Science.gov

Sample records for production metabolism scaling

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

    PubMed

    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.

  2. Biofuel production: an odyssey from metabolic engineering to fermentation scale-up

    PubMed Central

    Hollinshead, Whitney; He, Lian; Tang, Yinjie J.

    2014-01-01

    Metabolic engineering has developed microbial cell factories that can convert renewable carbon sources into biofuels. Current molecular biology tools can efficiently alter enzyme levels to redirect carbon fluxes toward biofuel production, but low product yield and titer in large bioreactors prevent the fulfillment of cheap biofuels. There are three major roadblocks preventing economical biofuel production. First, carbon fluxes from the substrate dissipate into a complex metabolic network. Besides the desired product, microbial hosts direct carbon flux to synthesize biomass, overflow metabolites, and heterologous enzymes. Second, microbial hosts need to oxidize a large portion of the substrate to generate both ATP and NAD(P)H to power biofuel synthesis. High cell maintenance, triggered by the metabolic burdens from genetic modifications, can significantly affect the ATP supply. Thereby, fermentation of advanced biofuels (such as biodiesel and hydrocarbons) often requires aerobic respiration to resolve the ATP shortage. Third, mass transfer limitations in large bioreactors create heterogeneous growth conditions and micro-environmental fluctuations (such as suboptimal O2 level and pH) that induce metabolic stresses and genetic instability. To overcome these limitations, fermentation engineering should merge with systems metabolic engineering. Modern fermentation engineers need to adopt new metabolic flux analysis tools that integrate kinetics, hydrodynamics, and 13C-proteomics, to reveal the dynamic physiologies of the microbial host under large bioreactor conditions. Based on metabolic analyses, fermentation engineers may employ rational pathway modifications, synthetic biology circuits, and bioreactor control algorithms to optimize large-scale biofuel production. PMID:25071754

  3. Systems metabolic engineering of microorganisms to achieve large-scale production of flavonoid scaffolds.

    PubMed

    Wu, Junjun; Du, Guocheng; Zhou, Jingwen; Chen, Jian

    2014-10-20

    Flavonoids possess pharmaceutical potential due to their health-promoting activities. The complex structures of these products make extraction from plants difficult, and chemical synthesis is limited because of the use of many toxic solvents. Microbial production offers an alternate way to produce these compounds on an industrial scale in a more economical and environment-friendly manner. However, at present microbial production has been achieved only on a laboratory scale and improvements and scale-up of these processes remain challenging. Naringenin and pinocembrin, which are flavonoid scaffolds and precursors for most of the flavonoids, are the model molecules that are key to solving the current issues restricting industrial production of these chemicals. The emergence of systems metabolic engineering, which combines systems biology with synthetic biology and evolutionary engineering at the systems level, offers new perspectives on strain and process optimization. In this review, current challenges in large-scale fermentation processes involving flavonoid scaffolds and the strategies and tools of systems metabolic engineering used to overcome these challenges are summarized. This will offer insights into overcoming the limitations and challenges of large-scale microbial production of these important pharmaceutical compounds.

  4. Genome-scale metabolic network guided engineering of Streptomyces tsukubaensis for FK506 production improvement

    PubMed Central

    2013-01-01

    Background FK506 is an important immunosuppressant, which can be produced by Streptomyces tsukubaensis. However, the production capacity of the strain is very low. Hereby, a computational guided engineering approach was proposed in order to improve the intracellular precursor and cofactor availability of FK506 in S. tsukubaensis. Results First, a genome-scale metabolic model of S. tsukubaensis was constructed based on its annotated genome and biochemical information. Subsequently, several potential genetic targets (knockout or overexpression) that guaranteed an improved yield of FK506 were identified by the recently developed methodology. To validate the model predictions, each target gene was manipulated in the parent strain D852, respectively. All the engineered strains showed a higher FK506 production, compared with D852. Furthermore, the combined effect of the genetic modifications was evaluated. Results showed that the strain HT-ΔGDH-DAZ with gdhA-deletion and dahp-, accA2-, zwf2-overexpression enhanced FK506 concentration up to 398.9 mg/L, compared with 143.5 mg/L of the parent strain D852. Finally, fed-batch fermentations of HT-ΔGDH-DAZ were carried out, which led to the FK506 production of 435.9 mg/L, 1.47-fold higher than the parent strain D852 (158.7 mg/L). Conclusions Results confirmed that the promising targets led to an increase in FK506 titer. The present work is the first attempt to engineer the primary precursor pathways to improve FK506 production in S. tsukubaensis with genome-scale metabolic network guided metabolic engineering. The relationship between model prediction and experimental results demonstrates the rationality and validity of this approach for target identification. This strategy can also be applied to the improvement of other important secondary metabolites. PMID:23705993

  5. Large-scale production of UDP-galactose and globotriose by coupling metabolically engineered bacteria.

    PubMed

    Koizumi, S; Endo, T; Tabata, K; Ozaki, A

    1998-09-01

    A large-scale production system of uridine 5'-diphospho-galactose (UDP-Gal) has been established by the combination of recombinant Escherichia coli and Corynebacterium ammoniagenes. Recombinant E. coli that overexpress the UDP-Gal biosynthetic genes galT, galK, and galU were generated. C. ammoniagenes contribute the production of uridine triphosphate (UTP), a substrate for UDP-Gal biosynthesis, from orotic acid, an inexpensive precursor of UTP. UDP-Gal accumulated to 72 mM (44 g/L) after a 21 h reaction starting with orotic acid and galactose. When E. coli cells that expressed the alpha1,4-galactosyltransferase gene of Neisseria gonorrhoeae were coupled with this UDP-Gal production system, 372 mM (188 g/L) globotriose (Galalpha1-4Galbeta1-4Glc), a trisaccharide portion of verotoxin receptor, was produced after a 36 h reaction starting with orotic acid, galactose, and lactose. No oligosaccharide by-products were observed in the reaction mixture. The production of globotriose was several times higher than that of UDP-Gal. The strategy of producing sugar nucleotides by combining metabolically engineered recombinant E. coli with a nucleoside 5'-triphosphate producing microorganism, and the concept of producing oligosaccharides by coupling sugar nucleotide production systems with glycosyltransferases, can be applied to the manufacture of other sugar nucleotides and oligosaccharides.

  6. Genome-scale modeling enables metabolic engineering of Saccharomyces cerevisiae for succinic acid production.

    PubMed

    Agren, Rasmus; Otero, José Manuel; Nielsen, Jens

    2013-07-01

    In this work, we describe the application of a genome-scale metabolic model and flux balance analysis for the prediction of succinic acid overproduction strategies in Saccharomyces cerevisiae. The top three single gene deletion strategies, Δmdh1, Δoac1, and Δdic1, were tested using knock-out strains cultivated anaerobically on glucose, coupled with physiological and DNA microarray characterization. While Δmdh1 and Δoac1 strains failed to produce succinate, Δdic1 produced 0.02 C-mol/C-mol glucose, in close agreement with model predictions (0.03 C-mol/C-mol glucose). Transcriptional profiling suggests that succinate formation is coupled to mitochondrial redox balancing, and more specifically, reductive TCA cycle activity. While far from industrial titers, this proof-of-concept suggests that in silico predictions coupled with experimental validation can be used to identify novel and non-intuitive metabolic engineering strategies.

  7. In silico method for modelling metabolism and gene product expression at genome scale

    SciTech Connect

    Lerman, Joshua A.; Hyduke, Daniel R.; Latif, Haythem; Portnoy, Vasiliy A.; Lewis, Nathan E.; Orth, Jeffrey D.; Rutledge, Alexandra C.; Smith, Richard D.; Adkins, Joshua N.; Zengler, Karsten; Palsson, Bernard O.

    2012-07-03

    Transcription and translation use raw materials and energy generated metabolically to create the macromolecular machinery responsible for all cellular functions, including metabolism. A biochemically accurate model of molecular biology and metabolism will facilitate comprehensive and quantitative computations of an organism's molecular constitution as a function of genetic and environmental parameters. Here we formulate a model of metabolism and macromolecular expression. Prototyping it using the simple microorganism Thermotoga maritima, we show our model accurately simulates variations in cellular composition and gene expression. Moreover, through in silico comparative transcriptomics, the model allows the discovery of new regulons and improving the genome and transcription unit annotations. Our method presents a framework for investigating molecular biology and cellular physiology in silico and may allow quantitative interpretation of multi-omics data sets in the context of an integrated biochemical description of an organism.

  8. Scaling metabolic rate fluctuations

    PubMed Central

    Labra, Fabio A.; Marquet, Pablo A.; Bozinovic, Francisco

    2007-01-01

    Complex ecological and economic systems show fluctuations in macroscopic quantities such as exchange rates, size of companies or populations that follow non-Gaussian tent-shaped probability distributions of growth rates with power-law decay, which suggests that fluctuations in complex systems may be governed by universal mechanisms, independent of particular details and idiosyncrasies. We propose here that metabolic rate within individual organisms may be considered as an example of an emergent property of a complex system and test the hypothesis that the probability distribution of fluctuations in the metabolic rate of individuals has a “universal” form regardless of body size or taxonomic affiliation. We examined data from 71 individuals belonging to 25 vertebrate species (birds, mammals, and lizards). We report three main results. First, for all these individuals and species, the distribution of metabolic rate fluctuations follows a tent-shaped distribution with power-law decay. Second, the standard deviation of metabolic rate fluctuations decays as a power-law function of both average metabolic rate and body mass, with exponents −0.352 and −1/4 respectively. Finally, we find that the distributions of metabolic rate fluctuations for different organisms can all be rescaled to a single parent distribution, supporting the existence of general principles underlying the structure and functioning of individual organisms. PMID:17578913

  9. Metabolic scaling in turtles.

    PubMed

    Ultsch, Gordon R

    2013-04-01

    Bennett and Dawson (1976) presented an analysis of the relationship of metabolic rate (MR) and body mass among turtles, based on 10 studies, but unlike most of other groups of ectotherms, there has been no update to include the many later reports on turtles. Here I present a review of the data on turtle metabolic rates at 20, 25, and 30°C, along with regression equations and graphical analyses from a large number of studies. Two generalities emerge: (1) reported metabolic rates for sea turtles are higher than for other chelonians, although it is not certain whether this is an intrinsic characteristic of sea turtles or an artifact related to experimental conditions (such as greater activity of sea turtles in metabolic chambers and the fact that a number of studies were done with the turtles out of water), and (2) the slopes of the log-log plots of metabolic rate (MR) vs. body mass [b in the allometric equation MR=a(mass)(b)] are mostly lower than previously reported in smaller studies.

  10. Form and metabolic scaling in colonial animals.

    PubMed

    Hartikainen, Hanna; Humphries, Stuart; Okamura, Beth

    2014-03-01

    Benthic colonial organisms exhibit a wide variation in size and shape and provide excellent model systems for testing the predictions of models that describe the scaling of metabolic rate with organism size. We tested the hypothesis that colony form will influence metabolic scaling and its derivatives by characterising metabolic and propagule production rates in three species of freshwater bryozoans that vary in morphology and module organisation and which demonstrate two- and three-dimensional growth forms. The results were evaluated with respect to predictions from two models for metabolic scaling. Isometric metabolic scaling in two-dimensional colonies supported predictions of a model based on dynamic energy budget theory (DEB) and not those of a model based on fractally branching supply networks. This metabolic isometry appears to be achieved by equivalent energy budgets of edge and central modules, in one species (Cristatella mucedo) via linear growth and in a second species (Lophopus crystallinus) by colony fission. Allometric scaling characterised colonies of a three-dimensional species (Fredericella sultana), also providing support for the DEB model. Isometric scaling of propagule production rates for C. mucedo and F. sultana suggests that the number of propagules produced in colonies increases in direct proportion with the number of modules within colonies. Feeding currents generated by bryozoans function in both food capture and respiration, thus linking metabolic scaling with dynamics of self-shading and resource capture. Metabolic rates fundamentally dictate organismal performance (e.g. growth, reproduction) and, as we show here, are linked with colony form. Metabolic profiles and associated variation in colony form should therefore influence the outcome of biotic interactions in habitats dominated by colonial animals and may drive patterns of macroevolution.

  11. Integrating large-scale functional genomics data to dissect metabolic networks for hydrogen production

    SciTech Connect

    Harwood, Caroline S

    2012-12-17

    The goal of this project is to identify gene networks that are critical for efficient biohydrogen production by leveraging variation in gene content and gene expression in independently isolated Rhodopseudomonas palustris strains. Coexpression methods were applied to large data sets that we have collected to define probabilistic causal gene networks. To our knowledge this a first systems level approach that takes advantage of strain-to strain variability to computationally define networks critical for a particular bacterial phenotypic trait.

  12. Metabolic scaling in solid tumours

    NASA Astrophysics Data System (ADS)

    Milotti, E.; Vyshemirsky, V.; Sega, M.; Stella, S.; Chignola, R.

    2013-06-01

    Tumour metabolism is an outstanding topic of cancer research, as it determines the growth rate and the global activity of tumours. Recently, by combining the diffusion of oxygen, nutrients, and metabolites in the extracellular environment, and the internal motions that mix live and dead cells, we derived a growth law of solid tumours which is linked to parameters at the cellular level. Here we use this growth law to obtain a metabolic scaling law for solid tumours, which is obeyed by tumours of different histotypes both in vitro and in vivo, and we display its relation with the fractal dimension of the distribution of live cells in the tumour mass. The scaling behaviour is related to measurable parameters, with potential applications in the clinical practice.

  13. Metabolic scaling in solid tumours

    PubMed Central

    Milotti, E.; Vyshemirsky, V.; Sega, M.; Stella, S.; Chignola, R.

    2013-01-01

    Tumour metabolism is an outstanding topic of cancer research, as it determines the growth rate and the global activity of tumours. Recently, by combining the diffusion of oxygen, nutrients, and metabolites in the extracellular environment, and the internal motions that mix live and dead cells, we derived a growth law of solid tumours which is linked to parameters at the cellular level1. Here we use this growth law to obtain a metabolic scaling law for solid tumours, which is obeyed by tumours of different histotypes both in vitro and in vivo, and we display its relation with the fractal dimension of the distribution of live cells in the tumour mass. The scaling behaviour is related to measurable parameters, with potential applications in the clinical practice. PMID:23727729

  14. Reconstruction and in silico analysis of an Actinoplanes sp. SE50/110 genome-scale metabolic model for acarbose production

    PubMed Central

    Wang, Yali; Xu, Nan; Ye, Chao; Liu, Liming; Shi, Zhongping; Wu, Jing

    2015-01-01

    Actinoplanes sp. SE50/110 produces the α-glucosidase inhibitor acarbose, which is used to treat type 2 diabetes mellitus. To obtain a comprehensive understanding of its cellular metabolism, a genome-scale metabolic model of strain SE50/110, iYLW1028, was reconstructed on the bases of the genome annotation, biochemical databases, and extensive literature mining. Model iYLW1028 comprises 1028 genes, 1128 metabolites, and 1219 reactions. One hundred and twenty-two and eighty one genes were essential for cell growth on acarbose synthesis and sucrose media, respectively, and the acarbose biosynthetic pathway in SE50/110 was expounded completely. Based on model predictions, the addition of arginine and histidine to the media increased acarbose production by 78 and 59%, respectively. Additionally, dissolved oxygen has a great effect on acarbose production based on model predictions. Furthermore, genes to be overexpressed for the overproduction of acarbose were identified, and the deletion of treY eliminated the formation of by-product component C. Model iYLW1028 is a useful platform for optimizing and systems metabolic engineering for acarbose production in Actinoplanes sp. SE50/110. PMID:26161077

  15. Genome-scale metabolic modeling to provide insight into the production of storage compounds during feast-famine cycles of activated sludge.

    PubMed

    Tajparast, Mohammad; Frigon, Dominic

    2013-01-01

    Studying storage metabolism during feast-famine cycles of activated sludge treatment systems provides profound insight in terms of both operational issues (e.g., foaming and bulking) and process optimization for the production of value added by-products (e.g., bioplastics). We examined the storage metabolism (including poly-β-hydroxybutyrate [PHB], glycogen, and triacylglycerols [TAGs]) during feast-famine cycles using two genome-scale metabolic models: Rhodococcus jostii RHA1 (iMT1174) and Escherichia coli K-12 (iAF1260) for growth on glucose, acetate, and succinate. The goal was to develop the proper objective function (OF) for the prediction of the main storage compound produced in activated sludge for given feast-famine cycle conditions. For the flux balance analysis, combinations of three OFs were tested. For all of them, the main OF was to maximize growth rates. Two additional sub-OFs were used: (1) minimization of biochemical fluxes, and (2) minimization of metabolic adjustments (MoMA) between the feast and famine periods. All (sub-)OFs predicted identical substrate-storage associations for the feast-famine growth of the above-mentioned metabolic models on a given substrate when glucose and acetate were set as sole carbon sources (i.e., glucose-glycogen and acetate-PHB), in agreement with experimental observations. However, in the case of succinate as substrate, the predictions depended on the network structure of the metabolic models such that the E. coli model predicted glycogen accumulation and the R. jostii model predicted PHB accumulation. While the accumulation of both PHB and glycogen was observed experimentally, PHB showed higher dynamics during an activated sludge feast-famine growth cycle with succinate as substrate. These results suggest that new modeling insights between metabolic predictions and population ecology will be necessary to properly predict metabolisms likely to emerge within the niches of activated sludge communities. Nonetheless

  16. Scaling the metabolic balance of the oceans.

    PubMed

    López-Urrutia, Angel; San Martin, Elena; Harris, Roger P; Irigoien, Xabier

    2006-06-06

    Oceanic communities are sources or sinks of CO2, depending on the balance between primary production and community respiration. The prediction of how global climate change will modify this metabolic balance of the oceans is limited by the lack of a comprehensive underlying theory. Here, we show that the balance between production and respiration is profoundly affected by environmental temperature. We extend the general metabolic theory of ecology to the production and respiration of oceanic communities and show that ecosystem rates can be reliably scaled from theoretical knowledge of organism physiology and measurement of population abundance. Our theory predicts that the differential temperature-dependence of respiration and photosynthesis at the organism level determines the response of the metabolic balance of the epipelagic ocean to changes in ambient temperature, a prediction that we support with empirical data over the global ocean. Furthermore, our model predicts that there will be a negative feedback of ocean communities to climate warming because they will capture less CO2 with a future increase in ocean temperature. This feedback of marine biota will further aggravate the anthropogenic effects on global warming.

