Protein engineering for metabolic engineering: current and next-generation tools

Science.gov (United States)

Marcheschi, Ryan J.; Gronenberg, Luisa S.; Liao, James C.

2014-01-01

Protein engineering in the context of metabolic engineering is increasingly important to the field of industrial biotechnology. As the demand for biologically-produced food, fuels, chemicals, food additives, and pharmaceuticals continues to grow, the ability to design and modify proteins to accomplish new functions will be required to meet the high productivity demands for the metabolism of engineered organisms. This article reviews advances of selecting, modeling, and engineering proteins to improve or alter their activity. Some of the methods have only recently been developed for general use and are just beginning to find greater application in the metabolic engineering community. We also discuss methods of generating random and targeted diversity in proteins to generate mutant libraries for analysis. Recent uses of these techniques to alter cofactor use, produce non-natural amino acids, alcohols, and carboxylic acids, and alter organism phenotypes are presented and discussed as examples of the successful engineering of proteins for metabolic engineering purposes. PMID:23589443

Metabolic engineering tools in model cyanobacteria.

Science.gov (United States)

Carroll, Austin L; Case, Anna E; Zhang, Angela; Atsumi, Shota

2018-03-26

Developing sustainable routes for producing chemicals and fuels is one of the most important challenges in metabolic engineering. Photoautotrophic hosts are particularly attractive because of their potential to utilize light as an energy source and CO 2 as a carbon substrate through photosynthesis. Cyanobacteria are unicellular organisms capable of photosynthesis and CO 2 fixation. While engineering in heterotrophs, such as Escherichia coli, has result in a plethora of tools for strain development and hosts capable of producing valuable chemicals efficiently, these techniques are not always directly transferable to cyanobacteria. However, recent efforts have led to an increase in the scope and scale of chemicals that cyanobacteria can produce. Adaptations of important metabolic engineering tools have also been optimized to function in photoautotrophic hosts, which include Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9, 13 C Metabolic Flux Analysis (MFA), and Genome-Scale Modeling (GSM). This review explores innovations in cyanobacterial metabolic engineering, and highlights how photoautotrophic metabolism has shaped their development. Copyright © 2018 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Obituary: Gordon Donaldson Obituary: Gordon Donaldson

Science.gov (United States)

Pegrum, Colin; Campbell, Archie; Hampshire, Damian

2013-07-01

Gordon Donaldson died in Glasgow on 28 November 2012 at the age of 71. He was born in Edinburgh and brought up and educated in Glasgow, which was his home city for much of his life. He was educated first at Glasgow Academy, and then with a scholarship at Christ's College Cambridge. Here he read Natural Sciences, finishing with first class honors in Physics. He then did a PhD on tunneling in superconductors in the Mond Laboratory, supervised by John Adkins. These were interesting times, since type II superconductors had only recently been identified, and the Mond was a leading player in the physics of vortices and other quantum effects. It was headed by Pippard and Shoenberg, and colleagues around that time were Brian Josephson, John Clarke, Colin Gough and John Waldram. On finishing his PhD in 1966 Gordon went straight to a lectureship at the University of Lancaster. In 1975 during a sabbatical at the University of California, Berkeley, with John Clarke's group, Gordon co-invented thin-film gradiometers with integrated DC SQUIDs. He then moved back to Glasgow, to the Department of Applied Physics at Strathclyde University, where he founded a new research group to make and use superconducting devices, especially SQUIDs and gradiometers. From modest beginnings the group grew steadily, acquiring new facilities and members, until in the 1990s it had over 20 members and a host of collaborators from elsewhere in Glasgow and abroad. With funding from the Wellcome Trust, Gordon and colleagues at Glasgow University and the Southern General Hospital in Glasgow set up a new biomagnetism facility in 1998 on the hospital campus to use SQUID gradiometers made at Strathclyde for measurements on patients and volunteers. Another of his main research interests was the use of SQUIDs for nondestructive evaluation (NDE). This started in the days before high temperature superconductors (HTS) with wire-wound gradiometers and niobium SQUIDs, soon moving on to miniature thin-film niobium

Genome-scale modeling for metabolic engineering.

Science.gov (United States)

Simeonidis, Evangelos; Price, Nathan D

2015-03-01

We focus on the application of constraint-based methodologies and, more specifically, flux balance analysis in the field of metabolic engineering, and enumerate recent developments and successes of the field. We also review computational frameworks that have been developed with the express purpose of automatically selecting optimal gene deletions for achieving improved production of a chemical of interest. The application of flux balance analysis methods in rational metabolic engineering requires a metabolic network reconstruction and a corresponding in silico metabolic model for the microorganism in question. For this reason, we additionally present a brief overview of automated reconstruction techniques. Finally, we emphasize the importance of integrating metabolic networks with regulatory information-an area which we expect will become increasingly important for metabolic engineering-and present recent developments in the field of metabolic and regulatory integration.

Plant metabolic modeling: achieving new insight into metabolism and metabolic engineering.

Science.gov (United States)

Baghalian, Kambiz; Hajirezaei, Mohammad-Reza; Schreiber, Falk

2014-10-01

Models are used to represent aspects of the real world for specific purposes, and mathematical models have opened up new approaches in studying the behavior and complexity of biological systems. However, modeling is often time-consuming and requires significant computational resources for data development, data analysis, and simulation. Computational modeling has been successfully applied as an aid for metabolic engineering in microorganisms. But such model-based approaches have only recently been extended to plant metabolic engineering, mainly due to greater pathway complexity in plants and their highly compartmentalized cellular structure. Recent progress in plant systems biology and bioinformatics has begun to disentangle this complexity and facilitate the creation of efficient plant metabolic models. This review highlights several aspects of plant metabolic modeling in the context of understanding, predicting and modifying complex plant metabolism. We discuss opportunities for engineering photosynthetic carbon metabolism, sucrose synthesis, and the tricarboxylic acid cycle in leaves and oil synthesis in seeds and the application of metabolic modeling to the study of plant acclimation to the environment. The aim of the review is to offer a current perspective for plant biologists without requiring specialized knowledge of bioinformatics or systems biology. © 2014 American Society of Plant Biologists. All rights reserved.

Modularization of genetic elements promotes synthetic metabolic engineering.

Science.gov (United States)

Qi, Hao; Li, Bing-Zhi; Zhang, Wen-Qian; Liu, Duo; Yuan, Ying-Jin

2015-11-15

In the context of emerging synthetic biology, metabolic engineering is moving to the next stage powered by new technologies. Systematical modularization of genetic elements makes it more convenient to engineer biological systems for chemical production or other desired purposes. In the past few years, progresses were made in engineering metabolic pathway using synthetic biology tools. Here, we spotlighted the topic of implementation of modularized genetic elements in metabolic engineering. First, we overviewed the principle developed for modularizing genetic elements and then discussed how the genetic modules advanced metabolic engineering studies. Next, we picked up some milestones of engineered metabolic pathway achieved in the past few years. Last, we discussed the rapid raised synthetic biology field of "building a genome" and the potential in metabolic engineering. Copyright © 2015 Elsevier Inc. All rights reserved.

Perspectives in metabolic engineering: understanding cellular regulation towards the control of metabolic routes.

Science.gov (United States)

Zadran, Sohila; Levine, Raphael D

2013-01-01

Metabolic engineering seeks to redirect metabolic pathways through the modification of specific biochemical reactions or the introduction of new ones with the use of recombinant technology. Many of the chemicals synthesized via introduction of product-specific enzymes or the reconstruction of entire metabolic pathways into engineered hosts that can sustain production and can synthesize high yields of the desired product as yields of natural product-derived compounds are frequently low, and chemical processes can be both energy and material expensive; current endeavors have focused on using biologically derived processes as alternatives to chemical synthesis. Such economically favorable manufacturing processes pursue goals related to sustainable development and "green chemistry". Metabolic engineering is a multidisciplinary approach, involving chemical engineering, molecular biology, biochemistry, and analytical chemistry. Recent advances in molecular biology, genome-scale models, theoretical understanding, and kinetic modeling has increased interest in using metabolic engineering to redirect metabolic fluxes for industrial and therapeutic purposes. The use of metabolic engineering has increased the productivity of industrially pertinent small molecules, alcohol-based biofuels, and biodiesel. Here, we highlight developments in the practical and theoretical strategies and technologies available for the metabolic engineering of simple systems and address current limitations.

Sinh-Gordon, cosh-Gordon, and Liouville equations for strings and multistrings in constant curvature spacetimes

International Nuclear Information System (INIS)

Larsen, A.L.; Sanchez, N.

1996-01-01

We find that the fundamental quadratic form of classical string propagation in (2+1)-dimensional constant curvature spacetimes solves the sinh-Gordon equation, the cosh-Gordon equation, or the Liouville equation. We show that in both de Sitter and anti endash de Sitter spacetimes (as well as in the 2+1 black hole anti endash de Sitter spacetime), all three equations must be included to cover the generic string dynamics. The generic properties of the string dynamics are directly extracted from the properties of these three equations and their associated potentials (irrespective of any solution). These results complete and generalize earlier discussions on this topic (until now, only the sinh-Gordon sector in de Sitter spacetime was known). We also construct new classes of multistring solutions, in terms of elliptic functions, to all three equations in both de Sitter and anti endash de Sitter spacetimes. Our results can be straightforwardly generalized to constant curvature spacetimes of arbitrary dimension, by replacing the sinh-Gordon equation, the cosh-Gordon equation, and the Liouville equation by their higher dimensional generalizations. copyright 1996 The American Physical Society

Modeling of Zymomonas mobilis central metabolism for novel metabolic engineering strategies.

Science.gov (United States)

Kalnenieks, Uldis; Pentjuss, Agris; Rutkis, Reinis; Stalidzans, Egils; Fell, David A

2014-01-01

Mathematical modeling of metabolism is essential for rational metabolic engineering. The present work focuses on several types of modeling approach to quantitative understanding of central metabolic network and energetics in the bioethanol-producing bacterium Zymomonas mobilis. Combined use of Flux Balance, Elementary Flux Mode, and thermodynamic analysis of its central metabolism, together with dynamic modeling of the core catabolic pathways, can help to design novel substrate and product pathways by systematically analyzing the solution space for metabolic engineering, and yields insights into the function of metabolic network, hardly achievable without applying modeling tools.

Nonlinear Klein-Gordon soliton mechanics

International Nuclear Information System (INIS)

Reinisch, G.

1992-01-01

Nonlinear Klein-Gordon solitary waves - or solitons in a loose sense - in n+1 dimensions, driven by very general external fields which must only satisfy continuity - together with regularity conditions at the boundaries of the system, obey a quite simple equation of motion. This equation is the exact generalization to this dynamical system of infinite number of degrees of freedom - which may be conservative or not - of the second Newton's law setting the basis of material point mechanics. In the restricted case of conservative nonlinear Klein-Gordon systems, where the external driving force is derivable from a potential energy, we recover the generalized Ehrenfest theorem which was itself the extension to such systems of the well-known Ehrenfest theorem in quantum mechanics. This review paper first displays a few (of one-dimensional sine-Gordon type) typical examples of the basic difficulties related to the trial construction of solitary-waves is proved and the derivation of the previous sine-Gordon examples from this theorem is displayed. Two-dimensional nonlinear solitary-wave patterns are considered, as well as a special emphasis is put on the applications to space-time complexity of 1-dim. sine-Gordon systems

Klein-Gordon oscillators in noncommutative phase space

International Nuclear Information System (INIS)

Wang Jianhua

2008-01-01

We study the Klein-Gordon oscillators in non-commutative (NC) phase space. We find that the Klein-Gordon oscillators in NC space and NC phase-space have a similar behaviour to the dynamics of a particle in commutative space moving in a uniform magnetic field. By solving the Klein-Gordon equation in NC phase space, we obtain the energy levels of the Klein-Gordon oscillators, where the additional terms related to the space-space and momentum-momentum non-commutativity are given explicitly. (authors)

Ultradiscrete sine-Gordon Equation over Symmetrized Max-Plus Algebra, and Noncommutative Discrete and Ultradiscrete sine-Gordon Equations

Directory of Open Access Journals (Sweden)

Kenichi Kondo

2013-11-01

Full Text Available Ultradiscretization with negative values is a long-standing problem and several attempts have been made to solve it. Among others, we focus on the symmetrized max-plus algebra, with which we ultradiscretize the discrete sine-Gordon equation. Another ultradiscretization of the discrete sine-Gordon equation has already been proposed by previous studies, but the equation and the solutions obtained here are considered to directly correspond to the discrete counterpart. We also propose a noncommutative discrete analogue of the sine-Gordon equation, reveal its relations to other integrable systems including the noncommutative discrete KP equation, and construct multisoliton solutions by a repeated application of Darboux transformations. Moreover, we derive a noncommutative ultradiscrete analogue of the sine-Gordon equation and its 1-soliton and 2-soliton solutions, using the symmetrized max-plus algebra. As a result, we have a complete set of commutative and noncommutative versions of continuous, discrete, and ultradiscrete sine-Gordon equations.

Computer-aided design for metabolic engineering.

Science.gov (United States)

Fernández-Castané, Alfred; Fehér, Tamás; Carbonell, Pablo; Pauthenier, Cyrille; Faulon, Jean-Loup

2014-12-20

The development and application of biotechnology-based strategies has had a great socio-economical impact and is likely to play a crucial role in the foundation of more sustainable and efficient industrial processes. Within biotechnology, metabolic engineering aims at the directed improvement of cellular properties, often with the goal of synthesizing a target chemical compound. The use of computer-aided design (CAD) tools, along with the continuously emerging advanced genetic engineering techniques have allowed metabolic engineering to broaden and streamline the process of heterologous compound-production. In this work, we review the CAD tools available for metabolic engineering with an emphasis, on retrosynthesis methodologies. Recent advances in genetic engineering strategies for pathway implementation and optimization are also reviewed as well as a range of bionalytical tools to validate in silico predictions. A case study applying retrosynthesis is presented as an experimental verification of the output from Retropath, the first complete automated computational pipeline applicable to metabolic engineering. Applying this CAD pipeline, together with genetic reassembly and optimization of culture conditions led to improved production of the plant flavonoid pinocembrin. Coupling CAD tools with advanced genetic engineering strategies and bioprocess optimization is crucial for enhanced product yields and will be of great value for the development of non-natural products through sustainable biotechnological processes. Copyright © 2014 Elsevier B.V. All rights reserved.

2017 Gordon Conference on Superconductivity

Energy Technology Data Exchange (ETDEWEB)

Chubukov, Andrey [Univ. of Minnesota, Twin Cities, MN (United States)

2017-11-14

The DOE award was for a 2017 Gordon Research conference on Superconductivity (GRC). The objective of GRC is to interchange the information about the latest theoretical and experimental developments in the area of superconductivity and to select most perspective directions for future research in this area.The goal of the Gordon Conference on Superconductivity is to present and discuss the latest results in the field of modern superconductivity, discuss new ideas and new directions of research in the area. It is a long-standing tradition of the Gordon conference on Superconductivity that the vast majority of participants are junior scientists. Funding for the conference would primarily be used to support junior researchers, particularly from under-represented groups. We had more 10 female speakers, some of them junior researchers, and some funding was used to support these speakers. The conference was held together with Gordon Research Seminar on Superconductivity, where almost all speakers and participants were junior scientists.

Systematic Applications of Metabolomics in Metabolic Engineering

Directory of Open Access Journals (Sweden)

Robert A. Dromms

2012-12-01

Full Text Available The goals of metabolic engineering are well-served by the biological information provided by metabolomics: information on how the cell is currently using its biochemical resources is perhaps one of the best ways to inform strategies to engineer a cell to produce a target compound. Using the analysis of extracellular or intracellular levels of the target compound (or a few closely related molecules to drive metabolic engineering is quite common. However, there is surprisingly little systematic use of metabolomics datasets, which simultaneously measure hundreds of metabolites rather than just a few, for that same purpose. Here, we review the most common systematic approaches to integrating metabolite data with metabolic engineering, with emphasis on existing efforts to use whole-metabolome datasets. We then review some of the most common approaches for computational modeling of cell-wide metabolism, including constraint-based models, and discuss current computational approaches that explicitly use metabolomics data. We conclude with discussion of the broader potential of computational approaches that systematically use metabolomics data to drive metabolic engineering.

Metabolic engineering in methanotrophic bacteria

Energy Technology Data Exchange (ETDEWEB)

Kalyuzhnaya, MG; Puri, AW; Lidstrom, ME

2015-05-01

Methane, as natural gas or biogas, is the least expensive source of carbon for (bio)chemical synthesis. Scalable biological upgrading of this simple alkane to chemicals and fuels can bring new sustainable solutions to a number of industries with large environmental footprints, such as natural gas/petroleum production, landfills, wastewater treatment, and livestock. Microbial biocatalysis with methane as a feedstock has been pursued off and on for almost a half century, with little enduring success. Today, biological engineering and systems biology provide new opportunities for metabolic system modulation and give new optimism to the concept of a methane-based bio-industry. Here we present an overview of the most recent advances pertaining to metabolic engineering of microbial methane utilization. Some ideas concerning metabolic improvements for production of acetyl-CoA and pyruvate, two main precursors for bioconversion, are presented. We also discuss main gaps in the current knowledge of aerobic methane utilization, which must be solved in order to release the full potential of methane-based biosystems. (C) 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

The 2013 Clusters, Nanocrystals & Nanostructures Gordon Research Conference/Gordon Research Seminar

Energy Technology Data Exchange (ETDEWEB)

Krauss, Todd D. [University of Rochester

2014-11-25

The fundamental properties of small particles and their potential for groundbreaking applications are among the most exciting areas of study in modern physics, chemistry, and materials science. The Clusters, Nanocrystals & Nanostructures Gordon ResearchConference and Gordon Research Seminar synthesize contributions from these inter-related fields that reflect the pivotal role of nano-particles at the interface between these disciplines. Size-dependent optical, electronic, magnetic and catalytic properties offer prospects for applications in many fields, and possible solutions for many of the grand challenges facing energy generation, consumption, delivery, and storage in the 21st century. The goal of the 2013 Clusters, Nanocrystals & Nanostructures Gordon Research Conference and Gordon Research Seminar is to continue the historical interdisciplinary tradition of this series and discuss the most recent advances, basic scientific questions, and emerging applications of clusters, nanocrystals, and nanostructures. The Clusters, Nanocrystals & Nanostructures GRC/GRS traditionally brings together the leading scientific groups that have made significant recent advances in one or more fundamental nanoscience or nanotechnology areas. Broad interests of the DOE BES and Solar Photochemistry Program addressed by this meeting include the areas of solar energy to fuels conversion, new photovoltaic systems, fundamental characterization of nanomaterials, magnetism, catalysis, and quantum physics. The vast majority of speakers and attendees will address either directly the topic of nanotechnology for photoinduced charge transfer, charge transport, and catalysis, or will have made significant contributions to related areas that will impact these fields indirectly. These topics have direct relevance to the mission of the DOE BES since it is this cutting-edge basic science that underpins our energy future.

Generalized sine-Gordon solitons

International Nuclear Information System (INIS)

Santos, C dos; Rubiera-Garcia, D

2011-01-01

In this paper, we construct analytical self-dual soliton solutions in (1+1) dimensions for two families of models which can be seen as generalizations of the sine-Gordon system but where the kinetic term is non-canonical. For that purpose we use a projection method applied to the sine-Gordon soliton. We focus our attention on the wall and lump-like soliton solutions of these k-field models. These solutions and their potentials reduce to those of the Klein-Gordon kink and the standard lump for the case of a canonical kinetic term. As we increase the nonlinearity on the kinetic term the corresponding potentials get modified and the nature of the soliton may change, in particular, undergoing a topology modification. The procedure constructed here is shown to be a sort of generalization of the deformation method for a specific class of k-field models. (paper)

Mass renormalization in sine-Gordon model

International Nuclear Information System (INIS)

Xu Bowei; Zhang Yumei

1991-09-01

With a general gaussian wave functional, we investigate the mass renormalization in the sine-Gordon model. At the phase transition point, the sine-Gordon system tends to a system of massless free bosons which possesses conformal symmetry. (author). 8 refs, 1 fig

The logics of metabolic regulation in bacteria challenges biosensor-based metabolic engineering

Directory of Open Access Journals (Sweden)

Matthieu Jules

2017-12-01

Full Text Available Synthetic Biology (SB aims at the rational design and engineering of novel biological functions and systems. By facilitating the engineering of living organisms, SB promises to facilitate the development of many new applications for health, biomanufacturing, and the environment. Over the last decade, SB promoted the construction of libraries of components enabling the fine-tuning of genetic circuits expression and the development of novel genome engineering methodologies for many organisms of interest. SB thus opened new perspectives in the field of metabolic engineering, which was until then mainly limited to (overproducing naturally synthesized metabolic compounds. To engineer efficient cell factories, it is key to precisely reroute cellular resources from the central carbon metabolism (CCM to the synthetic circuitry. This task is however difficult as there is still significant lack of knowledge regarding both the function of several metabolic components and the regulation of the CCM fluxes for many industrially important bacteria. Pyruvate is a pivotal metabolite at the heart of the CCM and a key precursor for the synthesis of several commodity compounds and fine chemicals. Numerous bacterial species can also use it as a carbon source when present in the environment but bacterial, pyruvate-specific uptake systems were to be discovered. This is an issue for metabolic engineering as one can imagine to make use of pyruvate transport systems to replenish synthetic metabolic pathways towards the synthesis of chemicals of interest. Here we describe a recent study (MBio 8(5: e00976-17, which identified and characterized a pyruvate transport system in the Gram-positive (G+ve bacterium Bacillus subtilis, a well-established biotechnological workhorse for the production of enzymes, fine chemicals and antibiotics. This study also revealed that the activity of the two-component system (TCS responsible for its induction is retro-inhibited by the level of

Engineering yeast metabolism for production of fuels and chemicals

DEFF Research Database (Denmark)

Nielsen, Jens

2016-01-01

faster development of metabolically engineered strains that can be used for production of fuels and chemicals. The yeast Saccharomyces cerevisiae is widely used for production of fuels, chemicals, pharmaceuticals and materials. Through metabolic engineering of this yeast a number of novel industrial...... as for metabolic design. In this lecture it will be demonstrated how the Design-Build-Test cycle of metabolic engineering has allowed for development of yeast cell factories for production of a range of different fuels and chemicals. Some examples of different technologies will be presented together with examples......Metabolic engineering relies on the Design-Build-Test cycle. This cycle includes technologies like mathematical modeling of metabolism, genome editing and advanced tools for phenotypic characterization. In recent years there have been advances in several of these technologies, which has enabled...

The 40th AAAS Gordon Conference on nuclear chemistry

International Nuclear Information System (INIS)

Seaborg, G.T.

1991-01-01

I am pleased to speak at the Fortieth Gordon Conference on Nuclear Chemistry. I served as Chairman of the first Gordon Conference on Nuclear Chemistry held June 23--27, 1952, at New Hampton, New Hampshire. In my remarks, during which I shall quote from my journal, I shall describe some of the background leading up to the first Gordon Conference on Nuclear Chemistry and my attendance at the first seven Gordon Conferences during the period 1952 through 1958. I shall also quote my description of my appearance as the featured speaker at the Silver Anniversary of the Gordon Research Conferences on December 27, 1956 held at the Commodore Hotel in New York City. I shall begin with reference to my participation in the predecessor to the Gordon Conferences, the Gibson Island Research Conferences 45 years ago, on Thursday, June 20, 1946, as a speaker. This was 15 years after the start of these conferences in 1931. Neil Gordon played a leading role in these conferences, which were named (in 1948) in his honor -- the Gordon Research Conferences -- soon after they were moved to Colby Junior College, New London, New Hampshire in 1947. W. George Parks became Director in 1947, Alexander Cruickshank became Assistant Director in 1947 and Director in 1968

The 40th AAAS Gordon Conference on nuclear chemistry

Energy Technology Data Exchange (ETDEWEB)

Seaborg, G.T.

1991-06-27

I am pleased to speak at the Fortieth Gordon Conference on Nuclear Chemistry. I served as Chairman of the first Gordon Conference on Nuclear Chemistry held June 23--27, 1952, at New Hampton, New Hampshire. In my remarks, during which I shall quote from my journal, I shall describe some of the background leading up to the first Gordon Conference on Nuclear Chemistry and my attendance at the first seven Gordon Conferences during the period 1952 through 1958. I shall also quote my description of my appearance as the featured speaker at the Silver Anniversary of the Gordon Research Conferences on December 27, 1956 held at the Commodore Hotel in New York City. I shall begin with reference to my participation in the predecessor to the Gordon Conferences, the Gibson Island Research Conferences 45 years ago, on Thursday, June 20, 1946, as a speaker. This was 15 years after the start of these conferences in 1931. Neil Gordon played a leading role in these conferences, which were named (in 1948) in his honor -- the Gordon Research Conferences -- soon after they were moved to Colby Junior College, New London, New Hampshire in 1947. W. George Parks became Director in 1947, Alexander Cruickshank became Assistant Director in 1947 and Director in 1968.

Recent advances in systems metabolic engineering tools and strategies.

Science.gov (United States)

Chae, Tong Un; Choi, So Young; Kim, Je Woong; Ko, Yoo-Sung; Lee, Sang Yup

2017-10-01

Metabolic engineering has been playing increasingly important roles in developing microbial cell factories for the production of various chemicals and materials to achieve sustainable chemical industry. Nowadays, many tools and strategies are available for performing systems metabolic engineering that allows systems-level metabolic engineering in more sophisticated and diverse ways by adopting rapidly advancing methodologies and tools of systems biology, synthetic biology and evolutionary engineering. As an outcome, development of more efficient microbial cell factories has become possible. Here, we review recent advances in systems metabolic engineering tools and strategies together with accompanying application examples. In addition, we describe how these tools and strategies work together in simultaneous and synergistic ways to develop novel microbial cell factories. Copyright © 2017 Elsevier Ltd. All rights reserved.

Genetic and metabolic engineering in diatoms.

Science.gov (United States)

Huang, Weichao; Daboussi, Fayza

2017-09-05

Diatoms have attracted considerable attention due to their success in diverse environmental conditions, which probably is a consequence of their complex origins. Studies of their metabolism will provide insight into their adaptation capacity and are a prerequisite for metabolic engineering. Several years of investigation have led to the development of the genome engineering tools required for such studies, and a profusion of appropriate tools is now available for exploring and exploiting the metabolism of these organisms. Diatoms are highly prized in industrial biotechnology, due to both their richness in natural lipids and carotenoids and their ability to produce recombinant proteins, of considerable value in diverse markets. This review provides an overview of recent advances in genetic engineering methods for diatoms, from the development of gene expression cassettes and gene delivery methods, to cutting-edge genome-editing technologies. It also highlights the contributions of these rapid developments to both basic and applied research: they have improved our understanding of key physiological processes; and they have made it possible to modify the natural metabolism to favour the production of specific compounds or to produce new compounds for green chemistry and pharmaceutical applications.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'. © 2017 The Author(s).

Engineering central metabolism – a grand challenge for plant biologists

DEFF Research Database (Denmark)

Sweetlove, Lee J.; Nielsen, Jens; Fernie, Alisdair R.

2017-01-01

The goal of increasing crop productivity and nutrient-use efficiency is being addressed by a number of ambitious research projects seeking to re-engineer photosynthetic biochemistry. Many of these projects will require the engineering of substantial changes in fluxes of central metabolism. However......, as has been amply demonstrated in simpler systems such as microbes, central metabolism is extremely difficult to rationally engineer. This is because of multiple layers of regulation that operate to maintain metabolic steady state and because of the highly connected nature of central metabolism....... In this review we discuss new approaches for metabolic engineering that have the potential to address these problems and dramatically improve the success with which we can rationally engineer central metabolism in plants. In particular, we advocate the adoption of an iterative ‘design-build-test-learn’ cycle...

Protein design in systems metabolic engineering for industrial strain development.

Science.gov (United States)

Chen, Zhen; Zeng, An-Ping

2013-05-01

Accelerating the process of industrial bacterial host strain development, aimed at increasing productivity, generating new bio-products or utilizing alternative feedstocks, requires the integration of complementary approaches to manipulate cellular metabolism and regulatory networks. Systems metabolic engineering extends the concept of classical metabolic engineering to the systems level by incorporating the techniques used in systems biology and synthetic biology, and offers a framework for the development of the next generation of industrial strains. As one of the most useful tools of systems metabolic engineering, protein design allows us to design and optimize cellular metabolism at a molecular level. Here, we review the current strategies of protein design for engineering cellular synthetic pathways, metabolic control systems and signaling pathways, and highlight the challenges of this subfield within the context of systems metabolic engineering. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Engineering microbial fatty acid metabolism for biofuels and biochemicals

DEFF Research Database (Denmark)

Marella, Eko Roy; Holkenbrink, Carina; Siewers, Verena

2017-01-01

microbial catalysis. This review summarizes the recent advances in the engineering of microbial metabolism for production of fatty acid-derived products. We highlight the efforts in engineering the central carbon metabolism, redox metabolism, controlling the chain length of the products, and obtaining...

Gauge symmetry of Sine-Gordon model

International Nuclear Information System (INIS)

Shen Jian-Min; Li Kang; Sheng Zhengmao.

1993-03-01

We have found that the strong coupled interaction of Sine-Gordon model is related to its weak coupled interaction by the su(2) gauge transformation. We therefore develop a semi-classical approach to deal with the infrared divergence in the conventional perturbation theory of the Hamiltonian of the quantum Sine-Gordon model. (author). 10 refs

Scaling in the sine-Gordon theory

International Nuclear Information System (INIS)

Ben-Abraham, S.I.

1976-01-01

It is shown that both the classical and the quantum sine-Gordon theory depend on a single scaling parameter and therefore the coupling constant cannot be freely chosen. To introduce a meaningful coupling constant it is proposed to include higher Fourier terms in the sine-Gordon potential. The two term case is exactly solvable. (Auth.)

Metabolite damage and repair in metabolic engineering design.

Science.gov (United States)

Sun, Jiayi; Jeffryes, James G; Henry, Christopher S; Bruner, Steven D; Hanson, Andrew D

2017-11-01

The necessarily sharp focus of metabolic engineering and metabolic synthetic biology on pathways and their fluxes has tended to divert attention from the damaging enzymatic and chemical side-reactions that pathway metabolites can undergo. Although historically overlooked and underappreciated, such metabolite damage reactions are now known to occur throughout metabolism and to generate (formerly enigmatic) peaks detected in metabolomics datasets. It is also now known that metabolite damage is often countered by dedicated repair enzymes that undo or prevent it. Metabolite damage and repair are highly relevant to engineered pathway design: metabolite damage reactions can reduce flux rates and product yields, and repair enzymes can provide robust, host-independent solutions. Herein, after introducing the core principles of metabolite damage and repair, we use case histories to document how damage and repair processes affect efficient operation of engineered pathways - particularly those that are heterologous, non-natural, or cell-free. We then review how metabolite damage reactions can be predicted, how repair reactions can be prospected, and how metabolite damage and repair can be built into genome-scale metabolic models. Lastly, we propose a versatile 'plug and play' set of well-characterized metabolite repair enzymes to solve metabolite damage problems known or likely to occur in metabolic engineering and synthetic biology projects. Copyright © 2017 International Metabolic Engineering Society. All rights reserved.

Systems metabolic engineering in an industrial setting.

Science.gov (United States)

Sagt, Cees M J

2013-03-01

Systems metabolic engineering is based on systems biology, synthetic biology, and evolutionary engineering and is now also applied in industry. Industrial use of systems metabolic engineering focuses on strain and process optimization. Since ambitious yields, titers, productivities, and low costs are key in an industrial setting, the use of effective and robust methods in systems metabolic engineering is becoming very important. Major improvements in the field of proteomics and metabolomics have been crucial in the development of genome-wide approaches in strain and process development. This is accompanied by a rapid increase in DNA sequencing and synthesis capacity. These developments enable the use of systems metabolic engineering in an industrial setting. Industrial systems metabolic engineering can be defined as the combined use of genome-wide genomics, transcriptomics, proteomics, and metabolomics to modify strains or processes. This approach has become very common since the technology for generating large data sets of all levels of the cellular processes has developed quite fast into robust, reliable, and affordable methods. The main challenge and scope of this mini review is how to translate these large data sets in relevant biological leads which can be tested for strain or process improvements. Experimental setup, heterogeneity of the culture, and sample pretreatment are important issues which are easily underrated. In addition, the process of structuring, filtering, and visualization of data is important, but also, the availability of a genetic toolbox and equipment for medium/high-throughput fermentation is a key success factor. For an efficient bioprocess, all the different components in this process have to work together. Therefore, mutual tuning of these components is an important strategy.

Two-Scale 13C Metabolic Flux Analysis for Metabolic Engineering.

Science.gov (United States)

Ando, David; Garcia Martin, Hector

2018-01-01

Accelerating the Design-Build-Test-Learn (DBTL) cycle in synthetic biology is critical to achieving rapid and facile bioengineering of organisms for the production of, e.g., biofuels and other chemicals. The Learn phase involves using data obtained from the Test phase to inform the next Design phase. As part of the Learn phase, mathematical models of metabolic fluxes give a mechanistic level of comprehension to cellular metabolism, isolating the principle drivers of metabolic behavior from the peripheral ones, and directing future experimental designs and engineering methodologies. Furthermore, the measurement of intracellular metabolic fluxes is specifically noteworthy as providing a rapid and easy-to-understand picture of how carbon and energy flow throughout the cell. Here, we present a detailed guide to performing metabolic flux analysis in the Learn phase of the DBTL cycle, where we show how one can take the isotope labeling data from a 13 C labeling experiment and immediately turn it into a determination of cellular fluxes that points in the direction of genetic engineering strategies that will advance the metabolic engineering process.For our modeling purposes we use the Joint BioEnergy Institute (JBEI) Quantitative Metabolic Modeling (jQMM) library, which provides an open-source, python-based framework for modeling internal metabolic fluxes and making actionable predictions on how to modify cellular metabolism for specific bioengineering goals. It presents a complete toolbox for performing different types of flux analysis such as Flux Balance Analysis, 13 C Metabolic Flux Analysis, and it introduces the capability to use 13 C labeling experimental data to constrain comprehensive genome-scale models through a technique called two-scale 13 C Metabolic Flux Analysis (2S- 13 C MFA) [1]. In addition to several other capabilities, the jQMM is also able to predict the effects of knockouts using the MoMA and ROOM methodologies. The use of the jQMM library is

Vacuum instability in the quantum sine-gordon model

International Nuclear Information System (INIS)

Bogolyubov, N.M.; Izergin, A.G.; Korepin, V.E.

1985-01-01

A review is given of papers dealing with regularization of the sine-Gordon model and the construction of the integrable lattice sine-Gordon (LSG) model. The regularization by means of LSG model seems to be much more natural as it is done in terms of initial boson fields entering Hamiltonian which describes relativistic scalar field with essentially nonlinear self-interaction. Changes in physical vacuum due to regularizations of the sine-Gordon model is shown

On Palacios-Gordon's theory of relativity

International Nuclear Information System (INIS)

Gulati, P.S.

1981-01-01

Since the early days of Einstein's special theory of relativity (1905), it is known that this theory suffers from some epistemological problems. Over the years, many theoreticians have endeavored to overcome these problems, rejecting either the 'Principle of Relativity' or the 'Light Principle'. Palacios and Gordon rejected the former and advanced an alternative theory governed by Voigt's transformation equations (1887). In the present paper, Palacios-Gordon's theory has been critically examined and some of its drawbacks are discovered. It becomes obvious that neither Einstein's special theory of relativity nor Palacios-Gordon's theory of relativity provides a flawless fit to the real world. It is speculated that suitable synthesis of these two theories might resolve all the controversial issues of special theory of relativity. (author)

Advancing metabolic engineering through systems biology of industrial microorganisms

DEFF Research Database (Denmark)

Dai, Zongjie; Nielsen, Jens

2015-01-01

resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review......Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable...... the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further....

Advances and prospects in metabolic engineering of Zymomonas mobilis.

Science.gov (United States)

Wang, Xia; He, Qiaoning; Yang, Yongfu; Wang, Jingwen; Haning, Katie; Hu, Yun; Wu, Bo; He, Mingxiong; Zhang, Yaoping; Bao, Jie; Contreras, Lydia M; Yang, Shihui

2018-04-05

Biorefinery of biomass-based biofuels and biochemicals by microorganisms is a competitive alternative of traditional petroleum refineries. Zymomonas mobilis is a natural ethanologen with many desirable characteristics, which makes it an ideal industrial microbial biocatalyst for commercial production of desirable bioproducts through metabolic engineering. In this review, we summarize the metabolic engineering progress achieved in Z. mobilis to expand its substrate and product ranges as well as to enhance its robustness against stressful conditions such as inhibitory compounds within the lignocellulosic hydrolysates and slurries. We also discuss a few metabolic engineering strategies that can be applied in Z. mobilis to further develop it as a robust workhorse for economic lignocellulosic bioproducts. In addition, we briefly review the progress of metabolic engineering in Z. mobilis related to the classical synthetic biology cycle of "Design-Build-Test-Learn", as well as the progress and potential to develop Z. mobilis as a model chassis for biorefinery practices in the synthetic biology era. Copyright © 2018 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Metabolic engineering of Yarrowia lipolytica for industrial applications.

Science.gov (United States)

Zhu, Quinn; Jackson, Ethel N

2015-12-01

Yarrowia lipolytica is a safe and robust yeast that has a history of industrial applications. Its physiological, metabolic and genomic characteristics have made it a superior host for metabolic engineering. The results of optimizing internal pathways and introducing new pathways have demonstrated that Y. lipolytica can be a platform cell factory for cost-effective production of chemicals and fuels derived from fatty acids, lipids and acetyl-CoA. Two products have been commercialized from metabolically engineered Y. lipolytica strains producing high amounts of omega-3 eicosapentaenoic acid, and more products are on the way to be produced at industrial scale. Here we review recent progress in metabolic engineering of Y. lipolytica for production of biodiesel fuel, functional fatty acids and carotenoids. Copyright © 2015 The Authors. Published by Elsevier Ltd.. All rights reserved.

Advancing metabolic engineering through systems biology of industrial microorganisms.

Science.gov (United States)

Dai, Zongjie; Nielsen, Jens

2015-12-01

Development of sustainable processes to produce bio-based compounds is necessary due to the severe environmental problems caused by the use of fossil resources. Metabolic engineering can facilitate the development of highly efficient cell factories to produce these compounds from renewable resources. The objective of systems biology is to gain a comprehensive and quantitative understanding of living cells and can hereby enhance our ability to characterize and predict cellular behavior. Systems biology of industrial microorganisms is therefore valuable for metabolic engineering. Here we review the application of systems biology tools for the identification of metabolic engineering targets which may lead to reduced development time for efficient cell factories. Finally, we present some perspectives of systems biology for advancing metabolic engineering further. Copyright © 2015 Elsevier Ltd. All rights reserved.

Gravity localization in sine-Gordon braneworlds

International Nuclear Information System (INIS)

Cruz, W.T.; Maluf, R.V.; Sousa, L.J.S.; Almeida, C.A.S.

2016-01-01

In this work we study two types of five-dimensional braneworld models given by sine-Gordon potentials. In both scenarios, the thick brane is generated by a real scalar field coupled to gravity. We focus our investigation on the localization of graviton field and the behaviour of the massive spectrum. In particular, we analyse the localization of massive modes by means of a relative probability method in a Quantum Mechanics context. Initially, considering a scalar field sine-Gordon potential, we find a localized state to the graviton at zero mode. However, when we consider a double sine-Gordon potential, the brane structure is changed allowing the existence of massive resonant states. The new results show how the existence of an internal structure can aid in the emergence of massive resonant modes on the brane.

Applications of computational modeling in metabolic engineering of yeast

DEFF Research Database (Denmark)

Kerkhoven, Eduard J.; Lahtvee, Petri-Jaan; Nielsen, Jens

2015-01-01

a preferred flux distribution. These methods point to strategies for altering gene expression; however, fluxes are often controlled by post-transcriptional events. Moreover, GEMs are usually not taking into account metabolic regulation, thermodynamics and enzyme kinetics. To facilitate metabolic engineering......, it is necessary to expand the modeling of metabolism to consider kinetics of individual processes. This review will give an overview about models available for metabolic engineering of yeast and discusses their applications....

Quantifying complexity in metabolic engineering using the LASER database

Directory of Open Access Journals (Sweden)

James D. Winkler

2016-12-01

Full Text Available We previously introduced the LASER database (Learning Assisted Strain EngineeRing, https://bitbucket.org/jdwinkler/laser_release (Winkler et al. 2015 to serve as a platform for understanding past and present metabolic engineering practices. Over the past year, LASER has been expanded by 50% to include over 600 engineered strains from 450 papers, including their growth conditions, genetic modifications, and other information in an easily searchable format. Here, we present the results of our efforts to use LASER as a means for defining the complexity of a metabolic engineering “design”. We evaluate two complexity metrics based on the concepts of construction difficulty and novelty. No correlation is observed between expected product yield and complexity, allowing minimization of complexity without a performance trade-off. We envision the use of such complexity metrics to filter and prioritize designs prior to implementation of metabolic engineering efforts, thereby potentially reducing the time, labor, and expenses of large-scale projects. Possible future developments based on an expanding LASER database are then discussed. Keywords: Metabolic engineering, Synthetic biology, Standardization, Design tools

[Improving industrial microbial stress resistance by metabolic engineering: a review].

Science.gov (United States)

Fu, Ruiyan; Li, Yin

2010-09-01

Metabolic engineering is a technologic platform for industrial strain improvement and aims not only at modifying microbial metabolic fluxes, but also improving the physiological performance of industrial microbes. Microbes will meet multiple stresses in industrial processes. Consequently, elicited gene responses might result in a decrease in overall cell fitness and the efficiency of biotransformation. Thus, it is crucial to develop robust and productive microbial strains that can be integrated into industrial-scale bioprocesses. In this review, we focus on the progress of these novel methods and strategies for engineering stress-tolerance phenotypes referring to rational metabolic engineering and inverse metabolic engineering in recent years. In addition, we also address problems existing in this area and future research needs of microbial physiological functionality engineering.

Engineering strategy of yeast metabolism for higher alcohol production

Directory of Open Access Journals (Sweden)

Shimizu Hiroshi

2011-09-01

Full Text Available Abstract Background While Saccharomyces cerevisiae is a promising host for cost-effective biorefinary processes due to its tolerance to various stresses during fermentation, the metabolically engineered S. cerevisiae strains exhibited rather limited production of higher alcohols than that of Escherichia coli. Since the structure of the central metabolism of S. cerevisiae is distinct from that of E. coli, there might be a problem in the structure of the central metabolism of S. cerevisiae. In this study, the potential production of higher alcohols by S. cerevisiae is compared to that of E. coli by employing metabolic simulation techniques. Based on the simulation results, novel metabolic engineering strategies for improving higher alcohol production by S. cerevisiae were investigated by in silico modifications of the metabolic models of S. cerevisiae. Results The metabolic simulations confirmed that the high production of butanols and propanols by the metabolically engineered E. coli strains is derived from the flexible behavior of their central metabolism. Reducing this flexibility by gene deletion is an effective strategy to restrict the metabolic states for producing target alcohols. In contrast, the lower yield using S. cerevisiae originates from the structurally limited flexibility of its central metabolism in which gene deletions severely reduced cell growth. Conclusions The metabolic simulation demonstrated that the poor productivity of S. cerevisiae was improved by the introduction of E. coli genes to compensate the structural difference. This suggested that gene supplementation is a promising strategy for the metabolic engineering of S. cerevisiae to produce higher alcohols which should be the next challenge for the synthetic bioengineering of S. cerevisiae for the efficient production of higher alcohols.

Next-generation genome-scale models for metabolic engineering

DEFF Research Database (Denmark)

King, Zachary A.; Lloyd, Colton J.; Feist, Adam M.

2015-01-01

Constraint-based reconstruction and analysis (COBRA) methods have become widely used tools for metabolic engineering in both academic and industrial laboratories. By employing a genome-scale in silico representation of the metabolic network of a host organism, COBRA methods can be used to predict...... examples of applying COBRA methods to strain optimization are presented and discussed. Then, an outlook is provided on the next generation of COBRA models and the new types of predictions they will enable for systems metabolic engineering....

Obituary: William Gordon (1918-2010)

Science.gov (United States)

Terzian, Yervant

2011-12-01

Bill Gordon was born in Paterson, New Jersey on January 8, 1918, and died in Ithaca, New York, on February 16, 2010. He is known as the engineer and ionospheric physicist who conceived and built the Arecibo giant radar/radio telescope. Bill graduated from Montclair State College in New Jersey and then in 1953 received his doctorate degree from Cornell University in electrical engineering, working under Henry Booker. During World War II he was in the Army where he studied the atmospheric conditions that affected radar transmissions. In the mid 1950s he began investigating giant antennas capable of studying the earths ionosphere. He succeeded in raising funds from the US Defense Department to construct the 1000 ft in diameter radar/radio telescope near the city of Arecibo on the island of Puerto Rico. The telescope was completed in 1963 under Bill's management, and he was its first Director. The huge fixed spherical antenna surface was made of a thin wire mesh allowing it to operate at frequencies up to about 600 MHz (50 cm wavelength). The spherical surface required complex 'line feeds' to correct for the spherical aberration, but allowed the telescope to track celestial radio sources by moving the line feeds which were supported by a platform suspended 500 ft above the reflector surface. Its sky coverage declination range was from -2 to +38 degrees. The large collecting area of the telescope made possible the detailed study of the physical properties of the earth's ionosphere. Measurements also included the rotation rates of the planets Mercury and Venus, radar imaging of the Moon and terrestrial planets. This new magastructure operated at low frequencies with its prime frequency at 430 MHz. One of Bill's passions was to make controlled experiments with the ionosphere. These so called 'heating experiments,' used a powerful HF radar transmitting from 5 to 10 MHz, to heat the ionosphere near the plasma frequency. The Arecibo radar then would study the heated

Applications of computational modeling in metabolic engineering of yeast.

Science.gov (United States)

Kerkhoven, Eduard J; Lahtvee, Petri-Jaan; Nielsen, Jens

2015-02-01

Generally, a microorganism's phenotype can be described by its pattern of metabolic fluxes. Although fluxes cannot be measured directly, inference of fluxes is well established. In biotechnology the aim is often to increase the capacity of specific fluxes. For this, metabolic engineering methods have been developed and applied extensively. Many of these rely on balancing of intracellular metabolites, redox, and energy fluxes, using genome-scale models (GEMs) that in combination with appropriate objective functions and constraints can be used to predict potential gene targets for obtaining a preferred flux distribution. These methods point to strategies for altering gene expression; however, fluxes are often controlled by post-transcriptional events. Moreover, GEMs are usually not taking into account metabolic regulation, thermodynamics and enzyme kinetics. To facilitate metabolic engineering, tools from synthetic biology have emerged, enabling integration and assembly of naturally nonexistent, but well-characterized components into a living organism. To describe these systems kinetic models are often used and to integrate these systems with the standard metabolic engineering approach, it is necessary to expand the modeling of metabolism to consider kinetics of individual processes. This review will give an overview about models available for metabolic engineering of yeast and discusses their applications. © FEMS 2015. All rights reserved. For permissions, please e-mail: journals.permission@oup.com.

Metabolite damage and repair in metabolic engineering design

Energy Technology Data Exchange (ETDEWEB)

Sun, Jiayi; Jeffryes, James G.; Henry, Christopher S.; Bruner, Steven D.; Hanson, Andrew D.

2017-11-01

The necessarily sharp focus of metabolic engineering and metabolic synthetic biology on pathways and their fluxes has tended to divert attention from the damaging enzymatic and chemical side-reactions that pathway metabolites can undergo. Although historically overlooked and underappreciated, such metabolite damage reactions are now known to occur throughout metabolism and to generate (formerly enigmatic) peaks detected in metabolomics datasets. It is also now known that metabolite damage is often countered by dedicated repair enzymes that undo or prevent it. Metabolite damage and repair are highly relevant to engineered pathway design: metabolite damage reactions can reduce flux rates and product yields, and repair enzymes can provide robust, host-independent solutions. Herein, after introducing the core principles of metabolite damage and repair, we use case histories to document how damage and repair processes affect efficient operation of engineered pathways - particularly those that are heterologous, non-natural, or cell-free. We then review how metabolite damage reactions can be predicted, how repair reactions can be prospected, and how metabolite damage and repair can be built into genome-scale metabolic models. Lastly, we propose a versatile 'plug and play' set of well-characterized metabolite repair enzymes to solve metabolite damage problems known or likely to occur in metabolic engineering and synthetic biology projects.

The Future of Metabolic Engineering and Synthetic Biology: Towards a Systematic Practice

Science.gov (United States)

Yadav, Vikramaditya G.; De Mey, Marjan; Lim, Chin Giaw; Ajikumar, Parayil Kumaran; Stephanopoulos, Gregory

2012-01-01

Industrial biotechnology promises to revolutionize conventional chemical manufacturing in the years ahead, largely owing to the excellent progress in our ability to re-engineer cellular metabolism. However, most successes of metabolic engineering have been confined to over-producing natively synthesized metabolites in E. coli and S. cerevisiae. A major reason for this development has been the descent of metabolic engineering, particularly secondary metabolic engineering, to a collection of demonstrations rather than a systematic practice with generalizable tools. Synthetic biology, a more recent development, faces similar criticisms. Herein, we attempt to lay down a framework around which bioreaction engineering can systematize itself just like chemical reaction engineering. Central to this undertaking is a new approach to engineering secondary metabolism known as ‘multivariate modular metabolic engineering’ (MMME), whose novelty lies in its assessment and elimination of regulatory and pathway bottlenecks by re-defining the metabolic network as a collection of distinct modules. After introducing the core principles of MMME, we shall then present a number of recent developments in secondary metabolic engineering that could potentially serve as its facilitators. It is hoped that the ever-declining costs of de novo gene synthesis; the improved use of bioinformatic tools to mine, sort and analyze biological data; and the increasing sensitivity and sophistication of investigational tools will make the maturation of microbial metabolic engineering an autocatalytic process. Encouraged by these advances, research groups across the world would take up the challenge of secondary metabolite production in simple hosts with renewed vigor, thereby adding to the range of products synthesized using metabolic engineering. PMID:22629571

Critical boundary sine-Gordon revisited

International Nuclear Information System (INIS)

Hasselfield, M.; Lee, Taejin; Semenoff, G.W.; Stamp, P.C.E.

2006-01-01

We revisit the exact solution of the two space-time dimensional quantum field theory of a free massless boson with a periodic boundary interaction and self-dual period. We analyze the model by using a mapping to free fermions with a boundary mass term originally suggested in Ref. [J. Polchinski, L. Thorlacius, Phys. Rev. D 50 (1994) 622]. We find that the entire SL (2, C) family of boundary states of a single boson are boundary sine-Gordon states and we derive a simple explicit expression for the boundary state in fermion variables and as a function of sine-Gordon coupling constants. We use this expression to compute the partition function. We observe that the solution of the model has a strong-weak coupling generalization of T-duality. We then examine a class of recently discovered conformal boundary states for compact bosons with radii which are rational numbers times the self-dual radius. These have simple expression in fermion variables. We postulate sine-Gordon-like field theories with discrete gauge symmetries for which they are the appropriate boundary states

The future of metabolic engineering and synthetic biology: towards a systematic practice.

