Access Journals (Sweden)

    Chengqiang Wang

    2017-07-01

    Full Text Available Efficient and cost-effective bioethanol production from lignocellulosic materials requires co-fermentation of the main hydrolyzed sugars, including glucose, xylose, and L-arabinose. Saccharomyces cerevisiae is a glucose-fermenting yeast that is traditionally used for ethanol production. Fermentation of L-arabinose is also possible after metabolic engineering. Transport into the cell is the first and rate-limiting step for L-arabinose metabolism. The galactose permease, Gal2p, is a non-specific, endogenous monosaccharide transporter that has been shown to transport L-arabinose. However, Gal2p-mediated transport of L-arabinose occurs at a low efficiency. In this study, homologous modeling and L-arabinose docking were used to predict amino acids in Gal2p that are crucial for L-arabinose transport. Nine amino acid residues in Gal2p were identified and were the focus for site-directed mutagenesis. In the Gal2p transport-deficient chassis cells, the capacity for L-arabinose transport of the different Gal2p mutants was compared by testing growth rates using L-arabinose as the sole carbon source. Almost all the tested mutations affected L-arabinose transport capacity. Among them, F85 is a unique site. The F85S, F85G, F85C, and F85T point mutations significantly increased L-arabinose transport activities, while, the F85E and F85R mutations decreased L-arabinose transport activities compared to the Gal2p-expressing wild-type strain. These results verified F85 as a key residue in L-arabinose transport. The F85S mutation, having the most significant effect, elevated the exponential growth rate by 40%. The F85S mutation also improved xylose transport efficiency and weakened the glucose transport preference. Overall, enhancing the L-arabinose transport capacity further improved the L-arabinose metabolism of engineered S. cerevisiae.

  18. Adapting Morphology to Multiple Tasks in Evolved Virtual Creatures

    DEFF Research Database (Denmark)

    Lessin, Dan; Fussell, Don; Miikkulainen, Risto

    2014-01-01

    The ESP method for evolving virtual creatures (Lessin et al., 2013) consisted of an encapsulation mechanism to preserve learned skills, a human-designed syllabus to build higherlevel skills by combining lower-level skills systematically, and a pandemonium mechanism to resolve conflicts between...... encapsulated skills in a single creature’s brain. Previous work with ESP showed that it is possible to evolve much more complex behavior than before, even when fundamental morphology (i.e., skeletal segments and joints) was evolved only for the first skill. This paper introduces a more general form of ESP...... in which full morphological development can continue beyond the first skill, allowing creatures to adapt their morphology to multiple tasks. This extension increases the variety and quality of evolved creature results significantly, while maintaining the original ESP system’s ability to incrementally...

  19. Orthogonally Evolved AI to Improve Difficulty Adjustment in Video Games

    DEFF Research Database (Denmark)

    Hintze, Arend; Olson, Randal; Lehman, Joel Anthony

    2016-01-01

    (i.e. agents subject to fewer generations of evolution) make for easier opponents, while highly-evolved agents are more challenging to overcome. In this publication we test a new approach for difficulty adjustment in games: orthogonally evolved AI, where the player receives support from collaborating...... agents that are co-evolved with opponent agents (where collaborators and opponents have orthogonal incentives). The advantage is that game difficulty can be adjusted more granularly by manipulating two independent axes: by having more or less adept collaborators, and by having more or less adept...... opponents. Furthermore, human interaction can modulate (and be informed by) the performance and behavior of collaborating agents. In this way, orthogonally evolved AI both facilitates smoother difficulty adjustment and enables new game experiences....