  17. Scaling the metabolic balance of the oceans

    PubMed Central

    López-Urrutia, Ángel; San Martin, Elena; Harris, Roger P.; Irigoien, Xabier

    2006-01-01

    Oceanic communities are sources or sinks of CO2, depending on the balance between primary production and community respiration. The prediction of how global climate change will modify this metabolic balance of the oceans is limited by the lack of a comprehensive underlying theory. Here, we show that the balance between production and respiration is profoundly affected by environmental temperature. We extend the general metabolic theory of ecology to the production and respiration of oceanic communities and show that ecosystem rates can be reliably scaled from theoretical knowledge of organism physiology and measurement of population abundance. Our theory predicts that the differential temperature-dependence of respiration and photosynthesis at the organism level determines the response of the metabolic balance of the epipelagic ocean to changes in ambient temperature, a prediction that we support with empirical data over the global ocean. Furthermore, our model predicts that there will be a negative feedback of ocean communities to climate warming because they will capture less CO2 with a future increase in ocean temperature. This feedback of marine biota will further aggravate the anthropogenic effects on global warming. PMID:16731624

  18. Ontogenetic and interspecific metabolic scaling in insects.

    PubMed

    Maino, James L; Kearney, Michael R

    2014-12-01

    Design constraints imposed by increasing size cause metabolic rate in animals to increase more slowly than mass. This ubiquitous biological phenomenon is referred to as metabolic scaling. However, mechanistic explanations for interspecific metabolic scaling do not apply to ontogenetic size changes within a species, implying different mechanisms for scaling phenomena. Here, we show that the dynamic energy budget theory approach of compartmentalizing biomass into reserve and structural components provides a unified framework for understanding ontogenetic and interspecific metabolic scaling. We formulate the theory for insects and show that it can account for ontogenetic metabolic scaling during the embryonic and larval phases, as well as the U-shaped respiration curve during pupation. After correcting for the predicted ontogenetic scaling effects, which we show to follow universal curves, the scaling of respiration between species is approximated by a three-quarters power law, supporting past empirical studies on insect metabolic scaling and our theoretical predictions. The ability to explain ontogenetic and interspecific metabolic scaling effects under one consistent framework suggests that the partitioning of biomass into reserve and structure is a necessary foundation to a general metabolic theory.

  19. Identification of metabolic engineering targets for the enhancement of 1,4-butanediol production in recombinant E. coli using large-scale kinetic models.

    PubMed

    Andreozzi, Stefano; Chakrabarti, Anirikh; Soh, Keng Cher; Burgard, Anthony; Yang, Tae Hoon; Van Dien, Stephen; Miskovic, Ljubisa; Hatzimanikatis, Vassily

    2016-05-01

    Rational metabolic engineering methods are increasingly employed in designing the commercially viable processes for the production of chemicals relevant to pharmaceutical, biotechnology, and food and beverage industries. With the growing availability of omics data and of methodologies capable to integrate the available data into models, mathematical modeling and computational analysis are becoming important in designing recombinant cellular organisms and optimizing cell performance with respect to desired criteria. In this contribution, we used the computational framework ORACLE (Optimization and Risk Analysis of Complex Living Entities) to analyze the physiology of recombinant Escherichia coli producing 1,4-butanediol (BDO) and to identify potential strategies for improved production of BDO. The framework allowed us to integrate data across multiple levels and to construct a population of large-scale kinetic models despite the lack of available information about kinetic properties of every enzyme in the metabolic pathways. We analyzed these models and we found that the enzymes that primarily control the fluxes leading to BDO production are part of central glycolysis, the lower branch of tricarboxylic acid (TCA) cycle and the novel BDO production route. Interestingly, among the enzymes between the glucose uptake and the BDO pathway, the enzymes belonging to the lower branch of TCA cycle have been identified as the most important for improving BDO production and yield. We also quantified the effects of changes of the target enzymes on other intracellular states like energy charge, cofactor levels, redox state, cellular growth, and byproduct formation. Independent earlier experiments on this strain confirmed that the computationally obtained conclusions are consistent with the experimentally tested designs, and the findings of the present studies can provide guidance for future work on strain improvement. Overall, these studies demonstrate the potential and

  20. Applications of genome-scale metabolic reconstructions

    PubMed Central

    Oberhardt, Matthew A; Palsson, Bernhard Ø; Papin, Jason A

    2009-01-01

    The availability and utility of genome-scale metabolic reconstructions have exploded since the first genome-scale reconstruction was published a decade ago. Reconstructions have now been built for a wide variety of organisms, and have been used toward five major ends: (1) contextualization of high-throughput data, (2) guidance of metabolic engineering, (3) directing hypothesis-driven discovery, (4) interrogation of multi-species relationships, and (5) network property discovery. In this review, we examine the many uses and future directions of genome-scale metabolic reconstructions, and we highlight trends and opportunities in the field that will make the greatest impact on many fields of biology. PMID:19888215

  1. Genome scale engineering techniques for metabolic engineering.

    PubMed

    Liu, Rongming; Bassalo, Marcelo C; Zeitoun, Ramsey I; Gill, Ryan T

    2015-11-01

    Metabolic engineering has expanded from a focus on designs requiring a small number of genetic modifications to increasingly complex designs driven by advances in genome-scale engineering technologies. Metabolic engineering has been generally defined by the use of iterative cycles of rational genome modifications, strain analysis and characterization, and a synthesis step that fuels additional hypothesis generation. This cycle mirrors the Design-Build-Test-Learn cycle followed throughout various engineering fields that has recently become a defining aspect of synthetic biology. This review will attempt to summarize recent genome-scale design, build, test, and learn technologies and relate their use to a range of metabolic engineering applications.

  2. Genome-scale modeling for metabolic engineering

    SciTech Connect

    Simeonidis, E; Price, ND

    2015-01-13

    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.

  3. Genome-scale modeling for metabolic engineering

    PubMed Central

    Simeonidis, Evangelos

    2015-01-01

    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. PMID:25578304

  4. Genome-scale modeling for metabolic engineering.

    PubMed

    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.

  5. The effect of heating rate on Escherichia coli metabolism, physiological stress, transcriptional response, and production of temperature-induced recombinant protein: a scale-down study.

    PubMed

    Caspeta, Luis; Flores, Noemí; Pérez, Néstor O; Bolívar, Francisco; Ramírez, Octavio T

    2009-02-01

    At the laboratory scale, sudden step increases from 30 to 42 degrees C can be readily accomplished when expressing heterologous proteins in heat-inducible systems. However, for large scale-cultures only slow ramp-type increases in temperature are possible due to heat transfer limitations, where the heating rate decreases as the scale increases. In this work, the transcriptional and metabolic responses of a recombinant Escherichia coli strain to temperature-induced synthesis of pre-proinsulin in high cell density cultures were examined at different heating rates. Heating rates of 6, 1.7, 0.8, and 0.4 degrees C/min were tested in a scale-down approach to mimic fermentors of 0.1, 5, 20, and 100 m(3), respectively. The highest yield and concentration of recombinant protein was obtained for the slowest heating rate. As the heating rate increased, the yield and maximum recombinant protein concentration decreased, whereas a larger fraction of carbon skeletons was lost as acetate, lactate, and formate. Compared to 30 degrees C, the mRNA levels of selected heat-shock genes at 38 and 42 degrees C, as quantified by qRT-PCR, increased between 2- to over 42-fold when cultures were induced at 6, 1.7, and 0.8 degrees C/min, but no increase was observed at 0.4 degrees C/min. Only small increases (between 1.5- and 4-fold) in the expression of the stress genes spoT and relA were observed at 42 degrees C for cultures induced at 1.7 and 6 degrees C/min, suggesting that cells subjected to slow temperature increases can adapt to stress. mRNA levels of genes from the transcription-translation machinery (tufB, rpoA, and tig) decreased between 40% and 80% at 6, 1.7 and 0.8 degrees C/min, whereas a transient increase occurred for 0.4 degrees C/min at 42 degrees C. mRNA levels of the gene coding for pre-proinsulin showed a similar profile to transcripts of heat-shock genes, reflecting a probable analogous induction mechanism. Altogether, the results obtained indicate that slow heating rates

  6. Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii

    SciTech Connect

    Nagarajan, H; Sahin, M; Nogales, J; Latif, H; Lovley, DR; Ebrahim, A; Zengler, K

    2013-11-25

    Background: The metabolic capabilities of acetogens to ferment a wide range of sugars, to grow autotrophically on H-2/CO2, and more importantly on synthesis gas (H-2/CO/CO2) make them very attractive candidates as production hosts for biofuels and biocommodities. Acetogenic metabolism is considered one of the earliest modes of bacterial metabolism. A thorough understanding of various factors governing the metabolism, in particular energy conservation mechanisms, is critical for metabolic engineering of acetogens for targeted production of desired chemicals. Results: Here, we present the genome-scale metabolic network of Clostridium ljungdahlii, the first such model for an acetogen. This genome-scale model (iHN637) consisting of 637 genes, 785 reactions, and 698 metabolites captures all the major central metabolic and biosynthetic pathways, in particular pathways involved in carbon fixation and energy conservation. A combination of metabolic modeling, with physiological and transcriptomic data provided insights into autotrophic metabolism as well as aided the characterization of a nitrate reduction pathway in C. ljungdahlii. Analysis of the iHN637 metabolic model revealed that flavin based electron bifurcation played a key role in energy conservation during autotrophic growth and helped identify genes for some of the critical steps in this mechanism. Conclusions: iHN637 represents a predictive model that recapitulates experimental data, and provides valuable insights into the metabolic response of C. ljungdahlii to genetic perturbations under various growth conditions. Thus, the model will be instrumental in guiding metabolic engineering of C. ljungdahlii for the industrial production of biocommodities and biofuels.

  7. Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii

    PubMed Central

    2013-01-01

    Background The metabolic capabilities of acetogens to ferment a wide range of sugars, to grow autotrophically on H2/CO2, and more importantly on synthesis gas (H2/CO/CO2) make them very attractive candidates as production hosts for biofuels and biocommodities. Acetogenic metabolism is considered one of the earliest modes of bacterial metabolism. A thorough understanding of various factors governing the metabolism, in particular energy conservation mechanisms, is critical for metabolic engineering of acetogens for targeted production of desired chemicals. Results Here, we present the genome-scale metabolic network of Clostridium ljungdahlii, the first such model for an acetogen. This genome-scale model (iHN637) consisting of 637 genes, 785 reactions, and 698 metabolites captures all the major central metabolic and biosynthetic pathways, in particular pathways involved in carbon fixation and energy conservation. A combination of metabolic modeling, with physiological and transcriptomic data provided insights into autotrophic metabolism as well as aided the characterization of a nitrate reduction pathway in C. ljungdahlii. Analysis of the iHN637 metabolic model revealed that flavin based electron bifurcation played a key role in energy conservation during autotrophic growth and helped identify genes for some of the critical steps in this mechanism. Conclusions iHN637 represents a predictive model that recapitulates experimental data, and provides valuable insights into the metabolic response of C. ljungdahlii to genetic perturbations under various growth conditions. Thus, the model will be instrumental in guiding metabolic engineering of C. ljungdahlii for the industrial production of biocommodities and biofuels. PMID:24274140

  8. Production of natural products through metabolic engineering of Saccharomyces cerevisiae.

    PubMed

    Krivoruchko, Anastasia; Nielsen, Jens

    2015-12-01

    Many high-value metabolites are produced in nature by organisms that are not ideal for large-scale production. Therefore, interest exists in expressing the biosynthetic pathways of these compounds in organisms that are more suitable for industrial production. Recent years have seen developments in both the discovery of various biosynthetic pathways, as well as development of metabolic engineering tools that allow reconstruction of complex pathways in microorganisms. In the present review we discuss recent advances in reconstruction of the biosynthetic pathways of various high-value products in the yeast Saccharomyces cerevisiae, a commonly used industrial microorganism. Key achievements in the production of different isoprenoids, aromatics and polyketides are presented and the metabolic engineering strategies underlying these accomplishments are discussed.

  9. Ontogenetic scaling of metabolism, growth, and assimilation: testing metabolic scaling theory with Manduca sexta larvae.

    PubMed

    Sears, Katie E; Kerkhoff, Andrew J; Messerman, Arianne; Itagaki, Haruhiko

    2012-01-01

    Metabolism, growth, and the assimilation of energy and materials are essential processes that are intricately related and depend heavily on animal size. However, models that relate the ontogenetic scaling of energy assimilation and metabolism to growth rely on assumptions that have yet to be rigorously tested. Based on detailed daily measurements of metabolism, growth, and assimilation in tobacco hornworms, Manduca sexta, we provide a first experimental test of the core assumptions of a metabolic scaling model of ontogenetic growth. Metabolic scaling parameters changed over development, in violation of the model assumptions. At the same time, the scaling of growth rate matches that of metabolic rate, with similar scaling exponents both across and within developmental instars. Rates of assimilation were much higher than expected during the first two instars and did not match the patterns of scaling of growth and metabolism, which suggests high costs of biosynthesis early in development. The rapid increase in size and discrete instars observed in larval insect development provide an ideal system for understanding how patterns of growth and metabolism emerge from fundamental cellular processes and the exchange of materials and energy between an organism and its environment.

  10. Genome-scale metabolic representation of Amycolatopsis balhimycina.

    PubMed

    Vongsangnak, Wanwipa; Figueiredo, Luís Filipe; Förster, Jochen; Weber, Tilmann; Thykaer, Jette; Stegmann, Evi; Wohlleben, Wolfgang; Nielsen, Jens

    2012-07-01

    Infection caused by methicillin-resistant Staphylococcus aureus (MRSA) is an increasing societal problem. Typically, glycopeptide antibiotics are used in the treatment of these infections. The most comprehensively studied glycopeptide antibiotic biosynthetic pathway is that of balhimycin biosynthesis in Amycolatopsis balhimycina. The balhimycin yield obtained by A. balhimycina is, however, low and there is therefore a need to improve balhimycin production. In this study, we performed genome sequencing, assembly and annotation analysis of A. balhimycina and further used these annotated data to reconstruct a genome-scale metabolic model for the organism. Here we generated an almost complete A. balhimycina genome sequence comprising 10,562,587 base pairs assembled into 2,153 contigs. The high GC-genome (∼ 69%) includes 8,585 open reading frames (ORFs). We used our integrative toolbox called SEQTOR for functional annotation and then integrated annotated data with biochemical and physiological information available for this organism to reconstruct a genome-scale metabolic model of A. balhimycina. The resulting metabolic model contains 583 ORFs as protein encoding genes (7% of the predicted 8,585 ORFs), 407 EC numbers, 647 metabolites and 1,363 metabolic reactions. During the analysis of the metabolic model, linear, quadratic and evolutionary programming algorithms using flux balance analysis (FBA), minimization of metabolic adjustment (MOMA), and OptGene, respectively were applied as well as phenotypic behavior and improved balhimycin production were simulated. The A. balhimycina model shows a good agreement between in silico data and experimental data and also identifies key reactions associated with increased balhimycin production. The reconstruction of the genome-scale metabolic model of A. balhimycina serves as a basis for physiological characterization. The model allows a rational design of engineering strategies for increasing balhimycin production in A

  11. Modeling cancer metabolism on a genome scale

    PubMed Central

    Yizhak, Keren; Chaneton, Barbara; Gottlieb, Eyal; Ruppin, Eytan

    2015-01-01

    Cancer cells have fundamentally altered cellular metabolism that is associated with their tumorigenicity and malignancy. In addition to the widely studied Warburg effect, several new key metabolic alterations in cancer have been established over the last decade, leading to the recognition that altered tumor metabolism is one of the hallmarks of cancer. Deciphering the full scope and functional implications of the dysregulated metabolism in cancer requires both the advancement of a variety of omics measurements and the advancement of computational approaches for the analysis and contextualization of the accumulated data. Encouragingly, while the metabolic network is highly interconnected and complex, it is at the same time probably the best characterized cellular network. Following, this review discusses the challenges that genome-scale modeling of cancer metabolism has been facing. We survey several recent studies demonstrating the first strides that have been done, testifying to the value of this approach in portraying a network-level view of the cancer metabolism and in identifying novel drug targets and biomarkers. Finally, we outline a few new steps that may further advance this field. PMID:26130389

  12. Modeling cancer metabolism on a genome scale.

    PubMed

    Yizhak, Keren; Chaneton, Barbara; Gottlieb, Eyal; Ruppin, Eytan

    2015-06-30

    Cancer cells have fundamentally altered cellular metabolism that is associated with their tumorigenicity and malignancy. In addition to the widely studied Warburg effect, several new key metabolic alterations in cancer have been established over the last decade, leading to the recognition that altered tumor metabolism is one of the hallmarks of cancer. Deciphering the full scope and functional implications of the dysregulated metabolism in cancer requires both the advancement of a variety of omics measurements and the advancement of computational approaches for the analysis and contextualization of the accumulated data. Encouragingly, while the metabolic network is highly interconnected and complex, it is at the same time probably the best characterized cellular network. Following, this review discusses the challenges that genome-scale modeling of cancer metabolism has been facing. We survey several recent studies demonstrating the first strides that have been done, testifying to the value of this approach in portraying a network-level view of the cancer metabolism and in identifying novel drug targets and biomarkers. Finally, we outline a few new steps that may further advance this field.

  13. Quantum metabolism explains the allometric scaling of metabolic rates

    PubMed Central

    Demetrius, Lloyd; Tuszynski, J. A.