Science.gov (United States)

Yadav, Vikramaditya G; De Mey, Marjan; Lim, Chin Giaw; Ajikumar, Parayil Kumaran; Stephanopoulos, Gregory

2012-05-01

Industrial biotechnology promises to revolutionize conventional chemical manufacturing in the years ahead, largely owing to the excellent progress in our ability to re-engineer cellular metabolism. However, most successes of metabolic engineering have been confined to over-producing natively synthesized metabolites in E. coli and S. cerevisiae. A major reason for this development has been the descent of metabolic engineering, particularly secondary metabolic engineering, to a collection of demonstrations rather than a systematic practice with generalizable tools. Synthetic biology, a more recent development, faces similar criticisms. Herein, we attempt to lay down a framework around which bioreaction engineering can systematize itself just like chemical reaction engineering. Central to this undertaking is a new approach to engineering secondary metabolism known as 'multivariate modular metabolic engineering' (MMME), whose novelty lies in its assessment and elimination of regulatory and pathway bottlenecks by re-defining the metabolic network as a collection of distinct modules. After introducing the core principles of MMME, we shall then present a number of recent developments in secondary metabolic engineering that could potentially serve as its facilitators. It is hoped that the ever-declining costs of de novo gene synthesis; the improved use of bioinformatic tools to mine, sort and analyze biological data; and the increasing sensitivity and sophistication of investigational tools will make the maturation of microbial metabolic engineering an autocatalytic process. Encouraged by these advances, research groups across the world would take up the challenge of secondary metabolite production in simple hosts with renewed vigor, thereby adding to the range of products synthesized using metabolic engineering. Copyright © 2011 Elsevier Inc. All rights reserved.

Production of amino acids - Genetic and metabolic engineering approaches.

Science.gov (United States)

Lee, Jin-Ho; Wendisch, Volker F

2017-12-01

The biotechnological production of amino acids occurs at the million-ton scale and annually about 6milliontons of l-glutamate and l-lysine are produced by Escherichia coli and Corynebacterium glutamicum strains. l-glutamate and l-lysine production from starch hydrolysates and molasses is very efficient and access to alternative carbon sources and new products has been enabled by metabolic engineering. This review focusses on genetic and metabolic engineering of amino acid producing strains. In particular, rational approaches involving modulation of transcriptional regulators, regulons, and attenuators will be discussed. To address current limitations of metabolic engineering, this article gives insights on recent systems metabolic engineering approaches based on functional tools and method such as genome reduction, amino acid sensors based on transcriptional regulators and riboswitches, CRISPR interference, small regulatory RNAs, DNA scaffolding, and optogenetic control, and discusses future prospects. Copyright © 2017 Elsevier Ltd. All rights reserved.

Balancing cellular redox metabolism in microbial electrosynthesis and electro fermentation - A chance for metabolic engineering.

Science.gov (United States)

Kracke, Frauke; Lai, Bin; Yu, Shiqin; Krömer, Jens O

2018-01-01

More and more microbes are discovered that are capable of extracellular electron transfer, a process in which they use external electrodes as electron donors or acceptors for metabolic reactions. This feature can be used to overcome cellular redox limitations and thus optimizing microbial production. The technologies, termed microbial electrosynthesis and electro-fermentation, have the potential to open novel bio-electro production platforms from sustainable energy and carbon sources. However, the performance of reported systems is currently limited by low electron transport rates between microbes and electrodes and our limited ability for targeted engineering of these systems due to remaining knowledge gaps about the underlying fundamental processes. Metabolic engineering offers many opportunities to optimize these processes, for instance by genetic engineering of pathways for electron transfer on the one hand and target product synthesis on the other hand. With this review, we summarize the status quo of knowledge and engineering attempts around chemical production in bio-electrochemical systems from a microbe perspective. Challenges associated with the introduction or enhancement of extracellular electron transfer capabilities into production hosts versus the engineering of target compound synthesis pathways in natural exoelectrogens are discussed. Recent advances of the research community in both directions are examined critically. Further, systems biology approaches, for instance using metabolic modelling, are examined for their potential to provide insight into fundamental processes and to identify targets for metabolic engineering. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Metabolic Engineering: Techniques for analysis of targets for genetic manipulations

DEFF Research Database (Denmark)

Nielsen, Jens Bredal

1998-01-01

Metabolic engineering has been defined as the purposeful modification of intermediary metabolism using recombinant DNA techniques. With this definition metabolic engineering includes: (1) inserting new pathways in microorganisms with the aim of producing novel metabolites, e.g., production...... of polyketides by Streptomyces; (2) production of heterologous peptides, e.g., production of human insulin, erythropoitin, and tPA; and (3) improvement of both new and existing processes, e.g., production of antibiotics and industrial enzymes. Metabolic engineering is a multidisciplinary approach, which involves...... input from chemical engineers, molecular biologists, biochemists, physiologists, and analytical chemists. Obviously, molecular biology is central in the production of novel products, as well as in the improvement of existing processes. However, in the latter case, input from other disciplines is pivotal...

Exact solutions of nonlinear generalizations of the Klein Gordon and Schrodinger equations

International Nuclear Information System (INIS)

Burt, P.B.

1978-01-01

Exact solutions of sine Gordon and multiple sine Gordon equations are constructed in terms of solutions of a linear base equation, the Klein Gordon equation and also in terms of nonlinear base equations where the nonlinearity is polynomial in the dependent variable. Further, exact solutions of nonlinear generalizations of the Schrodinger equation and of additional nonlinear generalizations of the Klein Gordon equation are constructed in terms of solutions of linear base equations. Finally, solutions with spherical symmetry, of nonlinear Klein Gordon equations are given. 14 references

Production of L-valine from metabolically engineered Corynebacterium glutamicum.

Science.gov (United States)

Wang, Xiaoyuan; Zhang, Hailing; Quinn, Peter J

2018-05-01

L-Valine is one of the three branched-chain amino acids (valine, leucine, and isoleucine) essential for animal health and important in metabolism; therefore, it is widely added in the products of food, medicine, and feed. L-Valine is predominantly produced through microbial fermentation, and the production efficiency largely depends on the quality of microorganisms. In recent years, continuing efforts have been made in revealing the mechanisms and regulation of L-valine biosynthesis in Corynebacterium glutamicum, the most utilitarian bacterium for amino acid production. Metabolic engineering based on the metabolic biosynthesis and regulation of L-valine provides an effective alternative to the traditional breeding for strain development. Industrially competitive L-valine-producing C. glutamicum strains have been constructed by genetically defined metabolic engineering. This article reviews the global metabolic and regulatory networks responsible for L-valine biosynthesis, the molecular mechanisms of regulation, and the strategies employed in C. glutamicum strain engineering.

Cytochrome P450-mediated metabolic engineering

DEFF Research Database (Denmark)

Renault, Hugues; Bassard, Jean-Étienne André; Hamberger, Björn Robert

2014-01-01

for the engineered bioproduction of such compounds. Two ground-breaking developments of commercial products driven by the engineering of P450s are the antimalarial drug precursor artemisinic acid and blue roses or carnations. Tedious optimizations were required to generate marketable products. Hurdles encountered...... in P450 engineering and their potential solutions are summarized here. Together with recent technical developments and novel approaches to metabolic engineering, the lessons from this pioneering work should considerably boost exploitation of the amazing P450 toolkit emerging from accelerated sequencing...

Combined Sinh-Cosh-Gordon equation: Symmetry reductions, exact ...

African Journals Online (AJOL)

Combined Sinh-Cosh-Gordon equation: Symmetry reductions, exact solutions and conservation laws. ... In this paper we study the combined sinh-cosh-Gordon equation, which arises in mathematical physics and has a wide range of scientific applications that range from chemical reactions to water surface gravity waves.

Metabolic engineering of biosynthetic pathway for production of renewable biofuels.

Science.gov (United States)

Singh, Vijai; Mani, Indra; Chaudhary, Dharmendra Kumar; Dhar, Pawan Kumar

2014-02-01

Metabolic engineering is an important area of research that involves editing genetic networks to overproduce a certain substance by the cells. Using a combination of genetic, metabolic, and modeling methods, useful substances have been synthesized in the past at industrial scale and in a cost-effective manner. Currently, metabolic engineering is being used to produce sufficient, economical, and eco-friendly biofuels. In the recent past, a number of efforts have been made towards engineering biosynthetic pathways for large scale and efficient production of biofuels from biomass. Given the adoption of metabolic engineering approaches by the biofuel industry, this paper reviews various approaches towards the production and enhancement of renewable biofuels such as ethanol, butanol, isopropanol, hydrogen, and biodiesel. We have also identified specific areas where more work needs to be done in the future.

Thomas Gordon's Communicative Pedagogy in Modern Educational Realities

Science.gov (United States)

Leshchenko, Maria; Isaieva, Svitlana

2014-01-01

In the article the principles, strategies, methods, techniques of communicative pedagogy of American scientist Thomas Gordon and system components of effective communication training for parents, teachers and administrators are enlightened. It has been determined that the main principle of Thomas Gordon's pedagogy is an interactive way of knowing…

Comparison of renormalization group schemes for sine-Gordon-type models

International Nuclear Information System (INIS)

Nandori, I.; Nagy, S.; Sailer, K.; Trombettoni, A.

2009-01-01

The scheme dependence of the renormalization group (RG) flow has been investigated in the local potential approximation for two-dimensional periodic, sine-Gordon type field-theoretic models discussing the applicability of various functional RG methods in detail. It was shown that scheme-independent determination of such physical parameters is possible as the critical frequency (temperature) at which Kosterlitz-Thouless-Berezinskii type phase transition takes place in the sine-Gordon and the layered sine-Gordon models, and the critical ratio characterizing the Ising-type phase transition of the massive sine-Gordon model. For the latter case, the Maxwell construction represents a strong constraint on the RG flow, which results in a scheme-independent infrared value for the critical ratio. For the massive sine-Gordon model also the shrinking of the domain of the phase with spontaneously broken periodicity is shown to take place due to the quantum fluctuations.

Integrating the protein and metabolic engineering toolkits for next-generation chemical biosynthesis.

Science.gov (United States)

Pirie, Christopher M; De Mey, Marjan; Jones Prather, Kristala L; Ajikumar, Parayil Kumaran

2013-04-19

Through microbial engineering, biosynthesis has the potential to produce thousands of chemicals used in everyday life. Metabolic engineering and synthetic biology are fields driven by the manipulation of genes, genetic regulatory systems, and enzymatic pathways for developing highly productive microbial strains. Fundamentally, it is the biochemical characteristics of the enzymes themselves that dictate flux through a biosynthetic pathway toward the product of interest. As metabolic engineers target sophisticated secondary metabolites, there has been little recognition of the reduced catalytic activity and increased substrate/product promiscuity of the corresponding enzymes compared to those of central metabolism. Thus, fine-tuning these enzymatic characteristics through protein engineering is paramount for developing high-productivity microbial strains for secondary metabolites. Here, we describe the importance of protein engineering for advancing metabolic engineering of secondary metabolism pathways. This pathway integrated enzyme optimization can enhance the collective toolkit of microbial engineering to shape the future of chemical manufacturing.

Metabolic Engineering of Probiotic Saccharomyces boulardii.

Science.gov (United States)

Liu, Jing-Jing; Kong, In Iok; Zhang, Guo-Chang; Jayakody, Lahiru N; Kim, Heejin; Xia, Peng-Fei; Kwak, Suryang; Sung, Bong Hyun; Sohn, Jung-Hoon; Walukiewicz, Hanna E; Rao, Christopher V; Jin, Yong-Su

2016-04-01

Saccharomyces boulardiiis a probiotic yeast that has been used for promoting gut health as well as preventing diarrheal diseases. This yeast not only exhibits beneficial phenotypes for gut health but also can stay longer in the gut than Saccharomyces cerevisiae Therefore, S. boulardiiis an attractive host for metabolic engineering to produce biomolecules of interest in the gut. However, the lack of auxotrophic strains with defined genetic backgrounds has hampered the use of this strain for metabolic engineering. Here, we report the development of well-defined auxotrophic mutants (leu2,ura3,his3, and trp1) through clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9-based genome editing. The resulting auxotrophic mutants can be used as a host for introducing various genetic perturbations, such as overexpression or deletion of a target gene, using existing genetic tools forS. cerevisiae We demonstrated the overexpression of a heterologous gene (lacZ), the correct localization of a target protein (red fluorescent protein) into mitochondria by using a protein localization signal, and the introduction of a heterologous metabolic pathway (xylose-assimilating pathway) in the genome ofS. boulardii We further demonstrated that human lysozyme, which is beneficial for human gut health, could be secreted by S. boulardii Our results suggest that more sophisticated genetic perturbations to improveS. boulardii can be performed without using a drug resistance marker, which is a prerequisite for in vivo applications using engineeredS. boulardii. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Engineering of sugar metabolism in Lactococcus lactis

NARCIS (Netherlands)

Pool, Weia Arianne

2008-01-01

Short English Summary Lactococcus lactis is a lactic acid bacterium used in the dairy industry. This thesis decribes the genetic engineering performed on the sugar metabolism of L. lactis. Besides our fundamental interest for sugar metabolism and its regulation in L. lactis, this project had the

Metabolic engineering of cyanobacteria for the synthesis of commodity products

NARCIS (Netherlands)

Angermayr, S.A.; Gorchs Rovira, A.; Hellingwerf, K.J.

2015-01-01

Through metabolic engineering cyanobacteria can be employed in biotechnology. Combining the capacity for oxygenic photosynthesis and carbon fixation with an engineered metabolic pathway allows carbon-based product formation from CO2, light, and water directly. Such cyanobacterial 'cell factories'

Metabolic Engineering for Probiotics and their Genome-Wide Expression Profiling.

Science.gov (United States)

Yadav, Ruby; Singh, Puneet K; Shukla, Pratyoosh

2018-01-01

Probiotic supplements in food industry have attracted a lot of attention and shown a remarkable growth in this field. Metabolic engineering (ME) approaches enable understanding their mechanism of action and increases possibility of designing probiotic strains with desired functions. Probiotic microorganisms generally referred as industrially important lactic acid bacteria (LAB) which are involved in fermenting dairy products, food, beverages and produces lactic acid as final product. A number of illustrations of metabolic engineering approaches in industrial probiotic bacteria have been described in this review including transcriptomic studies of Lactobacillus reuteri and improvement in exopolysaccharide (EPS) biosynthesis yield in Lactobacillus casei LC2W. This review summaries various metabolic engineering approaches for exploring metabolic pathways. These approaches enable evaluation of cellular metabolic state and effective editing of microbial genome or introduction of novel enzymes to redirect the carbon fluxes. In addition, various system biology tools such as in silico design commonly used for improving strain performance is also discussed. Finally, we discuss the integration of metabolic engineering and genome profiling which offers a new way to explore metabolic interactions, fluxomics and probiogenomics using probiotic bacteria like Bifidobacterium spp and Lactobacillus spp. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

The symmetries and conservation laws of some Gordon-type

Indian Academy of Sciences (India)

Conservation laws; Milne space-time; Gordon-type equations. Abstract. In this letter, the Lie point symmetries of a class of Gordon-type wave equations that arise in the Milne space-time are presented ... Pramana – Journal of Physics | News.

Computational methods in metabolic engineering for strain design.

Science.gov (United States)

Long, Matthew R; Ong, Wai Kit; Reed, Jennifer L

2015-08-01

Metabolic engineering uses genetic approaches to control microbial metabolism to produce desired compounds. Computational tools can identify new biological routes to chemicals and the changes needed in host metabolism to improve chemical production. Recent computational efforts have focused on exploring what compounds can be made biologically using native, heterologous, and/or enzymes with broad specificity. Additionally, computational methods have been developed to suggest different types of genetic modifications (e.g. gene deletion/addition or up/down regulation), as well as suggest strategies meeting different criteria (e.g. high yield, high productivity, or substrate co-utilization). Strategies to improve the runtime performances have also been developed, which allow for more complex metabolic engineering strategies to be identified. Future incorporation of kinetic considerations will further improve strain design algorithms. Copyright © 2015 Elsevier Ltd. All rights reserved.

Corynebacterium glutamicum for Sustainable Bioproduction: From Metabolic Physiology to Systems Metabolic Engineering.

Science.gov (United States)

Becker, Judith; Gießelmann, Gideon; Hoffmann, Sarah Lisa; Wittmann, Christoph

Since its discovery 60 years ago, Corynebacterium glutamicum has evolved into a workhorse for industrial biotechnology. Traditionally well known for its remarkable capacity to produce amino acids, this Gram-positive soil bacterium, has become a flexible, efficient production platform for various bulk and fine chemicals, materials, and biofuels. The central turnstile of all these achievements is our excellent understanding of its metabolism and physiology. This knowledge base, together with innovative systems metabolic engineering concepts, which integrate systems and synthetic biology into strain engineering, has upgraded C. glutamicum into one of the most successful industrial microorganisms in the world.

SBOLme: a Repository of SBOL Parts for Metabolic Engineering

KAUST Repository

Kuwahara, Hiroyuki

2017-01-12

The Synthetic Biology Open Language (SBOL) is a community-driven open language to promote standardization in synthetic biology. To support the use of SBOL in metabolic engineering, we developed SBOLme, the first open-access repository of SBOL 2-compliant biochemical parts for a wide range of metabolic engineering applications. The URL of our repository is http://www.cbrc.kaust.edu.sa/sbolme.

Metabolic engineering approaches for production of biochemicals in food and medicinal plants.

Science.gov (United States)

Wilson, Sarah A; Roberts, Susan C

2014-04-01

Historically, plants are a vital source of nutrients and pharmaceuticals. Recent advances in metabolic engineering have made it possible to not only increase the concentration of desired compounds, but also introduce novel biosynthetic pathways to a variety of species, allowing for enhanced nutritional or commercial value. To improve metabolic engineering capabilities, new transformation techniques have been developed to allow for gene specific silencing strategies or stacking of multiple genes within the same region of the chromosome. The 'omics' era has provided a new resource for elucidation of uncharacterized biosynthetic pathways, enabling novel metabolic engineering approaches. These resources are now allowing for advanced metabolic engineering of plant production systems, as well as the synthesis of increasingly complex products in engineered microbial hosts. The status of current metabolic engineering efforts is highlighted for the in vitro production of paclitaxel and the in vivo production of β-carotene in Golden Rice and other food crops. Copyright © 2014 Elsevier Ltd. All rights reserved.

Gordon Ramsay's Politeness Strategies in Masterchef and Masterchef Junior Us

OpenAIRE

Safa, Annisa Friska; Kurniawan, Eri

2015-01-01

This research aims to investigate the types of politeness strategies that are performed by Gordon Ramsay in judging the Masterchef US and Masterchef Junior US contestants' dishes and to reveal whether Gordon Ramsay performs any different politeness strategies between the Master chef and Masterchef Junior contestants. The data spring from Gordon Ramsay utterances, taken from the elimination test of two episodes of Masterchef season 4 (episode 9 and 12) and the elimination test of two episodes ...

Cell-free protein synthesis enabled rapid prototyping for metabolic engineering and synthetic biology

Directory of Open Access Journals (Sweden)

Lihong Jiang

2018-06-01

Full Text Available Advances in metabolic engineering and synthetic biology have facilitated the manufacturing of many valuable-added compounds and commodity chemicals using microbial cell factories in the past decade. However, due to complexity of cellular metabolism, the optimization of metabolic pathways for maximal production represents a grand challenge and an unavoidable barrier for metabolic engineering. Recently, cell-free protein synthesis system (CFPS has been emerging as an enabling alternative to address challenges in biomanufacturing. This review summarizes the recent progresses of CFPS in rapid prototyping of biosynthetic pathways and genetic circuits (biosensors to speed up design-build-test (DBT cycles of metabolic engineering and synthetic biology. Keywords: Cell-free protein synthesis, Metabolic pathway optimization, Genetic circuits, Metabolic engineering, Synthetic biology

Soliton solutions of coupled nonlinear Klein-Gordon equations

International Nuclear Information System (INIS)

Alagesan, T.; Chung, Y.; Nakkeeran, K.

2004-01-01

The coupled nonlinear Klein-Gordon equations are analyzed for their integrability properties in a systematic manner through Painleve test. From the Painleve test, by truncating the Laurent series at the constant level term, the Hirota bilinear form is identified, from which one-soliton solutions are derived. Then, the results are generalized to the two, three and N-coupled Klein-Gordon equations

Metabolic engineering of Bacillus subtilis fueled by systems biology: Recent advances and future directions.

Science.gov (United States)

Liu, Yanfeng; Li, Jianghua; Du, Guocheng; Chen, Jian; Liu, Long

By combining advanced omics technology and computational modeling, systems biologists have identified and inferred thousands of regulatory events and system-wide interactions of the bacterium Bacillus subtilis, which is commonly used both in the laboratory and in industry. This dissection of the multiple layers of regulatory networks and their interactions has provided invaluable information for unraveling regulatory mechanisms and guiding metabolic engineering. In this review, we discuss recent advances in the systems biology and metabolic engineering of B. subtilis and highlight current gaps in our understanding of global metabolism and global pathway engineering in this organism. We also propose future perspectives in the systems biology of B. subtilis and suggest ways that this approach can be used to guide metabolic engineering. Specifically, although hundreds of regulatory events have been identified or inferred via systems biology approaches, systematic investigation of the functionality of these events in vivo has lagged, thereby preventing the elucidation of regulatory mechanisms and further rational pathway engineering. In metabolic engineering, ignoring the engineering of multilayer regulation hinders metabolic flux redistribution. Post-translational engineering, allosteric engineering, and dynamic pathway analyses and control will also contribute to the modulation and control of the metabolism of engineered B. subtilis, ultimately producing the desired cellular traits. We hope this review will aid metabolic engineers in making full use of available systems biology datasets and approaches for the design and perfection of microbial cell factories through global metabolism optimization. Copyright © 2016 Elsevier Inc. All rights reserved.

On the supersymmetric sine-Gordon model

International Nuclear Information System (INIS)

Hruby, J.

1977-01-01

The sine-Gordon model as the theory of a massless scalar field in one space and one time dimension with interaction Lagrangian density proportional to cosβsub(phi) is generalized for a scalar superfield and it is shown that the solution of the supercovariant sine-Gordon equation is the ''supersoliton'', it is the superfield, which has all ordinary fields in two dimensions as a type of the soliton solution. We also obtain the massive Thirring model and the new equations of motion coupling the Fermi field and the Bose field. The notice about supersymmetric ''SLAC-BAG'' model is done

Metabolic Engineering of Oleaginous Yeasts for Production of Fuels and Chemicals

Directory of Open Access Journals (Sweden)

Shuobo Shi

2017-11-01

Full Text Available Oleaginous yeasts have been increasingly explored for production of chemicals and fuels via metabolic engineering. Particularly, there is a growing interest in using oleaginous yeasts for the synthesis of lipid-related products due to their high lipogenesis capability, robustness, and ability to utilize a variety of substrates. Most of the metabolic engineering studies in oleaginous yeasts focused on Yarrowia that already has plenty of genetic engineering tools. However, recent advances in systems biology and synthetic biology have provided new strategies and tools to engineer those oleaginous yeasts that have naturally high lipid accumulation but lack genetic tools, such as Rhodosporidium, Trichosporon, and Lipomyces. This review highlights recent accomplishments in metabolic engineering of oleaginous yeasts and recent advances in the development of genetic engineering tools in oleaginous yeasts within the last 3 years.

Essences in Metabolic Engineering of Lignan Biosynthesis

Directory of Open Access Journals (Sweden)

Honoo Satake

2015-05-01

Full Text Available Lignans are structurally and functionally diverse phytochemicals biosynthesized in diverse plant species and have received wide attentions as leading compounds of novel drugs for tumor treatment and healthy diets to reduce of the risks of lifestyle-related non-communicable diseases. However, the lineage-specific distribution and the low-amount of production in natural plants, some of which are endangered species, hinder the efficient and stable production of beneficial lignans. Accordingly, the development of new procedures for lignan production is of keen interest. Recent marked advances in the molecular and functional characterization of lignan biosynthetic enzymes and endogenous and exogenous factors for lignan biosynthesis have suggested new methods for the metabolic engineering of lignan biosynthesis cascades leading to the efficient, sustainable, and stable lignan production in plants, including plant cell/organ cultures. Optimization of light conditions, utilization of a wide range of elicitor treatments, and construction of transiently gene-transfected or transgenic lignan-biosynthesizing plants are mainly being attempted. This review will present the basic and latest knowledge regarding metabolic engineering of lignans based on their biosynthetic pathways and biological activities, and the perspectives in lignan production via metabolic engineering.

Abundant Interaction Solutions of Sine-Gordon Equation

Directory of Open Access Journals (Sweden)

DaZhao Lü

2012-01-01

Full Text Available With the help of computer symbolic computation software (e.g., Maple, abundant interaction solutions of sine-Gordon equation are obtained by means of a constructed Wronskian form expansion method. The method is based upon the forms and structures of Wronskian solutions of sine-Gordon equation, and the functions used in the Wronskian determinants do not satisfy linear partial differential equations. Such interaction solutions are difficultly obtained via other methods. And the method can be automatically carried out in computer.

SYSTEMS BIOLOGY AND METABOLIC ENGINEERING OF ARTHROSPIRA CELL FACTORIES

Directory of Open Access Journals (Sweden)

Amornpan Klanchui

2012-10-01

Full Text Available Arthrospira are attractive candidates to serve as cell factories for production of many valuable compounds useful for food, feed, fuel and pharmaceutical industries. In connection with the development of sustainable bioprocessing, it is a challenge to design and develop efficient Arthrospira cell factories which can certify effective conversion from the raw materials (i.e. CO2 and sun light into desired products. With the current availability of the genome sequences and metabolic models of Arthrospira, the development of Arthrospira factories can now be accelerated by means of systems biology and the metabolic engineering approach. Here, we review recent research involving the use of Arthrospira cell factories for industrial applications, as well as the exploitation of systems biology and the metabolic engineering approach for studying Arthrospira. The current status of genomics and proteomics through the development of the genome-scale metabolic model of Arthrospira, as well as the use of mathematical modeling to simulate the phenotypes resulting from the different metabolic engineering strategies are discussed. At the end, the perspective and future direction on Arthrospira cell factories for industrial biotechnology are presented.

A novel singular pattern in the sine-Gordon equation

International Nuclear Information System (INIS)

Huang, Debin

2003-01-01

By the scatter problem and the Backlund transformation of the sine-Gordon equation, we find a novel solution with the singularity of jumping phenomenon, which displays pattern structure similar respectively to soliton, kink, anti-kink and double pole solution with the different choice of the purely imaginary spectrum of the sine-Gordon equation

Oscillons in a perturbed signum-Gordon model

Science.gov (United States)

Klimas, P.; Streibel, J. S.; Wereszczynski, A.; Zakrzewski, W. J.

2018-04-01

We study various properties of a perturbed signum-Gordon model, which has been obtained through the dimensional reduction of the called `first BPS submodel of the Skyrme model'. This study is motivated by the observation that the first BPS submodel of the Skyrme model may be partially responsible for the good qualities of the rational map ansatz approximation to the solutions of the Skyrme model. We investigate the existence, stability and various properties of oscillons and other time-dependent states in this perturbed signum-Gordon model.

Dynamical symmetries of the Klein-Gordon equation

International Nuclear Information System (INIS)

Zhang Fulin; Chen Jingling

2009-01-01

The dynamical symmetries of the two-dimensional Klein-Gordon equations with equal scalar and vector potentials (ESVPs) are studied. The dynamical symmetries are considered in the plane and the sphere, respectively. The generators of the SO(3) group corresponding to the Coulomb potential and the SU(2) group corresponding to the harmonic oscillator potential are derived. Moreover, the generators in the sphere construct the Higgs algebra. With the help of the Casimir operators, the energy levels of the Klein-Gordon systems are yielded naturally

New quasi-periodic waves of the (2+1)-dimensional sine-Gordon system

International Nuclear Information System (INIS)

Hu, H.C.; Lou, S.Y.

2005-01-01

New exact solutions of the well-known (2+1)-dimensional sine-Gordon system are studied by introducing the modified mapping relations between the cubic nonlinear Klein-Gordon and sine-Gordon equations. Two arbitrary functions are included into the Jacobi elliptic function solutions. By proper selections of the arbitrary functions, new quasi-periodic wave solutions are obtained and displayed graphically

GORDON RAMSAY’S POLITENESS STRATEGIES IN MASTERCHEF AND MASTERCHEF JUNIOR US

OpenAIRE

Annisa Friska Safa; Eri Kurniawan

2015-01-01

Abstract This research aims to investigate the types of politeness strategies that are performed by Gordon Ramsay in judging the Masterchef US and Masterchef Junior US contestants’ dishes and to reveal whether Gordon Ramsay performs any different politeness strategies between the Master chef and Masterchef Junior contestants. The data spring from Gordon Ramsay utterances, taken from the elimination test of two episodes of Masterchef season 4 (episode 9 and 12) and the elimination test of ...

Evolutionary programming as a platform for in silico metabolic engineering

Directory of Open Access Journals (Sweden)

Förster Jochen

2005-12-01

Full Text Available Abstract Background Through genetic engineering it is possible to introduce targeted genetic changes and hereby engineer the metabolism of microbial cells with the objective to obtain desirable phenotypes. However, owing to the complexity of metabolic networks, both in terms of structure and regulation, it is often difficult to predict the effects of genetic modifications on the resulting phenotype. Recently genome-scale metabolic models have been compiled for several different microorganisms where structural and stoichiometric complexity is inherently accounted for. New algorithms are being developed by using genome-scale metabolic models that enable identification of gene knockout strategies for obtaining improved phenotypes. However, the problem of finding optimal gene deletion strategy is combinatorial and consequently the computational time increases exponentially with the size of the problem, and it is therefore interesting to develop new faster algorithms. Results In this study we report an evolutionary programming based method to rapidly identify gene deletion strategies for optimization of a desired phenotypic objective function. We illustrate the proposed method for two important design parameters in industrial fermentations, one linear and other non-linear, by using a genome-scale model of the yeast Saccharomyces cerevisiae. Potential metabolic engineering targets for improved production of succinic acid, glycerol and vanillin are identified and underlying flux changes for the predicted mutants are discussed. Conclusion We show that evolutionary programming enables solving large gene knockout problems in relatively short computational time. The proposed algorithm also allows the optimization of non-linear objective functions or incorporation of non-linear constraints and additionally provides a family of close to optimal solutions. The identified metabolic engineering strategies suggest that non-intuitive genetic modifications span

Metabolic engineering of Agrobacterium sp. ATCC31749 for curdlan production from cellobiose.

Science.gov (United States)

Shin, Hyun-Dong; Liu, Long; Kim, Mi-Kyoung; Park, Yong-Il; Chen, Rachel

2016-09-01

Curdlan is a commercial polysaccharide made by fermentation of Agrobacterium sp. Its anticipated expansion to larger volume markets demands improvement in its production efficiency. Metabolic engineering for strain improvement has so far been limited due to the lack of genetic tools. This research aimed to identify strong promoters and to engineer a strain that converts cellobiose efficiently to curdlan. Three strong promoters were identified and were used to install an energy-efficient cellobiose phosphorolysis mechanism in a curdlan-producing strain. The engineered strains were shown with enhanced ability to utilize cellobiose, resulting in a 2.5-fold increase in titer. The availability of metabolically engineered strain capable of producing β-glucan from cellobiose paves the way for its production from cellulose. The identified native promoters from Agrobacterium open up opportunities for further metabolic engineering for improved production of curdlan and other products. The success shown here marks the first such metabolic engineering effort in this microbe.

Mini-review: In vitro Metabolic Engineering for Biomanufacturing of High-value Products

Directory of Open Access Journals (Sweden)

Weihua Guo

Full Text Available With the breakthroughs in biomolecular engineering and synthetic biology, many valuable biologically active compound and commodity chemicals have been successfully manufactured using cell-based approaches in the past decade. However, because of the high complexity of cell metabolism, the identification and optimization of rate-limiting metabolic pathways for improving the product yield is often difficult, which represents a significant and unavoidable barrier of traditional in vivo metabolic engineering. Recently, some in vitro engineering approaches were proposed as alternative strategies to solve this problem. In brief, by reconstituting a biosynthetic pathway in a cell-free environment with the supplement of cofactors and substrates, the performance of each biosynthetic pathway could be evaluated and optimized systematically. Several value-added products, including chemicals, nutraceuticals, and drug precursors, have been biosynthesized as proof-of-concept demonstrations of in vitro metabolic engineering. This mini-review summarizes the recent progresses on the emerging topic of in vitro metabolic engineering and comments on the potential application of cell-free technology to speed up the “design-build-test” cycles of biomanufacturing. Keywords: Cell-free, Biosynthesis, Metabolic pathways, Design-build-test cycle

A Status Report on the Global Research in Microbial Metabolic Engineering

Energy Technology Data Exchange (ETDEWEB)

Joe, Min Ho; Lim, Sang Yong; Kim, Dong Ho

2008-09-15

Biotechnology industry is now a global 'Mega-Trend' and metabolic engineering technology has important role is this area. Therefore, many countries has made efforts in this field to produce top value added bio-products efficiently using microorganisms. It has been applied to increase the production of chemicals that are already produced by the host organism, to produce desired chemical substances from less expensive feedstock, and to generate products that are new to the host organism. Recent experimental advances, the so-called '-omics' technologies, mainly functional genomics, proteomics and metabolomics, have enabled wholesale generation of new genomic, transcriptomic, proteomic, and metabolomic data. This report provides the insights of the integrated view of metabolism generated by metabolic engineering for biotechnological applications of microbial metabolic engineering.

A Status Report on the Global Research in Microbial Metabolic Engineering

International Nuclear Information System (INIS)

Joe, Min Ho; Lim, Sang Yong; Kim, Dong Ho

2008-09-01

Biotechnology industry is now a global 'Mega-Trend' and metabolic engineering technology has important role is this area. Therefore, many countries has made efforts in this field to produce top value added bio-products efficiently using microorganisms. It has been applied to increase the production of chemicals that are already produced by the host organism, to produce desired chemical substances from less expensive feedstock, and to generate products that are new to the host organism. Recent experimental advances, the so-called '-omics' technologies, mainly functional genomics, proteomics and metabolomics, have enabled wholesale generation of new genomic, transcriptomic, proteomic, and metabolomic data. This report provides the insights of the integrated view of metabolism generated by metabolic engineering for biotechnological applications of microbial metabolic engineering

A Status Report on the Global Research in Microbial Metabolic Engineering

Energy Technology Data Exchange (ETDEWEB)

Joe, Min Ho; Lim, Sang Yong; Kim, Dong Ho

2008-09-15

Biotechnology industry is now a global 'Mega-Trend' and metabolic engineering technology has important role is this area. Therefore, many countries has made efforts in this field to produce top value added bio-products efficiently using microorganisms. It has been applied to increase the production of chemicals that are already produced by the host organism, to produce desired chemical substances from less expensive feedstock, and to generate products that are new to the host organism. Recent experimental advances, the so-called '-omics' technologies, mainly functional genomics, proteomics and metabolomics, have enabled wholesale generation of new genomic, transcriptomic, proteomic, and metabolomic data. This report provides the insights of the integrated view of metabolism generated by metabolic engineering for biotechnological applications of microbial metabolic engineering.

Microbial Development and Metabolic Engineering | Bioenergy | NREL

Science.gov (United States)

Diversity Our genetically engineered microbes utilize a variety of feedstock including cellulose, xylan , syngas, simple sugars, organic acids, and carbon dioxide (CO2). We have modified the metabolic pathways

Deriving metabolic engineering strategies from genome-scale modeling with flux ratio constraints.

Science.gov (United States)

Yen, Jiun Y; Nazem-Bokaee, Hadi; Freedman, Benjamin G; Athamneh, Ahmad I M; Senger, Ryan S

2013-05-01

Optimized production of bio-based fuels and chemicals from microbial cell factories is a central goal of systems metabolic engineering. To achieve this goal, a new computational method of using flux balance analysis with flux ratios (FBrAtio) was further developed in this research and applied to five case studies to evaluate and design metabolic engineering strategies. The approach was implemented using publicly available genome-scale metabolic flux models. Synthetic pathways were added to these models along with flux ratio constraints by FBrAtio to achieve increased (i) cellulose production from Arabidopsis thaliana; (ii) isobutanol production from Saccharomyces cerevisiae; (iii) acetone production from Synechocystis sp. PCC6803; (iv) H2 production from Escherichia coli MG1655; and (v) isopropanol, butanol, and ethanol (IBE) production from engineered Clostridium acetobutylicum. The FBrAtio approach was applied to each case to simulate a metabolic engineering strategy already implemented experimentally, and flux ratios were continually adjusted to find (i) the end-limit of increased production using the existing strategy, (ii) new potential strategies to increase production, and (iii) the impact of these metabolic engineering strategies on product yield and culture growth. The FBrAtio approach has the potential to design "fine-tuned" metabolic engineering strategies in silico that can be implemented directly with available genomic tools. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

AdS. Klein-Gordon equation

OpenAIRE

Bel, Ll.

2014-01-01

I propose a generalization of the Klein-Gordon equation in the framework of AdS space-time and exhibit a four parameter family of solutions among which there is a two parameter family of time-dependent bound states.

Bunched soliton states in weakly coupled sine-Gordon systems

DEFF Research Database (Denmark)

Grønbech-Jensen, N.; Samuelsen, Mogens Rugholm; Lomdahl, P. S.

1990-01-01

The interaction between solitons of two weakly coupled sine-Gordon systems is considered. In particular, the stability of bunched states is investigated, and perturbation results are compared with numerical results.......The interaction between solitons of two weakly coupled sine-Gordon systems is considered. In particular, the stability of bunched states is investigated, and perturbation results are compared with numerical results....

Use of genome-scale microbial models for metabolic engineering

DEFF Research Database (Denmark)

Patil, Kiran Raosaheb; Åkesson, M.; Nielsen, Jens

2004-01-01

Metabolic engineering serves as an integrated approach to design new cell factories by providing rational design procedures and valuable mathematical and experimental tools. Mathematical models have an important role for phenotypic analysis, but can also be used for the design of optimal metaboli...... network structures. The major challenge for metabolic engineering in the post-genomic era is to broaden its design methodologies to incorporate genome-scale biological data. Genome-scale stoichiometric models of microorganisms represent a first step in this direction....

On the prolongation structure and Backlund transformation for new non-linear Klein-Gordon equations

International Nuclear Information System (INIS)

Roy Chowdhury, A.; Mukherjee, J.

1986-07-01

We have considered the complete integrability of two nonlinear equations which are some kind of extensions of usual Sine-Gordon and Sinh-Gordon equations. The first one is of non-autonomous version of Sinh-Gordon system and the second is closely related to the usual Sine-Gordon theory. The first problem indicates how (x,t) dependent non-linear equations can be treated in the prolongation theory and how a Backlund map can be constructed. The second one is a variation of the usual Sine-Gordon equation and suggests that there may be other equations (similar to Sine-Gordon) which are completely integrable. In both cases we have been able to construct the Lax pair. We then construct an auto-Backlund map by following the idea of Konno and Wadati, for the generation of multisolution states. (author)

Cyanobacterial metabolic engineering for biofuel and chemical production.

Science.gov (United States)

Oliver, Neal J; Rabinovitch-Deere, Christine A; Carroll, Austin L; Nozzi, Nicole E; Case, Anna E; Atsumi, Shota

2016-12-01

Rising levels of atmospheric CO 2 are contributing to the global greenhouse effect. Large scale use of atmospheric CO 2 may be a sustainable and renewable means of chemical and liquid fuel production to mitigate global climate change. Photosynthetic organisms are an ideal platform for efficient, natural CO 2 conversion to a broad range of chemicals. Cyanobacteria are especially attractive for these purposes, due to their genetic malleability and relatively fast growth rate. Recent years have yielded a range of work in the metabolic engineering of cyanobacteria and have led to greater knowledge of the host metabolism. Understanding of endogenous and heterologous carbon regulation mechanisms leads to the expansion of productive capacity and chemical variety. This review discusses the recent progress in metabolic engineering of cyanobacteria for biofuel and bulk chemical production since 2014. Copyright © 2016 Elsevier Ltd. All rights reserved.

Metabolic Engineering for Substrate Co-utilization

Science.gov (United States)

Gawand, Pratish

Production of biofuels and bio-based chemicals is being increasingly pursued by chemical industry to reduce its dependence on petroleum. Lignocellulosic biomass (LCB) is an abundant source of sugars that can be used for producing biofuels and bio-based chemicals using fermentation. Hydrolysis of LCB results in a mixture of sugars mainly composed of glucose and xylose. Fermentation of such a sugar mixture presents multiple technical challenges at industrial scale. Most industrial microorganisms utilize sugars in a sequential manner due to the regulatory phenomenon of carbon catabolite repression (CCR). Due to sequential utilization of sugars, the LCB-based fermentation processes suffer low productivities and complicated operation. Performance of fermentation processes can be improved by metabolic engineering of microorganisms to obtain superior characteristics such as high product yield. With increased computational power and availability of complete genomes of microorganisms, use of model-based metabolic engineering is now a common practice. The problem of sequential sugar utilization, however, is a regulatory problem, and metabolic models have never been used to solve such regulatory problems. The focus of this thesis is to use model-guided metabolic engineering to construct industrial strains capable of co-utilizing sugars. First, we develop a novel bilevel optimization algorithm SimUp, that uses metabolic models to identify reaction deletion strategies to force co-utilization of two sugars. We then use SimUp to identify reaction deletion strategies to force glucose-xylose co-utilization in Escherichia coli. To validate SimUp predictions, we construct three mutants with multiple gene knockouts and test them for glucose-xylose utilization characteristics. Two mutants, designated as LMSE2 and LMSE5, are shown to co-utilize glucose and xylose in agreement with SimUp predictions. To understand the molecular mechanism involved in glucose-xylose co-utilization of the

Gordon Fraser (1943-2013)

CERN Document Server

2013-01-01

We were deeply saddened to learn that Gordon Fraser had passed away on 3 January. During his 25-year career at CERN, until his retirement in 2002, he made many valuable contributions to the Laboratory, in particular as editor of CERN Courier.   Gordon’s life in science began at Imperial College London, where he obtained a PhD with the theory group of the future Nobel laureate Abdus Salam. He then spent time at Tel Aviv University in Yuval Ne’eman’s group and at Brighton University, before changing career to become a journalist, at first for Computer Weekly in London. He moved into scientific editing at the Rutherford Appleton Laboratory in 1975 and it was from there that he was hired to join the publications team at CERN in 1977. By 1982 Gordon had become the editor of the CERN Courier. During his time at the helm, both particle physics and the Courier changed considerably. Under his careful stewardship aspects of publishing were outsourced, leading to a...

Design, Optimization and Application of Small Molecule Biosensor in Metabolic Engineering.

Science.gov (United States)

Liu, Yang; Liu, Ye; Wang, Meng

2017-01-01

The development of synthetic biology and metabolic engineering has painted a great future for the bio-based economy, including fuels, chemicals, and drugs produced from renewable feedstocks. With the rapid advance of genome-scale modeling, pathway assembling and genome engineering/editing, our ability to design and generate microbial cell factories with various phenotype becomes almost limitless. However, our lack of ability to measure and exert precise control over metabolite concentration related phenotypes becomes a bottleneck in metabolic engineering. Genetically encoded small molecule biosensors, which provide the means to couple metabolite concentration to measurable or actionable outputs, are highly promising solutions to the bottleneck. Here we review recent advances in the design, optimization and application of small molecule biosensor in metabolic engineering, with particular focus on optimization strategies for transcription factor (TF) based biosensors.

77 FR 51023 - R. Gordon Gooch v. Colonial Pipeline Company; Notice of Complaint

Science.gov (United States)

2012-08-23

... DEPARTMENT OF ENERGY Federal Energy Regulatory Commission [Docket No. OR12-24-000] R. Gordon Gooch...)), and section 343.2 of the Commission's regulations (18 CFR 343.2 (2012)), R. Gordon Gooch (Complainant..., and 100.6.0, as set forth more fully in the complaint. R. Gordon Gooch states that a copy of the...

2010 Tetrapyrroles, Chemistry & Biology of Gordon Research Conference

Energy Technology Data Exchange (ETDEWEB)

Angela Wilks

2010-07-30

The objective of the Chemistry & Biology of Tetrapyrroles Gordon Conference is to bring together researchers from diverse disciplines that otherwise would not interact. By bringing biologists, chemists, engineers and clinicians with a common interest in tetrapyrroles the conference provides a forum for cross-disciplinary ideas and collaboration. The perspective provided by biologists, chemists, and clinicians working in fields such as newly discovered defects in human porphyrin metabolism, the myriad of strategies for light harvesting in photosynthetic organisms, novel tetrapyrroles that serve as auxiliary chromophores or enzyme cofactors, synthetic strategies in the design of novel tetrapyrrole scaffolds, and tetrapyrrole based cell signaling and regulatory systems, makes this conference unique in the field. Over the years the growing evidence for the role of tetrapyrroles and their reactive intermediates in cell signaling and regulation has been of increasing importance at this conference. The 2010 conference on Chemistry & Biology of Tetrapyrroles will focus on many of these new frontiers as outlined in the preliminary program listed. Speakers will emphasize unpublished results and new findings in the field. The oral sessions will be followed by the highly interactive afternoon poster sessions. The poster sessions provide all conferees with the opportunity to present their latest research and to exchange ideas in a more informal setting. As in the past, this opportunity will continue during the nightly social gathering that takes place in the poster hall following the evening lectures. All conferees are encouraged to submit and present posters. At the conference the best poster in the areas of biology, chemistry and medicine will be selected by a panel of previous conference chairs.

On a rigorously classical approach to the Sine-Gordon theory

International Nuclear Information System (INIS)

Ulmer, W.

1979-01-01

It is shown that the continuum limit of an infinite set of coupled pendula yields the Sine-Gordon theory. The extension of the model to more dimensions with respect to the propagation yields a generalized Sine-Gordon equation for vector fields, containing Proca equations as a first order approximation. (author)

Kink-antikink interactions in a modified sine-Gordon model

International Nuclear Information System (INIS)

Peyrard, M.; Campbell, D.K.; Los Alamos National Lab., NM

1983-01-01

We study numerically the interactions of a kink (K) and an antikink (anti K) in a parametrically modified sine-Gordon model with potential V(PHI)=(1-r) 2 (1-cos PHI)/(1+r 2 +2r cos PHI). As the parameter r is varied from the pure sine-Gordon case (r=0) to values for which the model is not completely integrable (rnot=0), we find that a rich structure arises in the Kanti K collisions. For some regions of r(-0.20 4 model, and we show that the theory recently suggested for these collisions also applies quantitatively to the modified sine-Gordon model. In other regions of r we observe new scattering phenomena, which we present in detail numerically and discuss in a qualitative manner analytically. (orig.)

Pathway elucidation and metabolic engineering of specialized plant metabolites

DEFF Research Database (Denmark)

Salomonsen, Bo

A worldwide need to liberate ourselves from unsustainable petrochemicals has led to numerous metabolic engineering projects, mostly carried out in microbial hosts. Using systems biology for predicting and altering the metabolism of microorganisms towards production of a desired metabolite......, these projects have increased revenues on fermentative production of several biochemicals. The use of systems biology is, however, not limited to microorganisms. Recent advances in biotechnology methods have provided a wealth of data within functional genomics, metabolomics, transcriptomics, proteomics...... and fluxomics for a considerable number of organisms. Unfortunately, transferring the wealth of data to valuable information for metabolic engineering purposes is a non-obvious task. This PhD thesis describes a palate of tools used in generation of cell factories for production of specialized plant metabolites...

Towards systems metabolic engineering in Pichia pastoris.

Science.gov (United States)

Schwarzhans, Jan-Philipp; Luttermann, Tobias; Geier, Martina; Kalinowski, Jörn; Friehs, Karl

2017-11-01

The methylotrophic yeast Pichia pastoris is firmly established as a host for the production of recombinant proteins, frequently outperforming other heterologous hosts. Already, a sizeable amount of systems biology knowledge has been acquired for this non-conventional yeast. By applying various omics-technologies, productivity features have been thoroughly analyzed and optimized via genetic engineering. However, challenging clonal variability, limited vector repertoire and insufficient genome annotation have hampered further developments. Yet, in the last few years a reinvigorated effort to establish P. pastoris as a host for both protein and metabolite production is visible. A variety of compounds from terpenoids to polyketides have been synthesized, often exceeding the productivity of other microbial systems. The clonal variability was systematically investigated and strategies formulated to circumvent untargeted events, thereby streamlining the screening procedure. Promoters with novel regulatory properties were discovered or engineered from existing ones. The genetic tractability was increased via the transfer of popular manipulation and assembly techniques, as well as the creation of new ones. A second generation of sequencing projects culminated in the creation of the second best functionally annotated yeast genome. In combination with landmark physiological insights and increased output of omics-data, a good basis for the creation of refined genome-scale metabolic models was created. The first application of model-based metabolic engineering in P. pastoris showcased the potential of this approach. Recent efforts to establish yeast peroxisomes for compartmentalized metabolite synthesis appear to fit ideally with the well-studied high capacity peroxisomal machinery of P. pastoris. Here, these recent developments are collected and reviewed with the aim of supporting the establishment of systems metabolic engineering in P. pastoris. Copyright © 2017. Published

Key applications of plant metabolic engineering.

Directory of Open Access Journals (Sweden)

Warren Lau

2014-06-01

Full Text Available Great strides have been made in plant metabolic engineering over the last two decades, with notable success stories including Golden rice. Here, we discuss the field's progress in addressing four long-standing challenges: creating plants that satisfy their own nitrogen requirement, so reducing or eliminating the need for nitrogen fertilizer; enhancing the nutrient content of crop plants; engineering biofuel feed stocks that harbor easy-to-access fermentable saccharides by incorporating self-destructing lignin; and increasing photosynthetic efficiency. We also look to the future at emerging areas of research in this field.

Genetic Optimization Algorithm for Metabolic Engineering Revisited

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Tobias B. Alter

2018-05-01

Full Text Available To date, several independent methods and algorithms exist for exploiting constraint-based stoichiometric models to find metabolic engineering strategies that optimize microbial production performance. Optimization procedures based on metaheuristics facilitate a straightforward adaption and expansion of engineering objectives, as well as fitness functions, while being particularly suited for solving problems of high complexity. With the increasing interest in multi-scale models and a need for solving advanced engineering problems, we strive to advance genetic algorithms, which stand out due to their intuitive optimization principles and the proven usefulness in this field of research. A drawback of genetic algorithms is that premature convergence to sub-optimal solutions easily occurs if the optimization parameters are not adapted to the specific problem. Here, we conducted comprehensive parameter sensitivity analyses to study their impact on finding optimal strain designs. We further demonstrate the capability of genetic algorithms to simultaneously handle (i multiple, non-linear engineering objectives; (ii the identification of gene target-sets according to logical gene-protein-reaction associations; (iii minimization of the number of network perturbations; and (iv the insertion of non-native reactions, while employing genome-scale metabolic models. This framework adds a level of sophistication in terms of strain design robustness, which is exemplarily tested on succinate overproduction in Escherichia coli.

Production of anthocyanins in metabolically engineered microorganisms: Current status and perspectives

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Jian Zha

2017-12-01

Full Text Available Microbial production of plant-derived natural products by engineered microorganisms has achieved great success thanks to large extend to metabolic engineering and synthetic biology. Anthocyanins, the water-soluble colored pigments found in terrestrial plants that are responsible for the red, blue and purple coloration of many flowers and fruits, are extensively used in food and cosmetics industry; however, their current supply heavily relies on complex extraction from plant-based materials. A promising alternative is their sustainable production in metabolically engineered microbes. Here, we review the recent progress on anthocyanin biosynthesis in engineered bacteria, with a special focus on the systematic engineering modifications such as selection and engineering of biosynthetic enzymes, engineering of transportation, regulation of UDP-glucose supply, as well as process optimization. These promising engineering strategies will facilitate successful microbial production of anthocyanins in industry in the near future.