  20. Evolving the Evolving: Territory, Place and Rewilding in the California Delta

    Directory of Open Access Journals (Sweden)

    Brett Milligan

    2017-10-01

    Full Text Available Current planning and legislation in California’s Sacramento-San Joaquin Delta call for the large-scale ecological restoration of aquatic and terrestrial habitats. These ecological mandates have emerged in response to the region’s infrastructural transformation and the Delta’s predominant use as the central logistical hub in the state’s vast water conveyance network. Restoration is an attempt to recover what was externalized by the logic and abstractions of this logistical infrastructure. However, based on findings from our research, which examined how people are using restored and naturalized landscapes in the Delta and how these landscapes are currently planned for, we argue that as mitigatory response, restoration planning continues some of the same spatial abstractions and inequities by failing to account for the Delta as an urbanized, cultural and unique place. In interpreting how these conditions have come to be, we give attention to a pluralistic landscape approach and a coevolutionary reading of planning, policy, science and landscapes to discuss the conservation challenges presented by “Delta as an Evolving Place”. We suggest that for rewilding efforts to be successful in the Delta, a range of proactive, opportunistic, grounded and participatory tactics will be required to shift towards a more socio-ecological approach.

  1. (N+1)-dimensional Lorentzian evolving wormholes supported by polytropic matter

    Energy Technology Data Exchange (ETDEWEB)

    Cataldo, Mauricio [Universidad del Bio-Bio, Departamento de Fisica, Facultad de Ciencias, Concepcion (Chile); Arostica, Fernanda; Bahamonde, Sebastian [Universidad de Concepcion, Departamento de Fisica, Concepcion (Chile)

    2013-08-15

    In this paper we study (N+1)-dimensional evolving wormholes supported by energy satisfying a polytropic equation of state. The considered evolving wormhole models are described by a constant redshift function and generalizes the standard flat Friedmann-Robertson-Walker spacetime. The polytropic equation of state allows us to consider in (3+1)-dimensions generalizations of the phantom energy and the generalized Chaplygin gas sources. (orig.)

  2. Neurotransmitter transporters

    DEFF Research Database (Denmark)

    Gether, Ulrik; Andersen, Peter H; Larsson, Orla M

    2006-01-01

    The concentration of neurotransmitters in the extracellular space is tightly controlled by distinct classes of membrane transport proteins. This review focuses on the molecular function of two major classes of neurotransmitter transporter that are present in the cell membrane of neurons and....../or glial cells: the solute carrier (SLC)1 transporter family, which includes the transporters that mediate the Na(+)-dependent uptake of glutamate, and the SLC6 transporter family, which includes the transporters that mediate the Na(+)-dependent uptake of dopamine, 5-HT, norepinephrine, glycine and GABA....... Recent research has provided substantial insight into the structure and function of these transporters. In particular, the recent crystallizations of bacterial homologs are of the utmost importance, enabling the first reliable structural models of the mammalian neurotransmitter transporters...

  3. Energy transport in the penumbra.

    Science.gov (United States)

    Schlichenmaier, R.; Jahn, K.; Schmidt, H. U.

    1996-11-01

    The problem of energy transport in sunspot penumbrae is addressed. This paper presents the mathematical tools to investigate numerically the dynamics of a thin flux tube, which evolves in a 2D background formed by a magneto-static sunspot model. The goal is to study the role of interchange convection in penumbral energy transport and to examine the usefullness of thin flux tubes as a physical entity to explain observed penumbral features such as penumbral grains, bright and dark filaments and the Evershed flow.

  4. Transport processes in evolved stars: Theoretical and observational challenges - A tribute to Manuel Forestini

    Science.gov (United States)

    Charbonnel, C.

    Low and intermediate mass stars exhibit, at all the stages of their evolution, signatures of processes that require challenging modelling beyond the standard stellar theory. In this review we focus on the properties of these stars when they reach the giant phases of their evolution. We discuss in particular the spectroscopic diagnostics that probe the nucleosynthesis and the internal mixing mechanisms that drive RGB and AGB stars. We point out some long-standing theoretical challenges that still hinder a reliable evaluation of the contribution of these important stars to the chemical evolution of galaxies, and that could be solved in a very near future.

  5. Genomic analysis and D-xylose fermentation of three novel Spathaspora species: Spathaspora girioi sp. nov., Spathaspora hagerdaliae f. a., sp. nov. and Spathaspora gorwiae f. a., sp. nov.