    2010-01-01

    A general model explaining the origin of allometric laws of physiology is proposed based on coupled energy-transducing oscillator networks embedded in a physical d-dimensional space (d = 1, 2, 3). This approach integrates Mitchell's theory of chemi-osmosis with the Debye model of the thermal properties of solids. We derive a scaling rule that relates the energy generated by redox reactions in cells, the dimensionality of the physical space and the mean cycle time. Two major regimes are found corresponding to classical and quantum behaviour. The classical behaviour leads to allometric isometry while the quantum regime leads to scaling laws relating metabolic rate and body size that cover a broad range of exponents that depend on dimensionality and specific parameter values. The regimes are consistent with a range of behaviours encountered in micelles, plants and animals and provide a conceptual framework for a theory of the metabolic function of living systems. PMID:19734187

  14. Quantum metabolism explains the allometric scaling of metabolic rates.

    PubMed

    Demetrius, Lloyd; Tuszynski, J A

    2010-03-06

    A general model explaining the origin of allometric laws of physiology is proposed based on coupled energy-transducing oscillator networks embedded in a physical d-dimensional space (d = 1, 2, 3). This approach integrates Mitchell's theory of chemi-osmosis with the Debye model of the thermal properties of solids. We derive a scaling rule that relates the energy generated by redox reactions in cells, the dimensionality of the physical space and the mean cycle time. Two major regimes are found corresponding to classical and quantum behaviour. The classical behaviour leads to allometric isometry while the quantum regime leads to scaling laws relating metabolic rate and body size that cover a broad range of exponents that depend on dimensionality and specific parameter values. The regimes are consistent with a range of behaviours encountered in micelles, plants and animals and provide a conceptual framework for a theory of the metabolic function of living systems.

  15. Imaging the time-integrated cerebral metabolic activity with subcellular resolution through nanometer-scale detection of biosynthetic products deriving from (13)C-glucose.

    PubMed

    Takado, Yuhei; Knott, Graham; Humbel, Bruno M; Masoodi, Mojgan; Escrig, Stéphane; Meibom, Anders; Comment, Arnaud

    2015-11-01

    Glucose is the primary source of energy for the brain but also an important source of building blocks for proteins, lipids, and nucleic acids. Little is known about the use of glucose for biosynthesis in tissues at the cellular level. We demonstrate that local cerebral metabolic activity can be mapped in mouse brain tissue by quantitatively imaging the biosynthetic products deriving from [U-(13)C]glucose metabolism using a combination of in situ electron microscopy and secondary ion mass-spectroscopy (NanoSIMS). Images of the (13)C-label incorporated into cerebral ultrastructure with ca. 100 nm resolution allowed us to determine the timescale on which the metabolic products of glucose are incorporated into different cells, their sub-compartments and organelles. These were mapped in astrocytes and neurons in the different layers of the motor cortex. We see evidence for high metabolic activity in neurons via the nucleus (13)C enrichment. We observe that in all the major cell compartments, such as e.g. nucleus and Golgi apparatus, neurons incorporate substantially higher concentrations of (13)C-label than astrocytes.

  16. Synthetic metabolism: engineering biology at the protein and pathway scales.

    PubMed

    Martin, Collin H; Nielsen, David R; Solomon, Kevin V; Prather, Kristala L Jones

    2009-03-27

    Biocatalysis has become a powerful tool for the synthesis of high-value compounds, particularly so in the case of highly functionalized and/or stereoactive products. Nature has supplied thousands of enzymes and assembled them into numerous metabolic pathways. Although these native pathways can be use to produce natural bioproducts, there are many valuable and useful compounds that have no known natural biochemical route. Consequently, there is a need for both unnatural metabolic pathways and novel enzymatic activities upon which these pathways can be built. Here, we review the theoretical and experimental strategies for engineering synthetic metabolic pathways at the protein and pathway scales, and highlight the challenges that this subfield of synthetic biology currently faces.

  17. Next-generation genome-scale models for metabolic engineering.

    PubMed

    King, Zachary A; Lloyd, Colton J; Feist, Adam M; Palsson, Bernhard O

    2015-12-01

    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 optimal genetic modifications that improve the rate and yield of chemical production. A new generation of COBRA models and methods is now being developed--encompassing many biological processes and simulation strategies-and next-generation models enable new types of predictions. Here, three key 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.

  18. Construction of a Genome-Scale Metabolic Model of Arthrospira platensis NIES-39 and Metabolic Design for Cyanobacterial Bioproduction.

    PubMed

    Yoshikawa, Katsunori; Aikawa, Shimpei; Kojima, Yuta; Toya, Yoshihiro; Furusawa, Chikara; Kondo, Akihiko; Shimizu, Hiroshi

    2015-01-01

    Arthrospira (Spirulina) platensis is a promising feedstock and host strain for bioproduction because of its high accumulation of glycogen and superior characteristics for industrial production. Metabolic simulation using a genome-scale metabolic model and flux balance analysis is a powerful method that can be used to design metabolic engineering strategies for the improvement of target molecule production. In this study, we constructed a genome-scale metabolic model of A. platensis NIES-39 including 746 metabolic reactions and 673 metabolites, and developed novel strategies to improve the production of valuable metabolites, such as glycogen and ethanol. The simulation results obtained using the metabolic model showed high consistency with experimental results for growth rates under several trophic conditions and growth capabilities on various organic substrates. The metabolic model was further applied to design a metabolic network to improve the autotrophic production of glycogen and ethanol. Decreased flux of reactions related to the TCA cycle and phosphoenolpyruvate reaction were found to improve glycogen production. Furthermore, in silico knockout simulation indicated that deletion of genes related to the respiratory chain, such as NAD(P)H dehydrogenase and cytochrome-c oxidase, could enhance ethanol production by using ammonium as a nitrogen source.

  19. Metabolic engineering of biosynthetic pathway for production of renewable biofuels.

    PubMed

    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.

  20. Improved Succinate Production by Metabolic Engineering

    PubMed Central

    Cheng, Ke-Ke; Wang, Gen-Yu; Zeng, Jing; Zhang, Jian-An

    2013-01-01

    Succinate is a promising chemical which has wide applications and can be produced by biological route. The history of the biosuccinate production shows that the joint effort of different metabolic engineering approaches brings successful results. In order to enhance the succinate production, multiple metabolical strategies have been sought. In this review, different overproducers for succinate production, including natural succinate overproducers and metabolic engineered overproducers, are examined and the metabolic engineering strategies and performances are discussed. Modification of the mechanism of substrate transportation, knocking-out genes responsible for by-products accumulation, overexpression of the genes directly involved in the pathway, and improvement of internal NADH and ATP formation are some of the strategies applied. Combination of the appropriate genes from homologous and heterologous hosts, extension of substrate, integrated production of succinate, and other high-value-added products are expected to bring a desired objective of producing succinate from renewable resources economically and efficiently. PMID:23691505

  1. Improved succinate production by metabolic engineering.

    PubMed

    Cheng, Ke-Ke; Wang, Gen-Yu; Zeng, Jing; Zhang, Jian-An

    2013-01-01

    Succinate is a promising chemical which has wide applications and can be produced by biological route. The history of the biosuccinate production shows that the joint effort of different metabolic engineering approaches brings successful results. In order to enhance the succinate production, multiple metabolical strategies have been sought. In this review, different overproducers for succinate production, including natural succinate overproducers and metabolic engineered overproducers, are examined and the metabolic engineering strategies and performances are discussed. Modification of the mechanism of substrate transportation, knocking-out genes responsible for by-products accumulation, overexpression of the genes directly involved in the pathway, and improvement of internal NADH and ATP formation are some of the strategies applied. Combination of the appropriate genes from homologous and heterologous hosts, extension of substrate, integrated production of succinate, and other high-value-added products are expected to bring a desired objective of producing succinate from renewable resources economically and efficiently.

  2. Cyanobacterial metabolic engineering for biofuel and chemical production.

    PubMed

    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 CO2 are contributing to the global greenhouse effect. Large scale use of atmospheric CO2 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 CO2 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.

  3. Randomizing Genome-Scale Metabolic Networks

    PubMed Central

    Samal, Areejit; Martin, Olivier C.

    2011-01-01

    Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have “unusual” properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the network is not statistically different from expected in a motivated ensemble. However, when dealing with metabolic networks, the randomization of the network using edge exchange generates fictitious reactions that are biochemically meaningless. Here we provide several natural ensembles of randomized metabolic networks. A first constraint is to use valid biochemical reactions. Further constraints correspond to imposing appropriate functional constraints. We explain how to perform these randomizations with the help of Markov Chain Monte Carlo (MCMC) and show that they allow one to approach the properties of biological metabolic networks. The implication of the present work is that the observed global structural properties of real metabolic networks are likely to be the consequence of simple biochemical and functional constraints. PMID:21779409

  4. Zea mays iRS1563: a comprehensive genome-scale metabolic reconstruction of maize metabolism.

    PubMed

    Saha, Rajib; Suthers, Patrick F; Maranas, Costas D

    2011-01-01

    The scope and breadth of genome-scale metabolic reconstructions have continued to expand over the last decade. Herein, we introduce a genome-scale model for a plant with direct applications to food and bioenergy production (i.e., maize). Maize annotation is still underway, which introduces significant challenges in the association of metabolic functions to genes. The developed model is designed to meet rigorous standards on gene-protein-reaction (GPR) associations, elementally and charged balanced reactions and a biomass reaction abstracting the relative contribution of all biomass constituents. The metabolic network contains 1,563 genes and 1,825 metabolites involved in 1,985 reactions from primary and secondary maize metabolism. For approximately 42% of the reactions direct literature evidence for the participation of the reaction in maize was found. As many as 445 reactions and 369 metabolites are unique to the maize model compared to the AraGEM model for A. thaliana. 674 metabolites and 893 reactions are present in Zea mays iRS1563 that are not accounted for in maize C4GEM. All reactions are elementally and charged balanced and localized into six different compartments (i.e., cytoplasm, mitochondrion, plastid, peroxisome, vacuole and extracellular). GPR associations are also established based on the functional annotation information and homology prediction accounting for monofunctional, multifunctional and multimeric proteins, isozymes and protein complexes. We describe results from performing flux balance analysis under different physiological conditions, (i.e., photosynthesis, photorespiration and respiration) of a C4 plant and also explore model predictions against experimental observations for two naturally occurring mutants (i.e., bm1 and bm3). The developed model corresponds to the largest and more complete to-date effort at cataloguing metabolism for a plant species.

  5. Genome-scale analysis of the metabolic networks of oleaginous Zygomycete fungi.

    PubMed

    Vongsangnak, Wanwipa; Ruenwai, Rawisara; Tang, Xin; Hu, Xinjie; Zhang, Hao; Shen, Bairong; Song, Yuanda; Laoteng, Kobkul

    2013-05-25

    Microbial lipids are becoming an attractive option for the industrial production of foods and oleochemicals. To investigate the lipid physiology of the oleaginous microorganisms, at the system level, genome-scale metabolic networks of Mortierella alpina and Mucor circinelloides were constructed using bioinformatics and systems biology. As scaffolds for integrated data analysis focusing on lipid production, consensus metabolic routes governing fatty acid synthesis, and lipid storage and mobilisation were identified by comparative analysis of developed metabolic networks. Unique metabolic features were identified in individual fungi, particularly in NADPH metabolism and sterol biosynthesis, which might be related to differences in fungal lipid phenotypes. The frameworks detailing the metabolic relationship between M. alpina and M. circinelloides generated in this study is useful for further elucidation of the microbial oleaginicity, which might lead to the production improvement of microbial oils as alternative feedstocks for oleochemical industry.

  6. Metabolic scaling in animals: methods, empirical results, and theoretical explanations.

    PubMed

    White, Craig R; Kearney, Michael R

    2014-01-01

    Life on earth spans a size range of around 21 orders of magnitude across species and can span a range of more than 6 orders of magnitude within species of animal. The effect of size on physiology is, therefore, enormous and is typically expressed by how physiological phenomena scale with mass(b). When b ≠ 1 a trait does not vary in direct proportion to mass and is said to scale allometrically. The study of allometric scaling goes back to at least the time of Galileo Galilei, and published scaling relationships are now available for hundreds of traits. Here, the methods of scaling analysis are reviewed, using examples for a range of traits with an emphasis on those related to metabolism in animals. Where necessary, new relationships have been generated from published data using modern phylogenetically informed techniques. During recent decades one of the most controversial scaling relationships has been that between metabolic rate and body mass and a number of explanations have been proposed for the scaling of this trait. Examples of these mechanistic explanations for metabolic scaling are reviewed, and suggestions made for comparing between them. Finally, the conceptual links between metabolic scaling and ecological patterns are examined, emphasizing the distinction between (1) the hypothesis that size- and temperature-dependent variation among species and individuals in metabolic rate influences ecological processes at levels of organization from individuals to the biosphere and (2) mechanistic explanations for metabolic rate that may explain the size- and temperature-dependence of this trait.

  7. Yeast metabolic chassis designs for diverse biotechnological products

    PubMed Central

    Jouhten, Paula; Boruta, Tomasz; Andrejev, Sergej; Pereira, Filipa; Rocha, Isabel; Patil, Kiran Raosaheb

    2016-01-01

    The diversity of industrially important molecules for which microbial production routes have been experimentally demonstrated is rapidly increasing. The development of economically viable producer cells is, however, lagging behind, as it requires substantial engineering of the host metabolism. A chassis strain suitable for production of a range of molecules is therefore highly sought after but remains elusive. Here, we propose a genome-scale metabolic modeling approach to design chassis strains of Saccharomyces cerevisiae – a widely used microbial cell factory. For a group of 29 products covering a broad range of biochemistry and applications, we identified modular metabolic engineering strategies for re-routing carbon flux towards the desired product. We find distinct product families with shared targets forming the basis for the corresponding chassis cells. The design strategies include overexpression targets that group products by similarity in precursor and cofactor requirements, as well as gene deletion strategies for growth-product coupling that lead to non-intuitive product groups. Our results reveal the extent and the nature of flux re-routing necessary for producing a diverse range of products in a widely used cell factory and provide blueprints for constructing pre-optimized chassis strains. PMID:27430744

  8. Metabolic heat production by human and animal populations in cities

    NASA Astrophysics Data System (ADS)

    Stewart, Iain D.; Kennedy, Chris A.

    2016-12-01

    Anthropogenic heating from building energy use, vehicle fuel consumption, and human metabolism is a key term in the urban energy budget equation. Heating from human metabolism, however, is often excluded from urban energy budgets because it is widely observed to be negligible. Few reports for low-latitude cities are available to support this observation, and no reports exist on the contribution of domestic animals to urban heat budgets. To provide a more comprehensive view of metabolic heating in cities, we quantified all terms of the anthropogenic heat budget at metropolitan scale for the world's 26 largest cities, using a top-down statistical approach. Results show that metabolic heat release from human populations in mid-latitude cities (e.g. London, Tokyo, New York) accounts for 4-8% of annual anthropogenic heating, compared to 10-45% in high-density tropical cities (e.g. Cairo, Dhaka, Kolkata). Heat release from animal populations amounts to <1% of anthropogenic heating in all cities. Heat flux density from human and animal metabolism combined is highest in Mumbai—the world's most densely populated megacity—at 6.5 W m-2, surpassing heat production by electricity use in buildings (5.8 W m-2) and fuel combustion in vehicles (3.9 W m-2). These findings, along with recent output from global climate models, suggest that in the world's largest and most crowded cities, heat emissions from human metabolism alone can force measurable change in mean annual temperature at regional scale.

  9. Northern Florida reef tract benthic metabolism scaled by remote sensing

    USGS Publications Warehouse

    Brock, J.C.; Yates, K.K.; Halley, R.B.; Kuffner, I.B.; Wright, C.W.; Hatcher, B.G.

    2006-01-01

    Holistic rates of excess organic carbon production (E) and calcification for a 0.5 km2 segment of the backreef platform of the northern Florida reef tract (NFRT) were estimated by combining biotope mapping using remote sensing with community metabolic rates determined with a benthic incubation system. The use of ASTER multispectral satellite imaging for the spatial scaling of benthic metabolic processes resulted in errors in E and net calcification (G) of 48 and 431% respectively, relative to estimates obtained using AISA hyperspectral airborne scanning. At 19 and 125%, the E and G errors relative to the AISA-based estimates were less pronounced for an analysis that used IKONOS multispectral satellite imagery to spatially extrapolate the chamber process measurements. Our scaling analysis indicates that the holistic calcification rate of the backreef platform of the northern Florida reef tract is negligible at 0.07 g CaCO3 m-2 d-1. All of the mapped biotopes in this reef zone are net heterotrophic, resulting in an estimated holistic excess production rate of -0.56 g C m-2 d-1, and an overall gross primary production to respiration ratio of 0.85. Based on our finding of ubiquitous heterotrophy, we infer that the backreef platform of the NFRT is a sink for external inputs of suspended particulate organic matter. Further, our results suggest that the inward advection of inorganic nutrients is not a dominant forcing mechanism for benthic biogeochemical function in the NFRT. We suggest that the degradation of the northern Florida reef tract may parallel the community phase shifts documented within other reef systems polluted by organic detritus.

  10. Redirection of metabolism for hydrogen production

    SciTech Connect

    Harwood, Caroline S.