Evolutionary programming as a platform for in silico metabolic engineering

DEFF Research Database (Denmark)

Patil, Kiran Raosaheb; Rocha, Isabel; Förster, Jochen

2005-01-01

, and it is therefore interesting to develop new faster algorithms. Results In this study we report an evolutionary programming based method to rapidly identify gene deletion strategies for optimization of a desired phenotypic objective function. We illustrate the proposed method for two important design parameters...... of close to optimal solutions. The identified metabolic engineering strategies suggest that non-intuitive genetic modifications span several different pathways and may be necessary for solving challenging metabolic engineering problems....

Impact of systems biology on metabolic engineering of Saccharomyces cerevisiae

DEFF Research Database (Denmark)

Nielsen, Jens; Jewett, Michael Christopher

2008-01-01

in the industrial application of this yeast. Developments in genomics and high-throughput systems biology tools are enhancing one's ability to rapidly characterize cellular behaviour, which is valuable in the field of metabolic engineering where strain characterization is often the bottleneck in strain development...... programmes. Here, the impact of systems biology on metabolic engineering is reviewed and perspectives on the role of systems biology in the design of cell factories are given....

The application of microfluidic-based technologies in the cycle of metabolic engineering

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Xiaoyan Ma

2016-09-01

Full Text Available The process of metabolic engineering consists of multiple cycles of design, build, test and learn, which is typically laborious and time-consuming. To increase the efficiency and the rate of success of strain engineering, novel instrumentation must be applied. Microfluidics, the control of liquid flow in microstructures, has enabled flexible, accurate, automatic, and high-throughput manipulation of cells in liquid at picoliter to nanoliter scale. These attributes hold great promise in advancing metabolic engineering in terms of the phases of design, build, test and learn. To promote the application of microfluidic-based technologies in strain improvement, this review addressed the potentials of microfluidics and the related approaches in DNA assembly, transformation, strain screening, genotyping and phenotyping, and highlighted their adaptations for single-cell analysis. As a result, this facilitates in-depth understanding of the metabolic network, which in turn promote efficient optimization in the following cycles of strain engineering. Taken together, microfluidic-based technologies enable on-chip workflow, and could greatly accelerate the turnaround of metabolic engineering.

Continuum solutions of the Klein-Gordon equation

International Nuclear Information System (INIS)

Jansen, G.; Pusch, M.; Soff, G.

1987-10-01

We construct explicit solutions of the Klein-Gordon equation for continuum states. The role of the energy in the single-particle Klein-Gordon theory is elucidated. Special emphasis is laid on the determination of resonance states in the continuum for overcritical potentials. As examples for long-range interaction we depict solutions for the Coulomb potential of a point-like nucleus as an extended nucleus. The square-well potential and the exponential potential are treated to exemplify pecularities of short-range interactions. We also derive continuum solutions for a scalar interaction of square-well type. Finally we discuss the behaviour of a spin-0 particle in an external homogeneous magnetic field. (orig.)

The role of metabolic engineering in the production of secondary metabolites

DEFF Research Database (Denmark)

Nielsen, Jens Bredal

1998-01-01

In the production of secondary metabolites yield and productivity are the most important design parameters. The focus is therefore to direct the carbon fluxes towards the product of interest, and this can be obtained through metabolic engineering whereby directed genetic changes are introduced...... into the production strain. In this process it is, however, important to analyze the metabolic network through measurement of the intracellular metabolites and the flux distributions. Besides playing an important role in the optimization of existing processes, metabolic engineering also offers the possibility...

Noether's theorem and Steudel's conserved currents for the sine-Gordon equation

International Nuclear Information System (INIS)

Shadwick, W.F.

1980-01-01

A version of Noether's theorem appropriate for the extended Hamilton-Cartan formalism for regular first-order Lagrangians is proposed. Steudel's derivation of an infinite collection of conserved currents for the sine-Gordon equation is presented in this context and it is demonstrated that, as a consequence of the commutativity of the sine-Gordon Baecklund transformations, the conserved charges corresponding to these currents are in involution with respect to the natural Poisson bracket provided by the formalism. Thus one obtains the formal 'complete integrability' of the sine-Gordon equation as a consequence of the properties of the Baecklund transformation. (orig.)

Pi-kinks in a parametrically driven sine-Gordon chain

DEFF Research Database (Denmark)

Kivshar, Yuri S.; Grønbech-Jensen, Niels; Samuelsen, Mogens Rugholm

1992-01-01

We consider the sine-Gordon chain driven by a high-frequency parametric force in the presence of loss. Using an analytical approach based on the method of averaging in fast oscillations, we predict that such a parametric force may support propagation of π kinks, which are unstable in the standard...... sine-Gordon model. The steady-state velocity of the π kinks is calculated, and the analytical results are in good agreement with direct numerical simulations....

Hijacking CRISPR-Cas for high-throughput bacterial metabolic engineering: advances and prospects

DEFF Research Database (Denmark)

Mougiakos, Ioannis; Bosma, Elleke F.; Ganguly, Joyshree

2018-01-01

High engineering efficiencies are required for industrial strain development. Due to its user-friendliness and its stringency, CRISPR-Cas-based technologies have strongly increased genome engineering efficiencies in bacteria. This has enabled more rapid metabolic engineering of both the model host...... the range of organisms in which it can be used to create novel production hosts. This review analyses the current status of prokaryotic metabolic engineering towards the production of biotechnologically relevant products, based on the exploitation of different CRISPR-related DNA/RNA endonuclease variants....

Some Exact Solutions for a Klein Gordon Equation Algunas soluciones exactas para una ecuación de Klein Gordon

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H H Ortíz Álvarez

2012-12-01

Full Text Available In solving practical problems in science and engineering arises as a direct consequence differential equations that explains the dynamics of the phenomena.Finding exact solutions to this equations provides importan informationabout the behavior of physical systems. The Lie symmetry method allows tofind invariant solutions under certain groups of transformations for differentialequations.This method not very well known and used is of great importance inthe scientific community. By this approach it was possible to find several exactinvariant solutions for the Klein Gordon Equation uxx − utt = k(u. A particularcase, The Kolmogorov equation uxx − utt = k1u + k2un was considered.These equations appear in the study of relativistic and quantum physics. Thegeneral solutions found, could be used for future explorations on the study forother specific K(u functions. En la solución de problemas prácticos de las ciencias y la ingeniería surgen como consecuencia directa ecuaciones diferenciales que dan razón de la dinámica de los fenómenos. El encontrar soluciones exactas a estas ecuaciones proporciona información importante sobre el comportamiento de sistemas físicos. El método de las simetrías de Lie permite encontrar soluciones invariantes bajo ciertos grupos de transformaciones para ecuaciones diferenciales. Mediante este método fue posible encontrar familias de soluciones exactas invariantes para la ecuación de Klein Gordon uxx- utt = k(u: En particular, se consideró la ecuación de Kolmogorov uxx - utt = k1u + k2u n. Estas ecuaciones aparecen en el estudio de la física relativista y cuántica. Las soluciones generales encontradas podrían emplearse en futuros desarrollos en el estudio para otro tipo de funciones k(u.

The necessity of a theory of biology for tissue engineering: metabolism-repair systems.

Science.gov (United States)

Ganguli, Suman; Hunt, C Anthony

2004-01-01

Since there is no widely accepted global theory of biology, tissue engineering and bioengineering lack a theoretical understanding of the systems being engineered. By default, tissue engineering operates with a "reductionist" theoretical approach, inherited from traditional engineering of non-living materials. Long term, that approach is inadequate, since it ignores essential aspects of biology. Metabolism-repair systems are a theoretical framework which explicitly represents two "functional" aspects of living organisms: self-repair and self-replication. Since repair and replication are central to tissue engineering, we advance metabolism-repair systems as a potential theoretical framework for tissue engineering. We present an overview of the framework, and indicate directions to pursue for extending it to the context of tissue engineering. We focus on biological networks, both metabolic and cellular, as one such direction. The construction of these networks, in turn, depends on biological protocols. Together these concepts may help point the way to a global theory of biology appropriate for tissue engineering.

Generalized quantum sine-Gordon equation and its relation to the Thirring model in quantum field theory

International Nuclear Information System (INIS)

Skagerstam, B.K.

1976-01-01

We discuss a generalization of the conventional sine-Gordon quantum field theory by using methods recently developed by Coleman. As a result we can argue that the equivalence between the sine-Gordon theory and the massive Thirring model is unaffected if we perturb the sine-Gordon Hamiltonian by a bounded perturbation consisting of a continuous sum of sine-Gordon type interactions

Genome-scale modeling using flux ratio constraints to enable metabolic engineering of clostridial metabolism in silico.

Science.gov (United States)

McAnulty, Michael J; Yen, Jiun Y; Freedman, Benjamin G; Senger, Ryan S

2012-05-14

Genome-scale metabolic networks and flux models are an effective platform for linking an organism genotype to its phenotype. However, few modeling approaches offer predictive capabilities to evaluate potential metabolic engineering strategies in silico. A new method called "flux balance analysis with flux ratios (FBrAtio)" was developed in this research and applied to a new genome-scale model of Clostridium acetobutylicum ATCC 824 (iCAC490) that contains 707 metabolites and 794 reactions. FBrAtio was used to model wild-type metabolism and metabolically engineered strains of C. acetobutylicum where only flux ratio constraints and thermodynamic reversibility of reactions were required. The FBrAtio approach allowed solutions to be found through standard linear programming. Five flux ratio constraints were required to achieve a qualitative picture of wild-type metabolism for C. acetobutylicum for the production of: (i) acetate, (ii) lactate, (iii) butyrate, (iv) acetone, (v) butanol, (vi) ethanol, (vii) CO2 and (viii) H2. Results of this simulation study coincide with published experimental results and show the knockdown of the acetoacetyl-CoA transferase increases butanol to acetone selectivity, while the simultaneous over-expression of the aldehyde/alcohol dehydrogenase greatly increases ethanol production. FBrAtio is a promising new method for constraining genome-scale models using internal flux ratios. The method was effective for modeling wild-type and engineered strains of C. acetobutylicum.

Filtration of the classical knot concordance group and Casson-Gordon invariants

Science.gov (United States)

Kim, Taehee

2004-09-01

It is known that if every prime power branched cyclic cover of a knot in S(3) is a homology sphere, then the knot has vanishing Casson-Gordon invariants. We construct infinitely many examples of (topologically) non-slice knots in S(3) whose prime power branched cyclic covers are homology spheres. We show that these knots generate an infinite rank subgroup of scrf_{(1.0)}/scrf_{(1.5)} for which Casson-Gordon invariants vanish in Cochran-Orr-Teichner's filtration of the classical knot concordance group. As a corollary, it follows that Casson-Gordon invariants are not a complete set of obstructions to a second layer of Whitney disks.

Quantum Hall bilayers and the chiral sine-Gordon equation

International Nuclear Information System (INIS)

Naud, J.D.; Pryadko, Leonid P.; Sondhi, S.L.

2000-01-01

The edge state theory of a class of symmetric double-layer quantum Hall systems with interlayer electron tunneling reduces to the sum of a free field theory and a field theory of a chiral Bose field with a self-interaction of the sine-Gordon form. We argue that the perturbative renormalization group flow of this chiral sine-Gordon theory is distinct from the standard (non-chiral) sine-Gordon theory, contrary to a previous assertion by Renn, and that the theory is manifestly sensible only at a discrete set of values of the inverse period of the cosine interaction (β-circumflex). We obtain exact solutions for the spectra and correlation functions of the chiral sine-Gordon theory at the two values of β-circumflex at which electron tunneling in bilayers is not irrelevant. Of these, the marginal case (β-circumflex 2 =4) is of greatest interest: the spectrum of the interacting theory is that of two Majorana fermions with different, dynamically generated, velocities. For the experimentally observed bilayer 331 state at filling factor 1/2, this implies the trifurcation of electrons added to the edge. We also present a method for fermionizing the theory at the discrete points (β-circumflex 2 is an element of Z + ) by the introduction of auxiliary degrees of freedom that could prove useful in other problems involving quantum Hall multi-layers

New non-linear modified massless Klein-Gordon equation

Energy Technology Data Exchange (ETDEWEB)

Asenjo, Felipe A. [Universidad Adolfo Ibanez, UAI Physics Center, Santiago (Chile); Universidad Adolfo Ibanez, Facultad de Ingenieria y Ciencias, Santiago (Chile); Hojman, Sergio A. [Universidad Adolfo Ibanez, UAI Physics Center, Santiago (Chile); Universidad Adolfo Ibanez, Departamento de Ciencias, Facultad de Artes Liberales, Santiago (Chile); Universidad de Chile, Departamento de Fisica, Facultad de Ciencias, Santiago (Chile); Centro de Recursos Educativos Avanzados, CREA, Santiago (Chile)

2017-11-15

The massless Klein-Gordon equation on arbitrary curved backgrounds allows for solutions which develop ''tails'' inside the light cone and, therefore, do not strictly follow null geodesics as discovered by DeWitt and Brehme almost 60 years ago. A modification of the massless Klein-Gordon equation is presented, which always exhibits null geodesic propagation of waves on arbitrary curved spacetimes. This new equation is derived from a Lagrangian which exhibits current-current interaction. Its non-linearity is due to a self-coupling term which is related to the quantum mechanical Bohm potential. (orig.)

Symmetric and arbitrarily high-order Birkhoff-Hermite time integrators and their long-time behaviour for solving nonlinear Klein-Gordon equations

Science.gov (United States)

Liu, Changying; Iserles, Arieh; Wu, Xinyuan

2018-03-01

The Klein-Gordon equation with nonlinear potential occurs in a wide range of application areas in science and engineering. Its computation represents a major challenge. The main theme of this paper is the construction of symmetric and arbitrarily high-order time integrators for the nonlinear Klein-Gordon equation by integrating Birkhoff-Hermite interpolation polynomials. To this end, under the assumption of periodic boundary conditions, we begin with the formulation of the nonlinear Klein-Gordon equation as an abstract second-order ordinary differential equation (ODE) and its operator-variation-of-constants formula. We then derive a symmetric and arbitrarily high-order Birkhoff-Hermite time integration formula for the nonlinear abstract ODE. Accordingly, the stability, convergence and long-time behaviour are rigorously analysed once the spatial differential operator is approximated by an appropriate positive semi-definite matrix, subject to suitable temporal and spatial smoothness. A remarkable characteristic of this new approach is that the requirement of temporal smoothness is reduced compared with the traditional numerical methods for PDEs in the literature. Numerical results demonstrate the advantage and efficiency of our time integrators in comparison with the existing numerical approaches.

Metabolic engineering of lactic acid bacteria for the production of nutraceuticals

NARCIS (Netherlands)

Hugenholtz, J.; Sybesma, W.; Groot, M.N.; Wisselink, W.; Ladero, V.; Burgess, K.; Sinderen, van D.; Piard, J.C.; Eggink, G.; Smid, E.J.; Savoy, G.; Sesma, F.; Jansen, T.; Hols, P.; Kleerebezem, M.

2002-01-01

Lactic acid bacteria display a relatively simple and well-described metabolism where the sugar source is converted mainly to lactic acid. Here we will shortly describe metabolic engineering strategies on the level of sugar metabolism, that lead to either the efficient re-routing of the lactococcal

Microalgal bioengineering for sustainable energy development: Recent transgenesis and metabolic engineering strategies.

Science.gov (United States)

Banerjee, Chiranjib; Singh, Puneet Kumar; Shukla, Pratyoosh

2016-03-01

Exploring the efficiency of algae to produce remarkable products can be directly benefitted by studying its mechanism at systems level. Recent advents in biotechnology like flux balance analysis (FBA), genomics and in silico proteomics minimize the wet lab exertion. It is understood that FBA predicts the metabolic products, metabolic pathways and alternative pathway to maximize the desired product, and these are key components for microalgae bio-engineering. This review encompasses recent transgenesis techniques and metabolic engineering strategies applied to different microalgae for improving different traits. Further it also throws light on RNAi and riboswitch engineering based methods which may be advantageous for high throughput microalgal research. A valid and optimally designed microalga can be developed where every engineering strategies meet each other successfully and will definitely fulfill the market needs. It is also to be noted that Omics (viz. genetic and metabolic manipulation with bioinformatics) should be integrated to develop a strain which could prove to be a futuristic solution for sustainable development for energy. Copyright © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The Cauchy problem for non-linear Klein-Gordon equations

International Nuclear Information System (INIS)

Simon, J.C.H.; Taflin, E.

1993-01-01

We consider in R n+1 , n≥2, the non-linear Klein-Gordon equation. We prove for such an equation that there is neighbourhood of zero in a Hilbert space of initial conditions for which the Cauchy problem has global solutions and on which there is asymptotic completeness. The inverse of the wave operator linearizes the non-linear equation. If, moreover, the equation is manifestly Poincare covariant then the non-linear representation of the Poincare-Lie algebra, associated with the non-linear Klein-Gordon equation is integrated to a non-linear representation of the Poincare group on an invariant neighbourhood of zero in the Hilbert space. This representation is linearized by the inverse of the wave operator. The Hilbert space is, in both cases, the closure of the space of the differentiable vectors for the linear representation of the Poincare group, associated with the Klein-Gordon equation, with respect to a norm defined by the representation of the enveloping algebra. (orig.)

An integrable noncommutative version of the sine-Gordon system

International Nuclear Information System (INIS)

Grisaru, Marcus T.; Penati, Silvia

2003-01-01

Using the bicomplex approach we discuss an integrable noncommutative system in two-dimensional Euclidean space. It is described by an equation of motion which reduces to the ordinary sine-Gordon equation when the noncommutation parameter is removed, plus a constraint equation which is nontrivial only in the noncommutative case. The implications of this constraint, which is required by integrability but seems to reduce the space of classical solutions, remain to be understood. We show that the system has an infinite number of conserved currents and we give the general recursive relation for constructing them. For the particular cases of lower spin nontrivial currents we work out the explicit expressions and perform a direct check of their conservation. These currents reduce to the usual sine-Gordon currents in the commutative limit. We find classical 'localized' solutions to first order in the noncommutativity parameter and describe the Backlund transformations for our system. Finally, we comment on the relation of our noncommutative system to the commutative sine-Gordon system

Improved Triacylglycerol Production in Acinetobacter baylyi ADP1 by Metabolic Engineering

Directory of Open Access Journals (Sweden)

Karp Matti

2011-05-01

Full Text Available Abstract Background Triacylglycerols are used in various purposes including food applications, cosmetics, oleochemicals and biofuels. Currently the main sources for triacylglycerol are vegetable oils, and microbial triacylglycerol has been suggested as an alternative for these. Due to the low production rates and yields of microbial processes, the role of metabolic engineering has become more significant. As a robust model organism for genetic and metabolic studies, and for the natural capability to produce triacylglycerol, Acinetobacter baylyi ADP1 serves as an excellent organism for modelling the effects of metabolic engineering for energy molecule biosynthesis. Results Beneficial gene deletions regarding triacylglycerol production were screened by computational means exploiting the metabolic model of ADP1. Four deletions, acr1, poxB, dgkA, and a triacylglycerol lipase were chosen to be studied experimentally both separately and concurrently by constructing a knock-out strain (MT with three of the deletions. Improvements in triacylglycerol production were observed: the strain MT produced 5.6 fold more triacylglycerol (mg/g cell dry weight compared to the wild type strain, and the proportion of triacylglycerol in total lipids was increased by 8-fold. Conclusions In silico predictions of beneficial gene deletions were verified experimentally. The chosen single and multiple gene deletions affected beneficially the natural triacylglycerol metabolism of A. baylyi ADP1. This study demonstrates the importance of single gene deletions in triacylglycerol metabolism, and proposes Acinetobacter sp. ADP1 as a model system for bioenergetic studies regarding metabolic engineering.

Systems metabolic engineering design: fatty acid production as an emerging case study.

Science.gov (United States)

Tee, Ting Wei; Chowdhury, Anupam; Maranas, Costas D; Shanks, Jacqueline V

2014-05-01

Increasing demand for petroleum has stimulated industry to develop sustainable production of chemicals and biofuels using microbial cell factories. Fatty acids of chain lengths from C6 to C16 are propitious intermediates for the catalytic synthesis of industrial chemicals and diesel-like biofuels. The abundance of genetic information available for Escherichia coli and specifically, fatty acid metabolism in E. coli, supports this bacterium as a promising host for engineering a biocatalyst for the microbial production of fatty acids. Recent successes rooted in different features of systems metabolic engineering in the strain design of high-yielding medium chain fatty acid producing E. coli strains provide an emerging case study of design methods for effective strain design. Classical metabolic engineering and synthetic biology approaches enabled different and distinct design paths towards a high-yielding strain. Here we highlight a rational strain design process in systems biology, an integrated computational and experimental approach for carboxylic acid production, as an alternative method. Additional challenges inherent in achieving an optimal strain for commercialization of medium chain-length fatty acids will likely require a collection of strategies from systems metabolic engineering. Not only will the continued advancement in systems metabolic engineering result in these highly productive strains more quickly, this knowledge will extend more rapidly the carboxylic acid platform to the microbial production of carboxylic acids with alternate chain-lengths and functionalities. © 2014 Wiley Periodicals, Inc.

Dispersive estimates for the Schroedinger and Klein-Gordon equations

Energy Technology Data Exchange (ETDEWEB)

Kopylova, Elena A [Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow (Russian Federation)

2010-01-01

This is a survey of results on the long-time asymptotic behaviour of solutions of the Schroedinger and Klein-Gordon equations in weighted energy norms. Results obtained from 1975 to 2001 in the spectral scattering theory of Agmon, Jensen-Kato, Jensen-Nenciu, and Murata are described for the Schroedinger equation, along with the author's recent results obtained jointly with A.I. Komech for the Klein-Gordon equation. The methods used develop the spectral approach as applied to relativistic equations. Bibliography: 40 titles.

Extended sine-Gordon Equation Method and Its Application to Maccari's System

International Nuclear Information System (INIS)

Song Lina; Zhang Hongqing

2005-01-01

An extended sine-Gordon equation method is proposed to construct exact travelling wave solutions to Maccari's equation based upon a generalized sine-Gordon equation. It is shown that more new travelling wave solutions can be found by this new method, which include bell-shaped soliton solutions, kink-shaped soliton solutions, periodic wave solution, and new travelling waves.

Metabolic Engineering of Chemical Defence Pathways in Plant Disease Control

DEFF Research Database (Denmark)

Rook, Frederik

2016-01-01

on each topic. The chapter reviews the some of the scientific and technical challenges in metabolic engineering and the new possibilities emerging from recent technological developments. It concludes by discussing the outlook for bioengineered chemical defences as part of crop protection strategies, also...... with antimicrobial properties for use in crop protection. It presents an overview of the metabolic engineering efforts made in the area of plant chemical defence. For in-depth information on the characteristics of a specific class of chemical defence compounds, the reader is referred to the specialized reviews...

Considerations on the hyperbolic complex Klein-Gordon equation

International Nuclear Information System (INIS)

Ulrych, S.

2010-01-01

This article summarizes and consolidates investigations on hyperbolic complex numbers with respect to the Klein-Gordon equation for fermions and bosons. The hyperbolic complex numbers are applied in the sense that complex extensions of groups and algebras are performed not with the complex unit, but with the product of complex and hyperbolic unit. The modified complexification is the key ingredient for the theory. The Klein-Gordon equation is represented in this framework in the form of the first invariant of the Poincare group, the mass operator, in order to emphasize its geometric origin. The possibility of new interactions arising from hyperbolic complex gauge transformations is discussed.

Light-front quantization of the sine-Gordon model

International Nuclear Information System (INIS)

Burkardt, M.

1993-01-01

It is shown how to modify the canonical light-front quantization of the (1+1)-dimensional sine-Gordon model such that the zero-mode problem of light-front quantization is avoided. The canonical sine-Gordon Lagrangian is replaced by an effective Lagrangian which does not lead to divergences as k + =(k 0 +k 1 )/ √2 →0. After canonically quantizing the effective Lagrangian, one obtains the effective light-front Hamiltonian which agrees with the naive light-front (LF) Hamiltonian, up to one additional renormalization. The spectrum of the effective LF Hamiltonian is determined using discrete light-cone quantization and agrees with results from equal-time quantization

On classical solutions of the relativistic Vlasov-Klein-Gordon system

Directory of Open Access Journals (Sweden)

Michael Kunzinger

2005-01-01

Full Text Available We consider a collisionless ensemble of classical particles coupled with a Klein-Gordon field. For the resulting nonlinear system of partial differential equations, the relativistic Vlasov-Klein-Gordon system, we prove local-in-time existence of classical solutions and a continuation criterion which says that a solution can blow up only if the particle momenta become large. We also show that classical solutions are global in time in the one-dimensional case.

Modulation of sulfur metabolism enables efficient glucosinolate engineering

Directory of Open Access Journals (Sweden)

Geu-Flores Fernando

2011-01-01

Full Text Available Abstract Background Metabolic engineering in heterologous organisms is an attractive approach to achieve efficient production of valuable natural products. Glucosinolates represent a good example of such compounds as they are thought to be the cancer-preventive agents in cruciferous plants. We have recently demonstrated that it is feasible to engineer benzylglucosinolate (BGLS in the non-cruciferous plant Nicotiana benthamiana by transient expression of five genes from Arabidopsis thaliana. In the same study, we showed that co-expression of a sixth Arabidopsis gene, γ-glutamyl peptidase 1 (GGP1, resolved a metabolic bottleneck, thereby increasing BGLS accumulation. However, the accumulation did not reach the expected levels, leaving room for further optimization. Results To optimize heterologous glucosinolate production, we have in this study performed a comparative metabolite analysis of BGLS-producing N. benthamiana leaves in the presence or absence of GGP1. The analysis revealed that the increased BGLS levels in the presence of GGP1 were accompanied by a high accumulation of the last intermediate, desulfoBGLS, and a derivative thereof. This evidenced a bottleneck in the last step of the pathway, the transfer of sulfate from 3'-phosphoadenosine-5'-phosphosulfate (PAPS to desulfoBGLS by the sulfotransferase AtSOT16. While substitution of AtSOT16 with alternative sulfotransferases did not alleviate the bottleneck, experiments with the three genes involved in the formation and recycling of PAPS showed that co-expression of adenosine 5'-phosphosulfate kinase 2 (APK2 alone reduced the accumulation of desulfoBGLS and its derivative by more than 98% and increased BGLS accumulation 16-fold. Conclusion Adjusting sulfur metabolism by directing sulfur from primary to secondary metabolism leads to a remarkable improvement in BGLS accumulation and thereby represents an important step towards a clean and efficient production of glucosinolates in

Group-theoretical aspects of the discrete sine-Gordon equation

International Nuclear Information System (INIS)

Orfanidis, S.J.

1980-01-01

The group-theoretical interpretation of the sine-Gordon equation in terms of connection forms on fiber bundles is extended to the discrete case. Solutions of the discrete sine-Gordon equation induce surfaces on a lattice in the SU(2) group space. The inverse scattering representation, expressing the parallel transport of fibers, is implemented by means of finite rotations. Discrete Baecklund transformations are realized as gauge transformations. The three-dimensional inverse scattering representation is used to derive a discrete nonlinear sigma model, and the corresponding Baecklund transformation and Pohlmeyer's R transformation are constructed

The Genome-Based Metabolic Systems Engineering to Boost Levan Production in a Halophilic Bacterial Model.

Science.gov (United States)

Aydin, Busra; Ozer, Tugba; Oner, Ebru Toksoy; Arga, Kazim Yalcin

2018-03-01

Metabolic systems engineering is being used to redirect microbial metabolism for the overproduction of chemicals of interest with the aim of transforming microbial hosts into cellular factories. In this study, a genome-based metabolic systems engineering approach was designed and performed to improve biopolymer biosynthesis capability of a moderately halophilic bacterium Halomonas smyrnensis AAD6 T producing levan, which is a fructose homopolymer with many potential uses in various industries and medicine. For this purpose, the genome-scale metabolic model for AAD6 T was used to characterize the metabolic resource allocation, specifically to design metabolic engineering strategies for engineered bacteria with enhanced levan production capability. Simulations were performed in silico to determine optimal gene knockout strategies to develop new strains with enhanced levan production capability. The majority of the gene knockout strategies emphasized the vital role of the fructose uptake mechanism, and pointed out the fructose-specific phosphotransferase system (PTS fru ) as the most promising target for further metabolic engineering studies. Therefore, the PTS fru of AAD6 T was restructured with insertional mutagenesis and triparental mating techniques to construct a novel, engineered H. smyrnensis strain, BMA14. Fermentation experiments were carried out to demonstrate the high efficiency of the mutant strain BMA14 in terms of final levan concentration, sucrose consumption rate, and sucrose conversion efficiency, when compared to the AAD6 T . The genome-based metabolic systems engineering approach presented in this study might be considered an efficient framework to redirect microbial metabolism for the overproduction of chemicals of interest, and the novel strain BMA14 might be considered a potential microbial cell factory for further studies aimed to design levan production processes with lower production costs.

CRISPR/Cas9-coupled recombineering for metabolic engineering of Corynebacterium glutamicum.

Science.gov (United States)

Cho, Jae Sung; Choi, Kyeong Rok; Prabowo, Cindy Pricilia Surya; Shin, Jae Ho; Yang, Dongsoo; Jang, Jaedong; Lee, Sang Yup

2017-07-01

Genome engineering of Corynebacterium glutamicum, an important industrial microorganism for amino acids production, currently relies on random mutagenesis and inefficient double crossover events. Here we report a rapid genome engineering strategy to scarlessly knock out one or more genes in C. glutamicum in sequential and iterative manner. Recombinase RecT is used to incorporate synthetic single-stranded oligodeoxyribonucleotides into the genome and CRISPR/Cas9 to counter-select negative mutants. We completed the system by engineering the respective plasmids harboring CRISPR/Cas9 and RecT for efficient curing such that multiple gene targets can be done iteratively and final strains will be free of plasmids. To demonstrate the system, seven different mutants were constructed within two weeks to study the combinatorial deletion effects of three different genes on the production of γ-aminobutyric acid, an industrially relevant chemical of much interest. This genome engineering strategy will expedite metabolic engineering of C. glutamicum. Copyright © 2017 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering.

Science.gov (United States)

He, Fei; Murabito, Ettore; Westerhoff, Hans V

2016-04-01

Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out through in silico theoretical studies with the aim to guide and complement further in vitro and in vivo experimental efforts. Clearly, what counts is the result in vivo, not only in terms of maximal productivity but also robustness against environmental perturbations. Engineering an organism towards an increased production flux, however, often compromises that robustness. In this contribution, we review and investigate how various analytical approaches used in metabolic engineering and synthetic biology are related to concepts developed by systems and control engineering. While trade-offs between production optimality and cellular robustness have already been studied diagnostically and statically, the dynamics also matter. Integration of the dynamic design aspects of control engineering with the more diagnostic aspects of metabolic, hierarchical control and regulation analysis is leading to the new, conceptual and operational framework required for the design of robust and productive dynamic pathways. © 2016 The Author(s).

Microbial production of antioxidant food ingredients via metabolic engineering.

Science.gov (United States)

Lin, Yuheng; Jain, Rachit; Yan, Yajun

2014-04-01

Antioxidants are biological molecules with the ability to protect vital metabolites from harmful oxidation. Due to this fascinating role, their beneficial effects on human health are of paramount importance. Traditional approaches using solvent-based extraction from food/non-food sources and chemical synthesis are often expensive, exhaustive, and detrimental to the environment. With the advent of metabolic engineering tools, the successful reconstitution of heterologous pathways in Escherichia coli and other microorganisms provides a more exciting and amenable alternative to meet the increasing demand of natural antioxidants. In this review, we elucidate the recent progress in metabolic engineering efforts for the microbial production of antioxidant food ingredients - polyphenols, carotenoids, and antioxidant vitamins. Copyright © 2013 Elsevier Ltd. All rights reserved.

Metabolic engineering of strains: from industrial-scale to lab-scale chemical production.

Science.gov (United States)

Sun, Jie; Alper, Hal S

2015-03-01

A plethora of successful metabolic engineering case studies have been published over the past several decades. Here, we highlight a collection of microbially produced chemicals using a historical framework, starting with titers ranging from industrial scale (more than 50 g/L), to medium-scale (5-50 g/L), and lab-scale (0-5 g/L). Although engineered Escherichia coli and Saccharomyces cerevisiae emerge as prominent hosts in the literature as a result of well-developed genetic engineering tools, several novel native-producing strains are gaining attention. This review catalogs the current progress of metabolic engineering towards production of compounds such as acids, alcohols, amino acids, natural organic compounds, and others.

Fumaric acid production in Saccharomyces cerevisiae by in silico aided metabolic engineering.

Directory of Open Access Journals (Sweden)

Guoqiang Xu

Full Text Available Fumaric acid (FA is a promising biomass-derived building-block chemical. Bio-based FA production from renewable feedstock is a promising and sustainable alternative to petroleum-based chemical synthesis. Here we report on FA production by direct fermentation using metabolically engineered Saccharomyces cerevisiae with the aid of in silico analysis of a genome-scale metabolic model. First, FUM1 was selected as the target gene on the basis of extensive literature mining. Flux balance analysis (FBA revealed that FUM1 deletion can lead to FA production and slightly lower growth of S. cerevisiae. The engineered S. cerevisiae strain obtained by deleting FUM1 can produce FA up to a concentration of 610±31 mg L(-1 without any apparent change in growth in fed-batch culture. FT-IR and (1H and (13C NMR spectra confirmed that FA was synthesized by the engineered S. cerevisiae strain. FBA identified pyruvate carboxylase as one of the factors limiting higher FA production. When the RoPYC gene was introduced, S. cerevisiae produced 1134±48 mg L(-1 FA. Furthermore, the final engineered S. cerevisiae strain was able to produce 1675±52 mg L(-1 FA in batch culture when the SFC1 gene encoding a succinate-fumarate transporter was introduced. These results demonstrate that the model shows great predictive capability for metabolic engineering. Moreover, FA production in S. cerevisiae can be efficiently developed with the aid of in silico metabolic engineering.

Non-photosynthetic plastids as hosts for metabolic engineering.

Science.gov (United States)

Mellor, Silas Busck; Behrendorff, James B Y H; Nielsen, Agnieszka Zygadlo; Jensen, Poul Erik; Pribil, Mathias

2018-04-13

Using plants as hosts for production of complex, high-value compounds and therapeutic proteins has gained increasing momentum over the past decade. Recent advances in metabolic engineering techniques using synthetic biology have set the stage for production yields to become economically attractive, but more refined design strategies are required to increase product yields without compromising development and growth of the host system. The ability of plant cells to differentiate into various tissues in combination with a high level of cellular compartmentalization represents so far the most unexploited plant-specific resource. Plant cells contain organelles called plastids that retain their own genome, harbour unique biosynthetic pathways and differentiate into distinct plastid types upon environmental and developmental cues. Chloroplasts, the plastid type hosting the photosynthetic processes in green tissues, have proven to be suitable for high yield protein and bio-compound production. Unfortunately, chloroplast manipulation often affects photosynthetic efficiency and therefore plant fitness. In this respect, plastids of non-photosynthetic tissues, which have focused metabolisms for synthesis and storage of particular classes of compounds, might prove more suitable for engineering the production and storage of non-native metabolites without affecting plant fitness. This review provides the current state of knowledge on the molecular mechanisms involved in plastid differentiation and focuses on non-photosynthetic plastids as alternative biotechnological platforms for metabolic engineering. © 2018 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

2013 plant lipids Gordon Research conference and Gordon Research Seminar (January 27 - February 1, 2013 - Hotel Galvez, Galveston, TX)

Energy Technology Data Exchange (ETDEWEB)

Welti, Ruth

2012-11-01

Presenters will discuss the latest advances in plant and algal lipid metabolism, oil synthesis, lipid signaling, lipid visualization, lipid biotechnology and its applications, the physiological and developmental roles of lipids, and plant lipids in health. Sessions include: Producing Nutritional Lipids; Metabolic biochemistry in the next decade; Triacylglycerols: Metabolism, function, and as a target for engineering; Lipids in Protection, Reproduction, and Development; Genetic and Lipidomic Approaches to Understanding Lipid Metabolism and Signaling; Lipid Signaling in Stress Responses; New Insights on the Path to Triacylglycerols; Membrane Lipid Signaling; Lipid Visualization; Development of Biofuels and Industrial Lipids.

Realization of a unique time evolution unitary operator in Klein Gordon theory

International Nuclear Information System (INIS)

Balasubramanian, T.S.; Bhatia, S.Kr.

1986-01-01

The scattering theory for the Klein Gordon equation, with time-dependent potential and in a non-static space-time, is considered. Using the Klein Gordon equation formulated in the Hilbert space L 2 (R 3 ) and the Einstein's relativistic equation in the space L 2 (R 3 ,dx) and establishing the equivalence of the vacuum states of their linearized forms in the Hilbert space L 2 (R 3 ) with the help of unique symmetric symplectic operator, the time evolution unitary operator U(t) has been fixed for the Klein Gordon eqution, incorporating either the positive or negative frequencies, in the infinite dimensional Hilbert space L 2 (R 3 ). (author)

Fractional Klein-Gordon equation composed of Jumarie fractional derivative and its interpretation by a smoothness parameter

Science.gov (United States)

Ghosh, Uttam; Banerjee, Joydip; Sarkar, Susmita; Das, Shantanu

2018-06-01

Klein-Gordon equation is one of the basic steps towards relativistic quantum mechanics. In this paper, we have formulated fractional Klein-Gordon equation via Jumarie fractional derivative and found two types of solutions. Zero-mass solution satisfies photon criteria and non-zero mass satisfies general theory of relativity. Further, we have developed rest mass condition which leads us to the concept of hidden wave. Classical Klein-Gordon equation fails to explain a chargeless system as well as a single-particle system. Using the fractional Klein-Gordon equation, we can overcome the problem. The fractional Klein-Gordon equation also leads to the smoothness parameter which is the measurement of the bumpiness of space. Here, by using this smoothness parameter, we have defined and interpreted the various cases.

Integrable discretizations of the (2+1)-dimensional sinh-Gordon equation

International Nuclear Information System (INIS)

Hu, Xing-Biao; Yu, Guo-Fu

2007-01-01

In this paper, we propose two semi-discrete equations and one fully discrete equation and study them by Hirota's bilinear method. These equations have continuum limits into a system which admits the (2+1)-dimensional generalization of the sinh-Gordon equation. As a result, two integrable semi-discrete versions and one fully discrete version for the sinh-Gordon equation are found. Baecklund transformations, nonlinear superposition formulae, determinant solution and Lax pairs for these discrete versions are presented

On some classes of breather lattice solutions to the sinh-Gordon equation

International Nuclear Information System (INIS)

Fu Zuntao; Liu Shikuo

2007-01-01

In this paper, dependent and independent variable transformations are introduced to solve the sinh-Gordon equation by using the knowledge of the elliptic equation and Jacobian elliptic functions. It is shown that different kinds of solutions can be obtained to the sinh-Gordon equation, including breather lattice solutions and periodic wave solutions. (orig.)

Engineering the fatty acid metabolic pathway in Saccharomyces cerevisiae for advanced biofuel production

Directory of Open Access Journals (Sweden)

Xiaoling Tang

2015-12-01

Full Text Available Fatty acid-derived fuels and chemicals have attracted a great deal of attention in recent decades, due to their following properties of high compatibility to gasoline-based fuels and existing infrastructure for their direct utilization, storage and distribution. The yeast Saccharomyces cerevisiae is the ideal biofuel producing candidate, based on the wealth of available genetic information and versatile tools designed to manipulate its metabolic pathways. Engineering the fatty acid metabolic pathways in S. cerevisiae is an effective strategy to increase its fatty acid biosynthesis and provide more pathway precursors for production of targeted products. This review summarizes the recent progress in metabolic engineering of yeast cells for fatty acids and fatty acid derivatives production, including the regulation of acetyl-CoA biosynthesis, NADPH production, fatty acid elongation, and the accumulation of activated precursors of fatty acids for converting enzymes. By introducing specific enzymes in the engineered strains, a powerful platform with a scalable, controllable and economic route for advanced biofuel production has been established. Keywords: Metabolic engineering, Fatty acid biosynthesis, Fatty acid derivatives, Saccharomyces cerevisiae

Oscillating and rotating sine-Gordon system

DEFF Research Database (Denmark)

Olsen, O. H.; Samuelsen, Mogens Rugholm

1986-01-01

The interaction between a 2π kink and the background or vacuum is investigated in the pure sine-Gordon system. For an oscillating background (i.e., the k=0 part of the phonon spectrum) the 2π kink oscillates, while for increasing or decreasing vacuum two phenomena have been observed, depending...

Quantum Barro-Gordon game in monetary economics

Science.gov (United States)

Samadi, Ali Hussein; Montakhab, Afshin; Marzban, Hussein; Owjimehr, Sakine

2018-01-01

Classical game theory addresses decision problems in multi-agent environment where one rational agent's decision affects other agents' payoffs. Game theory has widespread application in economic, social and biological sciences. In recent years quantum versions of classical games have been proposed and studied. In this paper, we consider a quantum version of the classical Barro-Gordon game which captures the problem of time inconsistency in monetary economics. Such time inconsistency refers to the temptation of weak policy maker to implement high inflation when the public expects low inflation. The inconsistency arises when the public punishes the weak policy maker in the next cycle. We first present a quantum version of the Barro-Gordon game. Next, we show that in a particular case of the quantum game, time-consistent Nash equilibrium could be achieved when public expects low inflation, thus resolving the game.

Metabolic engineering in chemolithoautotrophic hosts for the production of fuels and chemicals.

Science.gov (United States)

Nybo, S Eric; Khan, Nymul E; Woolston, Benjamin M; Curtis, Wayne R

2015-07-01

The ability of autotrophic organisms to fix CO2 presents an opportunity to utilize this 'greenhouse gas' as an inexpensive substrate for biochemical production. Unlike conventional heterotrophic microorganisms that consume carbohydrates and amino acids, prokaryotic chemolithoautotrophs have evolved the capacity to utilize reduced chemical compounds to fix CO2 and drive metabolic processes. The use of chemolithoautotrophic hosts as production platforms has been renewed by the prospect of metabolically engineered commodity chemicals and fuels. Efforts such as the ARPA-E electrofuels program highlight both the potential and obstacles that chemolithoautotrophic biosynthetic platforms provide. This review surveys the numerous advances that have been made in chemolithoautotrophic metabolic engineering with a focus on hydrogen oxidizing bacteria such as the model chemolithoautotrophic organism (Ralstonia), the purple photosynthetic bacteria (Rhodobacter), and anaerobic acetogens. Two alternative strategies of microbial chassis development are considered: (1) introducing or enhancing autotrophic capabilities (carbon fixation, hydrogen utilization) in model heterotrophic organisms, or (2) improving tools for pathway engineering (transformation methods, promoters, vectors etc.) in native autotrophic organisms. Unique characteristics of autotrophic growth as they relate to bioreactor design and process development are also discussed in the context of challenges and opportunities for genetic manipulation of organisms as production platforms. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

De Novo Metabolic Engineering and the Promise of Synthetic DNA

Science.gov (United States)

Klein-Marcuschamer, Daniel; Yadav, Vikramaditya G.; Ghaderi, Adel; Stephanopoulos, Gregory N.

The uncertain price and tight supply of crude oil and the ever-increasing demand for clean energy have prompted heightened attention to the development of sustainable fuel technologies that ensure continued economic development while maintaining stewardship of the environment. In the face of these enormous challenges, biomass has emerged as a viable alternative to petroleum for the production of energy, chemicals, and materials owing to its abundance, inexpensiveness, and carbon-neutrality. Moreover, the immense ease and efficiency of biological systems at converting biomass-derived feedstocks into fuels, chemicals, and materials has generated renewed interest in biotechnology as a replacement for traditional chemical processes. Aided by the ever-expanding repertoire of microbial genetics and plant biotechnology, improved understanding of gene regulation and cellular metabolism, and incessantly accumulating gene and protein data, scientists are now contemplating engineering microbial cell factories to produce fuels, chemical feedstocks, polymers and pharmaceuticals in an economically and environmentally sustainable way. This goal resonates with that of metabolic engineering - the improvement of cellular properties through the intelligent design, rational modification, or directed evolution of biochemical pathways, and arguably, metabolic engineering seems best positioned to achieve the concomittant goals of environmental stewardship and economic prolificity.

Recent applications of synthetic biology tools for yeast metabolic engineering

DEFF Research Database (Denmark)

Jensen, Michael Krogh; Keasling, Jay

2015-01-01

to engineer microbial chemical factories has steadily decreased, improvement is still needed. Through the development of synthetic biology tools for key microbial hosts, it should be possible to further decrease the development times and improve the reliability of the resulting microorganism. Together...... with continuous decreases in price and improvements in DNA synthesis, assembly and sequencing, synthetic biology tools will rationalize time-consuming strain engineering, improve control of metabolic fluxes, and diversify screening assays for cellular metabolism. This review outlines some recently developed...... synthetic biology tools and their application to improve production of chemicals and fuels in yeast. Finally, we provide a perspective for the challenges that lie ahead....

Reshaping-induced spatiotemporal chaos in driven, damped sine-Gordon systems

International Nuclear Information System (INIS)

Chacon, R.

2007-01-01

Spatiotemporal chaos arising from the competition between sine-Gordon-breather and kink-antikink-pair solitons by reshaping an ac force is demonstrated. After introducing soliton collective coordinates, Melnikov's method is applied to the resulting effective equation of motion to estimate the parameter-space regions of the ac force where homoclinic bifurcations are induced. The analysis reveals that the chaos-order threshold exhibits sensitivity to small changes in the force shape. Computer simulations of the sine-Gordon system show good agreement with these theoretical predictions

Reshaping-induced spatiotemporal chaos in driven, damped sine-Gordon systems

Energy Technology Data Exchange (ETDEWEB)

Chacon, R. [Departamento de Electronica e Ingenieria Electromecanica, Escuela de Ingenierias Industriales, Universidad de Extremadura, E-06071 Badajoz (Spain)]. E-mail: rchacon@unex.es

2007-03-15

Spatiotemporal chaos arising from the competition between sine-Gordon-breather and kink-antikink-pair solitons by reshaping an ac force is demonstrated. After introducing soliton collective coordinates, Melnikov's method is applied to the resulting effective equation of motion to estimate the parameter-space regions of the ac force where homoclinic bifurcations are induced. The analysis reveals that the chaos-order threshold exhibits sensitivity to small changes in the force shape. Computer simulations of the sine-Gordon system show good agreement with these theoretical predictions.

On the applicability of the layered sine-Gordon model for Josephson-coupled high-Tc layered superconductors

International Nuclear Information System (INIS)

Nandori, I; Jentschura, U D; Nagy, S; Sailer, K; Vad, K; Meszaros, S

2007-01-01

We find a mapping of the layered sine-Gordon model to an equivalent gas of topological excitations and determine the long-range interaction potentials of the topological defects. This enables us to make a detailed comparison to the so-called layered vortex gas, which can be obtained from the layered Ginzburg-Landau model. The layered sine-Gordon model has been proposed in the literature as a candidate field-theoretical model for Josephson-coupled high-T c superconductors, and the implications of our analysis for the applicability of the layered sine-Gordon model to high-T c superconductors are discussed. We are led to the conjecture that the layered sine-Gordon and the layered vortex gas models belong to different universality classes. The determination of the critical temperature of the layered sine-Gordon model is based on a renormalization-group analysis

Volatile science? Metabolic engineering of terpenoids in plants

NARCIS (Netherlands)

Aharoni, A.; Jongsma, M.A.; Bouwmeester, H.J.

2005-01-01

Terpenoids are important for plant survival and also possess biological properties that are beneficial to humans. Here, we describe the state of the art in terpenoid metabolic engineering, showing that significant progress has been made over the past few years. Subcellular targeting of enzymes has

Applied and Environmental Microbiology Gordon Research Conference

Energy Technology Data Exchange (ETDEWEB)

Wall, Judy D.

2003-11-19

The main objective of the Gordon Research Conference on Applied and Environmental Microbiology was to present and discuss new, fundamental research findings on microorganisms, their activities in the environment, their ecosystem-level effects, and their environmental or commercial applications. To accomplish this goal, knowledge of microbial diversity, interactions and population dynamics was required. The genomic basis of microbial processes, the cycling of naturally occurring and hazardous substances, and methodologies to assess the functional relationships of microorganisms in their habitats were essential for understanding the ecological consequences of microbial activities and the formulation of generalizing principles. In the last decade, molecular technology has revealed that microbial diversity is far more extensive than the limited view obtained from culturing procedures. Great advances in environmental microbiology have resulted from the development and application of molecular approaches to ecology and molecular evolution. A further surprise resulting from the application of these new tools is the blurring of the distinction between pathogenic traits versus those considered non-pathogenic. This year's conference addressed the issues of biodiversity, its development, and the impact of stress on gene selection and expression. In addition microbial metabolic versatility with toxins such as heavy metals, antibiotics, and organic pollutants were discussed. The nine session topics were (1) biodiversity and the bacterial species, (2) mechanisms of biodiversification, (3) biofilms in health and environment, (4) a genomic view of microbial response to stress, (5) microbial use of toxic metals, (6) microbial mineral formation and dissolution, (7) power and limitations of antimicrobials, (8) biodegradation of organic pollutants, and (9) astrobiology. The Conference had an international profile: the Conference Vice-Chair, Dr. Gerard Muyzer, was from The Nether

Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

Science.gov (United States)

Chen, Bor-Sen; Wu, Chia-Chou

2013-01-01

Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering. PMID:24709875

Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering

Directory of Open Access Journals (Sweden)

Bor-Sen Chen

2013-10-01

Full Text Available Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.

The elliptic sine-Gordon equation in a half plane

International Nuclear Information System (INIS)

Pelloni, B; Pinotsis, D A

2010-01-01

We consider boundary value problems for the elliptic sine-Gordon equation posed in the half plane y > 0. This problem was considered in Gutshabash and Lipovskii (1994 J. Math. Sci. 68 197–201) using the classical inverse scattering transform approach. Given the limitations of this approach, the results obtained rely on a nonlinear constraint on the spectral data derived heuristically by analogy with the linearized case. We revisit the analysis of such problems using a recent generalization of the inverse scattering transform known as the Fokas method, and show that the nonlinear constraint of Gutshabash and Lipovskii (1994 J. Math. Sci. 68 197–201) is a consequence of the so-called global relation. We also show that this relation implies a stronger constraint on the spectral data, and in particular that no choice of boundary conditions can be associated with a decaying (possibly mod 2π) solution analogous to the pure soliton solutions of the usual, time-dependent sine-Gordon equation. We also briefly indicate how, in contrast to the evolutionary case, the elliptic sine-Gordon equation posed in the half plane does not admit linearisable boundary conditions

Metabolic engineering of yeast for lignocellulosic biofuel production.