    Science.gov (United States)

    Lopes, Mariana R; Morais, Camila G; Kominek, Jacek; Cadete, Raquel M; Soares, Marco A; Uetanabaro, Ana Paula T; Fonseca, César; Lachance, Marc-André; Hittinger, Chris Todd; Rosa, Carlos A

    2016-06-01

    Three novel D-xylose-fermenting yeast species of Spathaspora clade were recovered from rotting wood in regions of the Atlantic Rainforest ecosystem in Brazil. Differentiation of new species was based on analyses of the gene encoding the D1/D2 sequences of large subunit of rRNA and on 642 conserved, single-copy, orthologous genes from genome sequence assemblies from the newly described species and 15 closely-related Debaryomycetaceae/Metschnikowiaceae species. Spathaspora girioi sp. nov. produced unconjugated asci with a single elongated ascospore with curved ends; ascospore formation was not observed for the other two species. The three novel species ferment D-xylose with different efficiencies. Spathaspora hagerdaliae sp. nov. and Sp. girioi sp. nov. showed xylose reductase (XR) activity strictly dependent on NADPH, whereas Sp. gorwiae sp. nov. had XR activity that used both NADH and NADPH as co-factors. The genes that encode enzymes involved in D-xylose metabolism (XR, xylitol dehydrogenase and xylulokinase) were also identified for these novel species. The type strains are Sp. girioi sp. nov. UFMG-CM-Y302(T) (=CBS 13476), Sp. hagerdaliae f.a., sp. nov. UFMG-CM-Y303(T) (=CBS 13475) and Sp. gorwiae f.a., sp. nov. UFMG-CM-Y312(T) (=CBS 13472). © FEMS 2016. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

  6. Primary Progressive Multiple Sclerosis Evolving From Radiologically Isolated Syndrome.

    Science.gov (United States)

    Kantarci, Orhun H; Lebrun, Christine; Siva, Aksel; Keegan, Mark B; Azevedo, Christina J; Inglese, Matilde; Tintoré, Mar; Newton, Braeden D; Durand-Dubief, Francoise; Amato, Maria Pia; De Stefano, Nicola; Sormani, Maria Pia; Pelletier, Daniel; Okuda, Darin T

    2016-02-01

    The aim of this work was to evaluate the preprogressive phase in subjects with radiologically isolated syndrome (RIS) who evolve to primary progressive multiple sclerosis (PPMS). A multicenter RIS cohort was previously established. Demographic, clinical, and radiological characteristics of subjects with RIS that evolved directly to PPMS were compared to those that developed a relapsing disease course from onset (clinically isolated syndrome [CIS] or relapsing-remitting MS) and were also compared to two other population- and clinic-based PPMS cohorts. Of the 453 subjects with RIS, 128 evolved to symptomatic MS during the follow-up (113 developed a first acute clinical event consistent with CIS/MS, 15 evolved to PPMS). PPMS prevalence (11.7%) and onset age (mean ± standard deviation; 49.1 ± 12.1) in the RIS group were comparable to other PPMS populations (p > 0.05). Median time to PPMS was 3.5 years (range, 1.6-5.4). RIS evolved to PPMS more commonly in men (p = 0.005) and at an older age (p < 0.001) when compared to CIS/MS, independent of follow-up duration. Subjects who evolved to PPMS had more spinal cord lesions (100%) before symptomatic evolution than those that developed CIS/MS (64%) and those that remained asymptomatic (23%) within the follow-up period (P = 0.005). Other MRI characteristics in the preprogressive phase of PPMS were indistinguishable from CIS/MS. Subjects with RIS evolve to PPMS at the same frequency as expected from general MS populations in an age-dependent manner. Besides age, unequivocal presence of spinal cord lesions and being male predicted evolution to PPMS. Our findings further suggest that RIS is biologically part of the MS spectrum. © 2015 American Neurological Association.