    2011-11-28

    This project is to develop and apply techniques in metabolic engineering to improve the biocatalytic potential of the bacterium Rhodopseudomonas palustris for nitrogenase-catalyzed hydrogen gas production. R. palustris, is an ideal platform to develop as a biocatalyst for hydrogen gas production because it is an extremely versatile microbe that produces copious amounts of hydrogen by drawing on abundant natural resources of sunlight and biomass. Anoxygenic photosynthetic bacteria, such as R. palustris, generate hydrogen and ammonia during a process known as biological nitrogen fixation. This reaction is catalyzed by the enzyme nitrogenase and normally consumes nitrogen gas, ATP and electrons. The applied use of nitrogenase for hydrogen production is attractive because hydrogen is an obligatory product of this enzyme and is formed as the only product when nitrogen gas is not supplied. Our challenge is to understand the systems biology of R. palustris sufficiently well to be able to engineer cells to produce hydrogen continuously, as fast as possible and with as high a conversion efficiency as possible of light and electron donating substrates. For many experiments we started with a strain of R. palustris that produces hydrogen constitutively under all growth conditions. We then identified metabolic pathways and enzymes important for removal of electrons from electron-donating organic compounds and for their delivery to nitrogenase in whole R. palustris cells. For this we developed and applied improved techniques in 13C metabolic flux analysis. We identified reactions that are important for generating electrons for nitrogenase and that are yield-limiting for hydrogen production. We then increased hydrogen production by blocking alternative electron-utilizing metabolic pathways by mutagenesis. In addition we found that use of non-growing cells as biocatalysts for hydrogen gas production is an attractive option, because cells divert all resources away from growth and

  11. Metabolic engineering for higher alcohol production.

    PubMed

    Nozzi, Nicole E; Desai, Shuchi H; Case, Anna E; Atsumi, Shota

    2014-09-01

    Engineering microbial hosts for the production of higher alcohols looks to combine the benefits of renewable biological production with the useful chemical properties of larger alcohols. In this review we outline the array of metabolic engineering strategies employed for the efficient diversion of carbon flux from native biosynthetic pathways to the overproduction of a target alcohol. Strategies for pathway design from amino acid biosynthesis through 2-keto acids, from isoprenoid biosynthesis through pyrophosphate intermediates, from fatty acid biosynthesis and degradation by tailoring chain length specificity, and the use and expansion of natural solvent production pathways will be covered.

  12. The scaling and temperature dependence of vertebrate metabolism.

    PubMed

    White, Craig R; Phillips, Nicole F; Seymour, Roger S

    2006-03-22

    Body size and temperature are primary determinants of metabolic rate, and the standard metabolic rate (SMR) of animals ranging in size from unicells to mammals has been thought to be proportional to body mass (M) raised to the power of three-quarters for over 40 years. However, recent evidence from rigorously selected datasets suggests that this is not the case for birds and mammals. To determine whether the influence of body mass on the metabolic rate of vertebrates is indeed universal, we compiled SMR measurements for 938 species spanning six orders of magnitude variation in mass. When normalized to a common temperature of 38 degrees C, the SMR scaling exponents of fish, amphibians, reptiles, birds and mammals are significantly heterogeneous. This suggests both that there is no universal metabolic allometry and that models that attempt to explain only quarter-power scaling of metabolic rate are unlikely to succeed.

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

    PubMed

    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.

  14. Genome-scale models of bacterial metabolism: reconstruction and applications

    PubMed Central

    Durot, Maxime; Bourguignon, Pierre-Yves; Schachter, Vincent

    2009-01-01

    Genome-scale metabolic models bridge the gap between genome-derived biochemical information and metabolic phenotypes in a principled manner, providing a solid interpretative framework for experimental data related to metabolic states, and enabling simple in silico experiments with whole-cell metabolism. Models have been reconstructed for almost 20 bacterial species, so far mainly through expert curation efforts integrating information from the literature with genome annotation. A wide variety of computational methods exploiting metabolic models have been developed and applied to bacteria, yielding valuable insights into bacterial metabolism and evolution, and providing a sound basis for computer-assisted design in metabolic engineering. Recent advances in computational systems biology and high-throughput experimental technologies pave the way for the systematic reconstruction of metabolic models from genomes of new species, and a corresponding expansion of the scope of their applications. In this review, we provide an introduction to the key ideas of metabolic modeling, survey the methods, and resources that enable model reconstruction and refinement, and chart applications to the investigation of global properties of metabolic systems, the interpretation of experimental results, and the re-engineering of their biochemical capabilities. PMID:19067749

  15. Scaling the respiratory metabolism to phosphorus relationship in plant seedlings

    PubMed Central

    Wang, Zhi-Qiang; Huang, Heng; Deng, Jian-Ming; Liu, Jian-Quan

    2015-01-01

    There are empirical indications of an isometric scaling relationship between plants’ respiratory metabolism rates and nitrogen contents. To test the hypothesis that there may be a similar relationship between plants’ respiratory metabolism and phosphorus contents we used data obtained from 150 laboratory and field-grown seedlings representing 30 herbaceous species and 20 woody deciduous species. Our results show that whole-plant respiration rates strongly scaled to the 0.81-power of the whole-plant phosphorus content, across wide ranges of growth conditions and functional classifications. Moreover, we also found a similar scaling exponent between whole-plant respiration rates and total nitrogen contents for the same set of samples. The similarities of the metabolic scaling relationships suggest that similar mechanisms may be involved in the transport and storage of phosphorus and nitrogen in plants. PMID:26560344

  16. Universal scaling of respiratory metabolism, size and nitrogen in plants.

    PubMed

    Reich, Peter B; Tjoelker, Mark G; Machado, Jose-Luis; Oleksyn, Jacek

    2006-01-26

    The scaling of respiratory metabolism to body size in animals is considered to be a fundamental law of nature, and there is substantial evidence for an approximate (3/4)-power relation. Studies suggest that plant respiratory metabolism also scales as the (3/4)-power of mass, and that higher plant and animal scaling follow similar rules owing to the predominance of fractal-like transport networks and associated allometric scaling. Here, however, using data obtained from about 500 laboratory and field-grown plants from 43 species and four experiments, we show that whole-plant respiration rate scales approximately isometrically (scaling exponent approximately 1) with total plant mass in individual experiments and has no common relation across all data. Moreover, consistent with theories about biochemically based physiological scaling, isometric scaling of whole-plant respiration rate to total nitrogen content is observed within and across all data sets, with a single relation common to all data. This isometric scaling is unaffected by growth conditions including variation in light, nitrogen availability, temperature and atmospheric CO2 concentration, and is similar within or among species or functional groups. These findings suggest that plants and animals follow different metabolic scaling relations, driven by distinct mechanisms.

  17. Metabolic Engineering for the Production of Natural Products

    PubMed Central

    Pickens, Lauren B.; Tang, Yi; Chooi, Yit-Heng

    2014-01-01

    Natural products and natural product derived compounds play an important role in modern healthcare as frontline treatments for many diseases and as inspiration for chemically synthesized therapeutics. With advances in sequencing and recombinant DNA technology, many of the biosynthetic pathways responsible for the production of these chemically complex and pharmaceutically valuable compounds have been elucidated. With an ever expanding toolkit of biosynthetic components, metabolic engineering is an increasingly powerful method to improve natural product titers and generate novel compounds. Heterologous production platforms have enabled access to pathways from difficult to culture strains; systems biology and metabolic modeling tools have resulted in increasing predictive and analytic capabilities; advances in expression systems and regulation have enabled the fine-tuning of pathways for increased efficiency, and characterization of individual pathway components has facilitated the construction of hybrid pathways for the production of new compounds. These advances in the many aspects of metabolic engineering have not only yielded fascinating scientific discoveries but also make it an increasingly viable approach for the optimization of natural product biosynthesis. PMID:22432617

  18. Activity affects intraspecific body-size scaling of metabolic rate in ectothermic animals.

    PubMed

    Glazier, Douglas Stewart

    2009-10-01

    Metabolic rate is commonly thought to scale with body mass (M) to the 3/4 power. However, the metabolic scaling exponent (b) may vary with activity state, as has been shown chiefly for interspecific relationships. Here I use a meta-analysis of literature data to test whether b changes with activity level within species of ectothermic animals. Data for 19 species show that b is usually higher during active exercise (mean +/- 95% confidence limits = 0.918 +/- 0.038) than during rest (0.768 +/- 0.069). This significant upward shift in b to near 1 is consistent with the metabolic level boundaries hypothesis, which predicts that maximal metabolic rate during exercise should be chiefly influenced by volume-related muscular power production (scaling as M (1)). This dependence of b on activity level does not appear to be a simple temperature effect because body temperature in ectotherms changes very little during exercise.

  19. Multi-scale modeling for sustainable chemical production.

    PubMed

    Zhuang, Kai; Bakshi, Bhavik R; Herrgård, Markus J

    2013-09-01

    With recent advances in metabolic engineering, it is now technically possible to produce a wide portfolio of existing petrochemical products from biomass feedstock. In recent years, a number of modeling approaches have been developed to support the engineering and decision-making processes associated with the development and implementation of a sustainable biochemical industry. The temporal and spatial scales of modeling approaches for sustainable chemical production vary greatly, ranging from metabolic models that aid the design of fermentative microbial strains to material and monetary flow models that explore the ecological impacts of all economic activities. Research efforts that attempt to connect the models at different scales have been limited. Here, we review a number of existing modeling approaches and their applications at the scales of metabolism, bioreactor, overall process, chemical industry, economy, and ecosystem. In addition, we propose a multi-scale approach for integrating the existing models into a cohesive framework. The major benefit of this proposed framework is that the design and decision-making at each scale can be informed, guided, and constrained by simulations and predictions at every other scale. In addition, the development of this multi-scale framework would promote cohesive collaborations across multiple traditionally disconnected modeling disciplines to achieve sustainable chemical production.

  20. Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network

    PubMed Central

    Martín-Jiménez, Cynthia A.; Salazar-Barreto, Diego; Barreto, George E.; González, Janneth

    2017-01-01

    Astrocytes are the most abundant cells of the central nervous system; they have a predominant role in maintaining brain metabolism. In this sense, abnormal metabolic states have been found in different neuropathological diseases. Determination of metabolic states of astrocytes is difficult to model using current experimental approaches given the high number of reactions and metabolites present. Thus, genome-scale metabolic networks derived from transcriptomic data can be used as a framework to elucidate how astrocytes modulate human brain metabolic states during normal conditions and in neurodegenerative diseases. We performed a Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network with the purpose of elucidating a significant portion of the metabolic map of the astrocyte. This is the first global high-quality, manually curated metabolic reconstruction network of a human astrocyte. It includes 5,007 metabolites and 5,659 reactions distributed among 8 cell compartments, (extracellular, cytoplasm, mitochondria, endoplasmic reticle, Golgi apparatus, lysosome, peroxisome and nucleus). Using the reconstructed network, the metabolic capabilities of human astrocytes were calculated and compared both in normal and ischemic conditions. We identified reactions activated in these two states, which can be useful for understanding the astrocytic pathways that are affected during brain disease. Additionally, we also showed that the obtained flux distributions in the model, are in accordance with literature-based findings. Up to date, this is the most complete representation of the human astrocyte in terms of inclusion of genes, proteins, reactions and metabolic pathways, being a useful guide for in-silico analysis of several metabolic behaviors of the astrocyte during normal and pathologic states. PMID:28243200

  1. Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network.

    PubMed

    Martín-Jiménez, Cynthia A; Salazar-Barreto, Diego; Barreto, George E; González, Janneth

    2017-01-01

    Astrocytes are the most abundant cells of the central nervous system; they have a predominant role in maintaining brain metabolism. In this sense, abnormal metabolic states have been found in different neuropathological diseases. Determination of metabolic states of astrocytes is difficult to model using current experimental approaches given the high number of reactions and metabolites present. Thus, genome-scale metabolic networks derived from transcriptomic data can be used as a framework to elucidate how astrocytes modulate human brain metabolic states during normal conditions and in neurodegenerative diseases. We performed a Genome-Scale Reconstruction of the Human Astrocyte Metabolic Network with the purpose of elucidating a significant portion of the metabolic map of the astrocyte. This is the first global high-quality, manually curated metabolic reconstruction network of a human astrocyte. It includes 5,007 metabolites and 5,659 reactions distributed among 8 cell compartments, (extracellular, cytoplasm, mitochondria, endoplasmic reticle, Golgi apparatus, lysosome, peroxisome and nucleus). Using the reconstructed network, the metabolic capabilities of human astrocytes were calculated and compared both in normal and ischemic conditions. We identified reactions activated in these two states, which can be useful for understanding the astrocytic pathways that are affected during brain disease. Additionally, we also showed that the obtained flux distributions in the model, are in accordance with literature-based findings. Up to date, this is the most complete representation of the human astrocyte in terms of inclusion of genes, proteins, reactions and metabolic pathways, being a useful guide for in-silico analysis of several metabolic behaviors of the astrocyte during normal and pathologic states.

  2. Metabolic engineering of Corynebacterium glutamicum for L-arginine production.

    PubMed

    Park, Seok Hyun; Kim, Hyun Uk; Kim, Tae Yong; Park, Jun Seok; Kim, Suok-Su; Lee, Sang Yup

    2014-08-05

    L-arginine is an important amino acid for diverse industrial and health product applications. Here we report the development of metabolically engineered Corynebacterium glutamicum ATCC 21831 for the production of L-arginine. Random mutagenesis is first performed to increase the tolerance of C. glutamicum to L-arginine analogues, followed by systems metabolic engineering for further strain improvement, involving removal of regulatory repressors of arginine operon, optimization of NADPH level, disruption of L-glutamate exporter to increase L-arginine precursor and flux optimization of rate-limiting L-arginine biosynthetic reactions. Fed-batch fermentation of the final strain in 5 l and large-scale 1,500 l bioreactors allows production of 92.5 and 81.2 g l(-1) of L-arginine with the yields of 0.40 and 0.35 g L-arginine per gram carbon source (glucose plus sucrose), respectively. The systems metabolic engineering strategy described here will be useful for engineering Corynebacteria strains for the industrial production of L-arginine and related products.

  3. A genome-scale metabolic model of the lipid-accumulating yeast Yarrowia lipolytica

    PubMed Central

    2012-01-01

    Background Yarrowia lipolytica is an oleaginous yeast which has emerged as an important microorganism for several biotechnological processes, such as the production of organic acids, lipases and proteases. It is also considered a good candidate for single-cell oil production. Although some of its metabolic pathways are well studied, its metabolic engineering is hindered by the lack of a genome-scale model that integrates the current knowledge about its metabolism. Results Combining in silico tools and expert manual curation, we have produced an accurate genome-scale metabolic model for Y. lipolytica. Using a scaffold derived from a functional metabolic model of the well-studied but phylogenetically distant yeast S. cerevisiae, we mapped conserved reactions, rewrote gene associations, added species-specific reactions and inserted specialized copies of scaffold reactions to account for species-specific expansion of protein families. We used physiological measures obtained under lab conditions to validate our predictions. Conclusions Y. lipolytica iNL895 represents the first well-annotated metabolic model of an oleaginous yeast, providing a base for future metabolic improvement, and a starting point for the metabolic reconstruction of other species in the Yarrowia clade and other oleaginous yeasts. PMID:22558935

  4. Yeast metabolic engineering for hemicellulosic ethanol production.

    PubMed

    Van Vleet, J H; Jeffries, T W

    2009-06-01

    Efficient fermentation of hemicellulosic sugars is critical for the bioconversion of lignocellulosics to ethanol. Efficient sugar uptake through the heterologous expression of yeast and fungal xylose/glucose transporters can improve fermentation if other metabolic steps are not rate limiting. Rectification of cofactor imbalances through heterologous expression of fungal xylose isomerase or modification of cofactor requirements in the yeast oxidoreductase pathway can reduce xylitol production while increasing ethanol yields, but these changes often occur at the expense of xylose utilization rates. Genetic engineering and evolutionary adaptation to increase glycolytic flux coupled with transcriptomic and proteomic studies have identified targets for further modification, as have genomic and metabolic engineering studies in native xylose fermenting yeasts.

  5. Genome scale metabolic reconstruction of Chlorella variabilis for exploring its metabolic potential for biofuels.

    PubMed

    Juneja, Ankita; Chaplen, Frank W R; Murthy, Ganti S

    2016-08-01

    A compartmentalized genome scale metabolic network was reconstructed for Chlorella variabilis to offer insight into various metabolic potentials from this alga. The model, iAJ526, was reconstructed with 1455 reactions, 1236 metabolites and 526 genes. 21% of the reactions were transport reactions and about 81% of the total reactions were associated with enzymes. Along with gap filling reactions, 2 major sub-pathways were added to the model, chitosan synthesis and rhamnose metabolism. The reconstructed model had reaction participation of 4.3 metabolites per reaction and average lethality fraction of 0.21. The model was effective in capturing the growth of C. variabilis under three light conditions (white, red and red+blue light) with fair agreement. This reconstructed metabolic network will serve an important role in systems biology for further exploration of metabolism for specific target metabolites and enable improved characteristics in the strain through metabolic engineering.

  6. Metabolic heat production by human and animal populations in cities.

    PubMed

    Stewart, Iain D; Kennedy, Chris A

    2016-12-26

    Anthropogenic heating from building energy use, vehicle fuel consumption, and human metabolism is a key term in the urban energy budget equation. Heating from human metabolism, however, is often excluded from urban energy budgets because it is widely observed to be negligible. Few reports for low-latitude cities are available to support this observation, and no reports exist on the contribution of domestic animals to urban heat budgets. To provide a more comprehensive view of metabolic heating in cities, we quantified all terms of the anthropogenic heat budget at metropolitan scale for the world's 26 largest cities, using a top-down statistical approach. Results show that metabolic heat release from human populations in mid-latitude cities (e.g. London, Tokyo, New York) accounts for 4-8% of annual anthropogenic heating, compared to 10-45% in high-density tropical cities (e.g. Cairo, Dhaka, Kolkata). Heat release from animal populations amounts to <1% of anthropogenic heating in all cities. Heat flux density from human and animal metabolism combined is highest in Mumbai-the world's most densely populated megacity-at 6.5 W m(-2), surpassing heat production by electricity use in buildings (5.8 W m(-2)) and fuel combustion in vehicles (3.9 W m(-2)). These findings, along with recent output from global climate models, suggest that in the world's largest and most crowded cities, heat emissions from human metabolism alone can force measurable change in mean annual temperature at regional scale.