Science.gov (United States)

Jin, Yong-Su; Cate, Jamie Hd

2017-12-01

Production of biofuels from lignocellulosic biomass remains an unsolved challenge in industrial biotechnology. Efforts to use yeast for conversion face the question of which host organism to use, counterbalancing the ease of genetic manipulation with the promise of robust industrial phenotypes. Saccharomyces cerevisiae remains the premier host for metabolic engineering of biofuel pathways, due to its many genetic, systems and synthetic biology tools. Numerous engineering strategies for expanding substrate ranges and diversifying products of S. cerevisiae have been developed. Other yeasts generally lack these tools, yet harbor superior phenotypes that could be exploited in the harsh processes required for lignocellulosic biofuel production. These include thermotolerance, resistance to toxic compounds generated during plant biomass deconstruction, and wider carbon consumption capabilities. Although promising, these yeasts have yet to be widely exploited. By contrast, oleaginous yeasts such as Yarrowia lipolytica capable of producing high titers of lipids are rapidly advancing in terms of the tools available for their metabolic manipulation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Metabolic Engineering of Probiotic Saccharomyces boulardii

OpenAIRE

Liu, Jing-Jing; Kong, In Iok; Zhang, Guo-Chang; Jayakody, Lahiru N.; Kim, Heejin; Xia, Peng-Fei; Kwak, Suryang; Sung, Bong Hyun; Sohn, Jung-Hoon; Walukiewicz, Hanna E.; Rao, Christopher V.; Jin, Yong-Su

2016-01-01

Saccharomyces boulardii is a probiotic yeast that has been used for promoting gut health as well as preventing diarrheal diseases. This yeast not only exhibits beneficial phenotypes for gut health but also can stay longer in the gut than Saccharomyces cerevisiae. Therefore, S. boulardii is an attractive host for metabolic engineering to produce biomolecules of interest in the gut. However, the lack of auxotrophic strains with defined genetic backgrounds has hampered the use of this strain for...

Multiresonance modes in sine–Gordon brane models

Energy Technology Data Exchange (ETDEWEB)

Cruz, W.T., E-mail: wilamicruz@gmail.com [Instituto Federal de Educação, Ciência e Tecnologia do Ceará (IFCE), Campus Juazeiro do Norte, 63040-540 Juazeiro do Norte-Ceará (Brazil); Maluf, R.V., E-mail: r.v.maluf@fisica.ufc.br [Universidade Federal do Ceará (UFC), Departamento de Física, Campus do Pici, Fortaleza - CE, C.P. 6030, 60455-760 (Brazil); Dantas, D.M., E-mail: davi@fisica.ufc.br [Universidade Federal do Ceará (UFC), Departamento de Física, Campus do Pici, Fortaleza - CE, C.P. 6030, 60455-760 (Brazil); Almeida, C.A.S., E-mail: carlos@fisica.ufc.br [Universidade Federal do Ceará (UFC), Departamento de Física, Campus do Pici, Fortaleza - CE, C.P. 6030, 60455-760 (Brazil)

2016-12-15

In this work, we study the localization of the vector gauge field in two five-dimensional braneworlds generated by scalar fields coupled to gravity. The sine–Gordon like potentials are employed to produce different thick brane setups. A zero mode localized is obtained, and we show the existence of reverberations with the wave solutions indicating a quasi-localized massive mode. More interesting results are achieved when we propose a double sine–Gordon potential to the scalar field. The resulting thick brane shows a more detailed topology with the presence of an internal structure composed by two kinks. The massive spectrum of the gauge field is revalued on this scenario revealing the existence of various resonant modes. Furthermore, we compute the corrections to Coulomb law coming from these massive KK vector modes in these thick scenarios, which is concluded that the dilaton parameter regulates these corrections.

Multiresonance modes in sine–Gordon brane models

International Nuclear Information System (INIS)

Cruz, W.T.; Maluf, R.V.; Dantas, D.M.; Almeida, C.A.S.

2016-01-01

In this work, we study the localization of the vector gauge field in two five-dimensional braneworlds generated by scalar fields coupled to gravity. The sine–Gordon like potentials are employed to produce different thick brane setups. A zero mode localized is obtained, and we show the existence of reverberations with the wave solutions indicating a quasi-localized massive mode. More interesting results are achieved when we propose a double sine–Gordon potential to the scalar field. The resulting thick brane shows a more detailed topology with the presence of an internal structure composed by two kinks. The massive spectrum of the gauge field is revalued on this scenario revealing the existence of various resonant modes. Furthermore, we compute the corrections to Coulomb law coming from these massive KK vector modes in these thick scenarios, which is concluded that the dilaton parameter regulates these corrections.

2010 ELECTRODEPOSITION GORDON RESEARCH CONFERENCE, AUGUST 1-6, 2010

Energy Technology Data Exchange (ETDEWEB)

Peter Searson

2010-08-06

The 2010 Gordon Conference on Electrodeposition will present cutting-edge research on electrodeposition with emphasis on (i) advances in basic science, (ii) developments in next-generation technologies, and (iii) new and emerging areas. The Conference will feature a wide range of topics, from atomic scale processes, nucleation and growth, thin film deposition, and electrocrystallization, to applications of electrodeposition in devices including microelectronics, solar energy, and power sources. The Conference will bring together investigators from a wide range of scientific disciplines, including chemical engineering, materials science and engineering, physics, and chemistry. The Conference will feature invited speakers at the forefront of the field, and a late-breaking news session that will provide the opportunity for graduate students, post-docs, and junior faculty to participate. The collegial atmosphere of this Conference, with scientific talks and poster sessions, as well as opportunities for informal gatherings in the afternoons and evenings, provides an avenue for scientists from different disciplines to discuss current issues and promotes cross-disciplinary collaborations in the various research areas represented. The Conference will be held at Colby-Sawyer College, located in the Mt. Kearsarge-Lake Sunapee Region of New Hampshire. The surrounding mountains, forests, and lakes provide a beautiful setting for this conference. The attendance is limited so early application is strongly advised.

Metabolic engineering of volatile isoprenoids in plants and microbes.

Science.gov (United States)

Vickers, Claudia E; Bongers, Mareike; Liu, Qing; Delatte, Thierry; Bouwmeester, Harro

2014-08-01

The chemical properties and diversity of volatile isoprenoids lends them to a broad variety of biological roles. It also lends them to a host of biotechnological applications, both by taking advantage of their natural functions and by using them as industrial chemicals/chemical feedstocks. Natural functions include roles as insect attractants and repellents, abiotic stress protectants in pathogen defense, etc. Industrial applications include use as pharmaceuticals, flavours, fragrances, fuels, fuel additives, etc. Here we will examine the ways in which researchers have so far found to exploit volatile isoprenoids using biotechnology. Production and/or modification of volatiles using metabolic engineering in both plants and microorganisms are reviewed, including engineering through both mevalonate and methylerythritol diphosphate pathways. Recent advances are illustrated using several case studies (herbivores and bodyguards, isoprene, and monoterpene production in microbes). Systems and synthetic biology tools with particular utility for metabolic engineering are also reviewed. Finally, we discuss the practical realities of various applications in modern biotechnology, explore possible future applications, and examine the challenges of moving these technologies forward so that they can deliver tangible benefits. While this review focuses on volatile isoprenoids, many of the engineering approaches described here are also applicable to non-isoprenoid volatiles and to non-volatile isoprenoids. © 2014 John Wiley & Sons Ltd.

Critical properties of the double-frequency sine-Gordon model with applications

International Nuclear Information System (INIS)

Fabrizio, M.; Gogolin, A.O.; Nersesyan, A.A.

2000-01-01

We study the properties of the double-frequency sine-Gordon model in the vicinity of the Ising quantum phase transition displayed by this model. Using a mapping onto a generalized lattice quantum Ashkin-Teller model, we obtain critical and nearly-off-critical correlation functions of various operators. We discuss applications of the double-sine-Gordon model to one-dimensional physical systems, like spin chains in a staggered external field and interacting electrons in a staggered potential

Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering

DEFF Research Database (Denmark)

Cho, Changhee; Choi, So Young; Luo, Zi Wei

2015-01-01

The advent of various systems metabolic engineering tools and strategies has enabled more sophisticated engineering of microorganisms for the production of industrially useful fuels and chemicals. Advances in systems metabolic engineering have been made in overproducing natural chemicals...... and producing novel non-natural chemicals. In this paper, we review the tools and strategies of systems metabolic engineering employed for the development of microorganisms for the production of various industrially useful chemicals belonging to fuels, building block chemicals, and specialty chemicals......, in particular focusing on those reported in the last three years. It was aimed at providing the current landscape of systems metabolic engineering and suggesting directions to address future challenges towards successfully establishing processes for the bio-based production of fuels and chemicals from renewable...

Gordon Browni valitsuslaevuke sõitis karidele / Heiki Suurkask

Index Scriptorium Estoniae

Suurkask, Heiki, 1972-

2008-01-01

Briti peaministri Gordon Browni partei kaotas Inglismaa ja Walesi kohalikel valimistel. Autori väitel võis kõige rängema hoobi valitsusele anda madalaima, 10-protsendilise tulumaksumäära kaotamine

Metabolic engineering of microalgal based biofuel production: prospects and challenges

Directory of Open Access Journals (Sweden)

Chiranjib eBanerjee

2016-03-01

Full Text Available The current scenario in renewable energy is focused on development of alternate and sustainable energy sources, amongst which microalgae stands as one of the promising feedstock for biofuel production. It is well known that microalgae generate much larger amounts of biofuels in a shorter time than other sources based on plant seeds. However, the greatest challenge in a transition to algae-based biofuel production is the various other complications involved in microalgal cultivation, its harvesting, concentration, drying and lipid extraction. Several green microalgae accumulate lipids, especially triacylglycerols (TAGs, which are main precursors in the production of lipid. The various aspects on metabolic pathway analysis of an oleaginous microalgae i.e. Chlamydomonas reinhardtii have elucidated some novel metabolically important genes and this enhances the lipid production in this microalgae. Adding to it, various other aspects in metabolic engineering using OptFlux and effectual bioprocess design also gives an interactive snapshot of enhancing lipid production which ultimately improvises the oil yield. This article reviews the current status of microalgal based technologies for biofuel production, bioreactor process design, flux analysis and it also provides various strategies to increase lipids accumulation via metabolic engineering.

Biobased production of alkanes and alkenes through metabolic engineering of microorganisms

DEFF Research Database (Denmark)

Kang, Min Kyoung; Nielsen, Jens

2017-01-01

Advancement in metabolic engineering of microorganisms has enabled bio-based production of a range of chemicals, and such engineered microorganism can be used for sustainable production leading to reduced carbon dioxide emission there. One area that has attained much interest is microbial...... hydrocarbon biosynthesis, and in particular, alkanes and alkenes are important high-value chemicals as they can be utilized for a broad range of industrial purposes as well as ‘drop-in’ biofuels. Some microorganisms have the ability to biosynthesize alkanes and alkenes naturally, but their production level...... is extremely low. Therefore, there have been various attempts to recruit other microbial cell factories for production of alkanes and alkenes by applying metabolic engineering strategies. Here we review different pathways and involved enzymes for alkane and alkene production and discuss bottlenecks...

SBOLme: a Repository of SBOL Parts for Metabolic Engineering

KAUST Repository

Kuwahara, Hiroyuki; Cui, Xuefeng; Umarov, Ramzan; Grunberg, Raik; Myers, Chris J.; Gao, Xin

2017-01-01

The Synthetic Biology Open Language (SBOL) is a community-driven open language to promote standardization in synthetic biology. To support the use of SBOL in metabolic engineering, we developed SBOLme, the first open-access repository of SBOL 2

Invariant solutions of the supersymmetric sine-Gordon equation

International Nuclear Information System (INIS)

Grundland, A M; Hariton, A J; Snobl, L

2009-01-01

A comprehensive symmetry analysis of the N=1 supersymmetric sine-Gordon equation is performed. Two different forms of the supersymmetric system are considered. We begin by studying a system of partial differential equations corresponding to the coefficients of the various powers of the anticommuting independent variables. Next, we consider the super-sine-Gordon equation expressed in terms of a bosonic superfield involving anticommuting independent variables. In each case, a Lie (super)algebra of symmetries is determined and a classification of all subgroups having generic orbits of codimension 1 in the space of independent variables is performed. The method of symmetry reduction is systematically applied in order to derive invariant solutions of the supersymmetric model. Several types of algebraic, hyperbolic and doubly periodic solutions are obtained in explicit form.

Scattering of topological solitons on barriers and holes of deformed Sine-Gordon models

International Nuclear Information System (INIS)

Al-Alawi, Jassem H; Zakrzewski, Wojtek J

2008-01-01

We study various scattering properties of topological solitons in two classes of models, which are the generalizations of the Sine-Gordon model and which have recently been proposed by Bazeia et al. These two classes of models depend on a positive real nonzero parameter n but in this paper we consider the models only for its integer values as when n = 2 (for the first class) and n = 1 (for the second class), the model reduces to the Sine-Gordon one. We take the soliton solutions of these models (generalizations of the 'kink' solution of the Sine-Gordon model) and consider their scattering on potential holes and barriers. We present our results for n = 1, ..., 6. We find that, like in the Sine-Gordon models, the scattering on the barrier is very elastic while the scattering on the hole is inelastic and can, at times, lead to a reflection. We discuss the dependence of our results on n and find that the critical velocity for the transmission through the hole is lowest for n = 3

Correct use of the Gordon decomposition in the calculation of nucleon magnetic dipole moments

International Nuclear Information System (INIS)

Mekhfi, Mustapha

2008-01-01

We perform the calculation of the nucleon dipole magnetic moment in full detail using the Gordon decomposition of the free quark current. This calculation has become necessary because of frequent misuse of the Gordon decomposition by some authors in computing the nucleon dipole magnetic moment

Recent advances in microbial production of fuels and chemicals using tools and strategies of systems metabolic engineering.

Science.gov (United States)

Cho, Changhee; Choi, So Young; Luo, Zi Wei; Lee, Sang Yup

2015-11-15

The advent of various systems metabolic engineering tools and strategies has enabled more sophisticated engineering of microorganisms for the production of industrially useful fuels and chemicals. Advances in systems metabolic engineering have been made in overproducing natural chemicals and producing novel non-natural chemicals. In this paper, we review the tools and strategies of systems metabolic engineering employed for the development of microorganisms for the production of various industrially useful chemicals belonging to fuels, building block chemicals, and specialty chemicals, in particular focusing on those reported in the last three years. It was aimed at providing the current landscape of systems metabolic engineering and suggesting directions to address future challenges towards successfully establishing processes for the bio-based production of fuels and chemicals from renewable resources. Copyright © 2014 Elsevier Inc. All rights reserved.

Exact, multiple soliton solutions of the double sine Gordon equation

International Nuclear Information System (INIS)

Burt, P.B.

1978-01-01

Exact, particular solutions of the double sine Gordon equation in n dimensional space are constructed. Under certain restrictions these solutions are N solitons, where N <= 2q - 1 and q is the dimensionality of space-time. The method of solution, known as the base equation technique, relates solutions of nonlinear partial differential equations to solutions of linear partial differential equations. This method is reviewed and its applicability to the double sine Gordon equation shown explicitly. The N soliton solutions have the remarkable property that they collapse to a single soliton when the wave vectors are parallel. (author)

Metabolic engineering with systems biology tools to optimize production of prokaryotic secondary metabolites

DEFF Research Database (Denmark)

Kim, Hyun Uk; Charusanti, Pep; Lee, Sang Yup

2016-01-01

Metabolic engineering using systems biology tools is increasingly applied to overproduce secondary metabolites for their potential industrial production. In this Highlight, recent relevant metabolic engineering studies are analyzed with emphasis on host selection and engineering approaches...... for the optimal production of various prokaryotic secondary metabolites: native versus heterologous hosts (e.g., Escherichia coli) and rational versus random approaches. This comparative analysis is followed by discussions on systems biology tools deployed in optimizing the production of secondary metabolites....... The potential contributions of additional systems biology tools are also discussed in the context of current challenges encountered during optimization of secondary metabolite production....

Quantifying the metabolic capabilities of engineered Zymomonas mobilis using linear programming analysis

Directory of Open Access Journals (Sweden)

Tsantili Ivi C

2007-03-01

Full Text Available Abstract Background The need for discovery of alternative, renewable, environmentally friendly energy sources and the development of cost-efficient, "clean" methods for their conversion into higher fuels becomes imperative. Ethanol, whose significance as fuel has dramatically increased in the last decade, can be produced from hexoses and pentoses through microbial fermentation. Importantly, plant biomass, if appropriately and effectively decomposed, is a potential inexpensive and highly renewable source of the hexose and pentose mixture. Recently, the engineered (to also catabolize pentoses anaerobic bacterium Zymomonas mobilis has been widely discussed among the most promising microorganisms for the microbial production of ethanol fuel. However, Z. mobilis genome having been fully sequenced in 2005, there is still a small number of published studies of its in vivo physiology and limited use of the metabolic engineering experimental and computational toolboxes to understand its metabolic pathway interconnectivity and regulation towards the optimization of its hexose and pentose fermentation into ethanol. Results In this paper, we reconstructed the metabolic network of the engineered Z. mobilis to a level that it could be modelled using the metabolic engineering methodologies. We then used linear programming (LP analysis and identified the Z. mobilis metabolic boundaries with respect to various biological objectives, these boundaries being determined only by Z. mobilis network's stoichiometric connectivity. This study revealed the essential for bacterial growth reactions and elucidated the association between the metabolic pathways, especially regarding main product and byproduct formation. More specifically, the study indicated that ethanol and biomass production depend directly on anaerobic respiration stoichiometry and activity. Thus, enhanced understanding and improved means for analyzing anaerobic respiration and redox potential in vivo are

Genomics:GTL Contractor-Grantee Workshop IV and Metabolic Engineering Working Group Inter-Agency Conference on Metabolic Engineering 2006

Energy Technology Data Exchange (ETDEWEB)

Mansfield, Betty Kay [ORNL; Martin, Sheryl A [ORNL

2006-02-01

Welcome to the 2006 joint meeting of the fourth Genomics:GTL Contractor-Grantee Workshop and the six Metabolic Engineering Working Group Inter-Agency Conference. The vision and scope of the Genomics:GTL program continue to expand and encompass research and technology issues from diverse scientific disciplines, attracting broad interest and support from researchers at universities, DOE national laboratories, and industry. Metabolic engineering's vision is the targeted and purposeful alteration of metabolic pathways to improve the understanding and use of cellular pathways for chemical transformation, energy transduction, and supramolecular assembly. These two programs have much complementarity in both vision and technological approaches, as reflected in this joint workshop. GLT's challenge to the scientific community remains the further development and use of a broad array of innovative technologies and computational tools to systematically leverage the knowledge and capabilities brought to us by DNA sequencing projects. The goal is to seek a broad and predictive understanding of the functioning and control of complex systems--individual microbes, microbial communities, and plants. GTL's prominent position at the interface of the physical, computational, and biological sciences is both a strength and challenge. Microbes remain GTL's principal biological focus. In the complex 'simplicity' of microbes, they find capabilities needed by DOE and the nation for clean and secure energy, cleanup of environmental contamination, and sequestration of atmospheric carbon dioxide that contributes to global warming. An ongoing challenge for the entire GTL community is to demonstrate that the fundamental science conducted in each of your research projects brings us a step closer to biology-based solutions for these important national energy and environmental needs.

The sine-Gordon model revisited I

Energy Technology Data Exchange (ETDEWEB)

Niccoli, G.; Teschner, J.

2009-10-15

We study integrable lattice regularizations of the Sine-Gordon model with the help of the Separation of Variables method of Sklyanin and the Baxter Q-operators. This allows us to characterize the spectrum (eigenvalues and eigenstates) completely in terms of polynomial solutions of the Baxter equation with certain properties. This result is analogous to the completeness of the Bethe ansatz. (orig.)

2008 Multiphoton Processes Gordon Research Conferences - June 8-13, 2008

Energy Technology Data Exchange (ETDEWEB)

Mette B. Gaarde

2009-08-28

In 2008 the Gordon Research Conference on Multiphoton Processes is held for the 14th time. The meeting continues to evolve as it embraces both the rapid technological and intellectual growth in the field as well as the multi-disciplinary expertise of the participants. This time the sessions will focus on: (1) Attosecond Science; (2) Free-electron laser experiments and theory; (3) Ultrafast dynamics of molecules; (4) Laser control of molecules; (5) Ultrafast imaging; (6) Super-high intensity and x-rays; (7) Strong field processes in molecules; and (8) Control atoms with light and vice versa. The scientific program will blur traditional disciplinary boundaries as the presenters and discussion leaders involve chemists, physicists, and optical engineers, representing both experiment and theory. The broad range of expertise and different perspectives of attendees should provide a stimulating and unique environment for solving problems and developing new ideas in this rapidly evolving field.

Experimental Investigation of Trapped Sine-Gordon Solitons

DEFF Research Database (Denmark)

Davidson, A.; Dueholm, B.; Kryger, B.

1985-01-01

We have observed for the first time a single sine-Gordon soliton trapped in an annular Josephson junction. This system offers a unique possibility to study undisturbed soliton motion. In the context of perturbation theory, the soliton may be viewed as a relativistic particle moving under a uniform...

Filtration of the classical knot concordance group and Casson-Gordon invariants

OpenAIRE

Kim, Taehee

2002-01-01

It is known that if any prime power branched cyclic cover of a knot in the 3-sphere is a homology sphere, then the knot has vanishing Casson-Gordon invariants. We construct infinitely many examples of (topologically) non-slice knots in the 3-sphere whose prime power branched cyclic covers are homology spheres. We show that these knots generate an infinite rank subgroup of F_(1.0)/F_(1.5) for which Casson-Gordon invariants vanish in Cochran-Orr-Teichner's filtration of the classical knot conco...

Localized solutions of non-linear Klein--Gordon equations

International Nuclear Information System (INIS)

Werle, J.

1977-05-01

Nondissipative, stationary solutions for a class of nonlinear Klein-Gordon equations for a scalar field were found explicitly. Since the field is different from zero only inside a sphere of definite radius, the solutions are called quantum droplets

Critical values of the Yang-Yang functional in the quantum sine-Gordon model

International Nuclear Information System (INIS)

Lukyanov, Sergei L.

2011-01-01

The critical values of the Yang-Yang functional corresponding to the vacuum states of the sine-Gordon QFT in the finite-volume are studied. Two major applications are discussed: (i) generalization of Fendley-Saleur-Zamolodchikov relations to arbitrary values of the sine-Gordon coupling constant, and (ii) connection problem for a certain two-parameter family of solutions of the Painleve III equation.

Exact expectation values of local fields in the quantum sine-Gordon model

International Nuclear Information System (INIS)

Lukyanov, S.; Rossijskaya Akademiya Nauk, Chernogolovka; Zamolodchikov, A.; Rossijskaya Akademiya Nauk, Chernogolovka

1997-01-01

We propose an explicit expression for vacuum expectation values left angle e iaφ right angle of the exponential fields in the sine-Gordon model. Our expression agrees both with semi-classical results in the sine-Gordon theory and with perturbative calculations in the massive Thirring model. We use this expression to make new predictions about the large-distance asymptotic form of the two-point correlation function in the XXZ spin chain. (orig.)

Klein-Gordon oscillator with position-dependent mass in the rotating cosmic string spacetime

Science.gov (United States)

Wang, Bing-Qian; Long, Zheng-Wen; Long, Chao-Yun; Wu, Shu-Rui

2018-02-01

A spinless particle coupled covariantly to a uniform magnetic field parallel to the string in the background of the rotating cosmic string is studied. The energy levels of the electrically charged particle subject to the Klein-Gordon oscillator are analyzed. Afterwards, we consider the case of the position-dependent mass and show how these energy levels depend on the parameters in the problem. Remarkably, it shows that for the special case, the Klein-Gordon oscillator coupled covariantly to a homogeneous magnetic field with the position-dependent mass in the rotating cosmic string background has the similar behaviors to the Klein-Gordon equation with a Coulomb-type configuration in a rotating cosmic string background in the presence of an external magnetic field.

The Need for Integrated Approaches in Metabolic Engineering

Energy Technology Data Exchange (ETDEWEB)

Lechner, Anna; Brunk, Elizabeth; Keasling, Jay D.

2016-08-15

This review highlights state-of-the-art procedures for heterologous small-molecule biosynthesis, the associated bottlenecks, and new strategies that have the potential to accelerate future accomplishments in metabolic engineering. We emphasize that a combination of different approaches over multiple time and size scales must b e considered for successful pathway engineering in a heterologous host. We have classified these optimization procedures based on the "system" that is being manipulated: transcriptome, translatome, proteome, or reactome. By bridging multiple disciplines, including molecular biology, biochemistry, biophysics, and computational sciences, we can create an integral framework for the discovery and implementation of novel biosynthetic production routes.

Pilved Gordon Browni tuleviku kohal aina tumenevad / Hendrik Vosman

Index Scriptorium Estoniae

Vosman, Hendrik

2008-01-01

Briti peaministri Gordon Brownile on parlamendis opositsioonis olevad toorid suutnud oma edumaad leiboristide ees suurendada juba 28 %-punktini, peaministri maine kiire languse põhjuseks peetakse viimaste kuude maailma finantskriisi

Semiclassical approach to the quantization of the periodic solutions of the sine-Gordon equation

International Nuclear Information System (INIS)

Ghika, G.; Visinescu, M.

1978-01-01

The periodic solutions of the sine-Gordon equation are proved to be singular. For the semiclassical quantization of the periodic solutions we calculate the fluctuations around them and we use the path integrals in the Gaussian approximation in order to obtain the bound states of the sine-Gordon field equation. (author)

Engineering of metabolic pathways by artificial enzyme channels

Directory of Open Access Journals (Sweden)

Marlene ePröschel

2015-10-01

Full Text Available Application of industrial enzymes for production of valuable chemical compounds has greatly benefited from recent developments in Systems and Synthetic Biology. Both, in vivo and in vitro systems have been established, allowing conversion of simple into complex compounds. Metabolic engineering in living cells needs to be balanced which is achieved by controlling gene expression levels, translation, scaffolding, compartmentation and flux control. In vitro applications are often hampered by limited protein stability/half-life and insufficient rates of substrate conversion. To improve stability and catalytic activity, proteins are post-translationally modified and arranged in artificial metabolic channels. Within the review article we will first discuss the supramolecular organization of enzymes in living systems and secondly summarize current and future approaches to design artificial metabolic channels by additive manufacturing for the efficient production of desired products.

Review of Microfluidic Photobioreactor Technology for Metabolic Engineering and Synthetic Biology of Cyanobacteria and Microalgae

Directory of Open Access Journals (Sweden)

Ya-Tang Yang

2016-10-01

Full Text Available One goal of metabolic engineering and synthetic biology for cyanobacteria and microalgae is to engineer strains that can optimally produce biofuels and commodity chemicals. However, the current workflow is slow and labor intensive with respect to assembly of genetic parts and characterization of production yields because of the slow growth rates of these organisms. Here, we review recent progress in the microfluidic photobioreactors and identify opportunities and unmet needs in metabolic engineering and synthetic biology. Because of the unprecedented experimental resolution down to the single cell level, long-term real-time monitoring capability, and high throughput with low cost, microfluidic photobioreactor technology will be an indispensible tool to speed up the development process, advance fundamental knowledge, and realize the full potential of metabolic engineering and synthetic biology for cyanobacteria and microalgae.

Thermodynamic quantities for the Klein–Gordon equation

Indian Academy of Sciences (India)

We study some thermodynamic quantities for the Klein–Gordon equation with a linear plus inverselinear, scalar potential. We obtain the energy eigenvalues with the help of the quantization rule from the biconfluent Heun's equation.We use a method based on the Euler–MacLaurin formula to analytically compute thethermal ...

Gordon's model applied to nursing care of people with depression.

Science.gov (United States)

Temel, M; Kutlu, F Y

2015-12-01

Psychiatric nurses should consider the patient's biological, psychological and social aspects. Marjory Gordon's Functional Health Pattern Model ensures a holistic approach for the patient. To examine the effectiveness of Gordon's Functional Health Pattern Model in reducing depressive symptoms, increasing self-efficacy, coping with depression and increasing hope in people with depression. A quasi-experimental two-group pre-test and post-test design was adopted. Data were collected from April 2013 to May 2014 from people with depression at the psychiatry clinic of a state hospital in Turkey; they were assigned to the intervention (n = 34) or control group (n = 34). The intervention group received nursing care according to Gordon's Functional Health Pattern Model and routine care, while the control group received routine care only. The Beck Depression Inventory, Beck Hopelessness Scale and Depression Coping Self-Efficacy Scale were used. The intervention group had significantly lower scores on the Beck Depression Inventory and Beck Hopelessness Scale at the post-test and 3-month follow-up; they had higher scores on the Depression Coping Self-Efficacy Scale at the 3-month follow-up when compared with the control group. The study was conducted at only one psychiatry clinic. The intervention and control group patients were at the clinic at the same time and influenced each other. Moreover, because clinical routines were in progress during the study, the results cannot only be attributed to nursing interventions. Nursing models offer guidance for the care provided. Practices based on the models return more efficient and systematic caregiving results with fewer health problems. Gordon's Functional Health Pattern Model was effective in improving the health of people with depression and could be introduced as routine care with ongoing evaluation in psychiatric clinics. More research is needed to evaluate Gordon's Nursing Model effect on people with depression. Future

Bunched soliton states in weakly coupled sine-Gordon systems

International Nuclear Information System (INIS)

Gronbech-Jensen, N.; Samuelsen, M.R.; Lomdahl, P.S.; Blackburn, J.A.

1990-01-01

The interaction between solitons of two weakly coupled sine-Gordon systems is considered. In particular, the stability of bunched states is investigated, and perturbation results are compared with numerical results

Transcriptome data modeling for targeted plant metabolic engineering.

Science.gov (United States)

Yonekura-Sakakibara, Keiko; Fukushima, Atsushi; Saito, Kazuki

2013-04-01

The massive data generated by omics technologies require the power of bioinformatics, especially network analysis, for data mining and doing data-driven biology. Gene coexpression analysis, a network approach based on comprehensive gene expression data using microarrays, is becoming a standard tool for predicting gene function and elucidating the relationship between metabolic pathways. Differential and comparative gene coexpression analyses suggest a change in coexpression relationships and regulators controlling common and/or specific biological processes. In conjunction with the newly emerging genome editing technology, network analysis integrated with other omics data should pave the way for robust and practical plant metabolic engineering. Copyright © 2012 Elsevier Ltd. All rights reserved.

Quantum solitons and their classical relatives: Bethe Ansatz states in soliton sectors of the Sine--Gordon System

International Nuclear Information System (INIS)

Garbaczewski, P.

1982-01-01

Previously we have found that the semiclassical sine--Gordon/Thirring spectrum can be received in the absence of quantum solitons via the spin 1/2 approximation of the quantized sine--Gordon system on a lattice. Later on, we have recovered the Hilbert space of quantum soliton states for the sine--Gordon system. In the present paper we present a derivation of the Bethe Ansatz eigenstates for the generalized ice model in this soliton Hilbert space. We demonstrate that via ''Wick rotation'' of a fundamental parameter of the ice model one arrives at the Bethe Ansatz eigenstates of the quantum sine--Gordon system. The latter is a ''local transition matrix'' ancestor of the coventional sine--Gordon/Thirring model, as derived by Faddeev et al. within the quantum inverse-scattering method. Our result is essentially based on the N< infinity,Δ = 1,m<<1 regime. Consequently, the spectrum received, though resembling the semiclassical one, does not coincide with it at all

Boson-soliton scattering in the sine-Gordon model

International Nuclear Information System (INIS)

Lowe, M.

1979-01-01

In this paper the author calculates the boson-soliton scattering amplitudes for various processes in the sine-Gordon model to obtain results in agreement with the prediction of no-particle production and equality of ingoing and outgoing sets of momenta. (Auth.)

Sine-Gordon equation as a model of a nonlinear scalar field in the Duffin-Kemmer formalism

International Nuclear Information System (INIS)

Getmanov, B.S.

1980-01-01

The nonlinear self-interaction of a scalar field is studied in the Minkowski space-time of an arbitrary dimension. It is shown that the sine-Gordon equation can be considered as a model of the nonlinear scalar field in the Duffin-Kemmer formalism with a specific kind of nonlinearity. The ''V-A'' type interaction is found to be equivalent to the ''complex sine-Gordon'' model. Such a new formation of the sine-Gordon equation might be useful for search for its integrable generalizations

Current progress of targetron technology: development, improvement and application in metabolic engineering.

Science.gov (United States)

Liu, Ya-Jun; Zhang, Jie; Cui, Gu-Zhen; Cui, Qiu

2015-06-01

Targetrons are mobile group II introns that can recognize their DNA target sites by base-pairing RNA-DNA interactions with the aid of site-specific binding reverse transcriptases. Targetron technology stands out from recently developed gene targeting methods because of the flexibility, feasibility, and efficiency, and is particularly suitable for the genetic engineering of difficult microorganisms, including cellulolytic bacteria that are considered promising candidates for biomass conversion via consolidated bioprocessing. Along with the development of the thermotargetron method for thermophiles, targetron technology becomes increasingly important for the metabolic engineering of industrial microorganisms aiming at biofuel/chemical production. To summarize the current progress of targetron technology and provide new insights on the use of the technology, this paper reviews the retrohoming mechanisms of both mesophilic and thermophilic targetron methods based on various group II introns, investigates the improvement of targetron tools for high target efficiency and specificity, and discusses the current applications in the metabolic engineering for bacterial producers. Although there are still intellectual property and technical restrictions in targetron applications, we propose that targetron technology will contribute to both biochemistry research and the metabolic engineering for industrial productions. Copyright © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

NOAA Ship Gordon Gunter Underway Meteorological Data, Quality Controlled

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — NOAA Ship Gordon Gunter Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and Oceanographic System...

Experimental relationship between damping and stability of sine-Gordon solitons in Josephson junctions

DEFF Research Database (Denmark)

Davidson, A.; Pedersen, Niels Falsig; Dueholm, B.

1985-01-01

We show some experimental results which suggest that total damping, including surface loss, plays a fundamental role in limiting the stability of high-velocity sine-Gordon solitons in real Josephson tunnel junctions.......We show some experimental results which suggest that total damping, including surface loss, plays a fundamental role in limiting the stability of high-velocity sine-Gordon solitons in real Josephson tunnel junctions....

Advances in Metabolic Engineering of Cyanobacteria for Photosynthetic Biochemical Production

OpenAIRE

Lai, Martin C.; Lan, Ethan I.

2015-01-01

Engineering cyanobacteria into photosynthetic microbial cell factories for the production of biochemicals and biofuels is a promising approach toward sustainability. Cyanobacteria naturally grow on light and carbon dioxide, bypassing the need of fermentable plant biomass and arable land. By tapping into the central metabolism and rerouting carbon flux towards desirable compound production, cyanobacteria are engineered to directly convert CO2 into various chemicals. This review discusses the d...

Mitigating health risks associated with alcoholic beverages through metabolic engineering.

Science.gov (United States)

Jayakody, Lahiru N; Lane, Stephan; Kim, Heejin; Jin, Yong-Su

2016-02-01

Epidemiological studies have established a positive relationship between the occurrence of cancer and consumption of alcoholic beverages. Metabolic engineering of brewing yeast to reduce potential carcinogenic compounds in alcoholic beverage is technically feasible as well as economically promising. This review presents the mechanisms of formation of potentially carcinogenic components in alcoholic beverages, such as formaldehyde, acetaldehyde, ethyl carbamate, acrylamide, and heavy metals, and introduces effective genetic perturbations to minimize the concentrations of these harmful components. As precise and effective genome editing tools for polyploid yeast are now available, we envision that yeast metabolic engineering might open up new research directions for improving brewing yeast in order to ensure product safety as well as to increase overall quality of alcoholic beverages. Copyright © 2015 Elsevier Ltd. All rights reserved.

2012 Gordon Research Conference on Bioinspired Materials - Formal Schedule and Speaker/Poster Program

Energy Technology Data Exchange (ETDEWEB)

Chilkoti, Ashutosk [Duke Univ., Durham, NC (United States)

2012-06-29

The emerging, interdisciplinary field of Bioinspired Materials focuses on developing a fundamental understanding of the synthesis, directed self-assembly and hierarchical organization of natural occurring materials, and uses this understanding to engineer new bioinspired artificial materials for diverse applications. The inaugural 2012 Gordon Conference on Bioinspired Materials seeks to capture the excitement of this burgeoning field by a cutting-edge scientific program and roster of distinguished invited speakers and discussion leaders who will address the key issues in the field. The Conference will feature a wide range of topics, such as materials and devices from DNA, reprogramming the genetic code for design of new materials, peptide, protein and carbohydrate based materials, biomimetic systems, complexity in self-assembly, and biomedical applications of bioinspired materials.

Engineering of aromatic amino acid metabolism in Saccharomyces cerevisiae

NARCIS (Netherlands)

Vuralhan, Z.

2006-01-01

Saccharomyces cerevisiae is a popular industrial microorganism. It has since long been used in bread, beer and wine making. More recently it is also being applied for heterologous protein production and as a target organism for metabolic engineering. The work presented in this thesis describes how

Enhancing gold recovery from electronic waste via lixiviant metabolic engineering in Chromobacterium violaceum

Science.gov (United States)

Tay, Song Buck; Natarajan, Gayathri; Rahim, Muhammad Nadjad bin Abdul; Tan, Hwee Tong; Chung, Maxey Ching Ming; Ting, Yen Peng; Yew, Wen Shan

2013-01-01

Conventional leaching (extraction) methods for gold recovery from electronic waste involve the use of strong acids and pose considerable threat to the environment. The alternative use of bioleaching microbes for gold recovery is non-pollutive and relies on the secretion of a lixiviant or (bio)chemical such as cyanide for extraction of gold from electronic waste. However, widespread industrial use of bioleaching microbes has been constrained by the limited cyanogenic capabilities of lixiviant-producing microorganisms such as Chromobacterium violaceum. Here we show the construction of a metabolically-engineered strain of Chromobacterium violaceum that produces more (70%) cyanide lixiviant and recovers more than twice as much gold from electronic waste compared to wild-type bacteria. Comparative proteome analyses suggested the possibility of further enhancement in cyanogenesis through subsequent metabolic engineering. Our results demonstrated the utility of lixiviant metabolic engineering in the construction of enhanced bioleaching microbes for the bioleaching of precious metals from electronic waste. PMID:23868689

2012 Photosynthesis Gordon Research Conference and Seminar, JUL 7-13, 2012

Energy Technology Data Exchange (ETDEWEB)

Debus, Richard [Univ. of California, Riverside, CA (United States)

2012-07-13

The Gordon Research Conference on PHOTOSYNTHESIS was held at Davidson College, Davidson, North Carolina, July 8-13, 2012. The Conference was well-attended with 150 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. Of the 150 attendees, 65 voluntarily responded to a general inquiry regarding ethnicity which appears on our registration forms. Of the 65 respondents, 20% were Minorities$-$ 5% Hispanic, 15% Asian and 0% African American. Approximately 28% of the participants at the 2012 meeting were women. The Gordon Research Seminar on PHOTOSYNTHESIS held at Davidson College, Davidson, North Carolina, July 7-8, 2012.. The Conference was well-attended with 51 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. Of the 51 attendees, 22 voluntarily responded to a general inquiry regarding ethnicity which appears on our registration forms. Of the 22 respondents, 14% were Minorities $-$0% Hispanic, 14% Asian and 0% African American. Approximately 35% of the participants at the 2012 meeting were women. Focal points for talks and discussions will include: Artificial photosynthesis and solar energy conversion strategies; Engineering organisms for biofuels and hydrogen production; Electron transport, proton transport, and energy coupling; Photoprotection mechanisms; Photosynthetic reaction center structure and function, including rewiring reaction centers for artificial photosynthesis; Energy capture and light harvesting solutions, including quantum coherence; Structure of the oxygen evolving complex and the mechanism of oxygen production.

2010 Gordon Research Conference on Plasmonics, June 13-19 2010

Energy Technology Data Exchange (ETDEWEB)

Halas, Naomi [Rice Univ., Houston, TX (United States)

2010-06-18

The field of plasmonics lies at the forefront of current revolutionary developments in optics at nanoscale dimensions, with broad applications in the fields of biology, chemistry, and engineering. Advancing these applications will require an enhanced focus on the fundamental science of plasmonics in new and exotic regimes. This 2010 Gordon Conference on Plasmonics will focus on recent advances in fundamental and applied plasmonics. As with past conferences, this meeting will bring together top researchers and future leaders for substantial interactions between students, young speakers, and senior figures in the field. Participants should expect lively discussion during the sessions, intermingled with unstructured time where ideas move, collaborations form, and connections are made. Invited talks will cover a diverse range of topics, including active devices, coherence effects, metamaterials and cloaking, quantum optical phenomena, and plasmons in exotic media and in new wavelength regimes. At the conclusion of the conference, our final session will look forward and begin defining upcoming challenges and opportunities for plasmonics.

Oscillating particle-like solutions of nonlinear Klein-Gordon equation

International Nuclear Information System (INIS)

Bogolubsky, I.L.

1976-01-01

A denumerable set of oscillating spherically-symmetric particle-like solutions of the Klein-Gordon equation with cubic nonlinearity is found. Extended particles modelled by them turn out to be slightly radiating and long-lived

Relativistic supersymmetric quantum mechanics based on Klein-Gordon equation

International Nuclear Information System (INIS)

Znojil, Miloslav

2004-01-01

Witten's the non-relativistic formalism of supersymmetric quantum mechanics was based on a factorization and partnership between Schroedinger equations. We show how it accommodates a transition to the partnership between relativistic Klein-Gordon equations

Gordon Research Conference on Genetic Toxicology

Energy Technology Data Exchange (ETDEWEB)

Project Director Penelope Jeggo

2003-02-15

Genetic toxicology represents a study of the genetic damage that a cell can incur, the agents that induce such damage, the damage response mechanisms available to cells and organisms, and the potential consequences of such damage. Genotoxic agents are abundant in the environment and are also induced endogenously. The consequences of such damage can include carcinogenesis and teratogenesis. An understanding of genetic toxicology is essential to carry out risk evaluations of the impact of genotoxic agents and to assess how individual genetic differences influence the response to genotoxic damage. In recent years, the importance of maintaining genomic stability has become increasingly recognized, in part by the realization that failure of the damage response mechanisms underlies many, if not all, cancer incidence. The importance of these mechanisms is also underscored by their remarkable conservation between species, allowing the study of simple organisms to provide significant input into our understanding of the underlying mechanisms. It has also become clear that the damage response mechanisms interface closely with other aspects of cellular metabolism including replication, transcription and cell cycle regulation. Moreover, defects in many of these mechanisms, as observed for example in ataxia telangiectasia patients, confer disorders with associated developmental abnormalities demonstrating their essential roles during growth and development. In short, while a decade ago, a study of the impact of DNA damage was seen as a compartmentalized area of cellular research, it is now appreciated to lie at the centre of an array of cellular responses of crucial importance to human health. Consequently, this has become a dynamic and rapidly advancing area of research. The Genetic Toxicology Gordon Research Conference is biannual with an evolving change in the emphasis of the meetings. From evaluating the nature of genotoxic chemicals, which lay at the centre of the early

Soliton annihilation in the perturbed sine-Gordon system

DEFF Research Database (Denmark)

Pedersen, Niels Falsig; Samuelsen, Mogens Rugholm; Welner, D.

1984-01-01

Fluxon-antifluxon annihilation in the perturbed sine-Gordon equation with loss and driving terms is investigated. For the infinite line we find a simple analytic expression for the threshold driving term corresponding to annihilation. With the application of the results to a Josephson junction...

The complex sine-Gordon model on a half line

International Nuclear Information System (INIS)

Tzamtzis, Georgios

2003-01-01

In this thesis, we study the complex sine-Gordon model on a half line. The model in the bulk is an integrable (1+1) dimensional field theory which is U(1) gauge invariant and comprises a generalisation of the sine-Gordon theory. It accepts soliton and breather solutions. By introducing suitably selected boundary conditions we may consider the model on a half line. Through such conditions the model can be shown to remain integrable and various aspects of the boundary theory can be examined. The first chapter serves as a brief introduction to some basic concepts of integrability and soliton solutions. As an example of an integrable system with soliton solutions, the sine-Gordon model is presented both in the bulk and on a half line. These results will serve as a useful guide for the model at hand. The introduction finishes with a brief overview of the two methods that will be used on the fourth chapter in order to obtain the quantum spectrum of the boundary complex sine-Gordon model. In the second chapter the model is properly introduced along with a brief literature review. Different realisations of the model and their connexions are discussed. The vacuum of the theory is investigated. Soliton solutions are given and a discussion on the existence of breathers follows. Finally the collapse of breather solutions to single solitons is demonstrated and the chapter concludes with a different approach to the breather problem. In the third chapter, we construct the lowest conserved currents and through them we find suitable boundary conditions that allow for their conservation in the presence of a boundary. The boundary term is added to the Lagrangian and the vacuum is reexamined in the half line case. The reflection process of solitons from the boundary is studied and the time-delay is calculated. Finally we address the existence of boundary-bound states. In the fourth chapter we study the quantum complex sine-Gordon model. We begin with a brief overview of the theory in

Sine-Gordon breather form factors and quantum field equations

International Nuclear Information System (INIS)

Babujian, H; Karowski, M

2002-01-01

Using the results of previous investigations on sine-Gordon form factors, exact expressions of all breather matrix elements are obtained for several operators: all powers of the fundamental Bose field, general exponentials of it, the energy-momentum tensor and all higher currents. Formulae for the asymptotic behaviour of bosonic form factors are presented which are motivated by Weinberg's power counting theorem in perturbation theory. It is found that the quantum sine-Gordon field equation holds, and an exact relation between the 'bare' mass and the renormalized mass is obtained. Also a quantum version of a classical relation for the trace of the energy-momentum is proved. The eigenvalue problem for all higher conserved charges is solved. All results are compared with perturbative Feynman graph expansions and full agreement is found

Astronaut Gordon Cooper in centrifuge for tests

Science.gov (United States)

1963-01-01

Astronaut L. Gordon Cooper, prime pilot for the Mercury-Atlas 9 mission, is strapped into the gondola while undergoing tests in the centrifuge at the Naval Air Development Center, Johnsville, Pennsylvania. The centrifuge is used to investigate by simulation the pilot's capability to control the vehicle during the actual flight in its booster and reentry profile.

Engineering the spatial organization of metabolic pathways

DEFF Research Database (Denmark)

Albertsen, Line; Maury, Jerome; Bach, Lars Stougaard

One of the goals of metabolic engineering is to optimize the production of valuable metabolites in cell factories. In this context, modulating the gene expression and activity of enzymes are tools that have been extensively used. Another approach that is gaining interest is the engineering...... of the spatial organization of biosynthetic pathways. Several natural systems for ensuring optimal spatial arrangement of biosynthetic enzymes exist. Sequentially acting enzymes can for example be positioned in close proximity by attachment to cellular structures, up-concentration in membrane enclosed organelles...... or assembly into large complexes. The vision is that by positioning sequentially acting enzymes in close proximity, the cell can accelerate reaction rates and thereby prevent loss of intermediates through diffusion, degradation or competing pathways. The production of valuable metabolites in cell factories...

NLIE of Dirichlet sine-Gordon model for boundary bound states

International Nuclear Information System (INIS)

Ahn, Changrim; Bajnok, Zoltan; Palla, Laszlo; Ravanini, Francesco

2008-01-01

We investigate boundary bound states of sine-Gordon model on the finite-size strip with Dirichlet boundary conditions. For the purpose we derive the nonlinear integral equation (NLIE) for the boundary excited states from the Bethe ansatz equation of the inhomogeneous XXZ spin 1/2 chain with boundary imaginary roots discovered by Saleur and Skorik. Taking a large volume (IR) limit we calculate boundary energies, boundary reflection factors and boundary Luescher corrections and compare with the excited boundary states of the Dirichlet sine-Gordon model first considered by Dorey and Mattsson. We also consider the short distance limit and relate the IR scattering data with that of the UV conformal field theory

Systems biology and metabolic engineering of lactic acid bacteria for improved fermented foods

NARCIS (Netherlands)

Flahaut, N.A.L.; Vos, de W.M.

2014-01-01

Lactic acid bacteria have long been used in industrial dairy and other food fermentations that make use of their metabolic activities leading to products with specific organoleptic properties. Metabolic engineering is a rational approach to steer fermentations toward the production of desired

Metabolic engineering of Candida glabrata for diacetyl production.

Directory of Open Access Journals (Sweden)

Xiang Gao

Full Text Available In this study, Candida glabrata, an efficient pyruvate-producing strain, was metabolically engineered for the production of the food ingredient diacetyl. A diacetyl biosynthetic pathway was reconstructed based on genetic modifications and medium optimization. The former included (i channeling carbon flux into the diacetyl biosynthetic pathway by amplification of acetolactate synthase, (ii elimination of the branched pathway of α-acetolactate by deleting the ILV5 gene, and (iii restriction of diacetyl degradation by deleting the BDH gene. The resultant strain showed an almost 1∶1 co-production of α-acetolactate and diacetyl (0.95 g L(-1. Furthermore, addition of Fe3+ to the medium enhanced the conversion of α-acetolactate to diacetyl and resulted in a two-fold increase in diacetyl production (2.1 g L(-1. In addition, increased carbon flux was further channeled into diacetyl biosynthetic pathway and a titer of 4.7 g L(-1 of diacetyl was achieved by altering the vitamin level in the flask culture. Thus, this study illustrates that C. glabrata could be tailored as an attractive platform for enhanced biosynthesis of beneficial products from pyruvate by metabolic engineering strategies.

Arbitrarily large numbers of kink internal modes in inhomogeneous sine-Gordon equations

Energy Technology Data Exchange (ETDEWEB)

González, J.A., E-mail: jalbertgonz@yahoo.es [Department of Physics, Florida International University, Miami, FL 33199 (United States); Department of Natural Sciences, Miami Dade College, 627 SW 27th Ave., Miami, FL 33135 (United States); Bellorín, A., E-mail: alberto.bellorin@ucv.ve [Escuela de Física, Facultad de Ciencias, Universidad Central de Venezuela, Apartado Postal 47586, Caracas 1041-A (Venezuela, Bolivarian Republic of); García-Ñustes, M.A., E-mail: monica.garcia@pucv.cl [Instituto de Física, Pontificia Universidad Católica de Valparaíso, Casilla 4059 (Chile); Guerrero, L.E., E-mail: lguerre@usb.ve [Departamento de Física, Universidad Simón Bolívar, Apartado Postal 89000, Caracas 1080-A (Venezuela, Bolivarian Republic of); Jiménez, S., E-mail: s.jimenez@upm.es [Departamento de Matemática Aplicada a las TT.II., E.T.S.I. Telecomunicación, Universidad Politécnica de Madrid, 28040-Madrid (Spain); Vázquez, L., E-mail: lvazquez@fdi.ucm.es [Departamento de Matemática Aplicada, Facultad de Informática, Universidad Complutense de Madrid, 28040-Madrid (Spain)

2017-06-28

We prove analytically the existence of an infinite number of internal (shape) modes of sine-Gordon solitons in the presence of some inhomogeneous long-range forces, provided some conditions are satisfied. - Highlights: • We have found exact kink solutions to the perturbed sine-Gordon equation. • We have been able to study analytically the kink stability problem. • A kink equilibrated by an exponentially-localized perturbation has a finite number of oscillation modes. • A sufficiently broad equilibrating perturbation supports an infinite number of soliton internal modes.