  7. Improving L-arabinose utilization of pentose fermenting Saccharomyces cerevisiae cells by heterologous expression of L-arabinose transporting sugar transporters

    Directory of Open Access Journals (Sweden)

    Boles Eckhard

    2011-10-01

    Full Text Available Abstract Background Hydrolysates of plant biomass used for the production of lignocellulosic biofuels typically contain sugar mixtures consisting mainly of D-glucose and D-xylose, and minor amounts of L-arabinose. The yeast Saccharomyces cerevisiae is the preferred microorganism for the fermentative production of ethanol but is not able to ferment pentose sugars. Although D-xylose and L-arabinose fermenting S. cerevisiae strains have been constructed recently, pentose uptake is still a limiting step in mixed sugar fermentations. Results Here we described the cloning and characterization of two sugar transporters, AraT from the yeast Scheffersomyces stipitis and Stp2 from the plant Arabidopsis thaliana, which mediate the uptake of L-arabinose but not of D-glucose into S. cerevisiae cells. A yeast strain lacking all of its endogenous hexose transporter genes and expressing a bacterial L-arabinose utilization pathway could no longer take up and grow with L-arabinose as the only carbon source. Expression of the heterologous transporters supported uptake and utilization of L-arabinose especially at low L-arabinose concentrations but did not, or only very weakly, support D-glucose uptake and utilization. In contrast, the S. cerevisiae D-galactose transporter, Gal2, mediated uptake of both L-arabinose and D-glucose, especially at high concentrations. Conclusions Using a newly developed screening system we have identified two heterologous sugar transporters from a yeast and a plant which can support uptake and utilization of L-arabinose in L-arabinose fermenting S. cerevisiae cells, especially at low L-arabinose concentrations.

  8. GxySBA ABC transporter of Agrobacterium tumefaciens and its role in sugar utilization and vir gene expression.

    Science.gov (United States)

    Zhao, Jinlei; Binns, Andrew N

    2014-09-01

    Monosaccharides available in the extracellular milieu of Agrobacterium tumefaciens can be transported into the cytoplasm, or via the periplasmic sugar binding protein, ChvE, play a critical role in controlling virulence gene expression. The ChvE-MmsAB ABC transporter is involved in the utilization of a wide range of monosaccharide substrates but redundant transporters are likely given the ability of a chvE-mmsAB deletion strain to grow, albeit more slowly, in the presence of particular monosaccharides. In this study, a putative ABC transporter encoded by the gxySBA operon is identified and shown to be involved in the utilization of glucose, xylose, fucose, and arabinose, which are also substrates for the ChvE-MmsAB ABC transporter. Significantly, GxySBA is also shown to be the first characterized glucosamine ABC transporter. The divergently transcribed gene gxyR encodes a repressor of the gxySBA operon, the function of which can be relieved by a subset of the transported sugars, including glucose, xylose, and glucosamine, and this substrate-induced expression can be repressed by glycerol. Furthermore, deletion of the transporter can increase the sensitivity of the virulence gene expression system to certain sugars that regulate it. Collectively, the results reveal a remarkably diverse set of substrates for the GxySBA transporter and its contribution to the repression of sugar sensitivity by the virulence-controlling system, thereby facilitating the capacity of the bacterium to distinguish between the soil and plant environments. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

  9. Modeling and clustering users with evolving profiles in usage streams

    KAUST Repository

    Zhang, Chongsheng

    2012-09-01

    Today, there is an increasing need of data stream mining technology to discover important patterns on the fly. Existing data stream models and algorithms commonly assume that users\\' records or profiles in data streams will not be updated or revised once they arrive. Nevertheless, in various applications such asWeb usage, the records/profiles of the users can evolve along time. This kind of streaming data evolves in two forms, the streaming of tuples or transactions as in the case of traditional data streams, and more importantly, the evolving of user records/profiles inside the streams. Such data streams bring difficulties on modeling and clustering for exploring users\\' behaviors. In this paper, we propose three models to summarize this kind of data streams, which are the batch model, the Evolving Objects (EO) model and the Dynamic Data Stream (DDS) model. Through creating, updating and deleting user profiles, these models summarize the behaviors of each user as a profile object. Based upon these models, clustering algorithms are employed to discover interesting user groups from the profile objects. We have evaluated all the proposed models on a large real-world data set, showing that the DDS model summarizes the data streams with evolving tuples more efficiently and effectively, and provides better basis for clustering users than the other two models. © 2012 IEEE.