  7. Large-scale profiling of metabolic dysregulation in ovarian cancer.

    PubMed

    Ke, Chaofu; Hou, Yan; Zhang, Haiyu; Fan, Lijun; Ge, Tingting; Guo, Bing; Zhang, Fan; Yang, Kai; Wang, Jingtao; Lou, Ge; Li, Kang

    2015-02-01

    Ovarian cancer is the leading cause of death in gynecologic malignancies. Profiling of endogenous metabolites has potential to identify changes caused by cancer and provide inspiring insights into cancer metabolism. To systematically investigate ovarian cancer metabolism, we performed metabolic profiling of 448 plasma samples related to epithelial ovarian cancer (EOC) based on ultra-performance liquid chromatography mass spectrometry in both positive and negative modes. These unbiased metabolomic profiles could well distinguish EOC from benign ovarian tumor (BOT) and uterine fibroid (UF). Fifty-three metabolites were identified as specific biomarkers for EOC, and this is the first report of piperine, 3-indolepropionic acid, 5-hydroxyindoleacetaldehyde and hydroxyphenyllactate as metabolic biomarkers of EOC. The AUC values of these metabolites for discriminating EOC from BOT/UF and early-stage EOC from BOT/UF were 0.9100/0.9428 and 0.8385/0.8624, respectively. Meanwhile, our metabolites were able to distinguish early-stage EOC from late-stage EOC with an AUC of 0.8801. Importantly, analysis of dysregulated metabolic pathways extends our current understanding of EOC metabolism. Metabolic pathways in EOC patients are mainly characterized by abnormal phospholipid metabolism, altered l-tryptophan catabolism, aggressive fatty acid β-oxidation and aberrant metabolism of piperidine derivatives. Together, these metabolic pathways provide a foundation to support cancer development and progression. In conclusion, our large-scale plasma metabolomics study yielded fundamental insights into dysregulated metabolism in ovarian cancer, which could facilitate clinical diagnosis, therapy, prognosis and shed new lights on ovarian cancer pathogenesis.

  8. MEMOSys: Bioinformatics platform for genome-scale metabolic models

    PubMed Central

    2011-01-01

    Background Recent advances in genomic sequencing have enabled the use of genome sequencing in standard biological and biotechnological research projects. The challenge is how to integrate the large amount of data in order to gain novel biological insights. One way to leverage sequence data is to use genome-scale metabolic models. We have therefore designed and implemented a bioinformatics platform which supports the development of such metabolic models. Results MEMOSys (MEtabolic MOdel research and development System) is a versatile platform for the management, storage, and development of genome-scale metabolic models. It supports the development of new models by providing a built-in version control system which offers access to the complete developmental history. Moreover, the integrated web board, the authorization system, and the definition of user roles allow collaborations across departments and institutions. Research on existing models is facilitated by a search system, references to external databases, and a feature-rich comparison mechanism. MEMOSys provides customizable data exchange mechanisms using the SBML format to enable analysis in external tools. The web application is based on the Java EE framework and offers an intuitive user interface. It currently contains six annotated microbial metabolic models. Conclusions We have developed a web-based system designed to provide researchers a novel application facilitating the management and development of metabolic models. The system is freely available at http://www.icbi.at/MEMOSys. PMID:21276275

  9. Identifying all moiety conservation laws in genome-scale metabolic networks.

    PubMed

    De Martino, Andrea; De Martino, Daniele; Mulet, Roberto; Pagnani, Andrea

    2014-01-01

    The stoichiometry of a metabolic network gives rise to a set of conservation laws for the aggregate level of specific pools of metabolites, which, on one hand, pose dynamical constraints that cross-link the variations of metabolite concentrations and, on the other, provide key insight into a cell's metabolic production capabilities. When the conserved quantity identifies with a chemical moiety, extracting all such conservation laws from the stoichiometry amounts to finding all non-negative integer solutions of a linear system, a programming problem known to be NP-hard. We present an efficient strategy to compute the complete set of integer conservation laws of a genome-scale stoichiometric matrix, also providing a certificate for correctness and maximality of the solution. Our method is deployed for the analysis of moiety conservation relationships in two large-scale reconstructions of the metabolism of the bacterium E. coli, in six tissue-specific human metabolic networks, and, finally, in the human reactome as a whole, revealing that bacterial metabolism could be evolutionarily designed to cover broader production spectra than human metabolism. Convergence to the full set of moiety conservation laws in each case is achieved in extremely reduced computing times. In addition, we uncover a scaling relation that links the size of the independent pool basis to the number of metabolites, for which we present an analytical explanation.

  10. Automation on the generation of genome-scale metabolic models.

    PubMed

    Reyes, R; Gamermann, D; Montagud, A; Fuente, D; Triana, J; Urchueguía, J F; de Córdoba, P Fernández

    2012-12-01

    Nowadays, the reconstruction of genome-scale metabolic models is a nonautomatized and interactive process based on decision making. This lengthy process usually requires a full year of one person's work in order to satisfactory collect, analyze, and validate the list of all metabolic reactions present in a specific organism. In order to write this list, one manually has to go through a huge amount of genomic, metabolomic, and physiological information. Currently, there is no optimal algorithm that allows one to automatically go through all this information and generate the models taking into account probabilistic criteria of unicity and completeness that a biologist would consider. This work presents the automation of a methodology for the reconstruction of genome-scale metabolic models for any organism. The methodology that follows is the automatized version of the steps implemented manually for the reconstruction of the genome-scale metabolic model of a photosynthetic organism, Synechocystis sp. PCC6803. The steps for the reconstruction are implemented in a computational platform (COPABI) that generates the models from the probabilistic algorithms that have been developed. For validation of the developed algorithm robustness, the metabolic models of several organisms generated by the platform have been studied together with published models that have been manually curated. Network properties of the models, like connectivity and average shortest mean path of the different models, have been compared and analyzed.

  11. Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942.

    PubMed

    Triana, Julián; Montagud, Arnau; Siurana, Maria; Fuente, David; Urchueguía, Arantxa; Gamermann, Daniel; Torres, Javier; Tena, Jose; de Córdoba, Pedro Fernández; Urchueguía, Javier F

    2014-08-20

    The reconstruction of genome-scale metabolic models and their applications represent a great advantage of systems biology. Through their use as metabolic flux simulation models, production of industrially-interesting metabolites can be predicted. Due to the growing number of studies of metabolic models driven by the increasing genomic sequencing projects, it is important to conceptualize steps of reconstruction and analysis. We have focused our work in the cyanobacterium Synechococcus elongatus PCC7942, for which several analyses and insights are unveiled. A comprehensive approach has been used, which can be of interest to lead the process of manual curation and genome-scale metabolic analysis. The final model, iSyf715 includes 851 reactions and 838 metabolites. A biomass equation, which encompasses elementary building blocks to allow cell growth, is also included. The applicability of the model is finally demonstrated by simulating autotrophic growth conditions of Synechococcus elongatus PCC7942.

  12. Generation and Evaluation of a Genome-Scale Metabolic Network Model of Synechococcus elongatus PCC7942

    PubMed Central

    Triana, Julián; Montagud†, Arnau; Siurana, Maria; Fuente, David; Urchueguía, Arantxa; Gamermann, Daniel; Torres, Javier; Tena, Jose; de Córdoba, Pedro Fernández; Urchueguía, Javier F.

    2014-01-01

    The reconstruction of genome-scale metabolic models and their applications represent a great advantage of systems biology. Through their use as metabolic flux simulation models, production of industrially-interesting metabolites can be predicted. Due to the growing number of studies of metabolic models driven by the increasing genomic sequencing projects, it is important to conceptualize steps of reconstruction and analysis. We have focused our work in the cyanobacterium Synechococcus elongatus PCC7942, for which several analyses and insights are unveiled. A comprehensive approach has been used, which can be of interest to lead the process of manual curation and genome-scale metabolic analysis. The final model, iSyf715 includes 851 reactions and 838 metabolites. A biomass equation, which encompasses elementary building blocks to allow cell growth, is also included. The applicability of the model is finally demonstrated by simulating autotrophic growth conditions of Synechococcus elongatus PCC7942. PMID:25141288

  13. Genome-scale metabolic models: reconstruction and analysis.

    PubMed

    Baart, Gino J E; Martens, Dirk E

    2012-01-01

    Metabolism can be defined as the complete set of chemical reactions that occur in living organisms in order to maintain life. Enzymes are the main players in this process as they are responsible for catalyzing the chemical reactions. The enzyme-reaction relationships can be used for the reconstruction of a network of reactions, which leads to a metabolic model of metabolism. A genome-scale metabolic network of chemical reactions that take place inside a living organism is primarily reconstructed from the information that is present in its genome and the literature and involves steps such as functional annotation of the genome, identification of the associated reactions and determination of their stoichiometry, assignment of localization, determination of the biomass composition, estimation of energy requirements, and definition of model constraints. This information can be integrated into a stoichiometric model of metabolism that can be used for detailed analysis of the metabolic potential of the organism using constraint-based modeling approaches and hence is valuable in understanding its metabolic capabilities.

  14. A Quantitative System-Scale Characterization of the Metabolism of Clostridium acetobutylicum

    PubMed Central

    Yoo, Minyeong; Bestel-Corre, Gwenaelle; Croux, Christian; Riviere, Antoine; Meynial-Salles, Isabelle

    2015-01-01

    ABSTRACT Engineering industrial microorganisms for ambitious applications, for example, the production of second-generation biofuels such as butanol, is impeded by a lack of knowledge of primary metabolism and its regulation. A quantitative system-scale analysis was applied to the biofuel-producing bacterium Clostridium acetobutylicum, a microorganism used for the industrial production of solvent. An improved genome-scale model, iCac967, was first developed based on thorough biochemical characterizations of 15 key metabolic enzymes and on extensive literature analysis to acquire accurate fluxomic data. In parallel, quantitative transcriptomic and proteomic analyses were performed to assess the number of mRNA molecules per cell for all genes under acidogenic, solventogenic, and alcohologenic steady-state conditions as well as the number of cytosolic protein molecules per cell for approximately 700 genes under at least one of the three steady-state conditions. A complete fluxomic, transcriptomic, and proteomic analysis applied to different metabolic states allowed us to better understand the regulation of primary metabolism. Moreover, this analysis enabled the functional characterization of numerous enzymes involved in primary metabolism, including (i) the enzymes involved in the two different butanol pathways and their cofactor specificities, (ii) the primary hydrogenase and its redox partner, (iii) the major butyryl coenzyme A (butyryl-CoA) dehydrogenase, and (iv) the major glyceraldehyde-3-phosphate dehydrogenase. This study provides important information for further metabolic engineering of C. acetobutylicum to develop a commercial process for the production of n-butanol. PMID:26604256

  15. Heterogeneity of cells may explain allometric scaling of metabolic rate.

    PubMed

    Takemoto, Kazuhiro

    2015-04-01

    The origin of allometric scaling of metabolic rate is a long-standing question in biology. Several models have been proposed for explaining the origin; however, they have advantages and disadvantages. In particular, previous models only demonstrate either two important observations for the allometric scaling: the variability of scaling exponents and predominance of 3/4-power law. Thus, these models have a dispute over their validity. In this study, we propose a simple geometry model, and show that a hypothesis that total surface area of cells determines metabolic rate can reproduce these two observations by combining two concepts: the impact of cell sizes on metabolic rate and fractal-like (hierarchical) organization. The proposed model both theoretically and numerically demonstrates the approximately 3/4-power law although several different biological strategies are considered. The model validity is confirmed using empirical data. Furthermore, the model suggests the importance of heterogeneity of cell size for the emergence of the allometric scaling. The proposed model provides intuitive and unique insights into the origin of allometric scaling laws in biology, despite several limitations of the model.

  16. Predicting novel pathways in genome-scale metabolic networks.

    PubMed

    Schuster, Stefan; de Figueiredo, Luís F; Kaleta, Christoph

    2010-10-01

    Elementary-modes analysis has become a well-established theoretical tool in metabolic pathway analysis. It allows one to decompose complex metabolic networks into the smallest functional entities, which can be interpreted as biochemical pathways. This analysis has, in medium-size metabolic networks, led to the successful theoretical prediction of hitherto unknown pathways. For illustration, we discuss the example of the phosphoenolpyruvate-glyoxylate cycle in Escherichia coli. Elementary-modes analysis meets with the problem of combinatorial explosion in the number of pathways with increasing system size, which has hampered scaling it up to genome-wide models. We present a novel approach to overcoming this obstacle. That approach is based on elementary flux patterns, which are defined as sets of reactions representing the basic routes through a particular subsystem that are compatible with admissible fluxes in a (possibly) much larger metabolic network. The subsystem can be made up by reactions in which we are interested in, for example, reactions producing a certain metabolite. This allows one to predict novel metabolic pathways in genome-scale networks.

  17. 13C metabolic flux analysis at a genome-scale.

    PubMed

    Gopalakrishnan, Saratram; Maranas, Costas D

    2015-11-01

    Metabolic models used in 13C metabolic flux analysis generally include a limited number of reactions primarily from central metabolism. They typically omit degradation pathways, complete cofactor balances, and atom transition contributions for reactions outside central metabolism. This study addresses the impact on prediction fidelity of scaling-up mapping models to a genome-scale. The core mapping model employed in this study accounts for (75 reactions and 65 metabolites) primarily from central metabolism. The genome-scale metabolic mapping model (GSMM) (697 reaction and 595 metabolites) is constructed using as a basis the iAF1260 model upon eliminating reactions guaranteed not to carry flux based on growth and fermentation data for a minimal glucose growth medium. Labeling data for 17 amino acid fragments obtained from cells fed with glucose labeled at the second carbon was used to obtain fluxes and ranges. Metabolic fluxes and confidence intervals are estimated, for both core and genome-scale mapping models, by minimizing the sum of square of differences between predicted and experimentally measured labeling patterns using the EMU decomposition algorithm. Overall, we find that both topology and estimated values of the metabolic fluxes remain largely consistent between core and GSM model. Stepping up to a genome-scale mapping model leads to wider flux inference ranges for 20 key reactions present in the core model. The glycolysis flux range doubles due to the possibility of active gluconeogenesis, the TCA flux range expanded by 80% due to the availability of a bypass through arginine consistent with labeling data, and the transhydrogenase reaction flux was essentially unresolved due to the presence of as many as five routes for the inter-conversion of NADPH to NADH afforded by the genome-scale model. By globally accounting for ATP demands in the GSMM model the unused ATP decreased drastically with the lower bound matching the maintenance ATP requirement. A non

  18. Scaling of metabolic rate on body mass in small laboratory mammals

    NASA Technical Reports Server (NTRS)

    Pace, N.; Rahlmann, D. F.; Smith, A. H.

    1980-01-01

    The scaling of metabolic heat production rate on body mass is investigated for five species of small laboratory mammal in order to define selection of animals of metabolic rates and size range appropriate for the measurement of changes in the scaling relationship upon exposure to weightlessness in Shuttle/Spacelab experiment. Metabolic rates were measured according to oxygen consumption and carbon dioxide production for individual male and female Swiss-Webster mice, Syrian hamsters, Simonsen albino rats, Hartley guinea pigs and New Zealand white rabbits, which range in mass from 0.05 to 5 kg mature body size, at ages of 1, 2, 3, 5, 8, 12, 18 and 24 months. The metabolic intensity, defined as the heat produced per hour per kg body mass, is found to decrease dramatically with age until the animals are 6 to 8 months old, with little or no sex difference. When plotted on a logarithmic graph, the relation of metabolic rate to total body mass is found to obey a power law of index 0.676, which differs significantly from the classical value of 0.75. When the values for the mice are removed, however, an index of 0.749 is obtained. It is thus proposed that six male animals, 8 months of age, of each of the four remaining species be used to study the effects of gravitational loading on the metabolic energy requirements of terrestrial animals.

  19. Swimming in Light: A Large-Scale Computational Analysis of the Metabolism of Dinoroseobacter shibae

    PubMed Central

    Rex, Rene; Bill, Nelli; Schmidt-Hohagen, Kerstin; Schomburg, Dietmar

    2013-01-01

    The Roseobacter clade is a ubiquitous group of marine α-proteobacteria. To gain insight into the versatile metabolism of this clade, we took a constraint-based approach and created a genome-scale metabolic model (iDsh827) of Dinoroseobacter shibae DFL12T. Our model is the first accounting for the energy demand of motility, the light-driven ATP generation and experimentally determined specific biomass composition. To cover a large variety of environmental conditions, as well as plasmid and single gene knock-out mutants, we simulated 391,560 different physiological states using flux balance analysis. We analyzed our results with regard to energy metabolism, validated them experimentally, and revealed a pronounced metabolic response to the availability of light. Furthermore, we introduced the energy demand of motility as an important parameter in genome-scale metabolic models. The results of our simulations also gave insight into the changing usage of the two degradation routes for dimethylsulfoniopropionate, an abundant compound in the ocean. A side product of dimethylsulfoniopropionate degradation is dimethyl sulfide, which seeds cloud formation and thus enhances the reflection of sunlight. By our exhaustive simulations, we were able to identify single-gene knock-out mutants, which show an increased production of dimethyl sulfide. In addition to the single-gene knock-out simulations we studied the effect of plasmid loss on the metabolism. Moreover, we explored the possible use of a functioning phosphofructokinase for D. shibae. PMID:24098096

  20. Genome-Scale Metabolic Modeling of Archaea Lends Insight into Diversity of Metabolic Function

    PubMed Central

    2017-01-01

    Decades of biochemical, bioinformatic, and sequencing data are currently being systematically compiled into genome-scale metabolic reconstructions (GEMs). Such reconstructions are knowledge-bases useful for engineering, modeling, and comparative analysis. Here we review the fifteen GEMs of archaeal species that have been constructed to date. They represent primarily members of the Euryarchaeota with three-quarters comprising representative of methanogens. Unlike other reviews on GEMs, we specially focus on archaea. We briefly review the GEM construction process and the genealogy of the archaeal models. The major insights gained during the construction of these models are then reviewed with specific focus on novel metabolic pathway predictions and growth characteristics. Metabolic pathway usage is discussed in the context of the composition of each organism's biomass and their specific energy and growth requirements. We show how the metabolic models can be used to study the evolution of metabolism in archaea. Conservation of particular metabolic pathways can be studied by comparing reactions using the genes associated with their enzymes. This demonstrates the utility of GEMs to evolutionary studies, far beyond their original purpose of metabolic modeling; however, much needs to be done before archaeal models are as extensively complete as those for bacteria. PMID:28133437