Hydrogen production and metabolic flux analysis of metabolically engineered Escherichia coli strains

Energy Technology Data Exchange (ETDEWEB)

Kim, Seohyoung; Seol, Eunhee; Park, Sunghoon [Department of Chemical and Biochemical Engineering, Pusan National University, Busan 609-735 (Korea); Oh, You-Kwan [Bioenergy Research Center, Korea Institute of Energy Research, Daejeon 305-543 (Korea); Wang, G.Y. [Department of Oceanography, University of Hawaii at Manoa Honolulu, HI 96822 (United States)

2009-09-15

Escherichia coli can produce H{sub 2} from glucose via formate hydrogen lyase (FHL). In order to improve the H{sub 2} production rate and yield, metabolically engineered E. coli strains, which included pathway alterations in their H{sub 2} production and central carbon metabolism, were developed and characterized by batch experiments and metabolic flux analysis. Deletion of hycA, a negative regulator for FHL, resulted in twofold increase of FHL activity. Deletion of two uptake hydrogenases (1 (hya) and hydrogenase 2 (hyb)) increased H{sub 2} production yield from 1.20 mol/mol glucose to 1.48 mol/mol glucose. Deletion of lactate dehydrogenase (ldhA) and fumarate reductase (frdAB) further improved the H{sub 2} yield; 1.80 mol/mol glucose under high H{sub 2} pressure or 2.11 mol/mol glucose under reduced H{sub 2} pressure. Several batch experiments at varying concentrations of glucose (2.5-10 g/L) and yeast extract (0.3 or 3.0 g/L) were conducted for the strain containing all these genetic alternations, and their carbon and energy balances were analyzed. The metabolic flux analysis revealed that deletion of ldhA and frdAB directed most of the carbons from glucose to the glycolytic pathway leading to H{sub 2} production by FHL, not to the pentose phosphate pathway. (author)

Genome and metabolic engineering in non-conventional yeasts: Current advances and applications.

Science.gov (United States)

Löbs, Ann-Kathrin; Schwartz, Cory; Wheeldon, Ian

2017-09-01

Microbial production of chemicals and proteins from biomass-derived and waste sugar streams is a rapidly growing area of research and development. While the model yeast Saccharomyces cerevisia e is an excellent host for the conversion of glucose to ethanol, production of other chemicals from alternative substrates often requires extensive strain engineering. To avoid complex and intensive engineering of S. cerevisiae, other yeasts are often selected as hosts for bioprocessing based on their natural capacity to produce a desired product: for example, the efficient production and secretion of proteins, lipids, and primary metabolites that have value as commodity chemicals. Even when using yeasts with beneficial native phenotypes, metabolic engineering to increase yield, titer, and production rate is essential. The non-conventional yeasts Kluyveromyces lactis, K. marxianus, Scheffersomyces stipitis, Yarrowia lipolytica, Hansenula polymorpha and Pichia pastoris have been developed as eukaryotic hosts because of their desirable phenotypes, including thermotolerance, assimilation of diverse carbon sources, and high protein secretion. However, advanced metabolic engineering in these yeasts has been limited. This review outlines the challenges of using non-conventional yeasts for strain and pathway engineering, and discusses the developed solutions to these problems and the resulting applications in industrial biotechnology.

Rotationally symmetric breather-like solutions to the sine-Gordon equation

International Nuclear Information System (INIS)

Olsen, O.H.; Samuelsen, M.R.

1980-01-01

Breather-like solutions to the spherically symmetric sine-Gordon equation are examined numerically. Depending on the initial conditions they either exhibit a return effect or expand towards infinity. (orig.)

Solutions of the finite type of Sine-Gordon equation

International Nuclear Information System (INIS)

Zhao Guosong

1998-01-01

We use the technique of differential geometry to prove that the solutions of finite type of the sine-Gordon equation φ xx - φ yy = sin φ cosφ can be obtained from a system of ordinary differential equations

Metabolic Engineering for Production of Biorenewable Fuels and Chemicals: Contributions of Synthetic Biology

Directory of Open Access Journals (Sweden)

Laura R. Jarboe

2010-01-01

Full Text Available Production of fuels and chemicals through microbial fermentation of plant material is a desirable alternative to petrochemical-based production. Fermentative production of biorenewable fuels and chemicals requires the engineering of biocatalysts that can quickly and efficiently convert sugars to target products at a cost that is competitive with existing petrochemical-based processes. It is also important that biocatalysts be robust to extreme fermentation conditions, biomass-derived inhibitors, and their target products. Traditional metabolic engineering has made great advances in this area, but synthetic biology has contributed and will continue to contribute to this field, particularly with next-generation biofuels. This work reviews the use of metabolic engineering and synthetic biology in biocatalyst engineering for biorenewable fuels and chemicals production, such as ethanol, butanol, acetate, lactate, succinate, alanine, and xylitol. We also examine the existing challenges in this area and discuss strategies for improving biocatalyst tolerance to chemical inhibitors.

Quantum conserved charges in N=1 and N=2 supersymmetric sine-Gordon theories

International Nuclear Information System (INIS)

Kobayashi, Ken-ichiro; Uematsu, Tsuneo; Yu Yangzheng

1993-01-01

We investigate quantum conservation laws in the N=1 and N=2 supersymmetric sine-Gordon theories. We study conserved charges at the quantum level based on perturbation theory formulated in superspace. It will turn out that there exist extra conserved charges of the vertex operator type at the quantum level and they generate a quantum group symmetry in supersymmetric sine-Gordon systems. We also discuss the implication of the quantum group symmetry on the S-matrix structure. (orig.)

Metabolic Engineering of Microorganisms for the Production of Higher Alcohols

Science.gov (United States)

Choi, Yong Jun; Lee, Joungmin; Jang, Yu-Sin

2014-01-01

ABSTRACT Due to the increasing concerns about limited fossil resources and environmental problems, there has been much interest in developing biofuels from renewable biomass. Ethanol is currently used as a major biofuel, as it can be easily produced by existing fermentation technology, but it is not the best biofuel due to its low energy density, high vapor pressure, hygroscopy, and incompatibility with current infrastructure. Higher alcohols, including 1-propanol, 1-butanol, isobutanol, 2-methyl-1-butanol, and 3-methyl-1-butanol, which possess fuel properties more similar to those of petroleum-based fuel, have attracted particular interest as alternatives to ethanol. Since microorganisms isolated from nature do not allow production of these alcohols at high enough efficiencies, metabolic engineering has been employed to enhance their production. Here, we review recent advances in metabolic engineering of microorganisms for the production of higher alcohols. PMID:25182323

Non-photosynthetic plastids as hosts for metabolic engineering

DEFF Research Database (Denmark)

Mellor, Silas Busck; Behrendorff, James Bruce Yarnton H; Nielsen, Agnieszka Janina Zygadlo

2018-01-01

Using plants as hosts for production of complex, high-value compounds and therapeutic proteins has gained increasing momentum over the past decade. Recent advances in metabolic engineering techniques using synthetic biology have set the stage for production yields to become economically attractive......, but more refined design strategies are required to increase product yields without compromising development and growth of the host system. The ability of plant cells to differentiate into various tissues in combination with a high level of cellular compartmentalization represents so far the most...... in green tissues, have proven to be suitable for high yield protein and bio-compound production. Unfortunately, chloroplast manipulation often affects photosynthetic efficiency and therefore plant fitness. In this respect, plastids of non-photosynthetic tissues, which have focused metabolisms for synthesis...

Metabollic Engineering of Saccharomyces Cereviae a,omi acid metabolism for production of products of industrial interest

DEFF Research Database (Denmark)

Chen, Xiao

-based processes. This study has focused on metabolic engineering of the amino acid metabolism in S. cerevisiae for production of two types of chemicals of industrial interest. The first chemical is δ-(L-α-aminoadipyl)–L-cysteinyl–D-valine (LLD-ACV). ACV belongs to non-ribosomal peptides (NRPs), which......Saccharomyces cerevisiae is widely used in microbial production of chemicals, metabolites and proteins, mainly because genetic manipulation of S. cerevisiae is relatively easy and experiences from its wide application in the existing industrial fermentations directly benefit new S. cerevisiae...

Research Ship Robert Gordon Sproul Underway Meteorological Data, Quality Controlled

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — Research Ship Robert Gordon Sproul Underway Meteorological Data (delayed ~10 days for quality control) are from the Shipboard Automated Meteorological and...

The general Klein-Gordon-Schroedinger system: modulational instability and exact solutions

International Nuclear Information System (INIS)

Tang Xiaoyan; Ding Wei

2008-01-01

The general Klein-Gordon-Schroedinger (gKGS) system is studied where the cubic auto-interactions are introduced in both the nonlinear Schroedinger and the nonlinear Klein-Gordon fields. We first investigate the modulational instability (MI) of the system, and thus derive the general dispersion relation between the frequency and wavenumber of the modulating perturbations, which demonstrates many possibilities for the MI regions. Using the travelling wave reduction, the gKGS system is greatly simplified. Via a simple function expansion method, we obtain some exact travelling wave solutions. Under some special parameter values, some representative wave structures are graphically displayed including the kink, anti-kink, bright, dark, grey and periodic solitons

Analytical solutions for Dirac and Klein-Gordon equations using Backlund transformations

Energy Technology Data Exchange (ETDEWEB)

Zabadal, Jorge R.; Borges, Volnei, E-mail: jorge.zabadal@ufrgs.br, E-mail: borges@ufrgs.br [Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil). Dept. de Engenharia Mecanica; Ribeiro, Vinicius G., E-mail: vinicius_ribeiro@uniritter.edu.br [Centro Universitario Ritter dos Reis (UNIRITTER), Porto Alegre, RS (Brazil); Santos, Marcio, E-mail: marciophd@gmail.com [Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS (Brazil). Centro de Estudos Interdisciplinares

2015-07-01

This work presents a new analytical method for solving Klein-Gordon type equations via Backlund transformations. The method consists in mapping the Klein-Gordon model into a first order system of partial differential equations, which contains a generalized velocity field instead of the Dirac matrices. This system is a tensor model for quantum field theory whose space solution is wider than the Dirac model in the original form. Thus, after finding analytical expressions for the wave functions, the Maxwell field can be readily obtained from the Dirac equations, furnishing a self-consistent field solution for the Maxwell-Dirac system. Analytical and numerical results are reported. (author)

Metabolic engineering of microorganisms for biofuels production: from bugs to synthetic biology to fuels

Energy Technology Data Exchange (ETDEWEB)

Kuk Lee, Sung; Chou, Howard; Ham, Timothy S.; Soon Lee, Taek; Keasling, Jay D.

2009-12-02

The ability to generate microorganisms that can produce biofuels similar to petroleum-based transportation fuels would allow the use of existing engines and infrastructure and would save an enormous amount of capital required for replacing the current infrastructure to accommodate biofuels that have properties significantly different from petroleum-based fuels. Several groups have demonstrated the feasibility of manipulating microbes to produce molecules similar to petroleum-derived products, albeit at relatively low productivity (e.g. maximum butanol production is around 20 g/L). For cost-effective production of biofuels, the fuel-producing hosts and pathways must be engineered and optimized. Advances in metabolic engineering and synthetic biology will provide new tools for metabolic engineers to better understand how to rewire the cell in order to create the desired phenotypes for the production of economically viable biofuels.

Perturbation analysis of a parametrically changed sine-Gordon equation

DEFF Research Database (Denmark)

Sakai, S.; Samuelsen, Mogens Rugholm; Olsen, O. H.

1987-01-01

A long Josephson junction with a spatially varying inductance is a physical manifestation of a modified sine-Gordon equation with parametric perturbation. Soliton propagation in such Josephson junctions is discussed. First, for an adiabatic model where the inductance changes smoothly compared...

NOAA Ship Gordon Gunter Underway Meteorological Data, Near Real Time

Data.gov (United States)

National Oceanic and Atmospheric Administration, Department of Commerce — NOAA Ship Gordon Gunter Underway Meteorological Data (Near Real Time, updated daily) are from the Shipboard Automated Meteorological and Oceanographic System (SAMOS)...

From pathways to genomes and beyond. The metabolic engineering toolbox and its place in biofuels production

Energy Technology Data Exchange (ETDEWEB)

Liu, Leqian; Reed, Ben; Alper, Hal [Texas Univ., Austin, TX (United States). Dept. of Chemical Engineering

2011-07-01

Concerns about the availability of petroleum-derived fuels and chemicals have led to the exploration of metabolically engineered organisms as novel hosts for biofuels and chemicals production. However, the complexity inherent in metabolic and regulatory networks makes this undertaking a complex task. To address these limitations, metabolic engineering has adapted a wide-variety of tools for altering phenotypes. In this review, we will highlight traditional and recent metabolic engineering tools for optimizing cells including pathway-based, global, and genomic-enabled approaches. Specifically, we describe these tools as well as provide demonstrations of their effectiveness in optimizing biofuels production. However, each of these tools provides stepping stones towards the grand goal of biofuels production. Thus, developing methods for large-scale cellular optimization and integrative approaches are invaluable for further cell optimization. This review highlights the challenges that still must be met to accomplish this goal. (orig.)

Strange culinary encounters::stranger fetichism in "Jamie's Italian escape" and "Gordon's great escape"

OpenAIRE

Leer, Jonatan; Kjær, Katrine Meldgaard

2015-01-01

In this article, we examine the ways in which the encountering of 'other' food cultures is played out in the two travelogue cooking shows Gordon's Great Escape and Jamie's Italian Escape. We investigate how the two protagonist chefs Jamie Oliver and Gordon Ramsay imagine, meet and evaluate the ‘other’ food cultures in these programs, paying special attention to how the encounter with the local Indian and Italian is imagined to be a gateway to an authentic and/or primitive experience. Our main...

Metabolically engineered cells for the production of polyunsaturated fatty acids

DEFF Research Database (Denmark)

2005-01-01

The present invention relates to the construction and engineering of cells, more particularly microorganisms for producing PUFAs with four or more double bonds from non-fatty acid substrates through heterologous expression of an oxygen requiring pathway. The invention especially involves...... improvement of the PUFA content in the host organism through fermentation optimization, e.g. decreasing the temperature and/or designing an optimal medium, or through improving the flux towards fatty acids by metabolic engineering, e.g. through over-expression of fatty acid synthases, over-expression of other...

On Darboux transformation of the supersymmetric sine-Gordon equation

International Nuclear Information System (INIS)

Siddiq, M; Hassan, M; Saleem, U

2006-01-01

Darboux transformation is constructed for superfields of the super sine-Gordon equation and the superfields of the associated linear problem. The Darboux transformation is shown to be related to the super Baecklund transformation and is further used to obtain N super soliton solutions

Gordon Brown. Raudne minister istub peaministri toolile / Jürgen Tamme

Index Scriptorium Estoniae

Tamme, Jürgen

2007-01-01

Ilmunud ka: Postimees : na russkom jazõke 29. juuni lk. 8. Suurbritannia valitsuse rahandusministri Gordon Browni saamisest Tööpartei esimeheks ja peaministriks, tema elukäigust, haridusteest ning poliitikukarjäärist

Gender differences in ozone-induced pulmonary and metabolic health effects

Science.gov (United States)

SOT 2015 abstractGender differences in ozone-induced pulmonary and metabolic health effectsU.P. Kodavanti1, V.L. Bass2, M.C. Schladweiler1, C.J. Gordon3, K.A. Jarema3, P. Phillips3, A.D. Ledbetter1, D.B. Miller4, S. Snow5, J.E. Richards1. 1 EPHD, NHEERL, USEPA, Research Triangle ...

Toward systems metabolic engineering of Aspergillus and Pichia species for the production of chemicals and biofuels

DEFF Research Database (Denmark)

Caspeta, Luis; Nielsen, Jens

2013-01-01

trends in systems biology of Aspergillus and Pichia species, highlighting the relevance of these developments for systems metabolic engineering of these organisms for the production of hydrolytic enzymes, biofuels and chemicals from biomass. Metabolic engineering is moving from traditional methods...... for the production of hydrolytic enzymes, biofuels and chemicals from biomass. © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim....

Resveratrol biosynthesis: plant metabolic engineering for nutritional improvement of food.

Science.gov (United States)

Giovinazzo, Giovanna; Ingrosso, Ilaria; Paradiso, Annalisa; De Gara, Laura; Santino, Angelo

2012-09-01

The plant polyphenol trans-resveratrol (3, 5, 4'-trihydroxystilbene) mainly found in grape, peanut and other few plants, displays a wide range of biological effects. Numerous in vitro studies have described various biological effects of resveratrol. In order to provide more information regarding absorption, metabolism, and bioavailability of resveratrol, various research approaches have been performed, including in vitro, ex vivo, and in vivo models. In recent years, the induction of resveratrol synthesis in plants which normally do not accumulate such polyphenol, has been successfully achieved by molecular engineering. In this context, the ectopic production of resveratrol has been reported to have positive effects both on plant resistance to biotic stress and the enhancement of the nutritional value of several widely consumed fruits and vegetables. The metabolic engineering of plants offers the opportunity to change the content of specific phytonutrients in plant - derived foods. This review focuses on the latest findings regarding on resveratrol bioproduction and its effects on the prevention of the major pathological conditions in man.

Numerical simulation of the self-pumped long Josephson junction using a modified sine-Gordon model

International Nuclear Information System (INIS)

Sobolev, A.S.; Pankratov, A.L.; Mygind, J.

2006-01-01

We have numerically investigated the dynamics of a long Josephson junction (flux-flow oscillator) biased by a DC current in the presence of magnetic field. The study is performed in the frame of the modified sine-Gordon model, which includes the surface losses, RC-load at both FFO ends and the self-pumping effect. In our model the dumping parameter depends both on the spatial coordinate and the amplitude of the AC voltage. In order to find the DC FFO voltage the damping parameter has to be calculated by successive approximations and time integration of the perturbed sine-Gordon equation. The modified model, which accounts for the presence of the superconducting gap, gives better qualitative agreement with experimental results compare to the conventional sine-Gordon model

Solutions of the lattice sine–Gordon equation and the solitons of its cellular automaton

International Nuclear Information System (INIS)

Willox, R; Ramani, A; Grammaticos, B

2014-01-01

We analyse the solutions of the cellular automaton sine–Gordon equation and link them to solutions of the discrete, lattice, sine–Gordon. We show that while the ultradiscretizable, positive definite, solutions of the latter behave dispersively, certain parts of these dispersive waves nonetheless survive in the ultradiscrete limit, giving rise to the solutions of the cellular automaton. We examine the ultradiscrete solutions in the case of a generalized cellular automaton in which the dependent variable can assume non-integer values and we show that the collision of two solitary waves is inelastic, leading to the creation of a ‘bridge’ of constant height that links two outgoing structures. Based on the ultradiscrete form of the sine–Gordon equation we explain the appearance of this bridging region and we describe its interaction with a solitary wave. (paper)

Intermittent Switching between Soliton Dynamic States in a Perturbed Sine-Gordon Model

DEFF Research Database (Denmark)

Sørensen, Mads Peter; Arley, N.; Christiansen, Peter Leth

1983-01-01

Chaotic intermittency between soliton dynamic states has been found in a perturbed sine-Gordon system in the absence of an external ac driving term. The system is a model of a long Josephson oscillator with constant loss and bias current in an external magnetic field. The results predict the exis......Chaotic intermittency between soliton dynamic states has been found in a perturbed sine-Gordon system in the absence of an external ac driving term. The system is a model of a long Josephson oscillator with constant loss and bias current in an external magnetic field. The results predict...

Roughening in random sine-Gordon systems

International Nuclear Information System (INIS)

Schwartz, M.; Nattermann, T.

1991-01-01

We consider the spatial correlations of the optimal solutions of the random sine-Gordon equation as an example of the usefulness of a very simple ansatz relating the Fourier transforms of certain functions of the field Φ to the Fourier transform of the random fields. The dramatic change in the correlations when going from above to below two dimensions is directly attributed to the transfer from dominance of long range fluctuations of the randomness to the dominance of short range fluctuations. (orig.)

Production of biopharmaceutical proteins by yeast: Advances through metabolic engineering

DEFF Research Database (Denmark)

Nielsen, Jens

2013-01-01

Production of recombinant proteins for use as pharmaceuticals, so-called biopharmaceuticals, is a multi-billion dollar industry. Many different cell factories are used for the production of biopharmaceuticals, but the yeast Saccharomyces cerevisiae is an important cell factory as it is used for p...... production. The involvement of directed metabolic engineering through the integration of tools from genetic engineering, systems biology and mathematical modeling, is also discussed....... by yeast are human serum albumin, hepatitis vaccines and virus like particles used for vaccination against human papillomavirus. Here is given a brief overview of biopharmaceutical production by yeast and it is discussed how the secretory pathway can be engineered to ensure more efficient protein...

Genome and metabolic engineering in non-conventional yeasts: Current advances and applications

Directory of Open Access Journals (Sweden)

Ann-Kathrin Löbs

2017-09-01

Full Text Available Microbial production of chemicals and proteins from biomass-derived and waste sugar streams is a rapidly growing area of research and development. While the model yeast Saccharomyces cerevisiae is an excellent host for the conversion of glucose to ethanol, production of other chemicals from alternative substrates often requires extensive strain engineering. To avoid complex and intensive engineering of S. cerevisiae, other yeasts are often selected as hosts for bioprocessing based on their natural capacity to produce a desired product: for example, the efficient production and secretion of proteins, lipids, and primary metabolites that have value as commodity chemicals. Even when using yeasts with beneficial native phenotypes, metabolic engineering to increase yield, titer, and production rate is essential. The non-conventional yeasts Kluyveromyces lactis, K. marxianus, Scheffersomyces stipitis, Yarrowia lipolytica, Hansenula polymorpha and Pichia pastoris have been developed as eukaryotic hosts because of their desirable phenotypes, including thermotolerance, assimilation of diverse carbon sources, and high protein secretion. However, advanced metabolic engineering in these yeasts has been limited. This review outlines the challenges of using non-conventional yeasts for strain and pathway engineering, and discusses the developed solutions to these problems and the resulting applications in industrial biotechnology.

Biobased production of alkanes and alkenes through metabolic engineering of microorganisms

OpenAIRE

Kang, Min Kyoung; Nielsen, Jens

2017-01-01

Advancement in metabolic engineering of microorganisms has enabled bio-based production of a range of chemicals, and such engineered microorganism can be used for sustainable production leading to reduced carbon dioxide emission there. One area that has attained much interest is microbial hydrocarbon biosynthesis, and in particular, alkanes and alkenes are important high-value chemicals as they can be utilized for a broad range of industrial purposes as well as ?drop-in? biofuels. Some microo...

Sine-Gordon quantum field theory on the half-line with quantum boundary degrees of freedom

International Nuclear Information System (INIS)

Baseilhac, P.; Koizumi, K.

2003-01-01

The sine-Gordon model on the half-line with a dynamical boundary introduced by Delius and one of the authors is considered at quantum level. Classical boundary conditions associated with classical integrability are shown to be preserved at quantum level too. Non-local conserved charges are constructed explicitly in terms of the field and boundary operators. We solve the intertwining equation associated with a certain coideal subalgebra of U q (sl 2 -bar) generated by these non-local charges. The corresponding solution is shown to satisfy quantum boundary Yang-Baxter equations. Up to an exact relation between the quantization length of the boundary quantum mechanical system and the sine-Gordon coupling constant, we conjecture the soliton/antisoliton reflection matrix and bound states reflection matrices. The structure of the boundary state is then considered, and shown to be divided in two sectors. Also, depending on the sine-Gordon coupling constant a finite set of boundary bound states are identified. Taking the analytic continuation of the coupling, the corresponding boundary sinh-Gordon model is briefly discussed. In particular, the particle reflection factor enjoys weak-strong coupling duality

Homoclinic tubes and chaos in perturbed sine-Gordon equation

International Nuclear Information System (INIS)

Li, Y. Charles

2004-01-01

Sine-Gordon equation under a quasi-periodic perturbation or a chaotic perturbation is studied. Existence of a homoclinic tube is proved. Established are chaos associated with the homoclinic tube, and 'chaos cascade' referring to the embeddings of smaller scale chaos in larger scale chaos

Rotationally symmetric numerical solutions to the sine-Gordon equation

DEFF Research Database (Denmark)

Olsen, O. H.; Samuelsen, Mogens Rugholm

1981-01-01

We examine numerically the properties of solutions to the spherically symmetric sine-Gordon equation given an initial profile which coincides with the one-dimensional breather solution and refer to such solutions as ring waves. Expanding ring waves either exhibit a return effect or expand towards...

Is the energy density of the ground state of the sine-Gordon model unbounded from below for β2 > 8π?

International Nuclear Information System (INIS)

Faber, M; Ivanov, A N

2003-01-01

We discuss Coleman's theorem concerning the energy density of the ground state of the sine-Gordon model proved in Coleman S (1975 Phys. Rev. D 11 2088). According to this theorem the energy density of the ground state of the sine-Gordon model should be unbounded from below for coupling constants β 2 > 8π. The consequence of this theorem would be the non-existence of the quantum ground state of the sine-Gordon model for β 2 > 8π. We show that the energy density of the ground state in the sine-Gordon model is bounded from below even for β 2 > 8π. This result is discussed in relation to Coleman's theorem (Coleman S 1973 Commun. Math. Phys. 31 259), particle mass spectra and soliton-soliton scattering in the sine-Gordon model

'National Hero and Very Queer Fish': Empire, Sexuality and the British Remembrance of General Gordon, 1918-72.

Science.gov (United States)

Jones, Max

2015-01-01

This article presents the first detailed study of General Gordon's remembrance in Britain between 1918 and 1972. Previous scholars have exaggerated the impact of Lytton Strachey's Eminent Victorians (1918). Strachey damaged Gordon's reputation, but part one reveals how several commentators forcefully rebutted Eminent Victorians; official commemorations, books, radio plays, and films celebrated Gordon in the 1930s, as empire featured prominently in mass culture. Didactic uses of his example by the state diminished after 1945, but parts 2 and 3 show how writers used Gordon's story to engage with new debates about Britain's role in the world, immigration and sexuality. The article reveals how a fascination with the sexuality of heroes inspired men as diverse as Viscount Robin Maugham and East End gangster Ronnie Kray to identify with Gordon. Maugham's works and the feature film Khartoum (1966) expressed nostalgia for empire during decolonization, but American screenwriter Robert Ardrey also drew on his experiences in the Congo to present a dark vision of African savagery in Khartoum, a vision performed at Pinewood studios by black immigrants from London's slums. The article questions Edward Berenson's emphasis on the 'charismatic aura' of heroes, emphasizing instead the diversity of engagements inspired through different genre.

Hydrodynamic representation of the Klein-Gordon-Einstein equations in the weak field limit

International Nuclear Information System (INIS)

Suárez, Abril; Chavanis, Pierre-Henri

2015-01-01

Using a generalization of the Madelung transformation, we derive the hydrodynamic representation of the Klein-Gordon-Einstein equations in the weak field limit. We consider a complex self-interacting scalar field with an arbitrary potential of the form V(|ϕ| 2 ). We compare the results with simplified models in which the gravitational potential is introduced by hand in the Klein-Gordon equation, and assumed to satisfy a (generalized) Poisson equation. Nonrelativistic hydrodynamic equations based on the Schrodinger-Poisson equations or on the Gross-Pitaevskii-Poisson equations are recovered in the limit c → +∞. (paper)

Fredholm determinant representation of quantum correlation function for Sine-Gordon at special value of coupling constant

International Nuclear Information System (INIS)

Itoyama, H.; Korepin, V.E.; Thacker, H.B.

1992-01-01

In this paper, correlation functions of the Sine-Gordon model (which is equivalent of the Massive-Thirring model) are considered at the free fermion point. The authors derive a determinant formula for local correlation functions of the Sine-Gordon model, starting form Bethe ansatz wave function. Kernel of integral operator is trigonometric version of the one for Impenetrable Bosons

Metabolic engineering of Ustilago trichophora TZ1 for improved malic acid production

Directory of Open Access Journals (Sweden)

Thiemo Zambanini

2017-06-01

These results open up a wide range of possibilities for further optimization, especially combinatorial metabolic engineering to increase the flux from pyruvate to malic acid and to reduce by-product formation.

In-silico-driven metabolic engineering of Pseudomonas putida for enhanced production of poly-hydroxyalkanoates

NARCIS (Netherlands)

Poblete-Castro, I.; Binger, D.; Rodrigues, A.; Becker, J.; Martins Dos Santos, V.A.P.; Wittmann, C.

2013-01-01

Here, we present systems metabolic engineering driven by in-silico modeling to tailor Pseudomonas putida for synthesis of medium chain length PHAs on glucose. Using physiological properties of the parent wild type as constraints, elementary flux mode analysis of a large-scale model of the metabolism

Thermal sine-Gordon system in the presence of different types of dissipation

DEFF Research Database (Denmark)

Salerno, M.; Samuelsen, Mogens Rugholm; Svensmark, Henrik

1988-01-01

The effects of thermal fluctuations on solitons and phonons of the sine-Gordon system are investigated in the presence of a αφt-βφxxt dissipation. The analysis requires the assumption of a more general autocorrelation function for the noise than the one used in previous works. We verify that this......The effects of thermal fluctuations on solitons and phonons of the sine-Gordon system are investigated in the presence of a αφt-βφxxt dissipation. The analysis requires the assumption of a more general autocorrelation function for the noise than the one used in previous works. We verify...

Metabolic engineering of free-energy (ATP) conserving reactions in Saccharomyces cerevisiae

NARCIS (Netherlands)

De Kok, S.

2012-01-01

Metabolic engineering – the improvement of cellular activities by manipulation of enzymatic, transport and regulatory functions of the cell – has enabled the industrial production of a wide variety of biological molecules from renewable resources. Microbial production of fuels and chemicals thereby

From sine-Gordon to vacuumless systems in flat and curved spacetimes

Energy Technology Data Exchange (ETDEWEB)

Bazeia, D.; Moreira, D.C. [Universidade Federal da Paraiba, Departamento de Fisica, Joao Pessoa, PB (Brazil)

2017-12-15

In this work we start from the Higgs prototype model to introduce a new model, which makes a smooth transition between systems with well-located minima and systems that support no minima at all. We implement this possibility using the deformation procedure, which allows the obtaining a sine-Gordon-like model, controlled by a real parameter that gives rise to a family of models, reproducing the sine-Gordon and the so-called vacuumless models. We also study the thick brane scenarios associated with these models and investigate their stability and renormalization group flow. In particular, it is shown how gravity can change from the 5-dimensional warped geometry with a single extra dimension of infinite extent to the conventional 5-dimensional Minkowski geometry. (orig.)

Perturbed Coulomb Potentials in the Klein-Gordon Equation: Quasi-Exact Solution

Science.gov (United States)

Baradaran, M.; Panahi, H.

2018-05-01

Using the Lie algebraic approach, we present the quasi-exact solutions of the relativistic Klein-Gordon equation for perturbed Coulomb potentials namely the Cornell potential, the Kratzer potential and the Killingbeck potential. We calculate the general exact expressions for the energies, corresponding wave functions and the allowed values of the parameters of the potential within the representation space of sl(2) Lie algebra. In addition, we show that the considered equations can be transformed into the Heun's differential equations and then we reproduce the results using the associated special functions. Also, we study the special case of the Coulomb potential and show that in the non-relativistic limit, the solution of the Klein-Gordon equation converges to that of Schrödinger equation.

Yeast metabolic engineering--targeting sterol metabolism and terpenoid formation.

Science.gov (United States)

Wriessnegger, Tamara; Pichler, Harald

2013-07-01

Terpenoids comprise various structures conferring versatile functions to eukaryotes, for example in the form of prenyl-anchors they attach proteins to membranes. The physiology of eukaryotic membranes is fine-tuned by another terpenoid class, namely sterols. Evidence is accumulating that numerous membrane proteins require specific sterol structural features for function. Moreover, sterols are intermediates in the synthesis of steroids serving as hormones in higher eukaryotes. Like steroids many compounds of the terpenoid family do not contribute to membrane architecture, but serve as signalling, protective or attractant/repellent molecules. Particularly plants have developed a plenitude of terpenoid biosynthetic routes branching off early in the sterol biosynthesis pathway and, thereby, forming one of the largest groups of naturally occurring organic compounds. Many of these aromatic and volatile molecules are interesting for industrial application ranging from foods to pharmaceuticals. Combining the fortunate situation that sterol biosynthesis is highly conserved in eukaryotes with the amenability of yeasts to genetic and metabolic engineering, basically all naturally occurring terpenoids might be produced involving yeasts. Such engineered yeasts are useful for the study of biological functions and molecular interactions of terpenoids as well as for the large-scale production of high-value compounds, which are unavailable in sufficient amounts from natural sources due to their low abundance. Copyright © 2013 Elsevier Ltd. All rights reserved.

Metabolic engineering of Corynebacterium glutamicum for fermentative production of chemicals in biorefinery.

Science.gov (United States)

Baritugo, Kei-Anne; Kim, Hee Taek; David, Yokimiko; Choi, Jong-Il; Hong, Soon Ho; Jeong, Ki Jun; Choi, Jong Hyun; Joo, Jeong Chan; Park, Si Jae

2018-05-01

Bio-based production of industrially important chemicals provides an eco-friendly alternative to current petrochemical-based processes. Because of the limited supply of fossil fuel reserves, various technologies utilizing microbial host strains for the sustainable production of platform chemicals from renewable biomass have been developed. Corynebacterium glutamicum is a non-pathogenic industrial microbial species traditionally used for L-glutamate and L-lysine production. It is a promising species for industrial production of bio-based chemicals because of its flexible metabolism that allows the utilization of a broad spectrum of carbon sources and the production of various amino acids. Classical breeding, systems, synthetic biology, and metabolic engineering approaches have been used to improve its applications, ranging from traditional amino-acid production to modern biorefinery systems for production of value-added platform chemicals. This review describes recent advances in the development of genetic engineering tools and techniques for the establishment and optimization of metabolic pathways for bio-based production of major C2-C6 platform chemicals using recombinant C. glutamicum.

Confinement, solitons and the equivalence between the sine-Gordon and massive Thirring models

International Nuclear Information System (INIS)

Blas Achic, H.S.; Ferreira, L.A.

2000-01-01

We consider a two-dimensional integrable and conformally invariant field theory possessing two Dirac spinors and three scalar fields. The interaction couples bilinear terms in the spinors to exponentials of the scalars. Its integrability properties are based on the sl(2) affine Kac-Moody algebra, and it is a simple example of the so-called conformal affine Toda theories coupled to matter fields. We show, using bosonization techniques, that the classical equivalence between a U(1) Noether current and the topological current holds true at the quantum level, and then leads to a bag model like mechanism for the confinement of the spinor fields inside the solitons. By bosonizing the spinors we show that the theory decouples into a sine-Gordon model and free scalars. We construct the two-soliton solutions and show that their interactions lead to the same time delays as those for the sine-Gordon solitons. The model provides a good laboratory to test duality ideas in the context of the equivalence between the sine-Gordon and Thirring theories

Metabolic engineering of Saccharomyces cerevisiae: a key cell factory platform for future biorefineries.

Science.gov (United States)

Hong, Kuk-Ki; Nielsen, Jens

2012-08-01

Metabolic engineering is the enabling science of development of efficient cell factories for the production of fuels, chemicals, pharmaceuticals, and food ingredients through microbial fermentations. The yeast Saccharomyces cerevisiae is a key cell factory already used for the production of a wide range of industrial products, and here we review ongoing work, particularly in industry, on using this organism for the production of butanol, which can be used as biofuel, and isoprenoids, which can find a wide range of applications including as pharmaceuticals and as biodiesel. We also look into how engineering of yeast can lead to improved uptake of sugars that are present in biomass hydrolyzates, and hereby allow for utilization of biomass as feedstock in the production of fuels and chemicals employing S. cerevisiae. Finally, we discuss the perspectives of how technologies from systems biology and synthetic biology can be used to advance metabolic engineering of yeast.

The Klein-Gordon Operator on Möbius Strip Domains and the Klein Bottle in ℝn

International Nuclear Information System (INIS)

Kraußhar, Rolf Sören

2013-01-01

In this paper we present explicit formulas for the fundamental solution to the Klein-Gordon operator on some higher dimensional generalizations of the Möbius strip and the Klein bottle with values in distinct pinor bundles. The fundamental solution is described in terms of generalizations of the Weierstrass ℘ -function that are adapted to the context of these geometries. The explicit formulas for the kernel then allow us to express all solutions to the homogeneous and inhomogeneous Klein-Gordon problem with given boundary data in the context of these manifolds. In the case of the Klein bottle we are able to describe all null solutions of the Klein-Gordon equation in terms of finite linear combinations of the fundamental solution and its partial derivatives

Gordon Brown lubab valijal riigieelarvet ümber teha / Siim Trumm

Index Scriptorium Estoniae

Trumm, Siim

2007-01-01

Peaminister Gordon Brown kavandab mitmeid reforme, et viia riigivõim rahvale lähemale. Inglismaa kümne piirkonna inimestele antakse võimalus otsustada rahvahääletuse kaudu kohaliku eelarve jaotamise üle. Lisa: Browni ja leiboristide toetus kasvab

Nonlinear dynamics of a parametrically driven sine-Gordon system

DEFF Research Database (Denmark)

Grønbech-Jensen, Niels; Kivshar, Yuri S.; Samuelsen, Mogens Rugholm

1993-01-01

We consider a sine-Gordon system, driven by an ac parametric force in the presence of loss. It is demonstrated that a breather can be maintained in a steady state at half of the external frequency. In the small-amplitude limit the effect is described by an effective nonlinear Schrodinger equation...

Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals

DEFF Research Database (Denmark)

Jullesson, David; David, Florian; Pfleger, Brian

2015-01-01

Industrial bio-processes for fine chemical production are increasingly relying on cell factories developed through metabolic engineering and synthetic biology. The use of high throughput techniques and automation for the design of cell factories, and especially platform strains, has played...... chemicals that have reached the market, key metabolic engineering tools that have allowed this to happen and some of the companies that are currently utilizing these technologies for developing industrial production processes....... an important role in the transition from laboratory research to industrial production. Model organisms such as Saccharomyces cerevisiae and Escherichia coli remain widely used host strains for industrial production due to their robust and desirable traits. This review describes some of the bio-based fine...

2012 Gordon Research Conference on Microbial Stress Response, Schedule and Speaker/Poster Program

Energy Technology Data Exchange (ETDEWEB)

Donohue, Timothy J. [Univ. of Wisconsin, Madison, WI (United States)

2012-07-20

The Gordon Research Conference on Microbial Stress Response was held at Mount Holyoke College, South Hadley, Massachusetts, July 15-20, 2012. The Conference was well-attended with 180 participants. The 2012 Microbial Stress Responses Gordon Research Conference will provide a forum for the open reporting of recent discoveries on the diverse mechanisms employed by microbes to respond to stress. Approaches range from analysis at the molecular level (how are signals perceived and transmitted to change gene expression or function) to cellular and microbial community responses. Attached is a copy of the formal schedule and speaker program and the poster program.

Covariant form for the conserved currents of the sine-Gordon and Liouville theories

International Nuclear Information System (INIS)

Freedman, D.Z.; Massachusetts Inst. of Tech., Cambridge; Lerda, A.; Massachusetts Inst. of Tech., Cambridge; Penati, S.

1990-01-01

A conserved covariant fourth rank tensor current J μαβγ is constructed for these models both in flat and constant curvature space. For flat space, ∫ dx + J ++++ and its parity conjugate agree with well known results for the lowest grade sine-Gordon conserved charges. However potentially new charges such as ∫ dx + J +++- and ∫ dx + J +++α ε αβ x β either vanish or fail to be conserved because J μαβγ is not symmetric in μ↔γ. There is one curious exception for sine-Gordon models in anti-de Sitter space. (orig.)

Thermodynamic quantities for the Klein–Gordon equation with a ...

Indian Academy of Sciences (India)

2017-02-01

Feb 1, 2017 ... Abstract. We study some thermodynamic quantities for the Klein–Gordon equation with a linear plus inverse- linear, scalar potential. We obtain the energy eigenvalues with the help of the quantization rule from the biconfluent Heun's equation. We use a method based on the Euler–MacLaurin formula to ...

2012 Gordon Research Conference, Organometallic Chemistry, 8-13 2012

Energy Technology Data Exchange (ETDEWEB)

Hillhouse, Gregory [Univ. of Chicago, IL (United States)

2012-07-13

The 2012 Organometallic Chemistry Gordon Research Conference will highlight new basic science and fundamental applications of organometallic chemistry in industrial, academic, and national lab settings. Scientific themes of the conference will include chemical synthesis, reactivity, catalysis, polymer chemistry, bonding, and theory that involve transition-metal (and main-group) interactions with organic moieties.

TBA equations for excited states in the sine-Gordon model

International Nuclear Information System (INIS)

Balog, Janos; Hegedus, Arpad

2004-01-01

We propose thermodynamic Bethe ansatz (TBA) integral equations for multi-particle soliton (fermion) states in the sine-Gordon (massive Thirring) model. This is based on T-system and Y-system equations, which follow from the Bethe ansatz solution in the light-cone lattice formulation of the model. Even and odd charge sectors are treated on an equal footing, corresponding to periodic and twisted boundary conditions, respectively. The analytic properties of the Y-system functions are conjectured on the basis of the large volume solution of the system, which we find explicitly. A simple relation between the TBA Y-functions and the counting function variable of the alternative non-linear integral equation (Destri-de Vega equation) description of the model is given. At the special value β 2 = 6π of the sine-Gordon coupling, exact expressions for energy and momentum eigenvalues of one-particle states are found

Sex differences in diet and inhaled ozone (O3) induced metabolic impairment

Science.gov (United States)

APS 2015 abstract Sex differences in diet and inhaled ozone (O3) induced metabolic impairment U.P. Kodavanti1, V.L. Bass2, M.C. Schladweiler1, C.J. Gordon3, K.A. Jarema1, P. Phillips1, A.D. Ledbetter1, D.B. Miller4, S. Snow5, J.E. Richards1. 1 EPHD, NHEERL, USEPA, Research Triang...

Correlations between chaos in a perturbed sine-Gordon equation and a truncated model system

International Nuclear Information System (INIS)

Bishop, A.R.; Flesch, R.; Forests, M.G.; Overman, E.A.

1990-01-01

The purpose of this paper is to present a first step toward providing coordinates and associated dynamics for low-dimensional attractors in nearly integrable partial differential equations (pdes), in particular, where the truncated system reflects salient geometric properties of the pde. This is achieved by correlating: (1) numerical results on the bifurcations to temporal chaos with spatial coherence of the damped, periodically forced sine-Gordon equation with periodic boundary conditions; (2) an interpretation of the spatial and temporal bifurcation structures of this perturbed integrable system with regard to the exact structure of the sine-Gordon phase space; (3) a model dynamical systems problem, which is itself a perturbed integrable Hamiltonian system, derived from the perturbed sine-Gordon equation by a finite mode Fourier truncation in the nonlinear Schroedinger limit; and (4) the bifurcations to chaos in the truncated phase space. In particular, a potential source of chaos in both the pde and the model ordinary differential equation systems is focused on: the existence of homoclinic orbits in the unperturbed integrable phase space and their continuation in the perturbed problem. The evidence presented here supports the thesis that the chaotic attractors of the weakly perturbed periodic sine-Gordon system consists of low-dimensional metastable attacking states together with intermediate states that are O(1) unstable and correspond to homoclinic states in the integrable phase space. It is surmised that the chaotic dynamics on these attractors is due to the perturbation of these homocline integrable configurations

Exact solutions to some modified sine-Gordon equations

International Nuclear Information System (INIS)

Saermark, K.

1983-01-01

Exact, translational solutions to a number of modified sine-Gordon equations are presented. In deriving the equations and the solutions use is made of results from the theory of ordinary differential equations without moving critical points as given by Ince. It is found that kink-like solutions exist also in cases where the coefficients of the trigonometric terms are space- and time-dependent. (Auth.)

13C Metabolic Flux Analysis for systematic metabolic engineering of S. cerevisiae for overproduction of fatty acids.

Directory of Open Access Journals (Sweden)

Amit Ghosh

2016-10-01

Full Text Available Efficient redirection of microbial metabolism into the abundant production of desired bioproducts remains non-trivial. Here we used flux-based modeling approaches to improve yields of fatty acids in S. cerevisiae. We combined 13C labeling data with comprehensive genome-scale models to shed light onto microbial metabolism and improve metabolic engineering efforts. We concentrated on studying the balance of acetyl-CoA, a precursor metabolite for the biosynthesis of fatty acids. A genome-wide acetyl-CoA balance study showed ATP citrate lyase from Y. lipolytica as a robust source of cytoplasmic acetyl-CoA and malate synthase as a desirable target for down-regulation in terms of acetyl-CoA consumption. These genetic modifications were applied to S. cerevisiae WRY2, a strain that is capable of producing 460 mg L of free fatty acids. With the addition of ATP citrate lyase and down-regulation of malate synthase the engineered strain produced 26 per cent more free fatty acids. Further increases in free fatty acid production of 33 per cent were obtained by knocking out the cytoplasmic glycerol-3-phosphate dehydrogenase, which flux analysis had shown was competing for carbon flux upstream with the carbon flux through the acetyl-CoA production pathway in the cytoplasm. In total, the genetic interventions applied in this work increased fatty acid production by 70 per cent.

Separation Transformation and New Exact Solutions of the (N + 1)-dimensional Dispersive Double sine-Gordon Equation

International Nuclear Information System (INIS)

Tian Ye; Chen Jing; Zhang Zhifei

2012-01-01

In this paper, the separation transformation approach is extended to the (N + 1)-dimensional dispersive double sine-Gordon equation arising in many physical systems such as the spin dynamics in the B phase of 3 He superfluid. This equation is first reduced to a set of partial differential equations and a nonlinear ordinary differential equation. Then the general solutions of the set of partial differential equations are obtained and the nonlinear ordinary differential equation is solved by F-expansion method. Finally, many new exact solutions of the (N + 1)-dimensional dispersive double sine-Gordon equation are constructed explicitly via the separation transformation. For the case of N > 2, there is an arbitrary function in the exact solutions, which may reveal more novel nonlinear structures in the high-dimensional dispersive double sine-Gordon equation.

Metabolic engineering is key to a sustainable chemical industry.

Science.gov (United States)

Murphy, Annabel C

2011-08-01

The depletion of fossil fuel stocks will prohibit their use as the main feedstock of future industrial processes. Biocatalysis is being increasingly used to reduce fossil fuel reliance and to improve the sustainability, efficiency and cost of chemical production. Even with their current small market share, biocatalyzed processes already generate approximately US$50 billion and it has been estimated that they could be used to produce up to 20% of fine chemicals by 2020. Until the advent of molecular biological technologies, the compounds that were readily accessible from renewable biomass were restricted to naturally-occurring metabolites. However, metabolic engineering has considerably broadened the range of compounds now accessible, providing access to compounds that cannot be otherwise reliably sourced, as well as replacing established chemical processes. This review presents the case for continued efforts to promote the adoption of biocatalyzed processes, highlighting successful examples of industrial chemical production from biomass and/or via biocatalyzed processes. A selection of emerging technologies that may further extend the potential and sustainability of biocatalysis are also presented. As the field matures, metabolic engineering will be increasingly crucial in maintaining our quality of life into a future where our current resources and feedstocks cannot be relied upon.

Metabolic engineering with plants for a sustainable biobased economy.

Science.gov (United States)

Yoon, Jong Moon; Zhao, Le; Shanks, Jacqueline V

2013-01-01

Plants are bona fide sustainable organisms because they accumulate carbon and synthesize beneficial metabolites from photosynthesis. To meet the challenges to food security and health threatened by increasing population growth and depletion of nonrenewable natural resources, recent metabolic engineering efforts have shifted from single pathways to holistic approaches with multiple genes owing to integration of omics technologies. Successful engineering of plants results in the high yield of biomass components for primary food sources and biofuel feedstocks, pharmaceuticals, and platform chemicals through synthetic biology and systems biology strategies. Further discovery of undefined biosynthesis pathways in plants, integrative analysis of discrete omics data, and diversified process developments for production of platform chemicals are essential to overcome the hurdles for sustainable production of value-added biomolecules from plants.

Impact of synthetic biology and metabolic engineering on industrial production of fine chemicals.

Science.gov (United States)

Jullesson, David; David, Florian; Pfleger, Brian; Nielsen, Jens

2015-11-15

Industrial bio-processes for fine chemical production are increasingly relying on cell factories developed through metabolic engineering and synthetic biology. The use of high throughput techniques and automation for the design of cell factories, and especially platform strains, has played an important role in the transition from laboratory research to industrial production. Model organisms such as Saccharomyces cerevisiae and Escherichia coli remain widely used host strains for industrial production due to their robust and desirable traits. This review describes some of the bio-based fine chemicals that have reached the market, key metabolic engineering tools that have allowed this to happen and some of the companies that are currently utilizing these technologies for developing industrial production processes. Copyright © 2015 Elsevier Inc. All rights reserved.

Generating Solutions to Discrete sine-Gordon Equation from Modified Baecklund Transformation

International Nuclear Information System (INIS)

Kou Xin; Zhang Dajun; Shi Ying; Zhao Songlin

2011-01-01

We modify the bilinear Baecklund transformation for the discrete sine-Gordon equation and derive variety, of solutions by freely choosing parameters from the modified Baecklund transformation. Dynamics of solutions and continuum limits are also discussed. (general)

Modeling with a view to target identification in metabolic engineering: a critical evaluation of the available tools.

Science.gov (United States)

Maertens, Jo; Vanrolleghem, Peter A

2010-01-01

The state of the art tools for modeling metabolism, typically used in the domain of metabolic engineering, were reviewed. The tools considered are stoichiometric network analysis (elementary modes and extreme pathways), stoichiometric modeling (metabolic flux analysis, flux balance analysis, and carbon modeling), mechanistic and approximative modeling, cybernetic modeling, and multivariate statistics. In the context of metabolic engineering, one should be aware that the usefulness of these tools to optimize microbial metabolism for overproducing a target compound depends predominantly on the characteristic properties of that compound. Because of their shortcomings not all tools are suitable for every kind of optimization; issues like the dependence of the target compound's synthesis on severe (redox) constraints, the characteristics of its formation pathway, and the achievable/desired flux towards the target compound should play a role when choosing the optimization strategy.

Cytochrome P450-mediated metabolic engineering: current progress and future challenges.

Science.gov (United States)

Renault, Hugues; Bassard, Jean-Etienne; Hamberger, Björn; Werck-Reichhart, Danièle

2014-06-01

Cytochromes P450 catalyze a broad range of regiospecific, stereospecific and irreversible steps in the biosynthetic routes of plant natural metabolites with important applications in pharmaceutical, cosmetic, fragrance and flavour, or polymer industries. They are consequently essential drivers for the engineered bioproduction of such compounds. Two ground-breaking developments of commercial products driven by the engineering of P450s are the antimalarial drug precursor artemisinic acid and blue roses or carnations. Tedious optimizations were required to generate marketable products. Hurdles encountered in P450 engineering and their potential solutions are summarized here. Together with recent technical developments and novel approaches to metabolic engineering, the lessons from this pioneering work should considerably boost exploitation of the amazing P450 toolkit emerging from accelerated sequencing of plant genomes. Copyright © 2014 The Authors. Published by Elsevier Ltd.. All rights reserved.

Synthetic biology and regulatory networks: where metabolic systems biology meets control engineering

NARCIS (Netherlands)

He, F.; Murabito, E.; Westerhoff, H.V.