  10. Paenibacillus curdlanolyticus B-6 xylanase Xyn10C capable of producing a doubly arabinose-substituted xylose, α-L-Araf-(1→2)-[α-L-Araf-(1→3)]-D-Xylp, from rye arabinoxylan.

    Science.gov (United States)

    Imjongjairak, Siriluck; Jommuengbout, Pattaporn; Karpilanondh, Pirin; Katsuzaki, Hirotaka; Sakka, Makiko; Kimura, Tetsuya; Pason, Patthra; Tachaapaikoon, Chakrit; Romsaiyud, Jariya; Ratanakhanokchai, Khanok; Sakka, Kazuo

    2015-05-01

    Paenibacillus curdlanolyticus B-6 Xyn10C is a single module xylanase consisting of a glycoside hydrolase family-10 catalytic module. The recombinant enzyme, rXyn10C, was produced by Escherichia coli and characterized. rXyn10C was highly active toward soluble xylans derived from rye, birchwood, and oat spelt, and slightly active toward insoluble wheat arabinoxylan. It hydrolyzed xylooligosaccharides larger than xylotetraose to produce xylotriose, xylobiose, and xylose. When rye arabinoxylan and oat spelt xylan were treated with the enzyme and the hydrolysis products were analyzed by thin layer chromatography (TLC), two unknown hydrolysis products, U1 and U2, were detected in the upper position of xylose on a TLC plate. Electrospray ionization mass spectrometry and enzymatic analysis using Bacillus licheniformis α-L-arabinofuranosidase Axh43A indicated that U1 was α-L-Araf-(1→2)-[α-L-Araf-(1→3)]-D-Xylp and U2 was α-L-Araf-(1→2)-D-Xylp, suggesting that rXyn10C had strong activity toward a xylosidic linkage before and after a doubly arabinose-substituted xylose residue and was able to accommodate an α-1,2- and α-1,3-linked arabinose-substituted xylose unit in both the -1 and +1 subsites. A molecular docking study suggested that rXyn10C could accommodate a doubly arabinose-substituted xylose residue in its catalytic site, at subsite -1. This is the first report of a xylanase capable of producing α-L-Araf-(1→2)-[α-L-Araf-(1→3)]-D-Xylp from highly arabinosylated xylan. Copyright © 2015 Elsevier Inc. All rights reserved.

  11. Synthesis of Evolving Cells for Reconfigurable Manufacturing Systems

    Science.gov (United States)

    Padayachee, J.; Bright, G.

    2014-07-01

    The concept of Reconfigurable Manufacturing Systems (RMSs) was formulated due to the global necessity for production systems that are able to economically evolve according to changes in markets and products. Technologies and design methods are under development to enable RMSs to exhibit transformable system layouts, reconfigurable processes, cells and machines. Existing factory design methods and software have not yet advanced to include reconfigurable manufacturing concepts. This paper presents the underlying group technology framework for the design of manufacturing cells that are able to evolve according to a changing product mix by mechanisms of reconfiguration. The framework is based on a Norton- Bass forecast and time variant BOM models. An adaptation of legacy group technology methods is presented for the synthesis of evolving cells and two optimization problems are presented within this context.

  12. Evolving Systems: An Outcome of Fondest Hopes and Wildest Dreams

    Science.gov (United States)

    Frost, Susan A.; Balas, Mark J.

    2012-01-01

    New theory is presented for evolving systems, which are autonomously controlled subsystems that self-assemble into a new evolved system with a higher purpose. Evolving systems of aerospace structures often require additional control when assembling to maintain stability during the entire evolution process. This is the concept of Adaptive Key Component Control that operates through one specific component to maintain stability during the evolution. In addition, this control must often overcome persistent disturbances that occur while the evolution is in progress. Theoretical results will be presented for Adaptive Key Component control for persistent disturbance rejection. An illustrative example will demonstrate the Adaptive Key Component controller on a system composed of rigid body and flexible body modes.