  1. The metabolic control of schistosome egg production

    PubMed Central

    Pearce, Edward J.; Huang, Stanley Ching-Cheng

    2015-01-01

    Schistosomiasis is a Neglected Tropical Disease caused by infection with trematode parasites of the genus Schistosoma. Despite ongoing treatment programs, the prevalence of schistosomiasis has failed to decline and the disease remains a cause of severe morbidity in millions of people. Understanding the biology of egg production by schistosomes is critical since eggs allow transmission of the infection, and when trapped in host tissues induce the immune responses that are responsible for the pathologic changes that underlie disease development. Unusually among trematodes, adult schistosomes exhibit sexual dimorphism and display a fascinating codependency in that the female is dependent on the male to grow and sexually mature. Thus virgin females are developmentally stunted compared to females from mixed-sex infections and are unable to lay eggs. Moreover, fecund female schistosomes rapidly lose the ability to produce eggs when placed in tissue culture. Here we discuss the metabolic regulation of egg production in schistosomes, and in particular the critical role played by fatty acid oxidation in this process. PMID:25850569

  2. iAK692: A genome-scale metabolic model of Spirulina platensis C1

    PubMed Central

    2012-01-01

    Background Spirulina (Arthrospira) platensis is a well-known filamentous cyanobacterium used in the production of many industrial products, including high value compounds, healthy food supplements, animal feeds, pharmaceuticals and cosmetics, for example. It has been increasingly studied around the world for scientific purposes, especially for its genome, biology, physiology, and also for the analysis of its small-scale metabolic network. However, the overall description of the metabolic and biotechnological capabilities of S. platensis requires the development of a whole cellular metabolism model. Recently, the S. platensis C1 (Arthrospira sp. PCC9438) genome sequence has become available, allowing systems-level studies of this commercial cyanobacterium. Results In this work, we present the genome-scale metabolic network analysis of S. platensis C1, iAK692, its topological properties, and its metabolic capabilities and functions. The network was reconstructed from the S. platensis C1 annotated genomic sequence using Pathway Tools software to generate a preliminary network. Then, manual curation was performed based on a collective knowledge base and a combination of genomic, biochemical, and physiological information. The genome-scale metabolic model consists of 692 genes, 837 metabolites, and 875 reactions. We validated iAK692 by conducting fermentation experiments and simulating the model under autotrophic, heterotrophic, and mixotrophic growth conditions using COBRA toolbox. The model predictions under these growth conditions were consistent with the experimental results. The iAK692 model was further used to predict the unique active reactions and essential genes for each growth condition. Additionally, the metabolic states of iAK692 during autotrophic and mixotrophic growths were described by phenotypic phase plane (PhPP) analysis. Conclusions This study proposes the first genome-scale model of S. platensis C1, iAK692, which is a predictive metabolic platform

  3. The Metabolic Cost of Sound Production in Odontocete Cetaceans

    DTIC Science & Technology

    2011-09-30

    1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. The Metabolic Cost of Sound Production in Odontocete...strategy to help reduce the probability of masking from environmental sounds (NRC 2003). Although accumulating evidence from recent research...data on the metabolic cost of sound production for any marine mammal species. Given that changes in vocal behavior in response to masking noise

  4. Metabolic network alignment in large scale by network compression.

    PubMed

    Ay, Ferhat; Dang, Michael; Kahveci, Tamer

    2012-03-21

    Metabolic network alignment is a system scale comparative analysis that discovers important similarities and differences across different metabolisms and organisms. Although the problem of aligning metabolic networks has been considered in the past, the computational complexity of the existing solutions has so far limited their use to moderately sized networks. In this paper, we address the problem of aligning two metabolic networks, particularly when both of them are too large to be dealt with using existing methods. We develop a generic framework that can significantly improve the scale of the networks that can be aligned in practical time. Our framework has three major phases, namely the compression phase, the alignment phase and the refinement phase. For the first phase, we develop an algorithm which transforms the given networks to a compressed domain where they are summarized using fewer nodes, termed supernodes, and interactions. In the second phase, we carry out the alignment in the compressed domain using an existing network alignment method as our base algorithm. This alignment results in supernode mappings in the compressed domain, each of which are smaller instances of network alignment problem. In the third phase, we solve each of the instances using the base alignment algorithm to refine the alignment results. We provide a user defined parameter to control the number of compression levels which generally determines the tradeoff between the quality of the alignment versus how fast the algorithm runs. Our experiments on the networks from KEGG pathway database demonstrate that the compression method we propose reduces the sizes of metabolic networks by almost half at each compression level which provides an expected speedup of more than an order of magnitude. We also observe that the alignments obtained by only one level of compression capture the original alignment results with high accuracy. Together, these suggest that our framework results in

  5. Engineering strategy of yeast metabolism for higher alcohol production

    PubMed Central

    2011-01-01

    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. PMID:21902829

  6. Uncinate process length in birds scales with resting metabolic rate.

    PubMed

    Tickle, Peter; Nudds, Robert; Codd, Jonathan

    2009-05-27

    A fundamental function of the respiratory system is the supply of oxygen to meet metabolic demand. Morphological constraints on the supply of oxygen, such as the structure of the lung, have previously been studied in birds. Recent research has shown that uncinate processes (UP) are important respiratory structures in birds, facilitating inspiratory and expiratory movements of the ribs and sternum. Uncinate process length (UPL) is important for determining the mechanical advantage for these respiratory movements. Here we report on the relationship between UPL, body size, metabolic demand and locomotor specialisation in birds. UPL was found to scale isometrically with body mass. Process length is greatest in specialist diving birds, shortest in walking birds and intermediate length in all others relative to body size. Examination of the interaction between the length of the UP and metabolic demand indicated that, relative to body size, species with high metabolic rates have corresponding elongated UP. We propose that elongated UP confer an advantage on the supply of oxygen, perhaps by improving the mechanical advantage and reducing the energetic cost of movements of the ribs and sternum.

  7. Reconstructing genome-scale metabolic models with merlin

    PubMed Central

    Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C.; Rocha, Isabel

    2015-01-01

    The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) tool is a user-friendly Java application that aids the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs the major steps of the reconstruction process, including the functional genomic annotation of the whole genome and subsequent construction of the portfolio of reactions. Moreover, merlin includes tools for the identification and annotation of genes encoding transport proteins, generating the transport reactions for those carriers. It also performs the compartmentalisation of the model, predicting the organelle localisation of the proteins encoded in the genome and thus the localisation of the metabolites involved in the reactions promoted by such enzymes. The gene-proteins-reactions (GPR) associations are automatically generated and included in the model. Finally, merlin expedites the transition from genomic data to draft metabolic models reconstructions exported in the SBML standard format, allowing the user to have a preliminary view of the biochemical network, which can be manually curated within the environment provided by merlin. PMID:25845595

  8. Reconstructing genome-scale metabolic models with merlin.

    PubMed

    Dias, Oscar; Rocha, Miguel; Ferreira, Eugénio C; Rocha, Isabel

    2015-04-30

    The Metabolic Models Reconstruction Using Genome-Scale Information (merlin) tool is a user-friendly Java application that aids the reconstruction of genome-scale metabolic models for any organism that has its genome sequenced. It performs the major steps of the reconstruction process, including the functional genomic annotation of the whole genome and subsequent construction of the portfolio of reactions. Moreover, merlin includes tools for the identification and annotation of genes encoding transport proteins, generating the transport reactions for those carriers. It also performs the compartmentalisation of the model, predicting the organelle localisation of the proteins encoded in the genome and thus the localisation of the metabolites involved in the reactions promoted by such enzymes. The gene-proteins-reactions (GPR) associations are automatically generated and included in the model. Finally, merlin expedites the transition from genomic data to draft metabolic models reconstructions exported in the SBML standard format, allowing the user to have a preliminary view of the biochemical network, which can be manually curated within the environment provided by merlin.

  9. Towards large scale fermentative production of succinic acid.

    PubMed

    Jansen, Mickel L A; van Gulik, Walter M

    2014-12-01

    Fermentative production of succinic acid (SA) from renewable carbohydrate feed-stocks can have the economic and sustainability potential to replace petroleum-based production in the future, not only for existing markets, but also new larger volume markets. To accomplish this, extensive efforts have been undertaken in the field of strain construction and metabolic engineering to optimize SA production in the last decade. However, relatively little effort has been put into fermentation process development. The choice for a specific host organism determines to a large extent the process configuration, which in turn influences the environmental impact of the overall process. In the last five years, considerable progress has been achieved towards commercialization of fermentative production of SA. Several companies have demonstrated their confidence about the economic feasibility of fermentative SA production by transferring their processes from pilot to production scale.

  10. Genome-scale metabolic model of Pichia pastoris with native and humanized glycosylation of recombinant proteins.

    PubMed

    Irani, Zahra Azimzadeh; Kerkhoven, Eduard J; Shojaosadati, Seyed Abbas; Nielsen, Jens

    2016-05-01

    Pichia pastoris is used for commercial production of human therapeutic proteins, and genome-scale models of P. pastoris metabolism have been generated in the past to study the metabolism and associated protein production by this yeast. A major challenge with clinical usage of recombinant proteins produced by P. pastoris is the difference in N-glycosylation of proteins produced by humans and this yeast. However, through metabolic engineering, a P. pastoris strain capable of producing humanized N-glycosylated proteins was constructed. The current genome-scale models of P. pastoris do not address native nor humanized N-glycosylation, and we therefore developed ihGlycopastoris, an extension to the iLC915 model with both native and humanized N-glycosylation for recombinant protein production, but also an estimation of N-glycosylation of P. pastoris native proteins. This new model gives a better prediction of protein yield, demonstrates the effect of the different types of N-glycosylation of protein yield, and can be used to predict potential targets for strain improvement. The model represents a step towards a more complete description of protein production in P. pastoris, which is required for using these models to understand and optimize protein production processes.

  11. Segmented linear modeling of CHO fed-batch culture and its application to large scale production.

    PubMed

    Ben Yahia, Bassem; Gourevitch, Boris; Malphettes, Laetitia; Heinzle, Elmar

    2017-04-01

    We describe a systematic approach to model CHO metabolism during biopharmaceutical production across a wide range of cell culture conditions. To this end, we applied the metabolic steady state concept. We analyzed and modeled the production rates of metabolites as a function of the specific growth rate. First, the total number of metabolic steady state phases and the location of the breakpoints were determined by recursive partitioning. For this, the smoothed derivative of the metabolic rates with respect to the growth rate were used followed by hierarchical clustering of the obtained partition. We then applied a piecewise regression to the metabolic rates with the previously determined number of phases. This allowed identifying the growth rates at which the cells underwent a metabolic shift. The resulting model with piecewise linear relationships between metabolic rates and the growth rate did well describe cellular metabolism in the fed-batch cultures. Using the model structure and parameter values from a small-scale cell culture (2 L) training dataset, it was possible to predict metabolic rates of new fed-batch cultures just using the experimental specific growth rates. Such prediction was successful both at the laboratory scale with 2 L bioreactors but also at the production scale of 2000 L. This type of modeling provides a flexible framework to set a solid foundation for metabolic flux analysis and mechanistic type of modeling. Biotechnol. Bioeng. 2017;114: 785-797. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc.

  12. Classifying forest productivity at different scales

    SciTech Connect

    Graham, R.L.

    1991-01-01

    Spatial scale is an important consideration when evaluating, using, or constructing forest productivity classifications. First, the factors which dominate spatial variability in forest productivity are scale dependent. For example, within a stand, spatial variability in productivity is dominated by microsite differences; within a national forest such as the Cherokee National Forest, spatial variability is dominated by topography and land-use history (e.g., years since harvest); within a large region such as the southeast, spatial variability is dominated by climatic patterns. Second, classifications developed at different spatial scales are often used for different purposes. For example, stand-level classifications are often keys or rules used in the field to judge the quality or potential of a site. National-forest classifications are often presented as maps or tables and may be used in forest land planning. Regional classifications may be maps or tables and may be used to quantify or predict resource availability. These scale-related differences in controlling factors and purposes will affect both the methods and the data used to develop classifications. In this paper, I will illustrate these points by describing and comparing three forest productivity classifications, each developed for a specific purpose at a specific scale. My objective is not to argue for or against any of these particular classifications but rather to heighten awareness of the critical role that spatial scale plays in the use and development of forest productivity classifications. 8 refs., 2 figs., 1 tab.

  13. Metabolic Profiling of Geobacter sulfurreducens during Industrial Bioprocess Scale-Up.

    PubMed

    Muhamadali, Howbeer; Xu, Yun; Ellis, David I; Allwood, J William; Rattray, Nicholas J W; Correa, Elon; Alrabiah, Haitham; Lloyd, Jonathan R; Goodacre, Royston

    2015-05-15

    During the industrial scale-up of bioprocesses it is important to establish that the biological system has not changed significantly when moving from small laboratory-scale shake flasks or culturing bottles to an industrially relevant production level. Therefore, during upscaling of biomass production for a range of metal transformations, including the production of biogenic magnetite nanoparticles by Geobacter sulfurreducens, from 100-ml bench-scale to 5-liter fermentors, we applied Fourier transform infrared (FTIR) spectroscopy as a metabolic fingerprinting approach followed by the analysis of bacterial cell extracts by gas chromatography-mass spectrometry (GC-MS) for metabolic profiling. FTIR results clearly differentiated between the phenotypic changes associated with different growth phases as well as the two culturing conditions. Furthermore, the clustering patterns displayed by multivariate analysis were in agreement with the turbidimetric measurements, which displayed an extended lag phase for cells grown in a 5-liter bioreactor (24 h) compared to those grown in 100-ml serum bottles (6 h). GC-MS analysis of the cell extracts demonstrated an overall accumulation of fumarate during the lag phase under both culturing conditions, coinciding with the detected concentrations of oxaloacetate, pyruvate, nicotinamide, and glycerol-3-phosphate being at their lowest levels compared to other growth phases. These metabolites were overlaid onto a metabolic network of G. sulfurreducens, and taking into account the levels of these metabolites throughout the fermentation process, the limited availability of oxaloacetate and nicotinamide would seem to be the main metabolic bottleneck resulting from this scale-up process. Additional metabolite-feeding experiments were carried out to validate the above hypothesis. Nicotinamide supplementation (1 mM) did not display any significant effects on the lag phase of G. sulfurreducens cells grown in the 100-ml serum bottles. However

  14. The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy.

    PubMed

    Papin, Jason A; Price, Nathan D; Edwards, Jeremy S; Palsson B, Bernhard Ø

    2002-03-07

    Genome-scale metabolic networks can be characterized by a set of systemically independent and unique extreme pathways. These extreme pathways span a convex, high-dimensional space that circumscribes all potential steady-state flux distributions achievable by the defined metabolic network. Genome-scale extreme pathways associated with the production of non-essential amino acids in Haemophilus influenzae were computed. They offer valuable insight into the functioning of its metabolic network. Three key results were obtained. First, there were multiple internal flux maps corresponding to externally indistinguishable states. It was shown that there was an average of 37 internal states per unique exchange flux vector in H. influenzae when the network was used to produce a single amino acid while allowing carbon dioxide and acetate as carbon sinks. With the inclusion of succinate as an additional output, this ratio increased to 52, a 40% increase. Second, an analysis of the carbon fates illustrated that the extreme pathways were non-uniformly distributed across the carbon fate spectrum. In the detailed case study, 45% of the distinct carbon fate values associated with lysine production represented 85% of the extreme pathways. Third, this distribution fell between distinct systemic constraints. For lysine production, the carbon fate values that represented 85% of the pathways described above corresponded to only 2 distinct ratios of 1:1 and 4:1 between carbon dioxide and acetate. The present study analysed single outputs from one organism, and provides a start to genome-scale extreme pathways studies. These emergent system-level characterizations show the significance of metabolic extreme pathway analysis at the genome-scale.

  15. Reconstruction and analysis of a genome-scale metabolic model for Scheffersomyces stipitis

    PubMed Central

    2012-01-01

    Background Fermentation of xylose, the major component in hemicellulose, is essential for economic conversion of lignocellulosic biomass to fuels and chemicals. The yeast Scheffersomyces stipitis (formerly known as Pichia stipitis) has the highest known native capacity for xylose fermentation and possesses several genes for lignocellulose bioconversion in its genome. Understanding the metabolism of this yeast at a global scale, by reconstructing the genome scale metabolic model, is essential for manipulating its metabolic capabilities and for successful transfer of its capabilities to other industrial microbes. Results We present a genome-scale metabolic model for Scheffersomyces stipitis, a native xylose utilizing yeast. The model was reconstructed based on genome sequence annotation, detailed experimental investigation and known yeast physiology. Macromolecular composition of Scheffersomyces stipitis biomass was estimated experimentally and its ability to grow on different carbon, nitrogen, sulphur and phosphorus sources was determined by phenotype microarrays. The compartmentalized model, developed based on an iterative procedure, accounted for 814 genes, 1371 reactions, and 971 metabolites. In silico computed growth rates were compared with high-throughput phenotyping data and the model could predict the qualitative outcomes in 74% of substrates investigated. Model simulations were used to identify the biosynthetic requirements for anaerobic growth of Scheffersomyces stipitis on glucose and the results were validated with published literature. The bottlenecks in Scheffersomyces stipitis metabolic network for xylose uptake and nucleotide cofactor recycling were identified by in silico flux variability analysis. The scope of the model in enhancing the mechanistic understanding of microbial metabolism is demonstrated by identifying a mechanism for mitochondrial respiration and oxidative phosphorylation. Conclusion The genome-scale metabolic model developed for

  16. Microbial methanol formation: A major end product of pectin metabolism

    SciTech Connect

    Schink, B.; Zeikus, J.G.

    1980-01-01

    Various pectinolytic strains of Clostridium, Erwinia, and Pseudomonas species produced methanol as a major end product during growth on pectin but not on glucose of polygalacturonic acid. Pectin metabolism of Clostridium butyricum strain 4PI correlated with a final product concentration of 16 mM at the end of growth, and a 1:1 stoichiometry for methanol production and percent initial substrate methoxylation. Growth on pectin was associated with high activity of pectin methylesterase and the absence of methanol consumption. The ecological significance of pectin metabolism and the establishment of microbial methylotrophic metabolism in nature is discussed.