2016-01-01

Metabolic pathways can be engineered to maximize the synthesis of various products of interest. With the advent of computational systems biology, this endeavour is usually carried out throughin silicotheoretical studies with the aim to guide and complement furtherin vitroandin vivoexperimental

2012 PLANT CELL WALLS GORDON RESEARCH CONFERENCE AND GORDON RESEARCH SEMINAR, AUGUST 4-10, 2012

Energy Technology Data Exchange (ETDEWEB)

Rose, Jocelyn

2012-08-10

The sub-theme of this year’s meeting, ‘Cell Wall Research in a Post-Genome World’, will be a consideration of the dramatic technological changes that have occurred in the three years since the previous cell wall Gordon Conference in the area of DNA sequencing. New technologies are providing additional perspectives of plant cell wall biology across a rapidly growing number of species, highlighting a myriad of architectures, compositions, and functions in both "conventional" and specialized cell walls. This meeting will focus on addressing the knowledge gaps and technical challenges raised by such diversity, as well as our need to understand the underlying processes for critical applications such as crop improvement and bioenergy resource development.

Near-Integrability of Low-Dimensional Periodic Klein-Gordon Lattices

Directory of Open Access Journals (Sweden)

Ognyan Christov

2018-01-01

Full Text Available The low-dimensional periodic Klein-Gordon lattices are studied for integrability. We prove that the periodic lattice with two particles and certain nonlinear potential is nonintegrable. However, in the cases of up to six particles, we prove that their Birkhoff-Gustavson normal forms are integrable, which allows us to apply KAM theory in most cases.

A note on the three dimensional sine--Gordon equation

OpenAIRE

Shariati, Ahmad

1996-01-01

Using a simple ansatz for the solutions of the three dimensional generalization of the sine--Gordon and Toda model introduced by Konopelchenko and Rogers, a class of solutions is found by elementary methods. It is also shown that these equations are not evolution equations in the sense that solution to the initial value problem is not unique.

Phonons and solitons in the "thermal" sine-Gordon system

DEFF Research Database (Denmark)

Salerno, Mario; Jørgensen, E.; Samuelsen, Mogens Rugholm

1984-01-01

Standard methods of stochastic processes are used to study the coupling of the sine-Gordon system with a heat reservoir. As a result we find thermal phonons with an average energy of kB T per mode. The translational mode (zero mode) is found to carry an average energy of 1 / 2kBT. This last value...

The sine-Gordon model in the presence of defects

International Nuclear Information System (INIS)

Avan, Jean; Doikou, Anastasia

2013-01-01

The sine-Gordon model in the presence of dynamical integrable defects is investigated. This is an application of the algebraic formulation introduced for integrable defects in earlier works. The quantities in involution as well as the associated Lax pairs are explicitly extracted. Integrability i also shown using certain sewing constraints, which emerge as suitable continuity conditions.

Gordon Tullock and the Virginia School of Law and Economics

DEFF Research Database (Denmark)

Parisi, Francesco; Luppi, Barbara; Guerra, Alice

2017-01-01

In 1999 Gordon Tullock became Professor at the George Mason University Law School. Tullock’s arrival at George Mason brought the economics department and the law school close together. The work that resulted during those years consolidated the methodological foundations for a different way of thi...

DEVELOPMENT OF MICROORGANISMS FOR CELLULOSE-BIOFUEL CONSOLIDATED BIOPROCESSINGS: METABOLIC ENGINEERS' TRICKS

Directory of Open Access Journals (Sweden)

Roberto Mazzoli

2012-10-01

By starting from the description of natural enzyme systems for plant biomass degradation and natural metabolic pathways for some of the most valuable product (i.e. butanol, ethanol, and hydrogen biosynthesis, this review describes state-of-the-art bottlenecks and solutions for the development of recombinant microbial strains for cellulosic biofuel CBP by metabolic engineering. Complexed cellulases (i.e. cellulosomes benefit from stronger proximity effects and show enhanced synergy on insoluble substrates (i.e. crystalline cellulose with respect to free enzymes. For this reason, special attention was held on strategies involving cellulosome/designer cellulosome-bearing recombinant microorganisms.

2004 Atomic and Molecular Interactions Gordon Research Conference

International Nuclear Information System (INIS)

Dr. Paul J. Dagdigian

2004-01-01

The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference

2004 Atomic and Molecular Interactions Gordon Research Conference

Energy Technology Data Exchange (ETDEWEB)

Dr. Paul J. Dagdigian

2004-10-25

The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference.

Ab initio and Gordon--Kim intermolecular potentials for two nitrogen molecules

International Nuclear Information System (INIS)

Ree, F.H.; Winter, N.W.

1980-01-01

Both ab initio MO--LCAO--SCF and the electron-gas (or Gordon--Kim) methods have been used to compute the intermolecular potential (Phi) of N 2 molecules for seven different N 2 --N 2 orientations. The ab initio calculations were carried out using a [4s3p] contracted Gaussian basis set with and without 3d polarization functions. The larger basis set provides adequate results for Phi>0.002 hartree or intermolecular separations less than 6.5--7 bohr. We use a convenient analytic expression to represent the ab initio data in terms of the intermolecular distance and three angles defining the orientations of the two N 2 molecules. The Gordon--Kim method with Rae's self-exchange correction yields Phi, which agrees reasonably well over a large repulsive range. However, a detailed comparison of the electron kinetic energy contributions shows a large difference between the ab initio and the Gordon--Kim calculations. Using the ab initio data we derive an atom--atom potential of the two N 2 molecules. Although this expression does not accurately fit the data at some orientations, its spherical average agrees with the corresponding average of the ab initio Phi remarkably well. The spherically averaged ab initio Phi is also compared with the corresponding quantities derived from experimental considerations. The approach of the ab initio Phi to the classical quadrupole--quadrupole interaction at large intermolecular separation is also discussed

Metabolic network modeling of microbial interactions in natural and engineered environmental systems

Directory of Open Access Journals (Sweden)

Octavio ePerez-Garcia

2016-05-01

Full Text Available We review approaches to characterize metabolic interactions within microbial communities using Stoichiometric Metabolic Network (SMN models for applications in environmental and industrial biotechnology. SMN models are computational tools used to evaluate the metabolic engineering potential of various organisms. They have successfully been applied to design and optimize the microbial production of antibiotics, alcohols and amino acids by single strains. To date however, such models have been rarely applied to analyze and control the metabolism of more complex microbial communities. This is largely attributed to the diversity of microbial community functions, metabolisms and interactions. Here, we firstly review different types of microbial interaction and describe their relevance for natural and engineered environmental processes. Next, we provide a general description of the essential methods of the SMN modeling workflow including the steps of network reconstruction, simulation through Flux Balance Analysis (FBA, experimental data gathering, and model calibration. Then we broadly describe and compare four approaches to model microbial interactions using metabolic networks, i.e. i lumped networks, ii compartment per guild networks, iii bi-level optimization simulations and iv dynamic-SMN methods. These approaches can be used to integrate and analyze diverse microbial physiology, ecology and molecular community data. All of them (except the lumped approach are suitable for incorporating species abundance data but so far they have been used only to model simple communities of two to eight different species. Interactions based on substrate exchange and competition can be directly modeled using the above approaches. However, interactions based on metabolic feedbacks, such as product inhibition and synthropy require extensions to current models, incorporating gene regulation and compounding accumulation mechanisms. SMN models of microbial

Astronaut L. Gordon Cooper is assisted into his spacecraft for tests

Science.gov (United States)

1963-01-01

NASA and McDonnell Aircraft Corp. spacecraft technicians assist Astronaut L. Gordon Cooper into his spacecraft prior to undergoing tests in the altitude chamber. These tests are used to determine the operating characteristcs of the overall environmental control system.

Approximate treatment of two soliton solutions of the sine-Gordon equation

International Nuclear Information System (INIS)

Mihaly, L.

1979-05-01

The so called breather solution of the sine-Gordon equation is phenomenologically described by an appropri.ately choosen potential acting between two particles. For some applications the method proves to be equivalent to other classical and quantum calculations. (author)

2016-2017 Travel Expense Reports for Gordon Houlden, Ex-Governor

International Development Research Centre (IDRC) Digital Library (Canada)

Beata Bialic

Page 1. Purpose: Board meetings. Date(s):. 2016-05-15 to 2016-05-16. Destination(s):. Ottawa. Airfare: $979.19. Other. Transportation: $0.00. Accommodation: $0.00. Meals and. Incidentals: $0.00. Other: $0.00. Total: $979.19. Comments: 2016-2017 Travel Expense Reports for Gordon. Houlden, Ex-Governor.

Engineered nanomaterial-mediated changes in the metabolism of terrestrial plants

Energy Technology Data Exchange (ETDEWEB)

Hatami, Mehrnaz, E-mail: m-hatami@araku.ac.ir [Department of Medicinal Plants, Faculty of Agriculture and Natural Resources, Arak University, 38156-8-8349 Arak (Iran, Islamic Republic of); Kariman, Khalil [School of Earth and Environment M004, The University of Western Australia, Crawley, WA 6009 (Australia); Ghorbanpour, Mansour, E-mail: m-ghorbanpour@araku.ac.ir [Department of Medicinal Plants, Faculty of Agriculture and Natural Resources, Arak University, 38156-8-8349 Arak (Iran, Islamic Republic of)

2016-11-15

Engineered nanomaterials (ENMs) possess remarkable physicochemical characteristics suitable for different applications in medicine, pharmaceuticals, biotechnology, energy, cosmetics and electronics. Because of their ultrafine size and high surface reactivity, ENMs can enter plant cells and interact with intracellular structures and metabolic pathways which may produce toxicity or promote plant growth and development by diverse mechanisms. Depending on their type and concentration, ENMs can have positive or negative effects on photosynthesis, photochemical fluorescence and quantum yield as well as photosynthetic pigments status of the plants. Some studies have shown that ENMs can improve photosynthetic efficiency via increasing chlorophyll content and light absorption and also broadening the spectrum of captured light, suggesting that photosynthesis can be nano-engineered for harnessing more solar energy. Both up- and down-regulation of primary metabolites such as proteins and carbohydrates have been observed following exposure of plants to various ENMs. The potential capacity of ENMs for changing the rate of primary metabolites lies in their close relationship with activation and biosynthesis of the key enzymes. Several classes of secondary metabolites such as phenolics, flavonoids, and alkaloids have been shown to be induced (mostly accompanied by stress-related factors) in plants exposed to different ENMs, highlighting their great potential as elicitors to enhance both quantity and quality of biologically active secondary metabolites. Considering reports on both positive and negative effects of ENMs on plant metabolism, in-depth studies are warranted to figure out the most appropriate ENMs (type, size and optimal concentration) in order to achieve the desirable effect on specific metabolites in a given plant species. In this review, we summarize the studies performed on the impacts of ENMs on biosynthesis of plant primary and secondary metabolites and mention the

Engineered nanomaterial-mediated changes in the metabolism of terrestrial plants

International Nuclear Information System (INIS)

Hatami, Mehrnaz; Kariman, Khalil; Ghorbanpour, Mansour

2016-01-01

Engineered nanomaterials (ENMs) possess remarkable physicochemical characteristics suitable for different applications in medicine, pharmaceuticals, biotechnology, energy, cosmetics and electronics. Because of their ultrafine size and high surface reactivity, ENMs can enter plant cells and interact with intracellular structures and metabolic pathways which may produce toxicity or promote plant growth and development by diverse mechanisms. Depending on their type and concentration, ENMs can have positive or negative effects on photosynthesis, photochemical fluorescence and quantum yield as well as photosynthetic pigments status of the plants. Some studies have shown that ENMs can improve photosynthetic efficiency via increasing chlorophyll content and light absorption and also broadening the spectrum of captured light, suggesting that photosynthesis can be nano-engineered for harnessing more solar energy. Both up- and down-regulation of primary metabolites such as proteins and carbohydrates have been observed following exposure of plants to various ENMs. The potential capacity of ENMs for changing the rate of primary metabolites lies in their close relationship with activation and biosynthesis of the key enzymes. Several classes of secondary metabolites such as phenolics, flavonoids, and alkaloids have been shown to be induced (mostly accompanied by stress-related factors) in plants exposed to different ENMs, highlighting their great potential as elicitors to enhance both quantity and quality of biologically active secondary metabolites. Considering reports on both positive and negative effects of ENMs on plant metabolism, in-depth studies are warranted to figure out the most appropriate ENMs (type, size and optimal concentration) in order to achieve the desirable effect on specific metabolites in a given plant species. In this review, we summarize the studies performed on the impacts of ENMs on biosynthesis of plant primary and secondary metabolites and mention the

A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories

Directory of Open Access Journals (Sweden)

Amanda K. Fisher

2014-08-01

Full Text Available Microbial cell factories (MCFs are of considerable interest to convert low value renewable substrates to biofuels and high value chemicals. This review highlights the progress of computational models for the rational design of an MCF to produce a target bio-commodity. In particular, the rational design of an MCF involves: (i product selection, (ii de novo biosynthetic pathway identification (i.e., rational, heterologous, or artificial, (iii MCF chassis selection, (iv enzyme engineering of promiscuity to enable the formation of new products, and (v metabolic engineering to ensure optimal use of the pathway by the MCF host. Computational tools such as (i de novo biosynthetic pathway builders, (ii docking, (iii molecular dynamics (MD and steered MD (SMD, and (iv genome-scale metabolic flux modeling all play critical roles in the rational design of an MCF. Genome-scale metabolic flux models are of considerable use to the design process since they can reveal metabolic capabilities of MCF hosts. These can be used for host selection as well as optimizing precursors and cofactors of artificial de novo biosynthetic pathways. In addition, recent advances in genome-scale modeling have enabled the derivation of metabolic engineering strategies, which can be implemented using the genomic tools reviewed here as well.

Mass spectrometry characterisation of fatty acids from metabolically engineered soybean seeds.

Science.gov (United States)

Murad, André M; Vianna, Giovanni R; Machado, Alex M; da Cunha, Nicolau B; Coelho, Cíntia M; Lacerda, Valquiria A M; Coelho, Marly C; Rech, Elibio L

2014-05-01

Improving the quality and performance of soybean oil as biodiesel depends on the chemical composition of its fatty acids and requires an increase in monounsaturated acids and a reduction in polyunsaturated acids. Despite its current use as a source of biofuel, soybean oil contains an average of 25 % oleic acid and 13 % palmitic acid, which negatively impacts its oxidative stability and freezing point, causing a high rate of nitrogen oxide emission. Gas chromatography and ion mobility mass spectrometry were conducted on soybean fatty acids from metabolically engineered seed extracts to determine the nature of the structural oleic and palmitic acids. The soybean genes FAD2-1 and FatB were placed under the control of the 35SCaMV constitutive promoter, introduced to soybean embryonic axes by particle bombardment and down-regulated using RNA interference technology. Results indicate that the metabolically engineered plants exhibited a significant increase in oleic acid (up to 94.58 %) and a reduction in palmitic acid (to seed oil content. No structural differences were observed between the fatty acids of the transgenic and non-transgenic oil extracts.

Role of glycolytic intermediate in regulation: Improving lycopene production in Escherichia coli by engineering metabolic control

Energy Technology Data Exchange (ETDEWEB)

Farmer, W.R.; Liao, J.C.

2001-06-01

Metabolic engineering in the postgenomic era is expected to benefit from a full understanding of the biosynthetic capability of microorganisms as a result of the progress being made in bioinformatics and functional genomics. The immediate advantage of such information is to allow the rational design of novel pathways and the elimination of native reactions that are detrimental or unnecessary for the desired purpose. However, with the ability to manipulate metabolic pathways becoming more effective, metabolic engineering will need to face a new challenge: the reengineering of the regulatory hierarchy that controls gene expression in those pathways. In addition to constructing the genetic composition of a metabolic pathway, they propose that it will become just as important to consider the dynamics of pathways gene expression. It has been widely observed that high-level induction of a recombinant protein or pathway leads to growth retardation and reduced metabolic activity. These phenotypic characteristics result from the fact that the constant demands of production placed upon the cell interfere with its changing requirements for growth. They believe that this common situation in metabolic engineering can be alleviated by designing a dynamic controller that is able to sense the metabolic state of the cell and regulate the expression of the recombinant pathway accordingly. This approach, which is termed metabolic control engineering, involves redesigning the native regulatory circuits and applying them to the recombinant pathway. The general goal of such an effort will be to control the flux to the recombinant pathway adaptively according to the cell's metabolic state. The dynamically controlled recombinant pathway can potentially lead to enhanced production, minimized growth retardation, and reduced toxic by-product formation. The regulation of gene expression in response to the physiological state is also essential to the success of gene therapy. Here they

2004 Electron Donor Acceptor Interactions Gordon Conference - August 8-13, 2004

Energy Technology Data Exchange (ETDEWEB)

GUILFORD JONES; S ST

2005-09-14

The 2004 Gordon Conference on Donor/Acceptor Interactions will take place at Salve Regina University in Newport, Rhode Island on August 8-13, 2004. The conference will be devoted to the consequences of charge interaction and charge motion in molecular and materials systems.

Production of vanillin by metabolically engineered Escherichia coli.

Science.gov (United States)

Yoon, Sang-Hwal; Li, Cui; Kim, Ju-Eun; Lee, Sook-Hee; Yoon, Ji-Young; Choi, Myung-Suk; Seo, Weon-Taek; Yang, Jae-Kyung; Kim, Jae-Yeon; Kim, Seon-Won

2005-11-01

E. coli was metabolically engineered to produce vanillin by expression of the fcs and ech genes from Amycolatopsis sp. encoding feruloyl-CoA synthetase and enoyl-CoA hydratase/aldolase, respectively. Vanillin production was optimized by leaky expression of the genes, under the IPTG-inducible trc promoter, in complex 2YT medium. Supplementation with glucose, fructose, galactose, arabinose or glycerol severely decreased vanillin production. The highest vanillin production of 1.1 g l(-1) was obtained with cultivation for 48 h in 2YT medium with 0.2% (w/v) ferulate, without IPTG and no supplementation of carbon sources.

Nonlinear Fourier transforms for the sine-Gordon equation in the quarter plane

Science.gov (United States)

Huang, Lin; Lenells, Jonatan

2018-03-01

Using the Unified Transform, also known as the Fokas method, the solution of the sine-Gordon equation in the quarter plane can be expressed in terms of the solution of a matrix Riemann-Hilbert problem whose definition involves four spectral functions a , b , A , B. The functions a (k) and b (k) are defined via a nonlinear Fourier transform of the initial data, whereas A (k) and B (k) are defined via a nonlinear Fourier transform of the boundary values. In this paper, we provide an extensive study of these nonlinear Fourier transforms and the associated eigenfunctions under weak regularity and decay assumptions on the initial and boundary values. The results can be used to determine the long-time asymptotics of the sine-Gordon quarter-plane solution via nonlinear steepest descent techniques.

Metabolic engineering: the ultimate paradigm for continuous pharmaceutical manufacturing.

Science.gov (United States)

Yadav, Vikramaditya G; Stephanopoulos, Gregory

2014-07-01

Research and development (R&D) expenditures by pharmaceutical companies doubled over the past decade, yet candidate attrition rates and development times rose markedly during this period. Understandably, companies have begun downsizing their pipelines and diverting investments away from R&D in favor of manufacturing. It is estimated that transitioning to continuous manufacturing could enable companies to compete for a share in emerging markets. Accordingly, the model for continuous manufacturing that has emerged commences with the conversion of late-stage intermediates into the active pharmaceutical ingredient (API) in a series of continuous flow reactors, followed by continuous solid processing to form finished tablets. The use of flow reactions for API synthesis will certainly generate purer products at higher yields in shorter times compared to equivalent batch reactions. However, transitioning from batch to flow configuration simply alleviates transport limitations within the reaction milieu. As the catalogue of reactions used in flow syntheses is a subset of batch-based chemistries, molecules such as natural products will continue to evade drug prospectors. Also, it is uncertain whether flow synthesis can deliver improvements in the atom and energy economies of API production at the scales that would achieve the levels of revenue growth targeted by companies. Instead, it is argued that implementing metabolic engineering for the production of oxidized scaffolds as gateway molecules for flow-based addition of electrophiles is a more effective and scalable strategy for accessing natural product chemical space. This new paradigm for manufacturing, with metabolic engineering as its engine, would also permit rapid optimization of production variables and allow facile scale-up from gram to ton scale to meet material requirements for clinical trials, thus recasting manufacturing as a tool for discovery. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Transcriptomic Changes in Response to Putrescine Production in Metabolically Engineered Corynebacterium glutamicum

Directory of Open Access Journals (Sweden)

Zhen Li

2017-10-01

Full Text Available Putrescine is widely used in industrial production of bioplastics, pharmaceuticals, agrochemicals, and surfactants. Although engineered Corynebacterium glutamicum has been successfully used to produce high levels of putrescine, the overall cellular physiological and metabolic changes caused by overproduction of putrescine remains unclear. To reveal the transcriptional changes that occur in response to putrescine production in an engineered C. glutamicum strain, a comparative transcriptomic analysis was carried out. Overproduction of putrescine resulted in transcriptional downregulation of genes involved in glycolysis; the TCA cycle, pyruvate degradation, biosynthesis of some amino acids, oxidative phosphorylation; vitamin biosynthesis (thiamine and vitamin 6, metabolism of purine, pyrimidine and sulfur, and ATP-, NAD-, and NADPH-consuming enzymes. The transcriptional levels of genes involved in ornithine biosynthesis and NADPH-forming related enzymes were significantly upregulated in the putrescine producing C. glutamicum strain PUT-ALE. Comparative transcriptomic analysis provided some genetic modification strategies to further improve putrescine production. Repressing ATP- and NADPH-consuming enzyme coding gene expression via CRISPRi enhanced putrescine production.

Transcriptomic Changes in Response to Putrescine Production in Metabolically Engineered Corynebacterium glutamicum

Science.gov (United States)

Li, Zhen; Liu, Jian-Zhong

2017-01-01

Putrescine is widely used in industrial production of bioplastics, pharmaceuticals, agrochemicals, and surfactants. Although engineered Corynebacterium glutamicum has been successfully used to produce high levels of putrescine, the overall cellular physiological and metabolic changes caused by overproduction of putrescine remains unclear. To reveal the transcriptional changes that occur in response to putrescine production in an engineered C. glutamicum strain, a comparative transcriptomic analysis was carried out. Overproduction of putrescine resulted in transcriptional downregulation of genes involved in glycolysis; the TCA cycle, pyruvate degradation, biosynthesis of some amino acids, oxidative phosphorylation; vitamin biosynthesis (thiamine and vitamin 6), metabolism of purine, pyrimidine and sulfur, and ATP-, NAD-, and NADPH-consuming enzymes. The transcriptional levels of genes involved in ornithine biosynthesis and NADPH-forming related enzymes were significantly upregulated in the putrescine producing C. glutamicum strain PUT-ALE. Comparative transcriptomic analysis provided some genetic modification strategies to further improve putrescine production. Repressing ATP- and NADPH-consuming enzyme coding gene expression via CRISPRi enhanced putrescine production. PMID:29089930

Regularized integrable version of the one-dimensional quantum sine-Gordon model

International Nuclear Information System (INIS)

Japaridze, G.I.; Nersesyan, A.A.; Wiegmann, P.B.

1983-01-01

The authors derive a regularized exactly solvable version of the one-dimensional quantum sine-Gordon model proceeding from the exact solution of the U(1)-symmetric Thirring model. The ground state and the excitation spectrum are obtained in the region ν 2 < 8π. (Auth.)

Biofuel production in Escherichia coli. The role of metabolic engineering and synthetic biology

Energy Technology Data Exchange (ETDEWEB)

Clomburg, James M. [Rice Univ., Houston, TX (United States). Dept. of Chemical and Biomolecular Engineering; Gonzalez, Ramon [Rice Univ., Houston, TX (United States). Dept. of Chemical and Biomolecular Engineering; Rice Univ., Houston, TX (United States). Dept. of Bioengineering

2010-03-15

The microbial production of biofuels is a promising avenue for the development of viable processes for the generation of fuels from sustainable resources. In order to become cost and energy effective, these processes must utilize organisms that can be optimized to efficiently produce candidate fuels from a variety of feedstocks. Escherichia coli has become a promising host organism for the microbial production of biofuels in part due to the ease at which this organism can be manipulated. Advancements in metabolic engineering and synthetic biology have led to the ability to efficiently engineer E. coli as a biocatalyst for the production of a wide variety of potential biofuels from several biomass constituents. This review focuses on recent efforts devoted to engineering E. coli for the production of biofuels, with emphasis on the key aspects of both the utilization of a variety of substrates as well as the synthesis of several promising biofuels. Strategies for the efficient utilization of carbohydrates, carbohydrate mixtures, and noncarbohydrate carbon sources will be discussed along with engineering efforts for the exploitation of both fermentative and nonfermentative pathways for the production of candidate biofuels such as alcohols and higher carbon biofuels derived from fatty acid and isoprenoid pathways. Continued advancements in metabolic engineering and synthetic biology will help improve not only the titers, yields, and productivities of biofuels discussed herein, but also increase the potential range of compounds that can be produced. (orig.)

Thermodynamic Bethe ansatz for boundary sine-Gordon model

International Nuclear Information System (INIS)

Lee, Taejun; Rim, Chaiho

2003-01-01

(R-channel) TBA is elaborated to find the effective central charge dependence on the boundary parameters for the massless boundary sine-Gordon model with the coupling constant (8π)/β 2 =1+λ with λ a positive integer. Numerical analysis of the massless boundary TBA demonstrates that at an appropriate boundary parameter range (cusp point) there exists a singularity crossing phenomena and this effect should be included in TBA to have the right behavior of the effective central charge

Genome Sequencing of Streptomyces atratus SCSIOZH16 and Activation Production of Nocardamine via Metabolic Engineering

Directory of Open Access Journals (Sweden)

Yan Li

2018-06-01

Full Text Available The Actinomycetes are metabolically flexible microorganisms capable of producing a wide range of interesting compounds, including but by no means limited to, siderophores which have high affinity for ferric iron. In this study, we report the complete genome sequence of marine-derived Streptomyces atratus ZH16 and the activation of an embedded siderophore gene cluster via the application of metabolic engineering methods. The S. atratus ZH16 genome reveals that this strain has the potential to produce 26 categories of natural products (NPs barring the ilamycins. Our activation studies revealed S. atratus SCSIO ZH16 to be a promising source of the production of nocardamine-type (desferrioxamine compounds which are important in treating acute iron intoxication and performing ecological remediation. We conclude that metabolic engineering provides a highly effective strategy by which to discover drug-like compounds and new NPs in the genomic era.

Engineering from the Sea: Establishing How Australian Army Engineers Fit into Australia’s Amphibious Concept

Science.gov (United States)

2011-03-16

STUDIES MAJOR M.D. SCOTT AUSTRALIAN ARMY AY 10-11 Oral Defense Committee Member: Dr. John W. Gordon , Ph.D., Professor ofNational Security App...equivalent to a Private. 9 Ronald Ramsay McNicoll, The Royal Australian Engineers 1902 to 1919: The Second Volume of the History of the Royal...Special Collections Branch, Library of the Marine Corps, WWII Marianas Islands Collection, Box 4, Folder 2; and Ronald Ramsay McNicoll, The Royal

New exact solutions of (2 + 1)-dimensional Gardner equation via the new sine-Gordon equation expansion method

International Nuclear Information System (INIS)

Chen Yong; Yan Zhenya

2005-01-01

In this paper (2 + 1)-dimensional Gardner equation is investigated using a sine-Gordon equation expansion method, which was presented via a generalized sine-Gordon reduction equation and a new transformation. As a consequence, it is shown that the method is more powerful to obtain many types of new doubly periodic solutions of (2 + 1)-dimensional Gardner equation. In particular, solitary wave solutions are also given as simple limits of doubly periodic solutions

Development of biosensors and their application in metabolic engineering

DEFF Research Database (Denmark)

Zhang, Jie; Jensen, Michael Krogh; Keasling, Jay

2015-01-01

and ease of implementation with high-throughput analysis. Here we describe recent progress in biosensor development and their applications in a metabolic engineering context. We also highlight examples of how biosensors can be integrated with synthetic circuits to exert feedback regulation...... for the desired phenotypes. However, methods available for microbial genome diversification far exceed our ability to screen and select for those variants with optimal performance. Genetically encoded biosensors have shown the potential to address this gap, given their ability to respond to small molecule binding...

Systematic metabolic engineering of Methylomicrobium alcaliphilum 20Z for 2,3-butanediol production from methane.

Science.gov (United States)

Nguyen, Anh Duc; Hwang, In Yeub; Lee, Ok Kyung; Kim, Donghyuk; Kalyuzhnaya, Marina G; Mariyana, Rina; Hadiyati, Susila; Kim, Min Sik; Lee, Eun Yeol

2018-04-16

Methane is considered a next-generation feedstock, and methanotrophic cell-based biorefinery is attractive for production of a variety of high-value compounds from methane. In this work, we have metabolically engineered Methylomicrobium alcaliphilum 20Z for 2,3-butanediol (2,3-BDO) production from methane. The engineered strain 20Z/pBudK.p, harboring the 2,3-BDO synthesis gene cluster (budABC) from Klebsiella pneumoniae, accumulated 2,3-BDO in methane-fed shake flask cultures with a titer of 35.66 mg/L. Expression of the most efficient gene cluster was optimized using selection of promoters, translation initiation rates (TIR), and the combination of 2,3-BDO synthesis genes from different sources. A higher 2,3-BDO titer of 57.7 mg/L was measured in the 20Z/pNBM-Re strain with budA of K. pneumoniae and budB of Bacillus subtilis under the control of the Tac promoter. The genome-scale metabolic network reconstruction of M. alcaliphilum 20Z enabled in silico gene knockout predictions using an evolutionary programming method to couple growth and 2,3-BDO production. The ldh, ack, and mdh genes in M. alcaliphilum 20Z were identified as potential knockout targets. Pursuing these targets, a triple-mutant strain ∆ldh ∆ack ∆mdh was constructed, resulting in a further increase of the 2,3-BDO titer to 68.8 mg/L. The productivity of this optimized strain was then tested in a fed-batch stirred tank bioreactor, where final product concentrations of up to 86.2 mg/L with a yield of 0.0318 g-(2,3-BDO) /g-CH 4 were obtained under O 2 -limited conditions. This study first demonstrates the strategy of in silico simulation-guided metabolic engineering and represents a proof-of-concept for the production of value-added compounds using systematic approaches from engineered methanotrophs. Copyright © 2018 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Natural and modified promoters for tailored metabolic engineering of the yeast Saccharomyces cerevisiae

NARCIS (Netherlands)

Hubmann, Georg; Thevelein, Johan M; Nevoigt, Elke

2014-01-01

The ease of highly sophisticated genetic manipulations in the yeast Saccharomyces cerevisiae has initiated numerous initiatives towards development of metabolically engineered strains for novel applications beyond its traditional use in brewing, baking, and wine making. In fact, baker's yeast has

Metabolic engineering for the microbial production of isoprenoids: Carotenoids and isoprenoid-based biofuels

Directory of Open Access Journals (Sweden)

Fu-Xing Niu

2017-09-01

Full Text Available Isoprenoids are the most abundant and highly diverse group of natural products. Many isoprenoids have been used for pharmaceuticals, nutraceuticals, flavors, cosmetics, food additives and biofuels. Carotenoids and isoprenoid-based biofuels are two classes of important isoprenoids. These isoprenoids have been produced microbially through metabolic engineering and synthetic biology efforts. Herein, we briefly review the engineered biosynthetic pathways in well-characterized microbial systems for the production of carotenoids and several isoprenoid-based biofuels.

2014 Defects in Semiconductors Gordon Research Conference & Gordon Research Seminar. Research Area 1: Materials Science, 1.3 Physical Properties of Materials

Science.gov (United States)

2014-08-01

invite leading experts from the full range of industry to academia to cover the topics of wide bandgap nitride and oxide semiconductors , the...Tsukuba University) " Positron Annihilation Studies in InGaN" 12:10 pm - 12:30 pm Discussion 9 12:30 pm Lunch 1:30 pm - 4:00 pm Free Time 4:00 pm...SECURITY CLASSIFICATION OF: The Gordon Research Conference on DEFECTS IN SEMICONDUCTORS was held at Bentley University in Waltham, Massachusetts

Metabolic and process engineering for biodesulfurization in Gram-negative bacteria.

Science.gov (United States)

Martínez, I; El-Said Mohamed, M; Santos, V E; García, J L; García-Ochoa, F; Díaz, E

2017-11-20

Microbial desulfurization or biodesulfurization (BDS) is an attractive low-cost and environmentally friendly complementary technology to the hydrotreating chemical process based on the potential of certain bacteria to specifically remove sulfur from S-heterocyclic compounds of crude fuels that are recalcitrant to the chemical treatments. The 4S or Dsz sulfur specific pathway for dibenzothiophene (DBT) and alkyl-substituted DBTs, widely used as model S-heterocyclic compounds, has been extensively studied at the physiological, biochemical and genetic levels mainly in Gram-positive bacteria. Nevertheless, several Gram-negative bacteria have been also used in BDS because they are endowed with some properties, e.g., broad metabolic versatility and easy genetic and genomic manipulation, that make them suitable chassis for systems metabolic engineering strategies. A high number of recombinant bacteria, many of which are Pseudomonas strains, have been constructed to overcome the major bottlenecks of the desulfurization process, i.e., expression of the dsz operon, activity of the Dsz enzymes, retro-inhibition of the Dsz pathway, availability of reducing power, uptake-secretion of substrate and intermediates, tolerance to organic solvents and metals, and other host-specific limitations. However, to attain a BDS process with industrial applicability, it is necessary to apply all the knowledge and advances achieved at the genetic and metabolic levels to the process engineering level, i.e., kinetic modelling, scale-up of biphasic systems, enhancing mass transfer rates, biocatalyst separation, etc. The production of high-added value products derived from the organosulfur material present in oil can be regarded also as an economically viable process that has barely begun to be explored. Copyright © 2017 Elsevier B.V. All rights reserved.

Darboux Transformations for Energy-Dependent Potentials and the Klein–Gordon Equation

International Nuclear Information System (INIS)

Schulze-Halberg, Axel

2013-01-01

We construct explicit Darboux transformations for a generalized Schrödinger-type equation with energy-dependent potential, a special case of which is the stationary Klein–Gordon equation. Our results complement and generalize former findings (Lin et al., Phys Lett A 362:212–214, 2007).

Breather kink-antikink-pair conversion in the driven sine-Gordon system

DEFF Research Database (Denmark)

Lomdahl, P. S.; Olsen, O. H.; Samuelsen, Mogens Rugholm

1984-01-01

Breather excitations in the sine-Gordon equation influenced by constant driving forces are investigated—large driving forces cause the breather to split into a kk― (2π kink-2π antikink) pair while for small driving forces the breather excitations enter stationary modes. A perturbation method...

Logical inference approach to relativistic quantum mechanics: Derivation of the Klein–Gordon equation

International Nuclear Information System (INIS)

Donker, H.C.; Katsnelson, M.I.; De Raedt, H.; Michielsen, K.

2016-01-01

The logical inference approach to quantum theory, proposed earlier De Raedt et al. (2014), is considered in a relativistic setting. It is shown that the Klein–Gordon equation for a massive, charged, and spinless particle derives from the combination of the requirements that the space–time data collected by probing the particle is obtained from the most robust experiment and that on average, the classical relativistic equation of motion of a particle holds. - Highlights: • Logical inference applied to relativistic, massive, charged, and spinless particle experiments leads to the Klein–Gordon equation. • The relativistic Hamilton–Jacobi is scrutinized by employing a field description for the four-velocity. • Logical inference allows analysis of experiments with uncertainty in detection events and experimental conditions.

Approximate damped oscillatory solutions and error estimates for the perturbed Klein–Gordon equation

International Nuclear Information System (INIS)

Ye, Caier; Zhang, Weiguo

2015-01-01

Highlights: • Analyze the dynamical behavior of the planar dynamical system corresponding to the perturbed Klein–Gordon equation. • Present the relations between the properties of traveling wave solutions and the perturbation coefficient. • Obtain all explicit expressions of approximate damped oscillatory solutions. • Investigate error estimates between exact damped oscillatory solutions and the approximate solutions and give some numerical simulations. - Abstract: The influence of perturbation on traveling wave solutions of the perturbed Klein–Gordon equation is studied by applying the bifurcation method and qualitative theory of dynamical systems. All possible approximate damped oscillatory solutions for this equation are obtained by using undetermined coefficient method. Error estimates indicate that the approximate solutions are meaningful. The results of numerical simulations also establish our analysis

2008 Co2 Assimilation in Plants: Genome to Biome Gordon Research Conference - August 17-22

Energy Technology Data Exchange (ETDEWEB)

James V. Maroney

2009-08-12

Formerly entitled 'CO2 Fixation and Metabolism in Green Plants', this long-standing Gordon Research Conference has been held on a triennial basis since 1976. In 1990 the participants decided to alternate between sites in the U.S. and outside the U.S. The 2005 conference was held in Europe at the Centre Paul Langevin in Aussois, France, so the 2008 conference returns to a U.S. site - the University of New England in Biddeford, Maine. The 2008 conference covers basic plant research related to photosynthesis and the subsequent regulation and engineering of carbon assimilation. Approaches that range from post-genomic technologies and systems biology, through to fundamental biochemistry, physiology and molecular biology are integrated within ecological and agronomic contexts. As such, the meeting provides the rare opportunity of a single venue for discussing all aspects of the 'carbon-side' of photosynthesis - from genome to biome. The 2008 conference will include an emphasis on the central role of carbon assimilation by plants for developing new sources of bioenergy and for achieving a carbon-neutral planet. A special characteristic of this conference is its 'intimacy' with approximately 110 conferees, ranging from beginning graduate students and postdoctoral associates to leading senior plant scientists, engaged in open and forward-thinking discussions in an informal, friendly setting. With extended time devoted to discussion, and the encouragement to challenge dogma, it is unlike other meetings in the U.S. or abroad. Another novel feature of the conference is a session devoted to the latest 'hot off the press' findings by both established and early career scientists, picked from the abstracts. Together with an expanded poster discussion in the evening sessions, this session provides an opportunity for early career scientists to present interesting new data and to 'test drive' hypotheses in a collegial atmosphere.

News from the Library: Gordon Fraser presents his book, "Quantum Exodus"

CERN Multimedia

CERN Library

2012-01-01

The book "Quantum Exodus" will be presented by the author Gordon Fraser on Thursday 14 June at 4 P.M. in the Library, Building 52-1-052.   "Quantum Exodus" by Gordon Fraser, Oxford University Press, 2012. Here's what the publisher says about the book: "It was no accident that the Holocaust and the Atomic Bomb happened at the same time. (...) Atomic science had attracted a lot of Jewish talent, and as Albert Einstein and other quantum exiles scattered, they realized that they held the key to a weapon of unimaginable power. Convinced that their gentile counterparts in Germany had come to the same conclusion, and having witnessed what the Nazis were prepared to do, the exiles were afraid. They had to get to the Atomic Bomb first. The Nazis meanwhile had acquired a more pressing objective: their persecution of the Jews had evolved into extermination. Two dreadfu...

Expanding beyond canonical metabolism: Interfacing alternative elements, synthetic biology, and metabolic engineering

Directory of Open Access Journals (Sweden)

Kevin B. Reed

2018-03-01

Full Text Available Metabolic engineering offers an exquisite capacity to produce new molecules in a renewable manner. However, most industrial applications have focused on only a small subset of elements from the periodic table, centered around carbon biochemistry. This review aims to illustrate the expanse of chemical elements that can currently (and potentially be integrated into useful products using cellular systems. Specifically, we describe recent advances in expanding the cellular scope to include the halogens, selenium and the metalloids, and a variety of metal incorporations. These examples range from small molecules, heteroatom-linked uncommon elements, and natural products to biomining and nanotechnology applications. Collectively, this review covers the promise of an expanded range of elemental incorporations and the future impacts it may have on biotechnology.

Solitons and separable elliptic solutions of the sine-Gordon equation

International Nuclear Information System (INIS)

Bryan, A.C.; Haines, C.R.; Stuart, A.E.G.

1979-01-01

It is pointed out that the two-soliton (antisoliton) solutions of the sine-Gordon equation may be obtained as limiting cases of a separable, two-parameter family of elliptic solutions. The solitons are found on the boundary of the parameter space for the elliptic solutions when the latter are considered over their usual complex domain. (Auth.)

Numerical simulation of the self-pumped long Josephson junction using a modified sine-Gordon model

DEFF Research Database (Denmark)

Sobolev, A.; Pankratov, A.; Mygind, Jesper

2006-01-01

We have numerically investigated the dynamics of a long Josephson junction (flux-flow oscillator) biased by a DC current in the presence of magnetic field. The study is performed in the frame of the modified sine-Gordon model, which includes the surface losses, RC-load at both FFO ends and the self-pumping...... effect. In our model the dumping parameter depends both on the spatial coordinate and the amplitude of the AC voltage. In order to find the DC FFO voltage the damping parameter has to be calculated by successive approximations and time integration of the perturbed sine-Gordon equation. The modified model...

OptFlux: an open-source software platform for in silico metabolic engineering.

Science.gov (United States)

Rocha, Isabel; Maia, Paulo; Evangelista, Pedro; Vilaça, Paulo; Soares, Simão; Pinto, José P; Nielsen, Jens; Patil, Kiran R; Ferreira, Eugénio C; Rocha, Miguel

2010-04-19

Over the last few years a number of methods have been proposed for the phenotype simulation of microorganisms under different environmental and genetic conditions. These have been used as the basis to support the discovery of successful genetic modifications of the microbial metabolism to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. OptFlux is an open-source and modular software aimed at being the reference computational application in the field. It is the first tool to incorporate strain optimization tasks, i.e., the identification of Metabolic Engineering targets, using Evolutionary Algorithms/Simulated Annealing metaheuristics or the previously proposed OptKnock algorithm. It also allows the use of stoichiometric metabolic models for (i) phenotype simulation of both wild-type and mutant organisms, using the methods of Flux Balance Analysis, Minimization of Metabolic Adjustment or Regulatory on/off Minimization of Metabolic flux changes, (ii) Metabolic Flux Analysis, computing the admissible flux space given a set of measured fluxes, and (iii) pathway analysis through the calculation of Elementary Flux Modes. OptFlux also contemplates several methods for model simplification and other pre-processing operations aimed at reducing the search space for optimization algorithms. The software supports importing/exporting to several flat file formats and it is compatible with the SBML standard. OptFlux has a visualization module that allows the analysis of the model structure that is compatible with the layout information of Cell Designer, allowing the superimposition of simulation results with the model graph. The OptFlux software is freely available, together with documentation and other resources, thus bridging the gap from research in strain optimization

Extremely Thermophilic Microorganisms as Metabolic Engineering Platforms for Production of Fuels and Industrial Chemicals

Directory of Open Access Journals (Sweden)

Benjamin M Zeldes

2015-11-01

Full Text Available Enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. Thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. Genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few enzymatic steps. However, in the past several years, unprecedented progress has been made in establishing molecular genetics tools for extreme thermophiles to the point that the use of these microorganisms as metabolic engineering platforms has become possible. While in its early days, complex metabolic pathways have been altered or engineered into recombinant extreme thermophiles, such that the production of fuels and chemicals at elevated temperatures has become possible. Not only does this expand the thermal range for industrial biotechnology, it also potentially provides biodiverse options for specific biotransformations unique to these microorganisms. The list of extreme thermophiles growing optimally between 70 and 100°C with genetic toolkits currently available includes archaea and bacteria, aerobes and anaerobes, coming from genera such as Caldicellulosiruptor, Sulfolobus, Thermotoga, Thermococcus and Pyrococcus. These organisms exhibit unusual and potentially useful native metabolic capabilities, including cellulose degradation, metal solubilization, and RuBisCO-free carbon fixation. Those looking to design a thermal bioprocess now have a host of potential candidates to choose from, each with its own advantages and challenges that will influence its appropriateness for specific applications. Here, the issues and opportunities for extremely thermophilic metabolic engineering platforms are considered with an eye towards potential technological

Extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals

Science.gov (United States)

Zeldes, Benjamin M.; Keller, Matthew W.; Loder, Andrew J.; Straub, Christopher T.; Adams, Michael W. W.; Kelly, Robert M.

2015-01-01

Enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. Thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. Genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few enzymatic steps. However, in the past several years, unprecedented progress has been made in establishing molecular genetics tools for extreme thermophiles to the point that the use of these microorganisms as metabolic engineering platforms has become possible. While in its early days, complex metabolic pathways have been altered or engineered into recombinant extreme thermophiles, such that the production of fuels and chemicals at elevated temperatures has become possible. Not only does this expand the thermal range for industrial biotechnology, it also potentially provides biodiverse options for specific biotransformations unique to these microorganisms. The list of extreme thermophiles growing optimally between 70 and 100°C with genetic toolkits currently available includes archaea and bacteria, aerobes and anaerobes, coming from genera such as Caldicellulosiruptor, Sulfolobus, Thermotoga, Thermococcus, and Pyrococcus. These organisms exhibit unusual and potentially useful native metabolic capabilities, including cellulose degradation, metal solubilization, and RuBisCO-free carbon fixation. Those looking to design a thermal bioprocess now have a host of potential candidates to choose from, each with its own advantages and challenges that will influence its appropriateness for specific applications. Here, the issues and opportunities for extremely thermophilic metabolic engineering platforms are considered with an eye toward potential technological advantages for high

Application of a controllable degron strategy for metabolic engineering

DEFF Research Database (Denmark)

Knuf, Christoph; Maury, Jerome; Jacobsen, Simo Abdessamad

2014-01-01

In numerous cases of metabolic engineering, metabolite pools have to be increased in order to obtain flux into heterologous pathways. A simple tool for this would be the deletion of genes that would practically lead to a block of the natural pathway, so that the carbon can flow into the heterolog...... of intermediates of the mevalonate pathway around 2,3-oxidosqualene, which is the precursor for triterpenoids. Many triterpenoids are pharmaceutically relevant compounds which nowadays need to be extracted from plant material through an intricate and resource consuming process....

Experimental relationship between damping and stability of Sine-Gordon solitons in Josephson junctions

International Nuclear Information System (INIS)

Davidson, A.; Pedersen, N.F.; Dueholm, B.

1985-01-01

We show some experimental results which suggest that total damping, including surface loss, plays a fundamental role in limiting the stability of high-velocity Sine-Gordon solitons in real Josephson tunnel junctions

2010 Thin Film & Small Scale Mechanical Behavior Gordon Research Conference

Energy Technology Data Exchange (ETDEWEB)

Dr. Thomas Balk

2010-07-30

Over the past decades, it has been well established that the mechanical behavior of materials changes when they are confined geometrically at least in one dimension to small scale. It is the aim of the 2010 Gordon Conference on 'Thin Film and Small Scale Mechanical Behavior' to discuss cutting-edge research on elastic, plastic and time-dependent deformation as well as degradation mechanisms like fracture, fatigue and wear at small scales. As in the past, the conference will benefit from contributions from fundamental studies of physical mechanisms linked to material science and engineering reaching towards application in modern applications ranging from optical and microelectronic devices and nano- or micro-electrical mechanical systems to devices for energy production and storage. The conference will feature entirely new testing methodologies and in situ measurements as well as recent progress in atomistic and micromechanical modeling. Particularly, emerging topics in the area of energy conversion and storage, such as material for batteries will be highlighted. The study of small-scale mechanical phenomena in systems related to energy production, conversion or storage offer an enticing opportunity to materials scientists, who can provide new insight and investigate these phenomena with methods that have not previously been exploited.

A new sine-Gordon equation expansion algorithm to investigate some special nonlinear differential equations

International Nuclear Information System (INIS)

Yan Zhenya

2005-01-01

A new transformation method is developed using the general sine-Gordon travelling wave reduction equation and a generalized transformation. With the aid of symbolic computation, this method can be used to seek more types of solutions of nonlinear differential equations, which include not only the known solutions derived by some known methods but new solutions. Here we choose the double sine-Gordon equation, the Magma equation and the generalized Pochhammer-Chree (PC) equation to illustrate the method. As a result, many types of new doubly periodic solutions are obtained. Moreover when using the method to these special nonlinear differential equations, some transformations are firstly needed. The method can be also extended to other nonlinear differential equations

Validation of RetroPath, a computer-aided design tool for metabolic pathway engineering.

Science.gov (United States)

Fehér, Tamás; Planson, Anne-Gaëlle; Carbonell, Pablo; Fernández-Castané, Alfred; Grigoras, Ioana; Dariy, Ekaterina; Perret, Alain; Faulon, Jean-Loup

2014-11-01

Metabolic engineering has succeeded in biosynthesis of numerous commodity or high value compounds. However, the choice of pathways and enzymes used for production was many times made ad hoc, or required expert knowledge of the specific biochemical reactions. In order to rationalize the process of engineering producer strains, we developed the computer-aided design (CAD) tool RetroPath that explores and enumerates metabolic pathways connecting the endogenous metabolites of a chassis cell to the target compound. To experimentally validate our tool, we constructed 12 top-ranked enzyme combinations producing the flavonoid pinocembrin, four of which displayed significant yields. Namely, our tool queried the enzymes found in metabolic databases based on their annotated and predicted activities. Next, it ranked pathways based on the predicted efficiency of the available enzymes, the toxicity of the intermediate metabolites and the calculated maximum product flux. To implement the top-ranking pathway, our procedure narrowed down a list of nine million possible enzyme combinations to 12, a number easily assembled and tested. One round of metabolic network optimization based on RetroPath output further increased pinocembrin titers 17-fold. In total, 12 out of the 13 enzymes tested in this work displayed a relative performance that was in accordance with its predicted score. These results validate the ranking function of our CAD tool, and open the way to its utilization in the biosynthesis of novel compounds. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular Basis of Microbial One-Carbon Metabolism 2008 Gordon Research Conference (July 20-25, 2008)

Energy Technology Data Exchange (ETDEWEB)

Stephen W. Ragsdale

2009-08-12

One-carbon (C-1) compounds play a central role in microbial metabolism. C-1 compounds include methane, carbon monoxide, CO2, and methanol as well as coenzyme-bound one-carbon compounds (methyl-B12, CH3-H4folate, etc). Such compounds are of broad global importance because several C-1 compounds (e.g., CH4) are important energy sources, some (e.g., CO2 and CH4) are potent greenhouse gases, and others (e.g., CH2Cl2) are xenobiotics. They are central in pathways of energy metabolism and carbon fixation by microbes and many are of industrial interest. Research on the pathways of one-carbon metabolism has added greatly to our understanding of evolution, structural biology, enzyme mechanisms, gene regulation, ecology, and applied biology. The 2008 meeting will include recent important findings in the following areas: (a) genomics, metagenomics, and proteomic studies that have expanded our understanding of autotrophy and C-1 metabolism and the evolution of these pathways; (b) redox regulation of carbon cycles and the interrelationship between the carbon cycle and other biogeochemical cycles (sulfur, nitrogen, oxygen); (c) novel pathways for carbon assimilation; (d) biotechnology related to C-1 metabolism; (e) novel enzyme mechanisms including channeling of C-1 intermediates during metabolism; and (f) the relationship between metal homeostasis and the global carbon cycle. The conference has a diverse and gender-balanced slate of speakers and session leaders. The wide variety of disciplines brought to the study of C-1 metabolism make the field an excellent one in which to train young researchers.

