186,434 research outputs found
Optimization of the production of methyl ethyl ketone in recombinant Pseudomonas putida using large-scale kinetic models
No full textThe production of second generation of biofuels by conversion of inexpensive feedstocks is a basis for future bio-sustainable economy. Among many proposed molecules, methyl ethyl ketone (MEK) emerged as one of the most prominent fuel candidates due to its high-energy density, low emissions, and good transport properties. There is no known natural producer of MEK, but there were some recent studies to express its production pathway in different organisms. In all of these attempts, reported yields were very low. Among industrial workhorses such as E. coli and S. cerevisiae, P. putida has emerged as one of the most promising biofuel production hosts due to its tolerance to high toxicity compounds. For instance, it is reported that P. putida can grow in the presence of high concentrations of butanol1. This highly adaptive bacterium has been found to survive and grow on a broad range of substrates from pure caffeine to toxic industrial waste. In this study, we used the ORACLE framework to build, for the first time, a population of large-scale kinetic models of recombinant P. putida producing MEK. ORACLE2,3 (Optimization and Risk Analysis of Complex Living Entities) is a suite of computational tools capable of identifying enzymes with the highest impact on the production of target molecules. We started by embedding the MEK production pathway in the genome-scale model iJN7464 of P. putida, and then we derived a consistently reduced stoichiometric model. The obtained core model consists of 302 reactions and 210 mass balances distributed over cytosol, periplasm and extracellular environment. We then performed a series of tests to verify the consistency of the core model with its genome-scale counterpart. We next integrated fluxomics and metabolomics data from experiments and literature and performed Thermodynamic-Based Flux Analysis (TFA) to compute the thermodynamically feasible flux profiles that are consistent with the observed data. We further integrated the available information about the kinetic properties of enzymes involved in the modeled metabolic network. For reactions with missing or incomplete information about kinetic parameters, we performed a Monte Carlo sampling to generate missing information. We then constructed a population of 250’000 models, and we used these models to simultaneously optimize specific productivity of MEK and yield of MEK from glucose as a sole carbon source while taking into consideration the metabolic parameters such as catabolic and anabolic reduction charges. This way, we were able to identify enzymes that are potential candidates for metabolic engineering strategies towards obtaining a P. putida strain with improved specific productivity of MEK and its yield from glucose. This work demonstrates the potential and usefulness of ORACLE for optimizing production of biofuels and biochemicals in metabolic engineering and synthetic biology applications. 1. Rühl, J., Schmid, A. & Blank, L. M. Selected Pseudomonas putida strains able to grow in the presence of high butanol concentrations. Appl. Environ. Microbiol. 75, 4653–6 (2009). 2. Miskovic, L. & Hatzimanikatis, V. Production of biofuels and biochemicals: in need of an ORACLE. Trends in biotechnology 28, 391–7 (2010). 3. Chakrabarti, A., Miskovic, L., Soh, K. C. & Hatzimanikatis, V. Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints. Biotechnol. J. 8, 1043–57 (2013). 4. Nogales, J., Palsson, B. Ø. & Thiele, I. A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory. BMC Syst. Biol. 2, 79 (2008).LCS
Educating against the cultural politics and complicities of containment
No full textCapítulo do libro: Miskovic, M. (2013). Roma education in Europe. London: Routledge
Computational analysis of Pseudomonas Putida metabolism Using Large-scale Kinetic Models
No full textP. putida is a highly adaptive, non-pathogenic, soil bacterium that can grow on a wide range of substrates, and it is tolerant to high toxicity compounds. For these reasons, it emerged recently as one of the most promising production hosts for a wide range of chemicals. In this work, we performed a computational analysis of this organism to evaluate its metabolic capacities and design metabolic engineering strategies to improve its robustness to stress conditions. To this end, we first performed a thermodynamic curation of the genome-scale iJN1411 model of P. putida KT2440, and we then used redGEM and lumpGEM algorithms to derive a consistently reduced large-scale stoichiometric model of P. putida. We integrated experimental data into the resulting core stoichiometric model, and we computed the thermodynamically-consistent steady state of metabolic fluxes. We then used the ORACLE framework to generate a population of large-scale kinetic models around the computed steady state, and we employed these models in two studies. In the first study, for wild-type strain of P. putida KT2440 grown under aerobic conditions using glucose as a carbon source, we evaluated and validated the predictions of the generated kinetic models against a collection of experimental single-gene knockouts. In the second study, we analyzed the capacity of P. putida to adapt to increased energy demand and we identified potential metabolic engineering targets for improved resistance of this organism to stress conditions. This work demonstrates the potential and usefulness of kinetic models in rational metabolic engineering strategies for (i) understanding the physiology of production hosts, (ii) optimizing production pathways, and (iii) improving the metabolic responses of organisms to environmental stresses.LCS