  13. Computational Genetic Regulatory Networks Evolvable, Self-organizing Systems

    CERN Document Server

    Knabe, Johannes F

    2013-01-01

    Genetic Regulatory Networks (GRNs) in biological organisms are primary engines for cells to enact their engagements with environments, via incessant, continually active coupling. In differentiated multicellular organisms, tremendous complexity has arisen in the course of evolution of life on earth. Engineering and science have so far achieved no working system that can compare with this complexity, depth and scope of organization. Abstracting the dynamics of genetic regulatory control to a computational framework in which artificial GRNs in artificial simulated cells differentiate while connected in a changing topology, it is possible to apply Darwinian evolution in silico to study the capacity of such developmental/differentiated GRNs to evolve. In this volume an evolutionary GRN paradigm is investigated for its evolvability and robustness in models of biological clocks, in simple differentiated multicellularity, and in evolving artificial developing 'organisms' which grow and express an ontogeny starting fr...

  14. Study on evolving phases of accelerating generalized polygon beams.

    Science.gov (United States)

    Zhang, Yuntian; Dong, Fengliang; Qian, Kemao; Zhang, Qingchuan; Chu, Weiguo; Ma, Xuan; Wu, Xiaoping

    2016-03-07

    Recently, accelerating beam is becoming a hotspot in optics research. In this paper, we studied the evolving phases of accelerating generalized polygon beams (AGPBs) and proposed a novel method to generate this beam family. An important discovery has been made about reconstructing AGPBs only by evolving low-frequency phases in high power region, which confirms the dominant role of phase terms in the AGPBs' evolution. We also succeeded controlling the size and quantity of AGPB's intensity peaks in an easy and direct manner by manipulating the evolving phases in low frequency. This result not only explains the self-healing property of AGPBs but also confirms that AGPBs can be a great candidate to function as an optical tweezer to trap and free microparticles and microcreatures for certain purpose.

  15. Cosmic Biology How Life Could Evolve on Other Worlds

    CERN Document Server

    Irwin, Louis Neil

    2011-01-01

    It is very unlikely that little green humanoids are living on Mars. But what are the possible life forms that might exist in our Solar System and how might they have evolved? This uniquely authoritative and imaginative book on the possibilties for alien life addresses the intrinsic interest that we have about life on other worlds - reinforcing some of our assumptions and reshaping others. It introduces new possibilties that will enlarge our understanding of the issue overall, in particular the enormous range of environments and planetary conditions within which life might evolve. Cosmic Biology -discusses a broad range of possible environments where alien life might have evolved; -explains why carbon-based, water-borne life is more likely that its alternatives, but is not the only possiblity; -applies the principles of planetary science and modern biology to evolutionary scenarios on other worlds; -looks at the future fates of living systems, including those on Earth.

  16. Qualitative Functional Decomposition Analysis of Evolved Neuromorphic Flight Controllers

    Directory of Open Access Journals (Sweden)

    Sanjay K. Boddhu

    2012-01-01

    Full Text Available In the previous work, it was demonstrated that one can effectively employ CTRNN-EH (a neuromorphic variant of EH method methodology to evolve neuromorphic flight controllers for a flapping wing robot. This paper describes a novel frequency grouping-based analysis technique, developed to qualitatively decompose the evolved controllers into explainable functional control blocks. A summary of the previous work related to evolving flight controllers for two categories of the controller types, called autonomous and nonautonomous controllers, is provided, and the applicability of the newly developed decomposition analysis for both controller categories is demonstrated. Further, the paper concludes with appropriate discussion of ongoing work and implications for possible future work related to employing the CTRNN-EH methodology and the decomposition analysis techniques presented in this paper.

  17. Salmonella in selected foods by VIDAS immuno-concentration Salmonella plus selective plate method (Hektoen enteric, xylose lysine desoxycholate, bismuth sulfite): collaborative study.