  17. Plant Interactions Alter the Predictions of Metabolic Scaling Theory

    PubMed Central

    Lin, Yue; Berger, Uta; Grimm, Volker; Huth, Franka; Weiner, Jacob

    2013-01-01

    Metabolic scaling theory (MST) is an attempt to link physiological processes of individual organisms with macroecology. It predicts a power law relationship with an exponent of −4/3 between mean individual biomass and density during density-dependent mortality (self-thinning). Empirical tests have produced variable results, and the validity of MST is intensely debated. MST focuses on organisms’ internal physiological mechanisms but we hypothesize that ecological interactions can be more important in determining plant mass-density relationships induced by density. We employ an individual-based model of plant stand development that includes three elements: a model of individual plant growth based on MST, different modes of local competition (size-symmetric vs. -asymmetric), and different resource levels. Our model is consistent with the observed variation in the slopes of self-thinning trajectories. Slopes were significantly shallower than −4/3 if competition was size-symmetric. We conclude that when the size of survivors is influenced by strong ecological interactions, these can override predictions of MST, whereas when surviving plants are less affected by interactions, individual-level metabolic processes can scale up to the population level. MST, like thermodynamics or biomechanics, sets limits within which organisms can live and function, but there may be stronger limits determined by ecological interactions. In such cases MST will not be predictive. PMID:23460884

  18. Genome-scale metabolic model in guiding metabolic engineering of microbial improvement.

    PubMed

    Xu, Chuan; Liu, Lili; Zhang, Zhao; Jin, Danfeng; Qiu, Juanping; Chen, Ming

    2013-01-01

    In the past few decades, despite all the significant achievements in industrial microbial improvement, the approaches of traditional random mutation and selection as well as the rational metabolic engineering based on the local knowledge cannot meet today's needs. With rapid reconstructions and accurate in silico simulations, genome-scale metabolic model (GSMM) has become an indispensable tool to study the microbial metabolism and design strain improvements. In this review, we highlight the application of GSMM in guiding microbial improvements focusing on a systematic strategy and its achievements in different industrial fields. This strategy includes a repetitive process with four steps: essential data acquisition, GSMM reconstruction, constraints-based optimizing simulation, and experimental validation, in which the second and third steps are the centerpiece. The achievements presented here belong to different industrial application fields, including food and nutrients, biopharmaceuticals, biopolymers, microbial biofuel, and bioremediation. This strategy and its achievements demonstrate a momentous guidance of GSMM for metabolic engineering breeding of industrial microbes. More efforts are required to extend this kind of study in the meantime.

  19. Targeting metabolic disorders by natural products.

    PubMed

    Tabatabaei-Malazy, Ozra; Larijani, Bagher; Abdollahi, Mohammad

    2015-01-01

    The most prevalent metabolic disorders are diabetes mellitus, obesity, dyslipidemia, osteoporosis and metabolic syndrome, which are developed when normal metabolic processes are disturbed. The most common pathophysiologies of the above disorders are oxidative stress, Nrf2 pathways, epigenetic, and change in miRNA expression. There is a challenge in the prevention and treatment of metabolic disorders due to severe adverse effects of some synthetic drugs, their high cost, lack of safety and poverty in some conditions, and insufficient accessibility for the general population in the world. With increasing interest in shifting from synthetic drugs to phytotherapy as an alternative treatment, there is still a gap in scientific evidences of plant-derived therapeutic benefits. One reason may be slow rate of translation of animal studies' findings into human clinical trials. Since metabolic disorders are multifactorial, it seems that poly-herbal medications, or drug-herbal combination are needed for their treatment. However, further researches to determine the most effective plant-derived metabolites, and their cellular mechanism in order to set priorities for well-designed animal and clinical trials, and also more studies with strong scientific evidences such as systematic review and meta-analysis of controlled studies are needed.

  20. Comparative genome-scale metabolic modeling of actinomycetes: the topology of essential core metabolism.

    PubMed

    Alam, Mohammad Tauqeer; Medema, Marnix H; Takano, Eriko; Breitling, Rainer

    2011-07-21

    Actinomycetes are highly important bacteria. On one hand, some of them cause severe human and plant diseases, on the other hand, many species are known for their ability to produce antibiotics. Here we report the results of a comparative analysis of genome-scale metabolic models of 37 species of actinomycetes. Based on in silico knockouts we generated topological and genomic maps for each organism. Combining the collection of genome-wide models, we constructed a global enzyme association network to identify both a conserved "core network" and an "essential core network" of the entire group. As has been reported for low-degree metabolites in several organisms, low-degree enzymes (in linear pathways) turn out to be generally more essential than high-degree enzymes (in metabolic hubs).

  1. Metabolic engineering of Klebsiella pneumoniae based on in silico analysis and its pilot-scale application for 1,3-propanediol and 2,3-butanediol co-production.

    PubMed

    Park, Jong Myoung; Rathnasingh, Chelladurai; Song, Hyohak

    2017-03-01

    Klebsiella pneumoniae naturally produces relatively large amounts of 1,3-propanediol (1,3-PD) and 2,3-butanediol (2,3-BD) along with various byproducts using glycerol as a carbon source. The ldhA and mdh genes in K. pneumoniae were deleted based on its in silico gene knockout simulation with the criteria of maximizing 1,3-PD and 2,3-BD production and minimizing byproducts formation and cell growth retardation. In addition, the agitation speed, which is known to strongly affect 1,3-PD and 2,3-BD production in Klebsiella strains, was optimized. The K. pneumoniae ΔldhA Δmdh strain produced 125 g/L of diols (1,3-PD and 2,3-BD) with a productivity of 2.0 g/L/h in the lab-scale (5-L bioreactor) fed-batch fermentation using high-quality guaranteed reagent grade glycerol. To evaluate the industrial capacity of the constructed K. pneumoniae ΔldhA Δmdh strain, a pilot-scale (5000-L bioreactor) fed-batch fermentation was carried out using crude glycerol obtained from the industrial biodiesel plant. The pilot-scale fed-batch fermentation of the K. pneumoniae ΔldhA Δmdh strain produced 114 g/L of diols (70 g/L of 1,3-PD and 44 g/L of 2,3-BD), with a yield of 0.60 g diols per gram glycerol and a productivity of 2.2 g/L/h of diols, which should be suitable for the industrial co-production of 1,3-PD and 2,3-BD.

  2. Production of bulk chemicals via novel metabolic pathways in microorganisms.

    PubMed

    Shin, Jae Ho; Kim, Hyun Uk; Kim, Dong In; Lee, Sang Yup

    2013-11-01

    Metabolic engineering has been playing important roles in developing high performance microorganisms capable of producing various chemicals and materials from renewable biomass in a sustainable manner. Synthetic and systems biology are also contributing significantly to the creation of novel pathways and the whole cell-wide optimization of metabolic performance, respectively. In order to expand the spectrum of chemicals that can be produced biotechnologically, it is necessary to broaden the metabolic capacities of microorganisms. Expanding the metabolic pathways for biosynthesizing the target chemicals requires not only the enumeration of a series of known enzymes, but also the identification of biochemical gaps whose corresponding enzymes might not actually exist in nature; this issue is the focus of this paper. First, pathway prediction tools, effectively combining reactions that lead to the production of a target chemical, are analyzed in terms of logics representing chemical information, and designing and ranking the proposed metabolic pathways. Then, several approaches for potentially filling in the gaps of the novel metabolic pathway are suggested along with relevant examples, including the use of promiscuous enzymes that flexibly utilize different substrates, design of novel enzymes for non-natural reactions, and exploration of hypothetical proteins. Finally, strain optimization by systems metabolic engineering in the context of novel metabolic pathways constructed is briefly described. It is hoped that this review paper will provide logical ways of efficiently utilizing 'big' biological data to design and develop novel metabolic pathways for the production of various bulk chemicals that are currently produced from fossil resources.

  3. The Metabolic Cost of Click Production in Bottlenose Dolphins

    DTIC Science & Technology

    2013-09-30

    duration, and/or repetition rate of their acoustic signals as a strategy to help reduce the probability of masking from environmental sounds (NRC 2003...behavior are unknown. To date, the only empirical data on the metabolic cost of sound production as well as the metabolic cost of increasing the...previous work was on whistle and social sound production in bottlenose dolphins (Holt et al. 2011 a, b, Noren et al. 2011). There is currently no

  4. The Metabolic Costs of Sound Production in Odontocete Cetaceans

    DTIC Science & Technology

    2012-09-30

    1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. The Metabolic Costs of Sound Production in Odontocete...of their acoustic signals as a strategy to help reduce the probability of masking from environmental sounds (NRC 2003). Although accumulating...our knowledge, there is no empirical data on the metabolic cost of sound production for any marine mammal species. Given that changes in vocal

  5. The Metabolic Costs of Sound Production in Odontocete Cetaceans

    DTIC Science & Technology

    2013-09-30

    1 DISTRIBUTION STATEMENT A. Approved for public release; distribution is unlimited. The Metabolic Costs of Sound Production in Odontocete...or repetition rate of their acoustic signals as a strategy to help reduce the probability of masking from environmental sounds (NRC 2003...are unknown. To our knowledge, there is no empirical data on the metabolic cost of sound production for any marine mammal species. Given that

  6. Metabolic engineering for the production of plant isoquinoline alkaloids.

    PubMed

    Diamond, Andrew; Desgagné-Penix, Isabel

    2016-06-01

    Several plant isoquinoline alkaloids (PIAs) possess powerful pharmaceutical and biotechnological properties. Thus, PIA metabolism and its fascinating molecules, including morphine, colchicine and galanthamine, have attracted the attention of both the industry and researchers involved in plant science, biochemistry, chemical bioengineering and medicine. Currently, access and availability of high-value PIAs [commercialized (e.g. galanthamine) or not (e.g. narciclasine)] is limited by low concentration in nature, lack of cultivation or geographic access, seasonal production and risk of overharvesting wild plant species. Nevertheless, most commercial PIAs are still extracted from plant sources. Efforts to improve the production of PIA have largely been impaired by the lack of knowledge on PIA metabolism. With the development and integration of next-generation sequencing technologies, high-throughput proteomics and metabolomics analyses and bioinformatics, systems biology was used to unravel metabolic pathways allowing the use of metabolic engineering and synthetic biology approaches to increase production of valuable PIAs. Metabolic engineering provides opportunity to overcome issues related to restricted availability, diversification and productivity of plant alkaloids. Engineered plant, plant cells and microbial cell cultures can act as biofactories by offering their metabolic machinery for the purpose of optimizing the conditions and increasing the productivity of a specific alkaloid. In this article, is presented an update on the production of PIA in engineered plant, plant cell cultures and heterologous micro-organisms.

  7. Investigating host-pathogen behavior and their interaction using genome-scale metabolic network models.

    PubMed

    Sadhukhan, Priyanka P; Raghunathan, Anu

    2014-01-01

    Genome Scale Metabolic Modeling methods represent one way to compute whole cell function starting from the genome sequence of an organism and contribute towards understanding and predicting the genotype-phenotype relationship. About 80 models spanning all the kingdoms of life from archaea to eukaryotes have been built till date and used to interrogate cell phenotype under varying conditions. These models have been used to not only understand the flux distribution in evolutionary conserved pathways like glycolysis and the Krebs cycle but also in applications ranging from value added product formation in Escherichia coli to predicting inborn errors of Homo sapiens metabolism. This chapter describes a protocol that delineates the process of genome scale metabolic modeling for analysing host-pathogen behavior and interaction using flux balance analysis (FBA). The steps discussed in the process include (1) reconstruction of a metabolic network from the genome sequence, (2) its representation in a precise mathematical framework, (3) its translation to a model, and (4) the analysis using linear algebra and optimization. The methods for biological interpretations of computed cell phenotypes in the context of individual host and pathogen models and their integration are also discussed.

  8. Enumeration of smallest intervention strategies in genome-scale metabolic networks.

    PubMed

    von Kamp, Axel; Klamt, Steffen

    2014-01-01

    One ultimate goal of metabolic network modeling is the rational redesign of biochemical networks to optimize the production of certain compounds by cellular systems. Although several constraint-based optimization techniques have been developed for this purpose, methods for systematic enumeration of intervention strategies in genome-scale metabolic networks are still lacking. In principle, Minimal Cut Sets (MCSs; inclusion-minimal combinations of reaction or gene deletions that lead to the fulfilment of a given intervention goal) provide an exhaustive enumeration approach. However, their disadvantage is the combinatorial explosion in larger networks and the requirement to compute first the elementary modes (EMs) which itself is impractical in genome-scale networks. We present MCSEnumerator, a new method for effective enumeration of the smallest MCSs (with fewest interventions) in genome-scale metabolic network models. For this we combine two approaches, namely (i) the mapping of MCSs to EMs in a dual network, and (ii) a modified algorithm by which shortest EMs can be effectively determined in large networks. In this way, we can identify the smallest MCSs by calculating the shortest EMs in the dual network. Realistic application examples demonstrate that our algorithm is able to list thousands of the most efficient intervention strategies in genome-scale networks for various intervention problems. For instance, for the first time we could enumerate all synthetic lethals in E.coli with combinations of up to 5 reactions. We also applied the new algorithm exemplarily to compute strain designs for growth-coupled synthesis of different products (ethanol, fumarate, serine) by E.coli. We found numerous new engineering strategies partially requiring less knockouts and guaranteeing higher product yields (even without the assumption of optimal growth) than reported previously. The strength of the presented approach is that smallest intervention strategies can be quickly

  9. Metabolic engineering as a tool for enhanced lactic acid production.

    PubMed

    Upadhyaya, Bikram P; DeVeaux, Linda C; Christopher, Lew P

    2014-12-01

    Metabolic engineering is a powerful biotechnological tool that finds, among others, increased use in constructing microbial strains for higher lactic acid productivity, lower costs and reduced pollution. Engineering the metabolic pathways has concentrated on improving the lactic acid fermentation parameters, enhancing the acid tolerance of production organisms and their abilities to utilize a broad range of substrates, including fermentable biomass-derived sugars. Recent efforts have focused on metabolic engineering of lactic acid bacteria as they produce high yields and have a small genome size that facilitates their genetic manipulation. We summarize here the current trends in metabolic engineering techniques and strategies for manipulating lactic acid producing organisms developed to address and overcome major challenges in the lactic acid production process.

  10. Metabolic engineering for amino-, oligo-, and polysugar production in microbes.

    PubMed

    Hossain, Gazi Sakir; Shin, Hyun-Dong; Li, Jianghua; Wang, Miao; Du, Guocheng; Chen, Jian; Liu, Long

    2016-03-01

    Amino-, oligo-, and polysugars are important for both medicinal and industrial applications. Microbial processes used in production of such sugars are not only carbon-intensive and energy-demanding processes but also have other distinct disadvantages such as low productivity, low yields, and by-product contamination. Therefore, metabolic engineering has emerged as an effective tool for developing engineered strains to deliver production strategies for many valuable sugars, which were previously difficult to manufacture by other means, in necessary amounts to support their applications. In this review, the recent strategies used for metabolic engineering are summarized and future prospects of this technique are discussed. We hope that this review will contribute to the development of functional and high-value sugar production by metabolic engineering strategies.

  11. A Genome-Scale Model of Shewanella piezotolerans Simulates Mechanisms of Metabolic Diversity and Energy Conservation

    PubMed Central

    Dufault-Thompson, Keith; Jian, Huahua; Cheng, Ruixue; Li, Jiefu; Wang, Fengping

    2017-01-01

    ABSTRACT Shewanella piezotolerans strain WP3 belongs to the group 1 branch of the Shewanella genus and is a piezotolerant and psychrotolerant species isolated from the deep sea. In this study, a genome-scale model was constructed for WP3 using a combination of genome annotation, ortholog mapping, and physiological verification. The metabolic reconstruction contained 806 genes, 653 metabolites, and 922 reactions, including central metabolic functions that represented nonhomologous replacements between the group 1 and group 2 Shewanella species. Metabolic simulations with the WP3 model demonstrated consistency with existing knowledge about the physiology of the organism. A comparison of model simulations with experimental measurements verified the predicted growth profiles under increasing concentrations of carbon sources. The WP3 model was applied to study mechanisms of anaerobic respiration through investigating energy conservation, redox balancing, and the generation of proton motive force. Despite being an obligate respiratory organism, WP3 was predicted to use substrate-level phosphorylation as the primary source of energy conservation under anaerobic conditions, a trait previously identified in other Shewanella species. Further investigation of the ATP synthase activity revealed a positive correlation between the availability of reducing equivalents in the cell and the directionality of the ATP synthase reaction flux. Comparison of the WP3 model with an existing model of a group 2 species, Shewanella oneidensis MR-1, revealed that the WP3 model demonstrated greater flexibility in ATP production under the anaerobic conditions. Such flexibility could be advantageous to WP3 for its adaptation to fluctuating availability of organic carbon sources in the deep sea. IMPORTANCE The well-studied nature of the metabolic diversity of Shewanella bacteria makes species from this genus a promising platform for investigating the evolution of carbon metabolism and energy

  12. A Genome-Scale Model of Shewanella piezotolerans Simulates Mechanisms of Metabolic Diversity and Energy Conservation.