A short-story of sin
No full textA brief overview is given of the theory of surface-ion neutralization (SIN) by highlighting studies from the pioneering days to the present time. Emphasis is placed on the 1-electron time-dependent Newns-Anderson (TDNA) model, which has played such a key role in studying resonance charge transfer. Recently, a many-electron (ME) version of the TDNA approach has been formulated to treat two or more electron processes, such as Auger transitions. The equation-of-motion technique is used to obtain the TD coefficients from which the required SIN probabilities can be found. After outlining the ME method, two applications are described. The first deals with the Li+-Cs/W(110) system, while the second addresses the laser enhancement of SIN, in the case of Li+-KBr: and revises some earlier results.PT: J; CR: AMOS AT, 1986, PHYS LETT A, V118, P471 AMOS AT, 1992, SURF SCI LETT, V277, L100 BLANDIN A, 1976, J PHYSIQUE, V37, P369 BLOSS W, 1978, SURF SCI, V72, P277 BRAKO R, 1981, SURF SCI, V108, P253 BRAKO R, 1985, SOLID STATE COMMUN, V55, P633 BRAKO R, 1989, REP PROG PHYS, V52, P655 DAVISON SG, 1986, J ELECTROANAL CH INF, V204, P173 DAVISON SG, 1994, IN PRESS ELECTRONIC GOLDBERG EC, 1985, PHYS REV B, V32, P4375 GOLDBERG EC, 1992, PHYS REV B, V45, P8657 GOODMAN FO, 1993, PHYS REV B, V47, P10685 GRIMLEY TB, 1983, SURF SCI, V124, P305 HAGSTRUM HD, 1954, PHYS REV, V96, P325 HAGSTRUM HD, 1954, PHYS REV, V96, P336 HAGSTRUM HD, 1961, PHYS REV, V122, P83 LANGRETH DC, 1991, PHYS REV B, V43, P2541 LOS J, 1990, PHYS REP, V190, P133 MASSEY HSW, 1930, P CAMB PHILOS SOC, V26, P386 MASSEY HSW, 1931, P CAMB PHILOS SOC, V27, P469 MISKOVIC ZL, 1993, SOLID STATE COMMUN, V87, P883 NAKANISHI H, 1991, SURF SCI, V242, P410 OLIPHANT MLE, 1930, P R SOC LOND A-CONTA, V127, P388 SEBASTIAN KL, 1983, PHYS LETT A, V98, P39 SEBASTIAN KL, 1985, PHYS REV B, V31, P6976 SHEKHTER SS, 1937, ZH EKSP TEOR FIZ, V7, P750 SROUBEK Z, 1974, SURF SCI, V44, P47 SULSTON KW, 1987, SOLID STATE COMMUN, V62, P781 SULSTON KW, 1988, PHYS REV B, V37, P9121 SULSTON KW, 1993, J PHYS-CONDENS MAT, V5, P2134 TULLY JC, 1977, PHYS REV B, V16, P4324 YOSHIMORI A, 1984, PROG THEOR PHYS SUPP, V80, P203 YOSHIMORI A, 1984, SPRINGER SERIES SOLI, V59, P74 YOSHIMORI A, 1986, PROG SURF SCI, V21, P251; NR: 34; TC: 3; J9: PROG SURF SCI; PG: 14; GA: QX183Source type: Electronic(1
Author-wise bibliometric analysis based on entropy.
No full textAuthor-wise bibliometric analysis based on entropy.</p
Going Beyond Counting First Authors in Author Co-citation Analysis
No full textThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
Results of Experimental Production of Forage of Grasslands Established on Abnormal Soils in Vojvodina Province
No full textIn Vojvodina province there is a certain acreage under hydromorphic, alkaline hydromorphic and alkaline soils which are not suitable for cultivation and growing of row crops. The acreage is roughly about 320000 ha. These soils may be cultivated only a short interval because of their unfavorable physical and aerial-hydrological properties and mechanical texture. If we add that the suitable machinery and implements are expensive, it becomes clear why farmers are unwilling to make use of that land (Zivkovic et al., 1972). The results of several research projects dealing with that problem indicated the establishment of cultivated grasslands as an optimum solution (Mihalic et al., 1980; Miskovic et al., 1980, 1981, 1982). The objective of study was to examine possibilities of establishing cultivated grasslands on different abnormal soils with purpose of ensuring a cheap production of quality forage
Appropriate Similarity Measures for Author Cocitation Analysis
No full textWe provide a number of new insights into the methodological discussion about author cocitation analysis. We first argue that the use of the Pearson correlation for measuring the similarity between authors’ cocitation profiles is not very satisfactory. We then discuss what kind of similarity measures may be used as an alternative to the Pearson correlation. We consider three similarity measures in particular. One is the well-known cosine. The other two similarity measures have not been used before in the bibliometric literature. Finally, we show by means of an example that our findings have a high practical relevance.information science;Pearson correlation;cosine;similarity measure;author cocitation analysis
Dispelling the Myths Behind First-author Citation Counts
No full textWe conducted a full-scale evaluative citation analysis study of scholars in the XML research field to explore just how different from each other author rankings resulting from different citation counting methods actually are, and to demonstrate the capability of emerging data and tools on the Web in supporting more realistic citation counting methods. Our results contest some common arguments for the continued
use of first-author citation counts in the evaluation of scholars, such as high correlations between author rankings by first-author citation counts and other citation
counting methods, and high costs of using more realistic citation counting methods that are not well-supported by the ISI databases. It is argued that increasingly available digital full text research papers make it possible for citation analysis studies to go beyond what the ISI databases have directly supported and to employ more
sophisticated methods
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