Semiclassical versus exact quantization of the Sinh-Gordon model

Energy Technology Data Exchange (ETDEWEB)

Grossehelweg, Juliane

2009-12-15

In this work we investigate the semiclassics of the Sinh-Gordon model. The Sinh-Gordon model is integrable, its explicit solutions of the classical and the quantum model are well known. This allows for a comprehensive investigation of the semiclassical quantization of the classical model as well as of the semiclassical limit of the exact quantum solution. Semiclassical means in this case that the key objects of quantum theory are constructed as formal power series. A quantity playing an important role in the quantum theory is the Q-function. The purpose of this work is to investigate to what extend the classical integrability of the model admits of a construction of the semiclassical expansion of the Q-function. Therefore we used two conceptual independent approaches. In the one approach we start from the exact nonperturbative solution of the quantum model and calculate the semiclassical limit up to the next to leading order. Thereby we found the spectral curve, as well as the semiclassical expansion of the Q-function and of the eigenvalue of the monodromy matrix. In the other approach we constructed the first two orders of the semiclassical expansion of the Q-function, starting from the classical solution theory. The results of both approaches coincide. (orig.)

Rapport de frais de 2016-2017 pour Gordon Houlden | CRDI ...

International Development Research Centre (IDRC) Digital Library (Canada)

Accueil · À propos du CRDI · Obligation de rendre compte · Transparence · Déplacements et accueil. Rapport de frais de 2016-2017 pour Gordon Houlden. Total des frais de déplacement : CAD$3,444.37. Réunion du Conseil des gouverneurs. 15 mai 2016 au 16 mai 2016. CAD$979.19. Réunion du Conseil des ...

Rapport de frais de 2015-2016 pour Gordon Houlden | CRDI ...

International Development Research Centre (IDRC) Digital Library (Canada)

Accueil · À propos du CRDI · Obligation de rendre compte · Transparence · Déplacements et accueil. Rapport de frais de 2015-2016 pour Gordon Houlden. Total des frais de déplacement : CAD$2,798.04. Réunion du Conseil des gouverneurs. 16 novembre 2015 au 19 novembre 2015. CAD$1,093.39. Réunion du Conseil ...

Using Gordon's functional health patterns to organize a critical care orientation program.

Science.gov (United States)

Recker, D; O'Brien, C

1992-02-01

We have described how we revised our critical care orientation according to Gordon's FHPs. The process will require continuous review and revision. Research is necessary to determine the effectiveness of an orientation organized by a nursing framework in facilitating holistic nursing practice.

Suurbritannia valitsuse etteotsa asub täna shotlane Gordon Brown / Siim Trumm

Index Scriptorium Estoniae

Trumm, Siim

2007-01-01

Suurbritannia peaministriks ja Tööpartei juhiks sai endine rahandusminister Gordon Brown. Tema elukäigust, karjäärist ja poliitilistest prioriteetidest. Vt. samas: Suured väljakutsed ja küsitav toetus; Briti Tööpartei aseesimeheks valiti Harriet Harman

Internal oscillation frequencies and anharmonic effects for the double sine-Gordon kink

DEFF Research Database (Denmark)

Salerno, M.; Samuelsen, Mogens Rugholm

1989-01-01

A simple derivation of the small oscillation frequency around 4π-kink solutions of the double sine-Gordon equation is presented. Small corrections to these frequencies due to anharmonic effects are also numerically and analytically investigated. The analysis is based on energetic considerations...

Metabolic engineering of Escherichia coli for limonene and perillyl alcohol production.

Science.gov (United States)

Alonso-Gutierrez, Jorge; Chan, Rossana; Batth, Tanveer S; Adams, Paul D; Keasling, Jay D; Petzold, Christopher J; Lee, Taek Soon

2013-09-01

Limonene is a valuable monoterpene used in the production of several commodity chemicals and medicinal compounds. Among them, perillyl alcohol (POH) is a promising anti-cancer agent that can be produced by hydroxylation of limonene. We engineered E. coli with a heterologous mevalonate pathway and limonene synthase for production of limonene followed by coupling with a cytochrome P450, which specifically hydroxylates limonene to produce POH. A strain containing all mevalonate pathway genes in a single plasmid produced limonene at titers over 400mg/L from glucose, substantially higher than has been achieved in the past. Incorporation of a cytochrome P450 to hydroxylate limonene yielded approximately 100mg/L of POH. Further metabolic engineering of the pathway and in situ product recovery using anion exchange resins would make this engineered E. coli a potential production platform for any valuable limonene derivative. © 2013 Elsevier Inc. All rights reserved.

Nuclearity, split-property and duality for the Klein-Gordon field in curved spacetime

International Nuclear Information System (INIS)

Verch, R.

1993-05-01

Nuclearity, Split-Property and Duality are establihed for the nets of von Neumann algebras associated with the representations of distinguished states of the massive Klein-Gordon field propagating in particular classes of curved spacetimes. (orig.)

Coherence and chaos in the driven damped sine-Gordon equation: Measurement of the soliton spectrum

Energy Technology Data Exchange (ETDEWEB)

Overman, II, E A; McLaughlin, D W; Bishop, A R; Los Alamos National Lab., NM

1986-02-01

A numerical procedure is developed which measures the sine-Gordon soliton and radiation content of any field (PHI, PHIsub(t)) which is periodic in space. The procedure is applied to the field generated by a damped, driven sine-Gordon equation. This field can be either temporally periodic (locked to the driver) or chaotic. In either case the numerical measurement shows that the spatial structure can be described by only a few spatially localized (soliton wave-train) modes. The numerical procedure quantitatively identifies the presence, number and properties of these soliton wave-trains. For example, an increase of spatial symmetry is accompanied by the injection of additional solitons into the field. (orig.).

Uniform decay for a local dissipative Klein-Gordon-Schrodinger type system

Directory of Open Access Journals (Sweden)

Marilena N. Poulou

2012-10-01

Full Text Available In this article, we consider a nonlinear Klein-Gordon-Schrodinger type system in $mathbb{R}^n$, where the nonlinear term exists and the damping term is effective. We prove the existence and uniqueness of a global solution and its exponential decay. The result is achieved by using the multiplier technique.

Integrating biocompatible chemistry and manipulating cofactor partitioning in metabolically engineeredLactococcus lactisfor fermentative production of (3S)-acetoin

DEFF Research Database (Denmark)

Liu, Jianming; Solem, Christian; Jensen, Peter Ruhdal

2016-01-01

Biocompatible chemistry (BC), i.e. non-enzymatic chemical reactions compatible with living organisms, is increasingly used in conjunction with metabolically engineered microorganisms for producing compounds that do not usually occur naturally. Here we report production of one such compound, (3S......)-acetoin, a valuable precursor for chiral synthesis, using a metabolically engineered Lactococcus lactis strain growing under respiratory conditions with ferric iron serving as a BC component. The strain used has all competing product pathways inactivated, and an appropriate cofactor balance is achieved by fine...

Metabolic cartography: experimental quantification of metabolic fluxes from isotopic labelling studies.

Science.gov (United States)

O'Grady, John; Schwender, Jörg; Shachar-Hill, Yair; Morgan, John A

2012-03-01

For the past decade, flux maps have provided researchers with an in-depth perspective on plant metabolism. As a rapidly developing field, significant headway has been made recently in computation, experimentation, and overall understanding of metabolic flux analysis. These advances are particularly applicable to the study of plant metabolism. New dynamic computational methods such as non-stationary metabolic flux analysis are finding their place in the toolbox of metabolic engineering, allowing more organisms to be studied and decreasing the time necessary for experimentation, thereby opening new avenues by which to explore the vast diversity of plant metabolism. Also, improved methods of metabolite detection and measurement have been developed, enabling increasingly greater resolution of flux measurements and the analysis of a greater number of the multitude of plant metabolic pathways. Methods to deconvolute organelle-specific metabolism are employed with increasing effectiveness, elucidating the compartmental specificity inherent in plant metabolism. Advances in metabolite measurements have also enabled new types of experiments, such as the calculation of metabolic fluxes based on (13)CO(2) dynamic labelling data, and will continue to direct plant metabolic engineering. Newly calculated metabolic flux maps reveal surprising and useful information about plant metabolism, guiding future genetic engineering of crops to higher yields. Due to the significant level of complexity in plants, these methods in combination with other systems biology measurements are necessary to guide plant metabolic engineering in the future.

Design of an ectoine-responsive AraC mutant and its application in metabolic engineering of ectoine biosynthesis.

Science.gov (United States)

Chen, Wei; Zhang, Shan; Jiang, Peixia; Yao, Jun; He, Yongzhi; Chen, Lincai; Gui, Xiwu; Dong, Zhiyang; Tang, Shuang-Yan

2015-07-01

Advanced high-throughput screening methods for small molecules may have important applications in the metabolic engineering of the biosynthetic pathways of these molecules. Ectoine is an excellent osmoprotectant that has been widely used in cosmetics. In this study, the Escherichia coli regulatory protein AraC was engineered to recognize ectoine as its non-natural effector and to activate transcription upon ectoine binding. As an endogenous reporter of ectoine, the mutated AraC protein was successfully incorporated into high-throughput screening of ectoine hyper-producing strains. The ectoine biosynthetic cluster from Halomonas elongata was cloned into E. coli. By engineering the rate-limiting enzyme L-2,4-diaminobutyric acid (DABA) aminotransferase (EctB), ectoine production and the specific activity of the EctB mutant were increased. Thus, these results demonstrated the effectiveness of engineering regulatory proteins into sensitive and rapid screening tools for small molecules and highlighted the importance and efficacy of directed evolution strategies applied to the engineering of genetic components for yield improvement in the biosynthesis of small molecules. Copyright © 2015 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Persistent breather excitations in an ac-driven sine-Gordon system with loss

International Nuclear Information System (INIS)

Lomdahl, P.S.; Samuelsen, M.R.

1986-01-01

In a sine-Gordon system with loss and applied ac driver, a breather can be maintained as a persistent entrained oscillation if the driver is strong enough. The threshold field is determined by a perturbation method and compared to numerical experiments. Excellent agreement is found

Metabolic engineering of riboflavin production in Ashbya gossypii through pathway optimization.

Science.gov (United States)

Ledesma-Amaro, Rodrigo; Serrano-Amatriain, Cristina; Jiménez, Alberto; Revuelta, José Luis

2015-10-14

The industrial production of riboflavin mostly relies on the microbial fermentation of flavinogenic microorganisms and Ashbya gossypii is the main industrial producer of the vitamin. Accordingly, bioengineering strategies aimed at increasing riboflavin production in A. gossypii are highly valuable for industry. We analyze the contribution of all the RIB genes to the production of riboflavin in A. gossypii. Two important metabolic rate-limiting steps that limit the overproduction of riboflavin have been found: first, low mRNA levels of the RIB genes hindered the overproduction of riboflavin; second, the competition of the AMP branch for purinogenic precursors also represents a limitation for riboflavin overproduction. Thus, overexpression of the RIB genes resulted in a significant increase in riboflavin yield. Moreover, both the inactivation and the underexpression of the ADE12 gene, which controls the first step of the AMP branch, also proved to have a positive effect on riboflavin production. Accordingly, a strain that combines both the overexpression of the RIB genes and the underexpression of the ADE12 gene was engineered. This strain produced 523 mg/L of riboflavin (5.4-fold higher than the wild-type), which is the highest titer of riboflavin obtained by metabolic engineering in A. gossypii so far. Riboflavin production in A. gossypii is limited by a low transcription activity of the RIB genes. Flux limitation towards AMP provides committed substrate GTP for riboflavin overproduction without detrimental effects on biomass formation. A multiple-engineered Ashbya strain that produces up to 523 mg/L of riboflavin was generated.

Biobased organic acids production by metabolically engineered microorganisms

DEFF Research Database (Denmark)

Chen, Yun; Nielsen, Jens

2016-01-01

Bio-based production of organic acids via microbial fermentation has been traditionally used in food industry. With the recent desire to develop more sustainable bioprocesses for production of fuels, chemicals and materials, the market for microbial production of organic acids has been further...... expanded as organic acids constitute a key group among top building block chemicals that can be produced from renewable resources. Here we review the current status for production of citric acid and lactic acid, and we highlight the use of modern metabolic engineering technologies to develop high...... performance microbes for production of succinic acid and 3-hydroxypropionic acid. Also, the key limitations and challenges in microbial organic acids production are discussed...

Expanding the chemical palate of cells by combining systems biology and metabolic engineering.

Science.gov (United States)

Curran, Kathleen A; Alper, Hal S

2012-07-01

The field of Metabolic Engineering has recently undergone a transformation that has led to a rapid expansion of the chemical palate of cells. Now, it is conceivable to produce nearly any organic molecule of interest using a cellular host. Significant advances have been made in the production of biofuels, biopolymers and precursors, pharmaceuticals and nutraceuticals, and commodity and specialty chemicals. Much of this rapid expansion in the field has been, in part, due to synergies and advances in the area of systems biology. Specifically, the availability of functional genomics, metabolomics and transcriptomics data has resulted in the potential to produce a wealth of new products, both natural and non-natural, in cellular factories. The sheer amount and diversity of this data however, means that uncovering and unlocking novel chemistries and insights is a non-obvious exercise. To address this issue, a number of computational tools and experimental approaches have been developed to help expedite the design process to create new cellular factories. This review will highlight many of the systems biology enabling technologies that have reduced the design cycle for engineered hosts, highlight major advances in the expanded diversity of products that can be synthesized, and conclude with future prospects in the field of metabolic engineering. Copyright © 2012 Elsevier Inc. All rights reserved.

Improving production of ?-lactam antibiotics by Penicillium chrysogenum : Metabolic engineering based on transcriptome analysis

NARCIS (Netherlands)

Veiga, T.

2012-01-01

In Chapters 2-5 of this thesis, the applicability of transcriptome analysis to guide metabolic engineering strategies in P. chrysogenum is explored by investigating four cellular processes that are of potential relevance for industrial production of ?-lactam antibiotics: - Regulation of secondary

Spatial separation of photosynthesis and ethanol production by cell type-specific metabolic engineering of filamentous cyanobacteria.

Science.gov (United States)

Ehira, Shigeki; Takeuchi, Takuto; Higo, Akiyoshi

2018-02-01

Cyanobacteria, which perform oxygenic photosynthesis, have drawn attention as hosts for the direct production of biofuels and commodity chemicals from CO 2 and H 2 O using light energy. Although cyanobacteria capable of producing diverse chemicals have been generated by metabolic engineering, anaerobic non-photosynthetic culture conditions are often necessary for their production. In this study, we conducted cell type-specific metabolic engineering of the filamentous cyanobacterium Anabaena sp. PCC 7120, which forms a terminally differentiated cell called a heterocyst with a semi-regular spacing of 10-15 cells. Because heterocysts are specialized cells for nitrogen fixation, the intracellular oxygen level of heterocysts is maintained very low even when adjacent cells perform oxygenic photosynthesis. Pyruvate decarboxylase of Zymomonas mobilis and alcohol dehydrogenase of Synechocystis sp. PCC 6803 were exclusively expressed in heterocysts. Ethanol production was concomitant with nitrogen fixation in genetically engineered Anabaena sp. PCC 7120. Engineering of carbon metabolism in heterocysts improved ethanol production, and strain ET14, with an extra copy of the invB gene expressed from a heterocyst-specific promoter, produced 130.9 mg L -1 of ethanol after 9 days. ET14 produced 1681.9 mg L -1 of ethanol by increasing the CO 2 supply. Ethanol production per heterocyst cell was approximately threefold higher than that per cell of unicellular cyanobacterium. This study demonstrates the potential of heterocysts for anaerobic production of biofuels and commodity chemicals under oxygenic photosynthetic conditions.

Computational metabolic engineering strategies for growth-coupled biofuel production by Synechocystis

Directory of Open Access Journals (Sweden)

Kiyan Shabestary

2016-12-01

Full Text Available Chemical and fuel production by photosynthetic cyanobacteria is a promising technology but to date has not reached competitive rates and titers. Genome-scale metabolic modeling can reveal limitations in cyanobacteria metabolism and guide genetic engineering strategies to increase chemical production. Here, we used constraint-based modeling and optimization algorithms on a genome-scale model of Synechocystis PCC6803 to find ways to improve productivity of fermentative, fatty-acid, and terpene-derived fuels. OptGene and MOMA were used to find heuristics for knockout strategies that could increase biofuel productivity. OptKnock was used to find a set of knockouts that led to coupling between biofuel and growth. Our results show that high productivity of fermentation or reversed beta-oxidation derived alcohols such as 1-butanol requires elimination of NADH sinks, while terpenes and fatty-acid based fuels require creating imbalances in intracellular ATP and NADPH production and consumption. The FBA-predicted productivities of these fuels are at least 10-fold higher than those reported so far in the literature. We also discuss the physiological and practical feasibility of implementing these knockouts. This work gives insight into how cyanobacteria could be engineered to reach competitive biofuel productivities. Keywords: Cyanobacteria, Modeling, Flux balance analysis, Biofuel, MOMA, OptFlux, OptKnock

Discrete mKdV and discrete sine-Gordon flows on discrete space curves

International Nuclear Information System (INIS)

Inoguchi, Jun-ichi; Kajiwara, Kenji; Matsuura, Nozomu; Ohta, Yasuhiro

2014-01-01

In this paper, we consider the discrete deformation of the discrete space curves with constant torsion described by the discrete mKdV or the discrete sine-Gordon equations, and show that it is formulated as the torsion-preserving equidistant deformation on the osculating plane which satisfies the isoperimetric condition. The curve is reconstructed from the deformation data by using the Sym–Tafel formula. The isoperimetric equidistant deformation of the space curves does not preserve the torsion in general. However, it is possible to construct the torsion-preserving deformation by tuning the deformation parameters. Further, it is also possible to make an arbitrary choice of the deformation described by the discrete mKdV equation or by the discrete sine-Gordon equation at each step. We finally show that the discrete deformation of discrete space curves yields the discrete K-surfaces. (paper)

2009 Gordon Research Conference on Photochemistry: Formal Schedule and Speaker/Poster Program

Energy Technology Data Exchange (ETDEWEB)

Wasielewski, Michael [Northwestern Univ., Evanston, IL (United States)

2009-07-05

The impact of photochemistry on diverse fields ranging from materials and environmental science to biology and medicine has never been greater. The 2009 Gordon Conference on Photochemistry will highlight recent advances in these key areas while also presenting the latest research on new photochemical reactions and mechanistic studies. Session topics will include: development of new chromophores, light harvesting materials, solar energy conversion, photocontrolled biomolecules, light-triggered amplification reactions, and advanced bioimaging techniques. The Conference will continue its 45 year history of promoting interactions between fundamental and applied scientists, a hallmark of the Gordon Conferences. In addition, oral presentations, poster sessions and informal discussions will provide opportunities for junior scientists and students to present their own work and discuss their results with leaders in the field. Applicants to the Conference are encouraged to submit abstracts for poster presentations in order to gain visibility and feedback on their research. In addition, a number of poster abstracts will be selected for presentation as short talks.

On the equivalence between sine-Gordon model and Thirring model in the chirally broken phase of the Thirring model

International Nuclear Information System (INIS)

Faber, M.; Ivanov, A.N.

2001-01-01

We investigate the equivalence between Thirring model and sine-Gordon model in the chirally broken phase of the Thirring model. This is unlike all other available approaches where the fermion fields of the Thirring model were quantized in the chiral symmetric phase. In the path integral approach we show that the bosonized version of the massless Thirring model is described by a quantum field theory of a massless scalar field and exactly solvable, and the massive Thirring model bosonizes to the sine-Gordon model with a new relation between the coupling constants. We show that the non-perturbative vacuum of the chirally broken phase in the massless Thirring model can be described in complete analogy with the BCS ground state of superconductivity. The Mermin-Wagner theorem and Coleman's statement concerning the absence of Goldstone bosons in the 1+1-dimensional quantum field theories are discussed. We investigate the current algebra in the massless Thirring model and give a new value of the Schwinger term. We show that the topological current in the sine-Gordon model coincides with the Noether current responsible for the conservation of the fermion number in the Thirring model. This allows one to identify the topological charge in the sine-Gordon model with the fermion number. (orig.)

Quantum solitons and their classical relatives. II. ''Fermion--boson reciprocity'' and classical versus quantum problem for the sine-Gordon system

International Nuclear Information System (INIS)

Garbaczewski, P.

1981-01-01

Both quantum and classical sine--Gordon fields can be built out of the fundamental free neutral massive excitations, which quantally obey the Bose--Einstein statistics. At the roots of the ''boson-fermion reciprocity'' invented by Coleman, lies the spin 1/2 approximation of the underlying Bose system. By generalizing the coherent state methods to incorporate non-Fock quantum structures and to give account of the so-called boson transformation theory, we construct the carrier Hilbert space H/sub SG/ for quantum soliton operators. The h→0 limit of state expectation values of these operators among pure coherentlike states in H/sub SG/ reproduces the classical sine--Gordon field. The related (classical and quantum) spin 1/2 xyz Heisenberg model field is built out of the fundamental sine--Gordon excitations, and hence can be consistently defined on the appropriate subset of the quantum soliton Hilbert space H/sub x/yz . A correct classical limit is here shown to arise for the Heisenberg system: phase manifolds of the classical Heisenberg and sine--Gordon systems cannot be then viewed independently as a consequence of the quantum relation

Construction of expression vectors for metabolic engineering of the vanillin-producing actinomycete Amycolatopsis sp. ATCC 39116.

Science.gov (United States)

Fleige, Christian; Steinbüchel, Alexander

2014-01-01

Amycolatopsis sp. ATCC 39116 is able to synthesize the important flavoring agent vanillin from cheap natural substrates. The bacterium is therefore of great interest for the industry and used for the fermentative production of vanillin. In order to improve the production of natural vanillin with Amycolatopsis sp. ATCC 39116, the strain has been genetically engineered to optimize the metabolic flux towards the desired product. Extensive metabolic engineering was hitherto hampered, due to the lack of genetic tools like functional promoters and expression vectors. In this study, we report the establishment of a plasmid-based gene expression system for Amycolatopsis sp. ATCC 39116 that allows a further manipulation of the genotype. Four new Escherichia coli-Amycolatopsis shuttle vectors harboring different promoter elements were constructed, and the functionality of these regulatory elements was proven by the expression of the reporter gene gusA, encoding a β-glucuronidase. Glucuronidase activity was detected in all plasmid-harboring strains, and remarkable differences in the expression strength of the reporter gene depending on the used promoter were observed. The new expression vectors will promote the further genetic engineering of Amycolatopsis sp. ATCC 39116 to get insight into the metabolic network and to improve the strain for a more efficient industrial use.

Stabilization of breathers in a parametrically driven sine-Gordon system with loss

DEFF Research Database (Denmark)

Grønbech-Jensen, N.; Kivshar, Yu. S.; Samuelsen, Mogens Rugholm

1991-01-01

We demonstrate that in a parametrically driven sine-Gordon system with loss, a breather, if driven, can be maintained in a steady state at half the external frequency. In the small-amplitude limit the system is described by the effective perturbed nonlinear Schrödinger equation. For an arbitrary...

[Advances in metabolic engineering for the microbial production of naturally occurring terpenes-limonene and bisabolene: a mini review].

Science.gov (United States)

Pang, Yaru; Hu, Zhihui; Xiao, Dongguang; Yu, Aiqun

2018-01-25

Limonene (C₁₀H₁₆) and bisabolene (C₁₅H₂₄) are both naturally occurring terpenes in plants. Depending on the number of C₅ units, limonene and bisabolene are recognized as representative monoterpenes and sesquiterpenes, respectively. Limonene and bisabolene are important pharmaceutical and nutraceutical products used in the prevention and treatment of cancer and many other diseases. In addition, they can be used as starting materials to produce a range of commercially valuable products, such as pharmaceuticals, nutraceuticals, cosmetics, and biofuels. The low abundance or yield of limonene and bisabolene in plants renders their isolation from plant sources non-economically viable. Isolation of limonene and bisabolene from plants also suffers from low efficiency and often requires harsh reaction conditions, prolonged reaction times, and expensive equipment cost. Recently, the rapid developments in metabolic engineering of microbes provide a promising alternative route for producing these plant natural products. Therefore, producing limonene and bisabolene by engineering microbial cells into microbial factories is becoming an attractive alternative approach that can overcome the bottlenecks, making it more sustainable, environmentally friendly and economically competitive. Here, we reviewed the status of metabolic engineering of microbes that produce limonene and bisabolene including microbial hosts, key enzymes, metabolic pathways and engineering of limonene/bisabolene biosynthesis. Furthermore, key challenges and future perspectives were discussed.

Complex classical paths and the one-dimensional sine-Gordon system

International Nuclear Information System (INIS)

Millard, P.A.

1985-01-01

The semiclassical limit of the Green function for a particle in the one-dimensional sine-Gordon potential is obtained by summing over complex classical paths. The results are the same as those obtained in the less physically intuitive WKB approach. In addition to being of practical utility for solving quantum mechanical problems involving tunnelling, the classical path method may show how to deal with dense configuration of instantons. (orig.)

Dynamic gene expression for metabolic engineering of mammalian cells in culture.

Science.gov (United States)

Le, Huong; Vishwanathan, Nandita; Kantardjieff, Anne; Doo, Inseok; Srienc, Michael; Zheng, Xiaolu; Somia, Nikunj; Hu, Wei-Shou

2013-11-01

Recombinant mammalian cells are the major hosts for the production of protein therapeutics. In addition to high expression of the product gene, a hyper-producer must also harbor superior phenotypic traits related to metabolism, protein secretion, and growth control. Introduction of genes endowing the relevant hyper-productivity traits is a strategy frequently used to enhance the productivity. Most of such cell engineering efforts have been performed using constitutive expression systems. However, cells respond to various environmental cues and cellular events dynamically according to cellular needs. The use of inducible systems allows for time dependent expression, but requires external manipulation. Ideally, a transgene's expression should be synchronous to the host cell's own rhythm, and at levels appropriate for the objective. To that end, we identified genes with different expression dynamics and intensity ranges using pooled transcriptome data. Their promoters may be used to drive the expression of the transgenes following the desired dynamics. We isolated the promoter of the Thioredoxin-interacting protein (Txnip) gene and demonstrated its capability to drive transgene expression in concert with cell growth. We further employed this Chinese hamster promoter to engineer dynamic expression of the mouse GLUT5 fructose transporter in Chinese hamster ovary (CHO) cells, enabling them to utilize sugar according to cellular needs rather than in excess as typically seen in culture. Thus, less lactate was produced, resulting in a better growth rate, prolonged culture duration, and higher product titer. This approach illustrates a novel concept in metabolic engineering which can potentially be used to achieve dynamic control of cellular behaviors for enhanced process characteristics. © 2013 Published by Elsevier Inc.

Synthetic biology for engineering acetyl coenzyme a metabolism in yeast

DEFF Research Database (Denmark)

Nielsen, Jens

2014-01-01

The yeast Saccharomyces cerevisiae is a widely used cell factory for the production of fuels, chemicals, and pharmaceuticals. The use of this cell factory for cost-efficient production of novel fuels and chemicals requires high yields and low by-product production. Many industrially interesting...... chemicals are biosynthesized from acetyl coenzyme A (acetyl-CoA), which serves as a central precursor metabolite in yeast. To ensure high yields in production of these chemicals, it is necessary to engineer the central carbon metabolism so that ethanol production is minimized (or eliminated) and acetyl...

Perron-Frobenius operators and the Klein-Gordon equation

OpenAIRE

Canto-Martin, Francisco; Hedenmalm, Haakan; Montes-Rodriguez, Alfonso

2012-01-01

For a smooth curve Γ and a set Λ in the plane R2, let AC(Γ; Λ) be the space of finite Borel measures in the plane supported on Γ, absolutely continuous with respect to the arc length and whose Fourier transform vanishes on Λ. Following [12], we say that (Γ, Λ) is a Heisenberg uniqueness pair if AC(Γ; Λ) = {0}. In the context of a hyperbola Γ, the study of Heisenberg uniqueness pairs is the same as looking for uniqueness sets Λ of a collection of solutions to the Klein-Gordon equation. In t...

Engineering yeast metabolism for production of terpenoids for use as perfume ingredients, pharmaceuticals and biofuels.

Science.gov (United States)

Zhang, Yueping; Nielsen, Jens; Liu, Zihe

2017-12-01

Terpenoids represent a large class of natural products with significant commercial applications. These chemicals are currently mainly obtained through extraction from plants and microbes or through chemical synthesis. However, these sources often face challenges of unsustainability and low productivity. In order to address these issues, Escherichia coli and yeast have been metabolic engineered to produce non-native terpenoids. With recent reports of engineering yeast metabolism to produce several terpenoids at high yields, it has become possible to establish commercial yeast production of terpenoids that find applications as perfume ingredients, pharmaceuticals and advanced biofuels. In this review, we describe the strategies to rewire the yeast pathway for terpenoid biosynthesis. Recent advances will be discussed together with challenges and perspectives of yeast as a cell factory to produce different terpenoids. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Advances in metabolic engineering of yeast Saccharomyces cerevisiae for production of chemicals.

Science.gov (United States)

Borodina, Irina; Nielsen, Jens

2014-05-01

Yeast Saccharomyces cerevisiae is an important industrial host for production of enzymes, pharmaceutical and nutraceutical ingredients and recently also commodity chemicals and biofuels. Here, we review the advances in modeling and synthetic biology tools and how these tools can speed up the development of yeast cell factories. We also present an overview of metabolic engineering strategies for developing yeast strains for production of polymer monomers: lactic, succinic, and cis,cis-muconic acids. S. cerevisiae has already firmly established itself as a cell factory in industrial biotechnology and the advances in yeast strain engineering will stimulate development of novel yeast-based processes for chemicals production. Copyright © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications.

Science.gov (United States)

Lin, Jyun-Liang; Wagner, James M; Alper, Hal S

2017-12-01

Within the Design-Build-Test Cycle for strain engineering, rapid product detection and selection strategies remain challenging and limit overall throughput. Here we summarize a wide variety of modalities that transduce chemical concentrations into easily measured absorbance, luminescence, and fluorescence signals. Specifically, we cover protein-based biosensors (including transcription factors), nucleic acid-based biosensors, coupled enzyme reactions, bioorthogonal chemistry, and fluorescent and chromogenic dyes and substrates as modalities for detection. We focus on the use of these methods for strain engineering and enzyme discovery and conclude with remarks on the current and future state of biosensor development for application in the metabolic engineering field. Copyright © 2017 Elsevier Inc. All rights reserved.

Separable coordinates and particle creation I: the klein-Gordon equation

International Nuclear Information System (INIS)

Costa, Isaias

1987-01-01

A very simple derivation of the 10 orthogonal coordinate systems where the Klein-Gordon equation separates is presented. It is based on the conformal structure of the two dimensional Minkowski space. Horizons, proper time and acceleration of abserves that follow the time coordinate line, as well as other physical properties of the systems, are obtained. The relevance of these coordinates is discussed, specially in the context of quantum field theory in curved space. (author) [pt

Metabolic engineering of carbon overflow metabolism of Bacillus subtilis for improved N-acetyl-glucosamine production.

Science.gov (United States)

Ma, Wenlong; Liu, Yanfeng; Shin, Hyun-Dong; Li, Jianghua; Chen, Jian; Du, Guocheng; Liu, Long

2018-02-01

Bacillus subtilis is widely used as cell factories for the production of important industrial biochemicals. Although many studies have demonstrated the effects of organic acidic byproducts, such as acetate, on microbial fermentation, little is known about the effects of blocking the neutral byproduct overflow, such as acetoin, on bioproduction. In this study, we focused on the influences of modulating overflow metabolism on the production of N-acetyl-d-glucosamine (GlcNAc) in engineered B. subtilis. We found that acetoin overflow competes with GlcNAc production, and blocking acetoin overflow increased GlcNAc titer and yield by 1.38- and 1.39-fold, reaching 48.9 g/L and 0.32 g GlcNAc/g glucose, respectively. Further blocking acetate overflow inhibited cell growth and GlcNAc production may be induced by inhibiting glucose uptake. Taken together, our results show that blocking acetoin overflow is a promising strategy for enhancing GlcNAc production. The strategies developed in this work may be useful for engineering strains of B. subtilis for producing other important biochemicals. Copyright © 2017. Published by Elsevier Ltd.

Promiscuous activities of heterologous enzymes lead to unintended metabolic rerouting in Saccharomyces cerevisiae engineered to assimilate various sugars from renewable biomass.

Science.gov (United States)

Yun, Eun Ju; Oh, Eun Joong; Liu, Jing-Jing; Yu, Sora; Kim, Dong Hyun; Kwak, Suryang; Kim, Kyoung Heon; Jin, Yong-Su

2018-01-01

Understanding the global metabolic network, significantly perturbed upon promiscuous activities of foreign enzymes and different carbon sources, is crucial for systematic optimization of metabolic engineering of yeast Saccharomyces cerevisiae . Here, we studied the effects of promiscuous activities of overexpressed enzymes encoded by foreign genes on rerouting of metabolic fluxes of an engineered yeast capable of assimilating sugars from renewable biomass by profiling intracellular and extracellular metabolites. Unbiased metabolite profiling of the engineered S. cerevisiae strain EJ4 revealed promiscuous enzymatic activities of xylose reductase and xylitol dehydrogenase on galactose and galactitol, respectively, resulting in accumulation of galactitol and tagatose during galactose fermentation. Moreover, during glucose fermentation, a trisaccharide consisting of glucose accumulated outside of the cells probably owing to the promiscuous and transglycosylation activity of β-glucosidase expressed for hydrolyzing cellobiose. Meanwhile, higher accumulation of fatty acids and secondary metabolites was observed during xylose and cellobiose fermentations, respectively. The heterologous enzymes functionally expressed in S. cerevisiae showed promiscuous activities that led to unintended metabolic rerouting in strain EJ4. Such metabolic rerouting could result in a low yield and productivity of a final product due to the formation of unexpected metabolites. Furthermore, the global metabolic network can be significantly regulated by carbon sources, thus yielding different patterns of metabolite production. This metabolomic study can provide useful information for yeast strain improvement and systematic optimization of yeast metabolism to manufacture bio-based products.

Flux Balance Analysis Inspired Bioprocess Upgrading for Lycopene Production by a Metabolically Engineered Strain of Yarrowia lipolytica

Directory of Open Access Journals (Sweden)

Komi Nambou

2015-12-01

Full Text Available Genome-scale metabolic models embody a significant advantage of systems biology since their applications as metabolic flux simulation models enable predictions for the production of industrially-interesting metabolites. The biotechnological production of lycopene from Yarrowia lipolytica is an emerging scope that has not been fully scrutinized, especially for what concerns cultivation conditions of newly generated engineered strains. In this study, by combining flux balance analysis (FBA and Plackett-Burman design, we screened chemicals for lycopene production from a metabolically engineered strain of Y. lipolytica. Lycopene concentrations of 126 and 242 mg/L were achieved correspondingly from the FBA-independent and the FBA-assisted designed media in fed-batch cultivation mode. Transcriptional studies revealed upregulations of heterologous genes in media designed according to FBA, thus implying the efficiency of model predictions. Our study will potentially support upgraded lycopene and other terpenoids production from existing or prospect bioengineered strains of Y. lipolytica and/or closely related yeast species.

Recent advances in engineering propionyl-CoA metabolism for microbial production of value-added chemicals and biofuels.

Science.gov (United States)

Srirangan, Kajan; Bruder, Mark; Akawi, Lamees; Miscevic, Dragan; Kilpatrick, Shane; Moo-Young, Murray; Chou, C Perry

2017-09-01

Diminishing fossil fuel reserves and mounting environmental concerns associated with petrochemical manufacturing practices have generated significant interests in developing whole-cell biocatalytic systems for the production of value-added chemicals and biofuels. Although acetyl-CoA is a common natural biogenic precursor for the biosynthesis of numerous metabolites, propionyl-CoA is unpopular and non-native to most organisms. Nevertheless, with its C3-acyl moiety as a discrete building block, propionyl-CoA can serve as another key biogenic precursor to several biological products of industrial importance. As a result, engineering propionyl-CoA metabolism, particularly in genetically tractable hosts with the use of inexpensive feedstocks, has paved an avenue for novel biomanufacturing. Herein, we present a systematic review on manipulation of propionyl-CoA metabolism as well as relevant genetic and metabolic engineering strategies for microbial production of value-added chemicals and biofuels, including odd-chain alcohols and organic acids, bio(co)polymers and polyketides. [Formula: see text].

A no-man's-land of sex: Reading Stephen Gordon and "her" critics.

Science.gov (United States)

Costello, Katherine A

2018-04-03

One of the most read novels of lesbian, transgender, and queer criticism, Radclyffe Hall's novel The Well of Loneliness (1928) has given rise to numerous and contradictory interpretations of the protagonist Stephen Gordon's complex relationship to her body. Some have argued that she is a historically specific example of female masculinity, others that she is a lesbian who wishes she were more feminine, and others still that she is a prototypical transsexual character. Focusing on the exemplary essays by Jack Halberstam, Teresa de Lauretis, and Jay Prosser, I argue that the coexistence of mutually exclusive interpretations of Stephen Gordon's relationship to her femaleness suggests that the novel is, in fact, a demand to readers to unmoor identity from sex and to recognize what I call "sexual indeterminacy." Lesbian, transgender, and queer theory's tendency to elide the literariness of literary objects and their reliance on critique as the primary mode of reading and argumentation have made it impossible for critics to see that the novel is explicitly about what cannot be settled.

Lessons learned from metabolic engineering of cyanogenic glucosides

DEFF Research Database (Denmark)

Morant, Anne Vinther; Jørgensen, Kirsten; Jørgensen, Bodil

2007-01-01

Plants produce a plethora of secondary metabolites which constitute a wealth of potential pharmaceuticals, pro-vitamins, flavours, fragrances, colorants and toxins as well as a source of natural pesticides. Many of these valuable compounds are only synthesized in exotic plant species or in concen......Plants produce a plethora of secondary metabolites which constitute a wealth of potential pharmaceuticals, pro-vitamins, flavours, fragrances, colorants and toxins as well as a source of natural pesticides. Many of these valuable compounds are only synthesized in exotic plant species...... or in concentrations too low to facilitate commercialization. In some cases their presence constitutes a health hazard and renders the crops unsuitable for consumption. Metabolic engineering is a powerful tool to alter and ameliorate the secondary metabolite composition of crop plants and gain new desired traits...

Low-mode truncation methods in the sine-Gordon equation

International Nuclear Information System (INIS)

Xiong Chuyu.

1991-01-01

In this dissertation, the author studies the chaotic and coherent motions (i.e., low-dimensional chaotic attractor) in some near integrable partial differential equations, particularly the sine-Gordon equation and the nonlinear Schroedinger equation. In order to study the motions, he uses low mode truncation methods to reduce these partial differential equations to some truncated models (low-dimensional ordinary differential equations). By applying many methods available to low-dimensional ordinary differential equations, he can understand the low-dimensional chaotic attractor of PDE's much better. However, there are two important questions one needs to answer: (1) How many modes is good enough for the low mode truncated models to capture the dynamics uniformly? (2) Is the chaotic attractor in a low mode truncated model close to the chaotic attractor in the original PDE? And how close is? He has developed two groups of powerful methods to help to answer these two questions. They are the computation methods of continuation and local bifurcation, and local Lyapunov exponents and Lyapunov exponents. Using these methods, he concludes that the 2N-nls ODE is a good model for the sine-Gordon equation and the nonlinear Schroedinger equation provided one chooses a 'good' basis and uses 'enough' modes (where 'enough' depends on the parameters of the system but is small for the parameter studied here). Therefore, one can use 2N-nls ODE to study the chaos of PDE's in more depth

2010 Gordon Research Conference, Electrochemistry, January 9-15, 2010

Energy Technology Data Exchange (ETDEWEB)

Creager, Stephen [Clemson Univ., SC (United States)

2010-12-31

Electrochemical science plays a crucial role in many important technologies and is intimately involved in many natural phenomena. Several new Gordon Research Conferences have appeared recently that are dedicated to electrochemical technologies, however electrochemistry as a discipline continues to thrive and provide the underpinnings of these technologies. The 2010 Electrochemistry GRC will focus on a wide range of fundamental electrochemical phenomena and materials and on their application in areas involving energy storage, information storage, chemical analysis, and motion actuation. The meeting will include sessions dedicated to the following specific topics: electrochemical energy storage (e.g. batteries; at least two sessions); electrochemical motion actuation (e.g. electrokinesis); electrocatalysis; electrochemistry in digital information storage; and bioelectrochemistry (including bioanalysis). An Open Session devoted to highlighting the activities of {approx}10 young investigators and non-North American visitors via brief 10-minute talks, and two open poster sessions highlighting the contributions of approximately 60 conference participants including graduate students, will be held. Altogether the conference is expected to include approximately 90 presentations. As has been the case in the recent past, the meeting will bring together participants from academia, national labs, and the private sector, including senior and junior-level scientists, postdoctoral scientists, and graduate students for informal interactions and exchange of ideas. An affiliated Gordon-Kenan Research Seminar (GRS) will also be held with the conference. Special efforts will be made to invite participation from members of underrepresented groups.

Terpene metabolic engineering via nuclear or chloroplast genomes profoundly and globally impacts off-target pathways through metabolite signalling.

Science.gov (United States)

Pasoreck, Elise K; Su, Jin; Silverman, Ian M; Gosai, Sager J; Gregory, Brian D; Yuan, Joshua S; Daniell, Henry

2016-09-01

The impact of metabolic engineering on nontarget pathways and outcomes of metabolic engineering from different genomes are poorly understood questions. Therefore, squalene biosynthesis genes FARNESYL DIPHOSPHATE SYNTHASE (FPS) and SQUALENE SYNTHASE (SQS) were engineered via the Nicotiana tabacum chloroplast (C), nuclear (N) or both (CN) genomes to promote squalene biosynthesis. SQS levels were ~4300-fold higher in C and CN lines than in N, but all accumulated ~150-fold higher squalene due to substrate or storage limitations. Abnormal leaf and flower phenotypes, including lower pollen production and reduced fertility, were observed regardless of the compartment or level of transgene expression. Substantial changes in metabolomes of all lines were observed: levels of 65-120 unrelated metabolites, including the toxic alkaloid nicotine, changed by as much as 32-fold. Profound effects of transgenesis on nontarget gene expression included changes in the abundance of 19 076 transcripts by up to 2000-fold in CN; 7784 transcripts by up to 1400-fold in N; and 5224 transcripts by as much as 2200-fold in C. Transporter-related transcripts were induced, and cell cycle-associated transcripts were disproportionally repressed in all three lines. Transcriptome changes were validated by qRT-PCR. The mechanism underlying these large changes likely involves metabolite-mediated anterograde and/or retrograde signalling irrespective of the level of transgene expression or end product, due to imbalance of metabolic pools, offering new insight into both anticipated and unanticipated consequences of metabolic engineering. © 2016 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Patchoulol Production with Metabolically Engineered Corynebacterium glutamicum

Directory of Open Access Journals (Sweden)

Nadja A. Henke

2018-04-01

Full Text Available Patchoulol is a sesquiterpene alcohol and an important natural product for the perfume industry. Corynebacterium glutamicum is the prominent host for the fermentative production of amino acids with an average annual production volume of ~6 million tons. Due to its robustness and well established large-scale fermentation, C. glutamicum has been engineered for the production of a number of value-added compounds including terpenoids. Both C40 and C50 carotenoids, including the industrially relevant astaxanthin, and short-chain terpenes such as the sesquiterpene valencene can be produced with this organism. In this study, systematic metabolic engineering enabled construction of a patchoulol producing C. glutamicum strain by applying the following strategies: (i construction of a farnesyl pyrophosphate-producing platform strain by combining genomic deletions with heterologous expression of ispA from Escherichia coli; (ii prevention of carotenoid-like byproduct formation; (iii overproduction of limiting enzymes from the 2-c-methyl-d-erythritol 4-phosphate (MEP-pathway to increase precursor supply; and (iv heterologous expression of the plant patchoulol synthase gene PcPS from Pogostemon cablin. Additionally, a proof of principle liter-scale fermentation with a two-phase organic overlay-culture medium system for terpenoid capture was performed. To the best of our knowledge, the patchoulol titers demonstrated here are the highest reported to date with up to 60 mg L−1 and volumetric productivities of up to 18 mg L−1 d−1.

An Implicit Scheme of Lattice Boltzmann Method for Sine-Gordon Equation

International Nuclear Information System (INIS)

Hui-Lin, Lai; Chang-Feng, Ma

2008-01-01

We establish an implicit scheme of lattice Boltzmann method for simulating the sine-Gordon equation, which can be transformed into the explicit one, so the computation of the scheme is simple. Moreover, the parameter θ of the implicit scheme is independent of the relaxation time, which makes the model more flexible. The numerical results show that this method is very effective. (fundamental areas of phenomenology (including applications))

Renormalization group study of the multi-layer sine-gordon model

International Nuclear Information System (INIS)

Nandori, I.

2005-01-01

Complete text of publication follows. We analyze the phase structure of the system of coupled sine-Gordon (SG) type field theoric models. The 'pure,' SG model is periodic in the internal space spanned by the field variable. The central subjects of investigation is the multi-layer sine-Gordon (LSG) model, where the periodicity is broken partially by the coupling terms between the layers each of which is described by a scalar field, where the second term on the r.h.s. describes the interaction of the layers. Here, we dis- cuss the generalization of the results obtained for the two-layer sine-Gordon model found in the previous study. Besides the obvious field theoretical interest, the LSG model has been used to describe the vortex properties of high transition temperature superconductors, and the extension of the previous analysis to a general N-layer model is necessary for a description of the critical behaviour of vortices in realistic multi-layer systems. The couplings between the layers can be considered as mass terms. Since the periodicity of the LSG model has been broken only partially, the N-layer model has always a single zero mass eigenvalue. The presence of this single zero mass eigenvalue is found to be decisive with respect to the phase structure of the N-layer models. By a suitable rotation of the field variables, we identify the periodic mode (which corresponds to the zero mass eigenvalue) and N - 1 non-periodic modes (with explicit mass terms). The N - 1 non-periodic modes have a trivial IR scaling which holds independently of β which has been proven consistently using (i) the non-perturbative renormalization group study of the rotated model, (ii) the Gaussian integration about the vanishing-field saddle point. Due to the presence of the periodic mode the model undergoes a Kosterlitz-Thouless type phase transition which occurs at a coupling parameter β c 2 = 8Nπ, where N is the number of layers. The critical value β c 2 corresponds to the critical

Post-Gaussian Effective Potential of Double sine-Gordon Field

International Nuclear Information System (INIS)

Cai Weiran; Lou Senyue

2005-01-01

In the framework of the functional integral formalism, we calculate the effective potential of the double sine-Gordon (DsG) model up to the second order with an optimized expansion and the Coleman's normal-ordering prescription. Within the range of convergence, we make a comparison among the classical and the effective potential of the first and second order. The numerical analysis shows that the DsG post-Gaussian EP possesses some fine global properties and makes a substantial and a concordant quantum correction to the features of the classical potential.

2012 Gordon Research Conference, Electron donor-acceptor interactions, August 5-10 2012

Energy Technology Data Exchange (ETDEWEB)

McCusker, James [Michigan State Univ., East Lansing, MI (United States)

2012-08-10

The upcoming incarnation of the Gordon Research Conference on Electron Donor Acceptor Interactions will feature sessions on classic topics including proton-coupled electron transfer, dye-sensitized solar cells, and biological electron transfer, as well as emerging areas such as quantum coherence effects in donor-acceptor interactions, spintronics, and the application of donor-acceptor interactions in chemical synthesis.

Sine-Gordon 2-pi-kink dynamics in the presence of small perturbations

DEFF Research Database (Denmark)

Olsen, O. H.; Samuelsen, Mogens Rugholm

1983-01-01

The influence of external driving forces on the 2π-kink solution to the sine-Gordon equation is examined. The analysis is based on the approach that the solution to the problem can be divided into a 2π-kink part and a background or vacuum part. The behavior of the 2π kink depends strongly...

Simple connection between conservation laws in the Korteweg--de Vriesand sine-Gordon systems

International Nuclear Information System (INIS)

Chodos, A.

1980-01-01

An infinite sequence of conserved quantities follows from the Lax representation in both the Korteweg--de Vries and sine-Gordon systems. We show that these two sequences are related by a simple substitution. In an appendix, two different methods of deriving conservation laws from the Lax representation are presented

Overproduction of Geranylgeraniol by Metabolically Engineered Saccharomyces cerevisiae▿

Science.gov (United States)

Tokuhiro, Kenro; Muramatsu, Masayoshi; Ohto, Chikara; Kawaguchi, Toshiya; Obata, Shusei; Muramoto, Nobuhiko; Hirai, Masana; Takahashi, Haruo; Kondo, Akihiko; Sakuradani, Eiji; Shimizu, Sakayu

2009-01-01

(E, E, E)-Geranylgeraniol (GGOH) is a valuable starting material for perfumes and pharmaceutical products. In the yeast Saccharomyces cerevisiae, GGOH is synthesized from the end products of the mevalonate pathway through the sequential reactions of farnesyl diphosphate synthetase (encoded by the ERG20 gene), geranylgeranyl diphosphate synthase (the BTS1 gene), and some endogenous phosphatases. We demonstrated that overexpression of the diacylglycerol diphosphate phosphatase (DPP1) gene could promote GGOH production. We also found that overexpression of a BTS1-DPP1 fusion gene was more efficient for producing GGOH than coexpression of these genes separately. Overexpression of the hydroxymethylglutaryl-coenzyme A reductase (HMG1) gene, which encodes the major rate-limiting enzyme of the mevalonate pathway, resulted in overproduction of squalene (191.9 mg liter−1) rather than GGOH (0.2 mg liter−1) in test tube cultures. Coexpression of the BTS1-DPP1 fusion gene along with the HMG1 gene partially redirected the metabolic flux from squalene to GGOH. Additional expression of a BTS1-ERG20 fusion gene resulted in an almost complete shift of the flux to GGOH production (228.8 mg liter−1 GGOH and 6.5 mg liter−1 squalene). Finally, we constructed a diploid prototrophic strain coexpressing the HMG1, BTS1-DPP1, and BTS1-ERG20 genes from multicopy integration vectors. This strain attained 3.31 g liter−1 GGOH production in a 10-liter jar fermentor with gradual feeding of a mixed glucose and ethanol solution. The use of bifunctional fusion genes such as the BTS1-DPP1 and ERG20-BTS1 genes that code sequential enzymes in the metabolic pathway was an effective method for metabolic engineering. PMID:19592534

Engineering synergy in biotechnology

DEFF Research Database (Denmark)

Nielsen, Jens; Fussenegger, Martin; Keasling, Jay

2014-01-01

In this article, the author focuses on approaches in metabolic engineering and synthetic biology for the creation of efficient cell factories, which can be bused to convert biomass and other feedstocks for the generation of chemicals. Topics discussed include development of restriction enzymes......, engineering plasmids and recyclable markers, production of 1,3-propanediol using a metabolically engineered Escherichia coli and production of isobutanol by using metabolically engineered yeast....

Metabolic engineering of deinococcus radiodurans based on computational analysis and functional genomics

Energy Technology Data Exchange (ETDEWEB)

Edwards, Jeremy, S.