    Science.gov (United States)

    Lepper, Wendy A; Schultz, Ann M; Curiale, Michael S; Johnson, Ronald L

    2002-01-01

    The VIDAS Immuno-concentration Salmonella (ICS) plus selective plate method (Hektoen enteric, xylose lysine desoxycholate, bismuth sulfite) method for the detection of Salmonella was compared to the Bacteriological Analytical Manual (BAM)/AOAC culture method in a collaborative study. Thirty-two laboratories participated in the evaluation. Each laboratory tested one or more of the 6 test products: milk chocolate, nonfat dry milk, dried whole egg, soy flour, ground black pepper, and ground raw turkey. The 2 methods were in agreement for 1,297 of the 1,455 samples. Of the 158 samples not in agreement, 82 were VIDAS ICS plus selective plate-positive and BAM/AOAC-negative, and 76 were VIDAS ICS plus selective plate-negative and BAM/AOAC-positive.

  18. Comparison of SHF and SSF processes from steam-exploded wheat straw for ethanol production by xylose-fermenting and robust glucose-fermenting Saccharomyces cerevisiae strains

    DEFF Research Database (Denmark)

    Tomas Pejo, Elia; Oliva, Jose M.; Ballesteros, Mercedes

    2008-01-01

    , it showed an ethanol yield on consumed sugars of 0.43 g/g and a volumetric ethanol productivity of 0.7 g/Lh for the first 3 h. Ethanol concentrations obtained in SSF processes were in all cases higher than those from SHF at the same conditions. Furthermore, using the whole slurry, final ethanol......In this study, bioethanol production from steam-exploded wheat straw using different process configurations was evaluated using two Saccharomyces cerevisiae strains, F12 and Red Star. The strain F12 has been engineerically modified to allow xylose consumption as cereal straw contain considerable...... amounts of pentoses. Red Star is a robust hexose-fermenting strain used for industrial fuel ethanol fermentations and it was used for comparative purposes. The highest ethanol concentration, 23.7 g/L, was reached using the whole slurry (10%, w/v) and the recombinant strain (F12) in an SSF process...

  19. Furfural Production from d-Xylose and Xylan by Using Stable Nafion NR50 and NaCl in a Microwave-Assisted Biphasic Reaction

    Directory of Open Access Journals (Sweden)

    Sarah Le Guenic

    2016-08-01

    Full Text Available Pentose dehydration and direct transformation of xylan into furfural were performed in a water-cyclopentyl methyl ether (CPME biphasic system under microwave irradiation. Heated up between 170 and 190 °C in the presence of Nafion NR50 and NaCl, d-xylose, l-arabinose and xylan gave furfural with maximum yields of 80%, 42% and 55%, respectively. The influence of temperature and reaction time on the reaction kinetics was discussed. This study was also completed by the survey of different reactant ratios, such as organic layer-water or catalyst-inorganic salt ratios. The exchange between proton and cation induced by an excess of NaCl was monitored, and a synergetic effect between the remaining protons and the released HCl was also discovered.

  20. Kinetics of oxidation of D-arabinose and D-xylose by vanadium (V in the presence of manganese II as homogeneous catalyst

    Directory of Open Access Journals (Sweden)

    Ezekiel O. Odebunmi

    2010-12-01

    Full Text Available Kinetics of oxidation of D-arabinose and D-xylose by acidic solution of vanadium (V ions in the presence of manganese (II has been reported. First-order dependence of the reaction rate was observed on [sugars] and [H+] at low concentrations throughout the oxidation reaction and a zero-order dependence on [sugar] and [H+] was observed at high concentrations. First-order kinetics with respect to [Mn (II] was also observed throughout the oxidation for both sugars. The results indicate the effect of Cl- concentration is negligible. The reaction rates increase with the ionic strength of the medium. Various activation parameters were evaluated and provide further support to the proposed mechanism. Formic acid was reported as one of the oxidation products of these sugars.