2005-02-02

The objective of our work is to develop novel computational tools to analyze the Deinococcus radiodurans DNA repair pathways and the influence of the metabolic flux distribution on DNA repair. These tools will be applied to provide insights for metabolic engineering of strains capable of growing under nutrient poor conditions similar to those found in mixed contaminant sites of interest to the DOE. Over the entire grant period we accomplished all our specific aims and were also able to pursue new directions of research. Below, I will list the major accomplishments over the previous 3 years. (1) Performed Monte Carlo Simulations of RecA Mediated Pairing of Homologous DNA Molecules. (2) Developed a statistical approach to study the gene expression data from D. radiodurans. We have been studying the data from John Batista's. (3) Developed an expression profiling technology to generate very accurate and precise expression data. We followed up on results from John Batista's group using this approach. (4) Developed and put online a database for metabolic reconstructions. (5) We have developed and applied new Monte Carlo algorithms that are optimized for studying biological systems. (6) We developed a flux balance model for the D. radiodurans metabolic network

Operational Solution to the Nonlinear Klein-Gordon Equation

Science.gov (United States)

Bengochea, G.; Verde-Star, L.; Ortigueira, M.

2018-05-01

We obtain solutions of the nonlinear Klein-Gordon equation using a novel operational method combined with the Adomian polynomial expansion of nonlinear functions. Our operational method does not use any integral transforms nor integration processes. We illustrate the application of our method by solving several examples and present numerical results that show the accuracy of the truncated series approximations to the solutions. Supported by Grant SEP-CONACYT 220603, the first author was supported by SEP-PRODEP through the project UAM-PTC-630, the third author was supported by Portuguese National Funds through the FCT Foundation for Science and Technology under the project PEst-UID/EEA/00066/2013

Quantum aspects of the noncommutative Sine-Gordon model

International Nuclear Information System (INIS)

Kuerkcueoglu

2007-01-01

In this talk, I will first present some of the quantum field theoretical aspects of the integrable noncommutative sine-Gordon model proposed in [hep-th/0406065] using standard semi-classical methods. In particular, I will discuss the fluctuations at quadratic order around the static kink solution using the background field method. I will argue that at 0(θ 2 ) the spectrum of fluctuations remains essentially the same as that of the corresponding commutative theory. A brief analysis of one-loop two-point functions will also be presented and it will be followed by some remarks on the obstacles in determining the noncommutativity corrections to the quantum mass of the kink. (author)

Entanglement between smeared field operators in the Klein-Gordon vacuum

International Nuclear Information System (INIS)

Zych, Magdalena; Costa, Fabio; Kofler, Johannes; Brukner, Caslav

2010-01-01

Quantum field theory is the application of quantum physics to fields. It provides a theoretical framework widely used in particle physics and condensed matter physics. One of the most distinct features of quantum physics with respect to classical physics is entanglement or the existence of strong correlations between subsystems that can even be spacelike separated. In quantum fields, observables restricted to a region of space define a subsystem. While there are proofs on the existence of local observables that would allow a violation of Bell's inequalities in the vacuum states of quantum fields as well as some explicit but technically demanding schemes requiring an extreme fine-tuning of the interaction between the fields and detectors, an experimentally accessible entanglement witness for quantum fields is still missing. Here we introduce smeared field operators which allow reducing the vacuum to a system of two effective bosonic modes. The introduction of such collective observables is motivated by the fact that no physical probe has access to fields in single spatial (mathematical) points but rather smeared over finite volumes. We first give explicit collective observables whose correlations reveal vacuum entanglement in the Klein-Gordon field. We then show that the critical distance between the two regions of space above which two effective bosonic modes become separable is of the order of the Compton wavelength of the particle corresponding to the massive Klein-Gordon field.

L-Cysteine Production in Escherichia coli Based on Rational Metabolic Engineering and Modular Strategy.

Science.gov (United States)

Liu, Han; Fang, Guochen; Wu, Hui; Li, Zhimin; Ye, Qin

2018-05-01

L-cysteine is an amino acid with important physiological functions and has a wide range of applications in medicine, food, animal feed, and cosmetics industry. In this study, the L-cysteine synthesis in Escherichia coliEscherichia coli is divided into four modules: the transport module, sulfur module, precursor module, and degradation module. The engineered strain LH03 (overexpression of the feedback-insensitive cysE and the exporter ydeD in JM109) accumulated 45.8 mg L -1 of L-cysteine in 48 hr with yield of 0.4% g/g glucose. Further modifications of strains and culture conditions which based on the rational metabolic engineering and modular strategy improved the L-cysteine biosynthesis significantly. The engineered strain LH06 (with additional overexpression of serA, serC, and serB and double mutant of tnaA and sdaA in LH03) produced 620.9 mg L -1 of L-cysteine with yield of 6.0% g/g glucose, which increased the production by 12 times and the yield by 14 times more than those of LH03 in the original condition. In fed-batch fermentation performed in a 5-L reactor, the concentration of L-cysteine achieved 5.1 g L -1 in 32 hr. This work demonstrates that the combination of rational metabolic engineering and module strategy is a promising approach for increasing the L-cysteine production in E. coli. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On a Kubo-Martin-Schwinger state of the Sine-Gordon system

International Nuclear Information System (INIS)

Peskov, N.V.

1986-01-01

This paper considers the Sine-Gordon equation on a finite interval as a Hamiltonian system. A Gaussian measure is defined on an extension of the phase space. It is shown that the partition funciton Z employed in the statistical mechanics of the solitons is an integral with respect to this measure. An algebra of observables is defined and on it a state is constructed which satisfies the Kubo-Martin-Schwinger condition

In vitro metabolic engineering for the salvage synthesis of NAD(.).

Science.gov (United States)

Honda, Kohsuke; Hara, Naoya; Cheng, Maria; Nakamura, Anna; Mandai, Komako; Okano, Kenji; Ohtake, Hisao

2016-05-01

Excellent thermal and operational stabilities of thermophilic enzymes can greatly increase the applicability of biocatalysis in various industrial fields. However, thermophilic enzymes are generally incompatible with thermo-labile substrates, products, and cofactors, since they show the maximal activities at high temperatures. Despite their pivotal roles in a wide range of enzymatic redox reactions, NAD(P)(+) and NAD(P)H exhibit relatively low stabilities at high temperatures, tending to be a major obstacle in the long-term operation of biocatalytic chemical manufacturing with thermophilic enzymes. In this study, we constructed an in vitro artificial metabolic pathway for the salvage synthesis of NAD(+) from its degradation products by the combination of eight thermophilic enzymes. The enzymes were heterologously produced in recombinant Escherichia coli and the heat-treated crude extracts of the recombinant cells were directly used as enzyme solutions. When incubated with experimentally optimized concentrations of the enzymes at 60°C, the NAD(+) concentration could be kept almost constant for 15h. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Biosynthesis and metabolic engineering of palmitoleate production, an important contributor to human health and sustainable industry.

Science.gov (United States)

Wu, Yongmei; Li, Runzhi; Hildebrand, David F

2012-10-01

Palmitoleate (cis-Δ9-16:1) shows numerous health benefits such as increased cell membrane fluidity, reduced inflammation, protection of the cardiovascular system, and inhibition of oncogenesis. Plant oils containing this unusual fatty acid can also be sustainable feedstocks for producing industrially important and high-demand 1-octene. Vegetable oils rich in palmitoleate are the ideal candidates for biodiesel production. Several wild plants are known that can synthesize high levels of palmitoleate in seeds. However, low yields and poor agronomic characteristics of these plants limit their commercialization. Metabolic engineering has been developed to create oilseed crops that accumulate high levels of palmitoleate or other unusual fatty acids, and significant advances have been made recently in this field, particularly using the model plant Arabidopsis as the host. The engineered targets for enhancing palmitoleate synthesis include overexpression of Δ9 desaturase from mammals, yeast, fungi, and plants, down-regulating KASII, coexpression of an ACP-Δ9 desaturase in plastids and CoA-Δ9 desaturase in endoplasmic reticulum (ER), and optimizing the metabolic flux into triacylglycerols (TAGs). This review will mainly describe the recent progress towards producing palmitoleate in transgenic plants by metabolic engineering along with our current understanding of palmitoleate biosynthesis and its regulation, as well as highlighting the bottlenecks that require additional investigation by combining lipidomics, transgenics and other "-omics" tools. A brief review of reported health benefits and non-food uses of palmitoleate will also be covered. Copyright © 2012. Published by Elsevier Ltd.

Systems-wide metabolic pathway engineering in Corynebacterium glutamicum for bio-based production of diaminopentane.

Science.gov (United States)

Kind, Stefanie; Jeong, Weol Kyu; Schröder, Hartwig; Wittmann, Christoph

2010-07-01

In the present work the Gram-positive bacterium Corynebacterium glutamicum was engineered into an efficient, tailor-made production strain for diaminopentane (cadaverine), a highly attractive building block for bio-based polyamides. The engineering comprised expression of lysine decarboxylase (ldcC) from Escherichia coli, catalyzing the conversion of lysine into diaminopentane, and systems-wide metabolic engineering of central supporting pathways. Substantially re-designing the metabolism yielded superior strains with desirable properties such as (i) the release from unwanted feedback regulation at the level of aspartokinase and pyruvate carboxylase by introducing the point mutations lysC311 and pycA458, (ii) an optimized supply of the key precursor oxaloacetate by amplifying the anaplerotic enzyme, pyruvate carboxylase, and deleting phosphoenolpyruvate carboxykinase which otherwise removes oxaloacetate, (iii) enhanced biosynthetic flux via combined amplification of aspartokinase, dihydrodipicolinate reductase, diaminopimelate dehydrogenase and diaminopimelate decarboxylase, and (iv) attenuated flux into the threonine pathway competing with production by the leaky mutation hom59 in the homoserine dehydrogenase gene. Lysine decarboxylase proved to be a bottleneck for efficient production, since its in vitro activity and in vivo flux were closely correlated. To achieve an optimal strain having only stable genomic modifications, the combination of the strong constitutive C. glutamicum tuf promoter and optimized codon usage allowed efficient genome-based ldcC expression and resulted in a high diaminopentane yield of 200 mmol mol(-1). By supplementing the medium with 1 mgL(-1) pyridoxal, the cofactor of lysine decarboxylase, the yield was increased to 300 mmol mol(-1). In the production strain obtained, lysine secretion was almost completely abolished. Metabolic analysis, however, revealed substantial formation of an as yet unknown by-product. It was identified as an

Production of the sesquiterpenoid (+)-nootkatone by metabolic engineering of Pichia pastoris.

Science.gov (United States)

Wriessnegger, Tamara; Augustin, Peter; Engleder, Matthias; Leitner, Erich; Müller, Monika; Kaluzna, Iwona; Schürmann, Martin; Mink, Daniel; Zellnig, Günther; Schwab, Helmut; Pichler, Harald

2014-07-01

The sesquiterpenoid (+)-nootkatone is a highly demanded and highly valued aroma compound naturally found in grapefruit, pummelo or Nootka cypress tree. Extraction of (+)-nootkatone from plant material or its production by chemical synthesis suffers from low yields and the use of environmentally harmful methods, respectively. Lately, major attention has been paid to biotechnological approaches, using cell extracts or whole-cell systems for the production of (+)-nootkatone. In our study, the yeast Pichia pastoris initially was applied as whole-cell biocatalyst for the production of (+)-nootkatone from (+)-valencene, the abundant aroma compound of oranges. Therefore, we generated a strain co-expressing the premnaspirodiene oxygenase of Hyoscyamus muticus (HPO) and the Arabidopsis thaliana cytochrome P450 reductase (CPR) that hydroxylated extracellularly added (+)-valencene. Intracellular production of (+)-valencene by co-expression of valencene synthase from Callitropsis nootkatensis resolved the phase-transfer issues of (+)-valencene. Bi-phasic cultivations of P. pastoris resulted in the production of trans-nootkatol, which was oxidized to (+)-nootkatone by an intrinsic P. pastoris activity. Additional overexpression of a P. pastoris alcohol dehydrogenase and truncated hydroxy-methylglutaryl-CoA reductase (tHmg1p) significantly enhanced the (+)-nootkatone yield to 208mg L(-1) cell culture in bioreactor cultivations. Thus, metabolically engineered yeast P. pastoris represents a valuable, whole-cell system for high-level production of (+)-nootkatone from simple carbon sources. Copyright © 2014 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Metabolic engineering of β-carotene in orange fruit increases its in vivo antioxidant properties.

Science.gov (United States)

Pons, Elsa; Alquézar, Berta; Rodríguez, Ana; Martorell, Patricia; Genovés, Salvador; Ramón, Daniel; Rodrigo, María Jesús; Zacarías, Lorenzo; Peña, Leandro

2014-01-01

Orange is a major crop and an important source of health-promoting bioactive compounds. Increasing the levels of specific antioxidants in orange fruit through metabolic engineering could strengthen the fruit's health benefits. In this work, we have afforded enhancing the β-carotene content of orange fruit through blocking by RNA interference the expression of an endogenous β-carotene hydroxylase gene (Csβ-CHX) that is involved in the conversion of β-carotene into xanthophylls. Additionally, we have simultaneously overexpressed a key regulator gene of flowering transition, the FLOWERING LOCUS T from sweet orange (CsFT), in the transgenic juvenile plants, which allowed us to obtain fruit in an extremely short period of time. Silencing the Csβ-CHX gene resulted in oranges with a deep yellow ('golden') phenotype and significant increases (up to 36-fold) in β-carotene content in the pulp. The capacity of β-carotene-enriched oranges for protection against oxidative stress in vivo was assessed using Caenorhabditis elegans as experimental animal model. Golden oranges induced a 20% higher antioxidant effect than the isogenic control. This is the first example of the successful metabolic engineering of the β-carotene content (or the content of any other phytonutrient) in oranges and demonstrates the potential of genetic engineering for the nutritional enhancement of fruit tree crops. © 2013 Society for Experimental Biology, Association of Applied Biologists and John Wiley & Sons Ltd.

Closed-form expressions for integrals of MKdV and sine-Gordon maps

International Nuclear Information System (INIS)

Kamp, Peter H van der; Rojas, O; Quispel, G R W

2007-01-01

We present closed-form expressions for approximately N integrals of 2N-dimensional maps. The maps are obtained by travelling wave reductions of the modified Korteweg-de Vries equation and of the sine-Gordon equation, respectively. We provide the integrating factors corresponding to the integrals. Moreover we show how the integrals and the integrating factors relate to the staircase method

Grand partition function in field theory with applications to sine-Gordon field theory

International Nuclear Information System (INIS)

Samuel, S.

1978-01-01

Certain relativistic field theories are shown to be equivalent to the grand partition function of an interacting gas. Using the physical insight given by this analogy many field-theoretic results are obtained, particularly for the sine-Gordon field theory. The main results are enumerated in the summary to which the reader is referred

Metabolic engineering of a haploid strain derived from a triploid industrial yeast for producing cellulosic ethanol.

Science.gov (United States)

Kim, Soo Rin; Skerker, Jeffrey M; Kong, In Iok; Kim, Heejin; Maurer, Matthew J; Zhang, Guo-Chang; Peng, Dairong; Wei, Na; Arkin, Adam P; Jin, Yong-Su

2017-03-01

Many desired phenotypes for producing cellulosic biofuels are often observed in industrial Saccharomyces cerevisiae strains. However, many industrial yeast strains are polyploid and have low spore viability, making it difficult to use these strains for metabolic engineering applications. We selected the polyploid industrial strain S. cerevisiae ATCC 4124 exhibiting rapid glucose fermentation capability, high ethanol productivity, strong heat and inhibitor tolerance in order to construct an optimal yeast strain for producing cellulosic ethanol. Here, we focused on developing a general approach and high-throughput screening method to isolate stable haploid segregants derived from a polyploid parent, such as triploid ATCC 4124 with a poor spore viability. Specifically, we deleted the HO genes, performed random sporulation, and screened the resulting segregants based on growth rate, mating type, and ploidy. Only one stable haploid derivative (4124-S60) was isolated, while 14 other segregants with a stable mating type were aneuploid. The 4124-S60 strain inherited only a subset of desirable traits present in the parent strain, same as other aneuploids, suggesting that glucose fermentation and specific ethanol productivity are likely to be genetically complex traits and/or they might depend on ploidy. Nonetheless, the 4124-60 strain did inherit the ability to tolerate fermentation inhibitors. When additional genetic perturbations known to improve xylose fermentation were introduced into the 4124-60 strain, the resulting engineered strain (IIK1) was able to ferment a Miscanthus hydrolysate better than a previously engineered laboratory strain (SR8), built by making the same genetic changes. However, the IIK1 strain showed higher glycerol and xylitol yields than the SR8 strain. In order to decrease glycerol and xylitol production, an NADH-dependent acetate reduction pathway was introduced into the IIK1 strain. By consuming 2.4g/L of acetate, the resulting strain (IIK1A

1999 Gordon Research Conference on Mammalian DNA Repair. Final Progress Report

International Nuclear Information System (INIS)

NONE

1999-01-01

This Conference will examine DNA repair as the key component in genomic surveillance that is so crucial to the overall integrity and function of mammalian cells. Recent discoveries have catapulted the field of DNA repair into a pivotal position for fundamental investigations into oncology, aging, environmental health, and developmental biology. We hope to highlight the most promising and exciting avenues of research in robust discussions at this conference. This Mammalian DNA Repair Gordon Conference differs from the past conferences in this series, in which the programs were broader in scope, with respect to topics and biological systems covered. A conference sponsored by the Genetics Society in April 1998 emphasized recombinational mechanisms for double-strand break repair and the role of mismatch repair deficiency in colorectal cancer. These topics will therefore receive somewhat less emphasis in the upcoming Conference. In view of the recent mechanistic advances in mammalian DNA repair, an upcoming comprehensive DNA repair meeting next autumn at Hilton Head; and the limited enrollment for Gordon Conferences we have decided to focus session-by-session on particular areas of controversy and/or new developments specifically in mammalian systems. Thus, the principal presentations will draw upon results from other cellular systems only to the extent that they impact our understanding of mammalian DNA repair

Soliton scatterings by impurities in a short-length sine-Gordon chain

International Nuclear Information System (INIS)

Dikande, A.M.; Kofane, T.C.

1995-07-01

The scattering of soliton by impurities at the frontiers of a finite-length region of an infinite sine-Gordon chain is analyzed. The impurities consist of two isotopic inhomogeneities installed at the boundaries of the finite-length region. The soliton solution in the region is found in term of snoidal sine-Gordon soliton which properly takes into account the effects of the boundaries. By contrast, the soliton solutions in the neighboring sides of the region are obtained in terms of the so-called large-amplitude, localized kinks with limiting spatial extensions at x → ± ∞, which is equal ±π. Using the continuity of these soliton solutions at the frontiers as well as appropriate boundary conditions, it is shown that the soliton may be either i) reflected by the incident impurity; ii) trapped (with oscillating motions) between the two impurities (i.e. inside the infinite region); or iii) transmitted by the second impurity into the third, infinitely extended region. The threshold velocities for the reflection and transmission into different regions are found and shown to vary exponentially as a function of the length of the bounded region. The frequency of soliton oscillations between the impurities has also been calculated in some acceptable limit. (author). 28 refs, 1 fig

1999 Gordon Research Conference on Mammalian DNA Repair. Final Progress Report

Energy Technology Data Exchange (ETDEWEB)

NONE

1999-02-12

This Conference will examine DNA repair as the key component in genomic surveillance that is so crucial to the overall integrity and function of mammalian cells. Recent discoveries have catapulted the field of DNA repair into a pivotal position for fundamental investigations into oncology, aging, environmental health, and developmental biology. We hope to highlight the most promising and exciting avenues of research in robust discussions at this conference. This Mammalian DNA Repair Gordon Conference differs from the past conferences in this series, in which the programs were broader in scope, with respect to topics and biological systems covered. A conference sponsored by the Genetics Society in April 1998 emphasized recombinational mechanisms for double-strand break repair and the role of mismatch repair deficiency in colorectal cancer. These topics will therefore receive somewhat less emphasis in the upcoming Conference. In view of the recent mechanistic advances in mammalian DNA repair, an upcoming comprehensive DNA repair meeting next autumn at Hilton Head; and the limited enrollment for Gordon Conferences we have decided to focus session-by-session on particular areas of controversy and/or new developments specifically in mammalian systems. Thus, the principal presentations will draw upon results from other cellular systems only to the extent that they impact our understanding of mammalian DNA repair.

Introduction and expression of genes for metabolic engineering applications in Saccharomyces cerevisiae.

Science.gov (United States)

Da Silva, Nancy A; Srikrishnan, Sneha

2012-03-01

Metabolic pathway engineering in the yeast Saccharomyces cerevisiae leads to improved production of a wide range of compounds, ranging from ethanol (from biomass) to natural products such as sesquiterpenes. The introduction of multienzyme pathways requires precise control over the level and timing of expression of the associated genes. Gene number and promoter strength/regulation are two critical control points, and multiple studies have focused on modulating these in yeast. This MiniReview focuses on methods for introducing genes and controlling their copy number and on the many promoters (both constitutive and inducible) that have been successfully employed. The advantages and disadvantages of the methods will be presented, and applications to pathway engineering will be highlighted. © 2011 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Metabolic engineering of Saccharomyces cerevisiae for production of germacrene A, a precursor of beta-elemene

DEFF Research Database (Denmark)

Hu, Yating; Zhou, Yongjin J.; Bao, Jichen

2017-01-01

inefficient and suffers from limited natural resources. Here, we engineered a yeast cell factory for the sustainable production of germacrene A, which can be transformed to beta-elemene by a one-step chemical reaction in vitro. Two heterologous germacrene A synthases (GASs) converting farnesyl pyrophosphate...... (FPP) to germacrene A were evaluated in yeast for their ability to produce germacrene A. Thereafter, several metabolic engineering strategies were used to improve the production level. Overexpression of truncated 3-hydroxyl-3-methylglutaryl-CoA reductase and fusion of FPP synthase with GAS, led...

Metabolic engineering of Escherichia coli for production of mixed-acid fermentation end products

Directory of Open Access Journals (Sweden)

Andreas Hartmut Förster

2014-05-01

Full Text Available Mixed-acid fermentation end products have numerous applications in biotechnology. This is probably the main driving force for the development of multiple strains that are supposed to produce individual end products with high yields. The process of engineering Escherichia coli strains for applied production of ethanol, lactate, succinate, or acetate was initiated several decades ago and is still ongoing. This review follows the path of strain development from the general characteristics of aerobic versus anaerobic metabolism over the regulatory machinery that enables the different metabolic routes. Thereafter, major improvements for broadening the substrate spectrum of Escherichia coli towards cheap carbon sources like molasses or lignocellulose are highlighted before major routes of strain development for the production of ethanol, acetate, lactate and succinate are presented.

Schadenfreude as a mate-value-tracking mechanism. Replication and extension of Colyn and Gordon .

NARCIS (Netherlands)

van Dijk, W.W.; Ouwerkerk, J.W.; Smith, R.H.

2015-01-01

The present research provides a replication and extension of L. A. Colyn and A. K. Gordon's (2013) study on gender differences in schadenfreude. An experiment-in which both the gender of the unfortunate other and the dimension on which the misfortune occurred were manipulated-showed that female

Combination of traditional mutation and metabolic engineering to enhance ansamitocin P-3 production in Actinosynnema pretiosum.

Science.gov (United States)

Du, Zhi-Qiang; Zhang, Yuan; Qian, Zhi-Gang; Xiao, Han; Zhong, Jian-Jiang

2017-12-01

Ansamitocin P-3 (AP-3) is a maytansinoid with its most compelling antitumor activity, however, the low production titer of AP-3 greatly restricts its wide commercial application. In this work, a combinatorial approach including random mutation and metabolic engineering was conducted to enhance AP-3 biosynthesis in Actinosynnema pretiosum. First, a mutant strain M was isolated by N-methyl-N'-nitro-N-nitrosoguanidine mutation, which could produce AP-3 almost threefold that of wild type (WT) in 48 deep-well plates. Then, by overexpressing key biosynthetic genes asmUdpg and asm13-17 in the M strain, a further 60% increase of AP-3 production in 250-ml shake flasks was achieved in the engineered strain M-asmUdpg:asm13-17 compared to the M strain, and its maximum AP-3 production reached 582.7 mg/L, which is the highest as ever reported. Both the gene transcription levels and intracellular intermediate concentrations in AP-3 biosynthesis pathway were significantly increased in the M and M-asmUdpg:asm13-17 during fermentation compared to the WT. The good fermentation performance of the engineered strain was also confirmed in a lab-scale bioreactor. This work demonstrated that combination of random mutation and metabolic engineering could promote AP-3 biosynthesis and might be helpful for increasing the production of other industrially important secondary metabolites. © 2017 Wiley Periodicals, Inc.

Whitney towers, Gropes and Casson-Gordon style invariants of links

OpenAIRE

Kim, Min Hoon

2014-01-01

In this paper, we prove a conjecture of Friedl and Powell that their Casson-Gordon type invariant of 2-component link with linking number one is actually an obstruction to being height 3.5 Whitney tower/grope concordant to the Hopf Link. The proof employs the notion of solvable cobordism of 3-manifolds with boundary, which was introduced by Cha. We also prove that the Blanchfield form and the Alexander polynomial of links in $S^3$ give obstructions to height 3 Whitney tower/grope concordance....

C. Gordon Fullerton

Science.gov (United States)

1989-01-01

C. Gordon Fullerton is a research pilot at NASA's Dryden Flight Research Center, Edwards, California. His assignments include a variety of flight research and support activities piloting NASA's B-52 launch aircraft, the 747 Shuttle Carrier Aircraft (SCA), and other multi-engine and high performance aircraft. Fullerton, who has logged 382 hours in space flight, was a NASA astronaut from September 1969 until November 1986 when he joined the Flight Crew Branch at Dryden. In July 1988, he completed a 30-year career with the U.S. Air Force and retired as a colonel. As the project pilot on the NASA B-52 launch aircraft, Fullerton flew during the first six air launches of the commercially developed Pegasus space vehicle. He was involved in a series of development air launches of the X-38 Crew Recovery Vehicle and in the Pegasus launch of the X-43A Hyper-X advanced propulsion project. Fullerton also flies Dryden's DC-8 Airborne Science aircraft, regularly deployed worldwide to support a variety of research studies, including atmospheric physics, ground mapping and meteorology. In addition to these current activities, Fullerton has been involved in numerous other research programs at Dryden. He was the project pilot on the Propulsion Controlled Aircraft program, during which he successfully landed both a modified F-15 and an MD-11 transport with all control surfaces neutralized, using only engine thrust modulation for control. Assigned to evaluate the flying qualities of the Russian Tu-144 supersonic transport during two flights in 1998, he reached a speed of Mach 2 and became one of only two non-Russian pilots to fly that aircraft. He piloted a Convair 990 modified to test space shuttle landing gear components during many very high-speed landings. Other projects for which he has flown in the past include the C-140 JetStar Laminar Flow Control; F-111 Mission Adaptive Wing; F-14 Variable Sweep Flow Transition; Space Shuttle drag chute and F-111 crew module parachute tests

Glycerol positive promoters for tailored metabolic engineering of the yeast Saccharomyces cerevisiae.

Science.gov (United States)

Ho, Ping-Wei; Klein, Mathias; Futschik, Matthias; Nevoigt, Elke

2018-05-01

Glycerol offers several advantages as a substrate for biotechnological applications. An important step toward using the popular production host Saccharomyces cerevisiae for glycerol-based bioprocesses has been the fact that in recent studies commonly used S. cerevisiae strains were engineered to grow in synthetic medium containing glycerol as the sole carbon source. For metabolic engineering projects of S. cerevisiae growing on glycerol, characterized promoters are missing. In the current study, we used transcriptome analysis and a yECitrine-based fluorescence reporter assay to select and characterize 25 useful promoters. The promoters of the genes ALD4 and ADH2 showed 4.2-fold and 3-fold higher activities compared to the well-known strong TEF1 promoter. Moreover, the collection contains promoters with graded activities in synthetic glycerol medium and different degrees of glucose repression. To demonstrate the general applicability of the promoter collection, we successfully used a subset of the characterized promoters with graded activities in order to optimize growth on glycerol in an engineered derivative of CEN.PK, in which glycerol catabolism exclusively occurs via a non-native DHA pathway.

Increasing galactose consumption by Saccharomyces cerevisiae through metabolic engineering of the GAL gene regulatory network

DEFF Research Database (Denmark)

Østergaard, Simon; Olsson, Lisbeth; Johnston, M.

2000-01-01

Increasing the flux through central carbon metabolism is difficult because of rigidity in regulatory structures, at both the genetic and the enzymatic levels. Here we describe metabolic engineering of a regulatory network to obtain a balanced increase in the activity of all the enzymes in the pat...... media. The improved galactose consumption of the gal mutants did not favor biomass formation, but rather caused excessive respiro-fermentative metabolism, with the ethanol production rate increasing linearly with glycolytic flux....... by eliminating three known negative regulators of the GAL system: Gale, Gal80, and Mig1. This led to a 41% increase in flux through the galactose utilization pathway compared with the wild-type strain. This is of significant interest within the field of biotechnology since galactose is present in many industrial...

Assessment of soil-gas, seep, and soil contamination at the North Range Road Landfill, Fort Gordon, Georgia, 2008-2009

Science.gov (United States)

Landmeyer, James E.; Falls, W. Fred; Ratliff, W. Hagan; Wellborn, John B.

2011-01-01

Soil gas, seeps, and soil were assessed for contaminants at the North Range Road Landfill at Fort Gordon, Georgia, from October 2008 to September 2009. The assessment included delineating organic contaminants present in soil-gas samples beneath the area estimated to be the landfill and in water samples collected from three seeps at the base of the landfill. Inorganic contaminants were determined in three seep samples and in soil samples. This assessment was conducted to provide environmental contamination data to Fort Gordon pursuant to requirements for the Resource Conservation and Recovery Act Part B Hazardous Waste Permit process.

Metabolic engineering of Escherichia coli for the production of riboflavin

Science.gov (United States)

2014-01-01

Background Riboflavin (vitamin B2), the precursor of the flavin cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), is used commercially as an animal feed supplement and food colorant. E. coli is a robust host for various genetic manipulations and has been employed for efficient production of biofuels, polymers, amino acids, and bulk chemicals. Thus, the aim of this study was to understand the metabolic capacity of E. coli for the riboflavin production by modification of central metabolism, riboflavin biosynthesis pathway and optimization of the fermentation conditions. Results The basic producer RF01S, in which the riboflavin biosynthesis genes ribABDEC from E. coli were overexpressed under the control of the inducible trc promoter, could accumulate 229.1 mg/L of riboflavin. Further engineering was performed by examining the impact of expression of zwf (encodes glucose 6-phosphate dehydrogenase) and gnd (encodes 6-phosphogluconate dehydrogenase) from Corynebacterium glutamicum and pgl (encodes 6-phosphogluconolactonase) from E. coli on riboflavin production. Deleting pgi (encodes glucose-6-phosphate isomerase) and genes of Entner-Doudoroff (ED) pathway successfully redirected the carbon flux into the oxidative pentose phosphate pathway, and overexpressing the acs (encodes acetyl-CoA synthetase) reduced the acetate accumulation. These modifications increased riboflavin production to 585.2 mg/L. By further modulating the expression of ribF (encodes riboflavin kinase) for reducing the conversion of riboflavin to FMN in RF05S, the final engineering strain RF05S-M40 could produce 1036.1 mg/L riboflavin in LB medium at 37°C. After optimizing the fermentation conditions, strain RF05S-M40 produced 2702.8 mg/L riboflavin in the optimized semi-defined medium, which was a value nearly 12-fold higher than that of RF01S, with a yield of 137.5 mg riboflavin/g glucose. Conclusions The engineered strain RF05S-M40 has the highest yield among all

Metabolic engineering of Escherichia coli for the production of riboflavin.

Science.gov (United States)

Lin, Zhenquan; Xu, Zhibo; Li, Yifan; Wang, Zhiwen; Chen, Tao; Zhao, Xueming

2014-07-16

Riboflavin (vitamin B2), the precursor of the flavin cofactors flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD), is used commercially as an animal feed supplement and food colorant. E. coli is a robust host for various genetic manipulations and has been employed for efficient production of biofuels, polymers, amino acids, and bulk chemicals. Thus, the aim of this study was to understand the metabolic capacity of E. coli for the riboflavin production by modification of central metabolism, riboflavin biosynthesis pathway and optimization of the fermentation conditions. The basic producer RF01S, in which the riboflavin biosynthesis genes ribABDEC from E. coli were overexpressed under the control of the inducible trc promoter, could accumulate 229.1 mg/L of riboflavin. Further engineering was performed by examining the impact of expression of zwf (encodes glucose 6-phosphate dehydrogenase) and gnd (encodes 6-phosphogluconate dehydrogenase) from Corynebacterium glutamicum and pgl (encodes 6-phosphogluconolactonase) from E. coli on riboflavin production. Deleting pgi (encodes glucose-6-phosphate isomerase) and genes of Entner-Doudoroff (ED) pathway successfully redirected the carbon flux into the oxidative pentose phosphate pathway, and overexpressing the acs (encodes acetyl-CoA synthetase) reduced the acetate accumulation. These modifications increased riboflavin production to 585.2 mg/L. By further modulating the expression of ribF (encodes riboflavin kinase) for reducing the conversion of riboflavin to FMN in RF05S, the final engineering strain RF05S-M40 could produce 1036.1 mg/L riboflavin in LB medium at 37°C. After optimizing the fermentation conditions, strain RF05S-M40 produced 2702.8 mg/L riboflavin in the optimized semi-defined medium, which was a value nearly 12-fold higher than that of RF01S, with a yield of 137.5 mg riboflavin/g glucose. The engineered strain RF05S-M40 has the highest yield among all reported riboflavin production

Bound State Solutions of the Klein-Gordon Equation for the Mathews-Lakshmanan Oscillator

International Nuclear Information System (INIS)

Schulze-Halberg, Axel; Wang, Jie

2014-01-01

We study a boundary-value problem for the Klein-Gordon equation that is inspired by the well-known Mathews-Lakshmanan oscillator model. By establishing a link to the spheroidal equation, we show that our problem admits an infinite number of discrete energies, together with associated solutions that form an orthogonal set in a weighted L 2 -Hilbert space. (author)

2011 GASEOUS IONS GORDON RESEARCH CONFERENCE

Energy Technology Data Exchange (ETDEWEB)

Scott Anderson

2011-03-04

The Gaseous Ions: Structures, Energetics and Reactions Gordon Research Conference will focus on ions and their interactions with molecules, surfaces, electrons, and light. The conference will cover theory and experiments, and systems ranging from molecular to biological to clusters to materials. The meeting goal continues to be bringing together scientists interested in fundamentals, with those applying fundamental phenomena to a wide range of practical problems. Each of the ten conference sessions will focus on a topic within this spectrum, and there will also be poster sessions for contributed papers, with sufficient space and time to allow all participants to present their latest results. To encourage active participation by young investigators, about ten of the poster abstracts will be selected for 15 minute 'hot topic' talks during the conference sessions. Hot topic selection will be done about a month before the meeting. Funds should be available to offset the participation cost for young investigators.

Sine-Gordon equation and its application to tectonic stress transfer

Science.gov (United States)

Bykov, Victor G.

2014-07-01

An overview is given on remarkable progress that has been made in theoretical studies of solitons and other nonlinear wave patterns, excited during the deformation of fault block (fragmented) geological media. The models that are compliant with the classical and perturbed sine-Gordon equations have only been chosen. In these mathematical models, the rotation angle of blocks (fragments) and their translatory displacement of the medium are used as dynamic variables. A brief description of the known models and their geophysical and geodynamic applications is given. These models reproduce the kinematic and dynamic features of the traveling deformation front (kink, soliton) generated in the fragmented media. It is demonstrated that the sine-Gordon equation is applicable to the description of series of the observed seismic data, modeling of strain waves, as well as the features related to fault dynamics and the subduction slab, including slow earthquakes, periodicity of episodic tremor and slow slip (ETS) events, and migration pattern of tremors. The study shows that simple heuristic models and analytical and numerical computations can explain triggering of seismicity by transient processes, such as stress changes associated with solitary strain waves in crustal faults. The need to develop the above-mentioned new (nonlinear) mathematical models of the deformed fault and fragmented media was caused by the reason that it is impossible to explain a lot of the observed effects, particularly, slow redistribution and migration of stresses in the lithosphere, within the framework of the linear elasticity theory.

Combining metabolic engineering and biocompatible chemistry for high-yield production of homo-diacetyl and homo-(S,S)-2,3-butanediol.

Science.gov (United States)

Liu, Jianming; Chan, Siu Hung Joshua; Brock-Nannestad, Theis; Chen, Jun; Lee, Sang Yup; Solem, Christian; Jensen, Peter Ruhdal

2016-07-01

Biocompatible chemistry is gaining increasing attention because of its potential within biotechnology for expanding the repertoire of biological transformations carried out by enzymes. Here we demonstrate how biocompatible chemistry can be used for synthesizing valuable compounds as well as for linking metabolic pathways to achieve redox balance and rescued growth. By comprehensive rerouting of metabolism, activation of respiration, and finally metal ion catalysis, we successfully managed to convert the homolactic bacterium Lactococcus lactis into a homo-diacetyl producer with high titer (95mM or 8.2g/L) and high yield (87% of the theoretical maximum). Subsequently, the pathway was extended to (S,S)-2,3-butanediol (S-BDO) through efficiently linking two metabolic pathways via chemical catalysis. This resulted in efficient homo-S-BDO production with a titer of 74mM (6.7g/L) S-BDO and a yield of 82%. The diacetyl and S-BDO production rates and yields obtained are the highest ever reported, demonstrating the promising combination of metabolic engineering and biocompatible chemistry as well as the great potential of L. lactis as a new production platform. Copyright © 2016 International Metabolic Engineering Society. Published by Elsevier Inc. All rights reserved.

Exact Mass-Coupling Relation for the Homogeneous Sine-Gordon Model.

Science.gov (United States)

Bajnok, Zoltán; Balog, János; Ito, Katsushi; Satoh, Yuji; Tóth, Gábor Zsolt

2016-05-06

We derive the exact mass-coupling relation of the simplest multiscale quantum integrable model, i.e., the homogeneous sine-Gordon model with two mass scales. The relation is obtained by comparing the perturbed conformal field theory description of the model valid at short distances to the large distance bootstrap description based on the model's integrability. In particular, we find a differential equation for the relation by constructing conserved tensor currents, which satisfy a generalization of the Θ sum rule Ward identity. The mass-coupling relation is written in terms of hypergeometric functions.

Partial Internal Control Recovery on 1-D Klein-Gordon Systems

Directory of Open Access Journals (Sweden)

Iwan Pranoto

2010-03-01

Full Text Available In this exposition, a technique to recover internal control on a distributed parameter system is reported. The system is described by 1-D Klein-Gordon partial differential equation with a time-varying parameter. We would like to recover the internal control applied to the system if we know some limited information about the output. We use a method called sentinel method to recover the internal control. It involves some construction of a linear functional, and we show that this construction relates closely to the exact controllability problem.

Non-existence of global solutions to generalized dissipative Klein-Gordon equations with positive energy

Directory of Open Access Journals (Sweden)

Maxim Olegovich Korpusov

2012-07-01

Full Text Available In this article the initial-boundary-value problem for generalized dissipative high-order equation of Klein-Gordon type is considered. We continue our study of nonlinear hyperbolic equations and systems with arbitrary positive energy. The modified concavity method by Levine is used for proving blow-up of solutions.

Medicine is not health care, food is health care: plant metabolic engineering, diet and human health.

Science.gov (United States)

Martin, Cathie; Li, Jie

2017-11-01

Contents 699 I. 699 II. 700 III. 700 IV. 706 V. 707 VI. 714 714 References 714 SUMMARY: Plants make substantial contributions to our health through our diets, providing macronutrients for energy and growth as well as essential vitamins and phytonutrients that protect us from chronic diseases. Imbalances in our food can lead to deficiency diseases or obesity and associated metabolic disorders, increased risk of cardiovascular diseases and cancer. Nutritional security is now a global challenge which can be addressed, at least in part, through plant metabolic engineering for nutritional improvement of foods that are accessible to and eaten by many. We review the progress that has been made in nutritional enhancement of foods, both improvements through breeding and through biotechnology and the engineering principles on which increased phytonutrient levels are based. We also consider the evidence, where available, that such foods do enhance health and protect against chronic diseases. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Development of Renewable Biofuels Technology by Transcriptomic Analysis and Metabolic Engineering of Diatoms

Energy Technology Data Exchange (ETDEWEB)

Hildebrand, Mark [Univ. of California, San Diego, CA (United States)

2013-11-18

There is enormous interest in developing renewable sources of liquid fuels because of depletion of fossil fuel reserves, dependence on foreign sources, and increasing atmospheric CO₂ levels. Algae produce neutral lipids that are readily converted into liquid fuels such as biodiesel or JP-8 equivalent, and are attractive sources because they are far more productive than plants (yielding 10 -100’s of time more lipid per land area), and can be grown on non-cultivatable land with non-potable (brackish or salt) water sources. Unicellular algae known as diatoms were the most thoroughly characterized species in the National Renewable Energy Laboratory’s Aquatic Species Program, whose goal was to develop microalgae as renewable fuel sources. Lipid accumulation in microalgae is generally induced by nutrient limitation, which involves a change in environmental conditions. Intrinsic variability in cellular response to environmental changes prevents a high degree of control over the process. Nutrient limitation also inhibits biomass accumulation; therefore a tradeoff between high biomass and lipid production occurs. The goal of this project was to develop metabolic engineering approaches for diatoms to enable induction of lipid accumulation by controllable manipulation of intracellular processes rather than from external environmental conditions, and to manipulate carbon partitioning within the cell between lipid and carbohydrate synthesis to enable both abundant biomass and lipid accumulation. There were two specific objectives for this project; Objective 1:To perform comparative transcriptomic analysis in T. pseudonana and C. cryptica of lipid accumulation resulting from silicon and nitrogen limitation, to identify common and key regulatory steps involved in controlling lipid accumulation and carbon partitioning; and Objective 2: To metabolically engineer the cell to alter carbon partitioning to either trigger lipid induction without the need for nutrient

Scattering of the double sine-Gordon kinks

Science.gov (United States)

Gani, Vakhid A.; Marjaneh, Aliakbar Moradi; Askari, Alidad; Belendryasova, Ekaterina; Saadatmand, Danial

2018-04-01

We study the scattering of kink and antikink of the double sine-Gordon model. There is a critical value of the initial velocity v_{{cr}} of the colliding kinks, which separates different regimes of the collision. At v_{in}>v_{cr} we observe kinks reflection, while at v_{in}

What distinguishes the Gordon Research Conference on Oceans and Human Health? A retrospective 2008-2012.

Science.gov (United States)

Doyle, John J

2013-05-01

This piece is being submitted as a short commentary for the special edition on Oceans and Human Health (OHH). It is written from the perspective of a student who has attended all three biennial Gordon Research Conferences and Seminars on OHH beginning in 2008.

Exact Travelling Solutions of Discrete sine-Gordon Equation via Extended Tanh-Function Approach

International Nuclear Information System (INIS)

Dai Chaoqing; Zhang Jiefang

2006-01-01

In this paper, we generalize the extended tanh-function approach, which was used to find new exact travelling wave solutions of nonlinear partial differential equations or coupled nonlinear partial differential equations, to nonlinear differential-difference equations. As illustration, two series of exact travelling wave solutions of the discrete sine-Gordon equation are obtained by means of the extended tanh-function approach.

Exact Solutions to a Combined sinh-cosh-Gordon Equation

International Nuclear Information System (INIS)

Wei Long

2010-01-01

Based on a transformed Painleve property and the variable separated ODE method, a function transformation method is proposed to search for exact solutions of some partial differential equations (PDEs) with hyperbolic or exponential functions. This approach provides a more systematical and convenient handling of the solution process of this kind of nonlinear equations. Its key point is to eradicate the hyperbolic or exponential terms by a transformed Painleve property and reduce the given PDEs to a variable-coefficient ordinary differential equations, then we seek for solutions to the resulting equations by some methods. As an application, exact solutions for the combined sinh-cosh-Gordon equation are formally derived. (general)

Construction of wave operator for two-dimensional Klein-Gordon-Schrodinger systems with Yukawa coupling

Directory of Open Access Journals (Sweden)

Kai Tsuruta

2013-05-01

Full Text Available We prove the existence of the wave operator for the Klein-Gordon-Schrodinger system with Yukawa coupling. This non-linearity type is below Strichartz scaling, and therefore classic perturbation methods will fail in any Strichartz space. Instead, we follow the "first iteration method" to handle these critical non-linearities.

Engineering of metabolic control

Science.gov (United States)

Liao, James C.

2004-03-16

The invention features a method of producing heterologous molecules in cells under the regulatory control of a metabolite and metabolic flux. The method can enhance the synthesis of heterologous polypeptides and metabolites.

Biosynthetic Pathway and Metabolic Engineering of Plant Dihydrochalcones.

Science.gov (United States)

Ibdah, Mwafaq; Martens, Stefan; Gang, David R

2018-03-14

Dihydrochalcones are plant natural products containing the phenylpropanoid backbone and derived from the plant-specific phenylpropanoid pathway. Dihydrochalcone compounds are important in plant growth and response to stresses and, thus, can have large impacts on agricultural activity. In recent years, these compounds have also received increased attention from the biomedical community for their potential as anticancer treatments and other benefits for human health. However, they are typically produced at relatively low levels in plants. Therefore, an attractive alternative is to express the plant biosynthetic pathway genes in microbial hosts and to engineer the metabolic pathway/host to improve the production of these metabolites. In the present review, we discuss in detail the functions of genes and enzymes involved in the biosynthetic pathway of the dihydrochalcones and the recent strategies and achievements used in the reconstruction of multi-enzyme pathways in microorganisms in efforts to be able to attain higher amounts of desired dihydrochalcones.

Scattering of sine-Gordon kinks on potential wells

International Nuclear Information System (INIS)

Piette, Bernard; Zakrzewski, W J

2007-01-01

We study the scattering properties of sine-Gordon kinks on obstructions in the form of finite size potential 'wells'. We model this by making the coefficient of the cos(ψ) - 1 term in the Lagrangian position dependent. We show that when the kinks find themselves in the well they radiate and then interact with this radiation. As a result of this energy loss, the kinks become trapped for small velocities while at higher velocities they are transmitted with a loss of energy. However, the interaction with the radiation can produce 'unexpected' reflections by the well. We present two simple models which capture the gross features of this behaviour. Both involve standing waves either at the edges of the well or in the well itself

The anarchitecture of Gordon Matta-Clark: political autonomism and aesthetic activism

Directory of Open Access Journals (Sweden)

Jorge Vasconcelos

2012-12-01

Full Text Available We intend to consider the contemporary relationships between art, politics and resistance, from the 1960s and 1970s artistic practices, established by the american architect, performer and autonomist activist, Gordon Matta-Clark (1943-1978. We will use, especially for such a task, the concepts proposed by Gilles Deleuze (and Felix Guattari, notably in his book What is philosophy?, of the “becoming-revolutionary of art”, “creative fabulation” and “acts of creation / acts of resistance”.

Deletion of acetyl-CoA synthetases I and II increases production of 3-hydroxypropionate by the metabolically-engineered hyperthermophile Pyrococcus furiosus.

Science.gov (United States)

Thorgersen, Michael P; Lipscomb, Gina L; Schut, Gerrit J; Kelly, Robert M; Adams, Michael W W

2014-03-01

The heterotrophic, hyperthermophilic archaeon Pyrococcus furiosus is a new addition to the growing list of genetically-tractable microorganisms suitable for metabolic engineering to produce liquid fuels and industrial chemicals. P. furiosus was recently engineered to generate 3-hydroxypropionate (3-HP) from CO₂ and acetyl-CoA by the heterologous-expression of three enzymes from the CO₂ fixation cycle of the thermoacidophilic archaeon Metallosphaera sedula using a thermally-triggered induction system. The acetyl-CoA for this pathway is generated from glucose catabolism that in wild-type P. furiosus is converted to acetate with concurrent ATP production by the heterotetrameric (α₂β₂) acetyl-CoA synthetase (ACS). Hence ACS in the engineered 3-HP production strain (MW56) competes with the heterologous pathway for acetyl-CoA. Herein we show that strains of MW56 lacking the α-subunit of either of the two ACSs previously characterized from P. furiosus (ACSI and ACSII) exhibit a three-fold increase in specific 3-HP production. The ΔACSIα strain displayed only a minor defect in growth on either maltose or peptides, while no growth defect on these substrates was observed with the ΔACSIIα strain. Deletion of individual and multiple ACS subunits was also shown to decrease CoA release activity for several different CoA ester substrates in addition to acetyl-CoA, information that will be extremely useful for future metabolic engineering endeavors in P. furiosus. Copyright © 2014 International Metabolic Engineering Society. All rights reserved.

Chaotic oscillations of the Klein-Gordon equation with distributed energy pumping and van der Pol boundary regulation and distributed time-varying coefficients

Directory of Open Access Journals (Sweden)

Bo Sun

2014-09-01

Full Text Available Consider the Klein-Gordon equation with variable coefficients, a van der Pol cubic nonlinearity in one of the boundary conditions and a spatially distributed antidamping term, we use a variable-substitution technique together with the analogy with the 1-dimensional wave equation to prove that for the Klein-Gordon equation chaos occurs for a class of equations and boundary conditions when system parameters enter a certain regime. Chaotic and nonchaotic profiles of solutions are illustrated by computer graphics.

American Recovery and Reinvestment Act (ARRA) Federal Energy Management Program Technical Assistance Project 282 Renewable Energy Opportunities at Fort Gordon, Georgia

Energy Technology Data Exchange (ETDEWEB)

Boyd, Brian K.; Gorrissen, Willy J.; Hand, James R.; Horner, Jacob A.; Orrell, Alice C.; Russo, Bryan J.; Weimar, Mark R.; Williamson, Jennifer L.; Nesse, Ronald J.

2010-09-30

This document provides an overview of renewable resource potential at Fort Gordon, based primarily upon analysis of secondary data sources supplemented with limited on-site evaluations. This effort focuses on grid-connected generation of electricity from renewable energy sources and also on ground source heat pumps for heating and cooling buildings. The effort was funded by the American Recovery and Reinvestment Act (ARRA) as follow-on to the 2005 Department of Defense (DoD) Renewables Assessment. The site visit to Fort Gordon took place on March 9, 2010.

Quadratic algebras applied to noncommutative integration of the Klein-Gordon equation: Four-dimensional quadratic algebras containing three-dimensional nilpotent lie algebras

International Nuclear Information System (INIS)

Varaksin, O.L.; Firstov, V.V.; Shapovalov, A.V.

1995-01-01

The study is continued on noncommutative integration of linear partial differential equations in application to the exact integration of quantum-mechanical equations in a Riemann space. That method gives solutions to the Klein-Gordon equation when the set of noncommutative symmetry operations for that equation forms a quadratic algebra consisting of one second-order operator and of first-order operators forming a Lie algebra. The paper is a continuation of, where a single nontrivial example is used to demonstrate noncommutative integration of the Klein-Gordon equation in a Riemann space not permitting variable separation

OptFlux: an open-source software platform for in silico metabolic engineering

DEFF Research Database (Denmark)

Rocha, I.; Maia, P.; Evangelista, P.

2010-01-01

to address industrial goals. However, the use of these methods has been restricted to bioinformaticians or other expert researchers. The main aim of this work is, therefore, to provide a user-friendly computational tool for Metabolic Engineering applications. Results: OptFlux is an open-source and modular...... available a number of useful tools. Its open-source nature invites contributions by all those interested in making their methods available for the community. Given its plug-in based architecture it can be extended with new functionalities. Currently, several plug-ins are being developed, including network...