    PubMed

    Dufault-Thompson, Keith; Jian, Huahua; Cheng, Ruixue; Li, Jiefu; Wang, Fengping; Zhang, Ying

    2017-01-01

    Shewanella piezotolerans strain WP3 belongs to the group 1 branch of the Shewanella genus and is a piezotolerant and psychrotolerant species isolated from the deep sea. In this study, a genome-scale model was constructed for WP3 using a combination of genome annotation, ortholog mapping, and physiological verification. The metabolic reconstruction contained 806 genes, 653 metabolites, and 922 reactions, including central metabolic functions that represented nonhomologous replacements between the group 1 and group 2 Shewanella species. Metabolic simulations with the WP3 model demonstrated consistency with existing knowledge about the physiology of the organism. A comparison of model simulations with experimental measurements verified the predicted growth profiles under increasing concentrations of carbon sources. The WP3 model was applied to study mechanisms of anaerobic respiration through investigating energy conservation, redox balancing, and the generation of proton motive force. Despite being an obligate respiratory organism, WP3 was predicted to use substrate-level phosphorylation as the primary source of energy conservation under anaerobic conditions, a trait previously identified in other Shewanella species. Further investigation of the ATP synthase activity revealed a positive correlation between the availability of reducing equivalents in the cell and the directionality of the ATP synthase reaction flux. Comparison of the WP3 model with an existing model of a group 2 species, Shewanella oneidensis MR-1, revealed that the WP3 model demonstrated greater flexibility in ATP production under the anaerobic conditions. Such flexibility could be advantageous to WP3 for its adaptation to fluctuating availability of organic carbon sources in the deep sea. IMPORTANCE The well-studied nature of the metabolic diversity of Shewanella bacteria makes species from this genus a promising platform for investigating the evolution of carbon metabolism and energy conservation

  13. Scaling of standard metabolic rate in estuarine crocodiles Crocodylus porosus.

    PubMed

    Seymour, Roger S; Gienger, C M; Brien, Matthew L; Tracy, Christopher R; Charlie Manolis, S; Webb, Grahame J W; Christian, Keith A

    2013-05-01

    Standard metabolic rate (SMR, ml O2 min(-1)) of captive Crocodylus porosus at 30 °C scales with body mass (kg) according to the equation, SMR = 1.01 M(0.829), in animals ranging in body mass of 3.3 orders of magnitude (0.19-389 kg). The exponent is significantly higher than 0.75, so does not conform to quarter-power scaling theory, but rather is likely an emergent property with no single explanation. SMR at 1 kg body mass is similar to the literature for C. porosus and for alligators. The high exponent is not related to feeding, growth, or obesity of captive animals. The log-transformed data appear slightly curved, mainly because SMR is somewhat low in many of the largest animals (291-389 kg). A 3-parameter model is scarcely different from the linear one, but reveals a declining exponent between 0.862 and 0.798. A non-linear model on arithmetic axes overestimates SMR in 70% of the smallest animals and does not satisfactorily represent the data.

  14. GRCop-84 Scaled Up for Production

    NASA Technical Reports Server (NTRS)

    Ellis, David L.

    2004-01-01

    GRCop-84 (Cu-8 at.% Cr-4 at.% Nb) was developed at the NASA Glenn Research Center for use in regeneratively cooled rocket engine main combustion chamber liners. The alloy has demonstrated high elevated-temperature strength, excellent creep resistance, long low-cycle-fatigue lives, low thermal expansion, and good thermal conductivity on a laboratory scale. The combination of properties has led to interest from the Rocketdyne Division of Boeing, Aerojet, and Pratt & Whitney for their new engines. Under the Space Launch Initiative/Next Generation Launch Technology program, GRCop-84 is being taken out of the laboratory and put into a full-scale production environment.

  15. Genome-scale metabolic flux analysis of Streptomyces lividans growing on a complex medium.

    PubMed

    D'Huys, Pieter-Jan; Lule, Ivan; Vercammen, Dominique; Anné, Jozef; Van Impe, Jan F; Bernaerts, Kristel

    2012-09-15

    Constraint-based metabolic modeling comprises various excellent tools to assess experimentally observed phenotypic behavior of micro-organisms in terms of intracellular metabolic fluxes. In combination with genome-scale metabolic networks, micro-organisms can be investigated in much more detail and under more complex environmental conditions. Although complex media are ubiquitously applied in industrial fermentations and are often a prerequisite for high protein secretion yields, such multi-component conditions are seldom investigated using genome-scale flux analysis. In this paper, a systematic and integrative approach is presented to determine metabolic fluxes in Streptomyces lividans TK24 grown on a nutritious and complex medium. Genome-scale flux balance analysis and randomized sampling of the solution space are combined to extract maximum information from exometabolome profiles. It is shown that biomass maximization cannot predict the observed metabolite production pattern as such. Although this cellular objective commonly applies to batch fermentation data, both input and output constraints are required to reproduce the measured biomass production rate. Rich media hence not necessarily lead to maximum biomass growth. To eventually identify a unique intracellular flux vector, a hierarchical optimization of cellular objectives is adopted. Out of various tested secondary objectives, maximization of the ATP yield per flux unit returns the closest agreement with the maximum frequency in flux histograms. This unique flux estimation is hence considered as a reasonable approximation for the biological fluxes. Flux maps for different growth phases show no active oxidative part of the pentose phosphate pathway, but NADPH generation in the TCA cycle and NADPH transdehydrogenase activity are most important in fulfilling the NADPH balance. Amino acids contribute to biomass growth by augmenting the pool of available amino acids and by boosting the TCA cycle, particularly

  16. Improvements in fermentative biological hydrogen production through metabolic engineering.

    PubMed

    Hallenbeck, Patrick C; Ghosh, Dipankar

    2012-03-01

    Replacement of fossil fuels with alternative energies is increasingly imperative in light of impending climate change and fossil fuel shortages. Biohydrogen has several potential advantages over other biofuels. Dark fermentation as a means of producing biohydrogen is attractive since a variety of readily available waste streams can be used. However, at present its practical application is prevented by the low yields obtained. Here the basic metabolisms leading to hydrogen production are outlined and current research to increase yields, either through modification of existing pathways, or by metabolic engineering to create new, higher yielding, pathways, is discussed. Inactivation of competing reactions and manipulation of culture conditions has lead to higher hydrogen yields, near those predicted by metabolic schemes. However, to be useful, hydrogen production must be increased beyond present limits. Several possibilities for surpassing those limits using metabolic engineering are presented.

  17. Plant Metabolic Engineering Strategies for the Production of Pharmaceutical Terpenoids

    PubMed Central

    Lu, Xu; Tang, Kexuan; Li, Ping

    2016-01-01

    Pharmaceutical terpenoids belong to the most diverse class of natural products. They have significant curative effects on a variety of diseases, such as cancer, cardiovascular diseases, malaria and Alzheimer’s disease. Nowadays, elicitors, including biotic and abiotic elicitors, are often used to activate the pathway of secondary metabolism and enhance the production of target terpenoids. Based on Agrobacterium-mediated genetic transformation, several plant metabolic engineering strategies hold great promise to regulate the biosynthesis of pharmaceutical terpenoids. Overexpressing terpenoids biosynthesis pathway genes in homologous and ectopic plants is an effective strategy to enhance the yield of pharmaceutical terpenoids. Another strategy is to suppress the expression of competitive metabolic pathways. In addition, global regulation which includes regulating the relative transcription factors, endogenous phytohormones and primary metabolism could also markedly increase their yield. All these strategies offer great opportunities to enhance the supply of scarce terpenoids drugs, reduce the price of expensive drugs and improve people’s standards of living. PMID:27877181

  18. Reducing maintenance metabolism by metabolic engineering of respiration improves riboflavin production by Bacillus subtilis.

    PubMed

    Zamboni, Nicola; Mouncey, Nigel; Hohmann, Hans-Peter; Sauer, Uwe

    2003-01-01

    We present redirection of electron flow to more efficient proton pumping branches within respiratory chains as a generally applicable metabolic engineering strategy, which tailors microbial metabolism to the specific requirements of high cell density processes by improving product and biomass yields. For the example of riboflavin production by Bacillus subtilis, we reduced the rate of maintenance metabolism by about 40% in a cytochrome bd oxidase knockout mutant. Since the putative Yth and the caa(3) oxidases were of minor importance, the most likely explanation for this improvement is translocation of two protons per transported electron via the remaining cytochrome aa(3) oxidase, instead of only one proton via the bd oxidase. The reduction of maintenance metabolism, in turn, significantly improved the yield of recombinant riboflavin and B. subtilis biomass in fed-batch cultures.

  19. Scale up of proteoliposome derived Cochleate production.

    PubMed

    Zayas, Caridad; Bracho, Gustavo; Lastre, Miriam; González, Domingo; Gil, Danay; Acevedo, Reinaldo; del Campo, Judith; Taboada, Carlos; Solís, Rosa L; Barberá, Ramón; Pérez, Oliver

    2006-04-12

    Cochleate are highly stable structures with promising immunological features. Cochleate structures are usually obtaining from commercial lipids. Proteoliposome derived Cochleate are derived from an outer membrane vesicles of Neisseria meningitidis B. Previously, we obtained Cochleates using dialysis procedures. In order to increase the production process, we used a crossflow system (CFS) that allows easy scale up to obtain large batches in an aseptic environment. The raw material and solutions used in the production process are already approved for human application. This work demonstrates that CFS is very efficient process to obtain Cochleate structures with a yield of more than 80% and the immunogenicity comparable to that obtained by dialysis membrane.

  20. The Metabolic Costs of Sound Production in Odontocete Cetaceans

    DTIC Science & Technology

    2010-09-30

    1 DISTRIBUTION STATEMENT A: Approved for public release; distribution is unlimited. The Metabolic Costs of Sound Production in Odontocete...of masking from environmental sounds (NRC 2003). Although accumulating evidence from recent research (Scheifele et al. 2005, Holt et al. 2009, Parks...potential energetic costs of such compensation behavior are unknown. To our knowledge, there is no empirical data on the metabolic cost of sound

  1. The Metabolic Cost of Click Production in Bottlenose Dolphins

    DTIC Science & Technology

    2012-09-30

    of their acoustic signals as a strategy to help reduce the probability of masking from environmental sounds (NRC 2003). Although accumulating...date, the only empirical data on the metabolic cost of sound production as well as the metabolic cost of increasing the amplitude of acoustic signals...dolphins producing whistles and other communicative sounds (Holt et al. 2011 a, b, Noren et al. 2011). There is currently no information on energy

  2. Cardiac Metabolism in Heart Failure - Implications beyond ATP production

    PubMed Central

    Doenst, Torsten; Nguyen, T. Dung; Abel, E. Dale

    2013-01-01

    The heart has a high rate of ATP production and turnover which is required to maintain its continuous mechanical work. Perturbations in ATP generating processes may therefore affect contractile function directly. Characterizing cardiac metabolism in heart failure revealed several metabolic alterations termed metabolic remodeling, ranging from changes in substrate utilization to mitochondrial dysfunction, ultimately resulting in ATP deficiency and impaired contractility. However, ATP depletion is not the only relevant consequence of metabolic remodeling during heart failure. By providing cellular building blocks and signaling molecules, metabolic pathways control essential processes such as cell growth and regeneration. Thus, alterations in cardiac metabolism may also affect the progression to heart failure by mechanisms beyond ATP supply. Our aim is therefore to highlight that metabolic remodeling in heart failure not only results in impaired cardiac energetics, but also induces other processes implicated in the development of heart failure such as structural remodeling and oxidative stress. Accordingly, modulating cardiac metabolism in heart failure may have significant therapeutic relevance that goes beyond the energetic aspect. PMID:23989714

  3. Replica scaling specifications for materials and production

    NASA Astrophysics Data System (ADS)

    Aune, R. B.; Lindgard, J.; Nygard, K.; Olden, V.

    1995-03-01

    Laboratory experiments of repeatable full scale precision tests on reinforced concrete elements exposed to blast loads require considerable resources, and are in many cases impossible with the test equipment available nationally and internationally. In this respect testing of scaled structural elements is advantageous. Model laws must be applied, and the effect of relaxations of a strict model law application must be well understood. The objective of this report is to give specifications for production of reinforced concrete slabs in replica scaling. Three slabs with different dimensions are included: 300 x 300 x 30 mm (P1), 1000 x 1000 x 100 mm (P2) and 3000 x 3000 x 300 mm (P3). Concrete mixes are developed for all three slabs. Concrete quality comply with C35, and similitude in the compressive strength between the mixes is required. Use of replica scaled accumulated aggregate grading curves was a part of the scope of work. Specifications for production of deformed bars with diameters 1.6 mm and 5.3 mm for P1 and P2, respectively, are developed. The material properties of the deformed bars comply with the Norwegian quality K500TE for reinforcement. Acceptable similitude between the stress-strain curves for the two dimensions is obtained.

  4. Effects of hyperglycemia on bone metabolism and bone matrix in goldfish scales.

    PubMed

    Kitamura, Kei-Ichiro; Andoh, Tadashi; Okesaku, Wakana; Tazaki, Yuya; Ogai, Kazuhiro; Sugitani, Kayo; Kobayashi, Isao; Suzuki, Nobuo; Chen, Wenxi; Ikegame, Mika; Hattori, Atsuhiko

    2017-01-01

    Increased risk of fracture associated with type 2 diabetes has been a topic of recent concern. Fracture risk is related to a decrease in bone strength, which can be affected by bone metabolism and the quality of the bone. To investigate the cause of the increased fracture rate in patients with diabetes through analyses of bone metabolism and bone matrix protein properties, we used goldfish scales as a bone model for hyperglycemia. Using the scales of seven alloxan-treated and seven vehicle-treated control goldfish, we assessed bone metabolism by analyzing the activity of marker enzymes and mRNA expression of marker genes, and we measured the change in molecular weight of scale matrix proteins with SDS-PAGE. After only a 2-week exposure to hyperglycemia, the molecular weight of α- and β-fractions of bone matrix collagen proteins changed incrementally in the regenerating scales of hyperglycemic goldfish compared with those of euglycemic goldfish. In addition, the relative ratio of the γ-fraction significantly increased, and a δ-fraction appeared after adding glyceraldehyde-a candidate for the formation of advanced glycation end products in diabetes-to isolated type 1 collagen in vitro. The enzymatic activity and mRNA expression of osteoblast and osteoclast markers were not significantly different between hyperglycemic and euglycemic goldfish scales. These results indicate that hyperglycemia is likely to affect bone quality through glycation of matrix collagen from an early stage of hyperglycemia. Therefore, non-enzymatic glycation of collagen fibers in bone matrix may lead to the deterioration of bone quality from the onset of diabetes.

  5. Unit Price Scaling Trends for Chemical Products

    SciTech Connect

    Qi, Wei; Sathre, Roger; William R. Morrow, III; Shehabi, Arman

    2015-08-01

    To facilitate early-stage life-cycle techno-economic modeling of emerging technologies, here we identify scaling relations between unit price and sales quantity for a variety of chemical products of three categories - metal salts, organic compounds, and solvents. We collect price quotations for lab-scale and bulk purchases of chemicals from both U.S. and Chinese suppliers. We apply a log-log linear regression model to estimate the price discount effect. Using the median discount factor of each category, one can infer bulk prices of products for which only lab-scale prices are available. We conduct out-of-sample tests showing that most of the price proxies deviate from their actual reference prices by a factor less than ten. We also apply the bootstrap method to determine if a sample median discount factor should be accepted for price approximation. We find that appropriate discount factors for metal salts and for solvents are both -0.56, while that for organic compounds is -0.67 and is less representative due to greater extent of product heterogeneity within this category.

  6. Universal scaling of production rates across mammalian lineages.

    PubMed

    Hamilton, Marcus J; Davidson, Ana D; Sibly, Richard M; Brown, James H

    2011-02-22

    Over many millions of years of independent evolution, placental, marsupial and monotreme mammals have diverged conspicuously in physiology, life history and reproductive ecology. The differences in life histories are particularly striking. Compared with placentals, marsupials exhibit shorter pregnancy, smaller size of offspring at birth and longer period of lactation in the pouch. Monotremes also exhibit short pregnancy, but incubate embryos in eggs, followed by a long period of post-hatching lactation. Using a large sample of mammalian species, we show that, remarkably, despite their very different life histories, the scaling of production rates is statistically indistinguishable across mammalian lineages. Apparently all mammals are subject to the same fundamental metabolic constraints on productivity, because they share similar body designs, vascular systems and costs of producing new tissue.

  7. Universal scaling of production rates across mammalian lineages

    PubMed Central

    Hamilton, Marcus J.; Davidson, Ana D.; Sibly, Richard M.; Brown, James H.

    2011-01-01

    Over many millions of years of independent evolution, placental, marsupial and monotreme mammals have diverged conspicuously in physiology, life history and reproductive ecology. The differences in life histories are particularly striking. Compared with placentals, marsupials exhibit shorter pregnancy, smaller size of offspring at birth and longer period of lactation in the pouch. Monotremes also exhibit short pregnancy, but incubate embryos in eggs, followed by a long period of post-hatching lactation. Using a large sample of mammalian species, we show that, remarkably, despite their very different life histories, the scaling of production rates is statistically indistinguishable across mammalian lineages. Apparently all mammals are subject to the same fundamental metabolic constraints on productivity, because they share similar body designs, vascular systems and costs of producing new tissue. PMID:20798111

  8. Metabolic Engineering of Microalgal Based Biofuel Production: Prospects and Challenges

    PubMed Central

    Banerjee, Chiranjib; Dubey, Kashyap K.; Shukla, Pratyoosh

    2016-01-01

    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. PMID:27065986

  9. Design and application of genome-scale reconstructed metabolic models.

    PubMed

    Rocha, Isabel; Förster, Jochen; Nielsen, Jens

    2008-01-01

    In this chapter, the process for the reconstruction of genome-scale metabolic networks is described, and some of the main applications of such models are illustrated. The reconstruction process can be viewed as an iterative process where information obtained from several sources is combined to construct a preliminary set of reactions and constraints. This involves steps such as genome annotation; identification of the reactions from the annotated genome sequence and available literature; determination of the reaction stoichiometry; definition of compartmentation and assignment of localization; determination of the biomass composition; measurement, calculation, or fitting of energy requirements; and definition of additional constraints. The reaction and constraint sets, after debugging, may be integrated into a stoichiometric model that can be used for simulation using tools such as Flux Balance Analysis (Section 3.8). From the flux distributions obtained, physiologic parameters such as growth yields or minimal medium components can be calculated, and their distance from similar experimental data provides a basis from where the model may need to be improved.

  10. Metabolic analyses elucidate non-trivial gene targets for amplifying dihydroartemisinic acid production in yeast

    PubMed Central

    Misra, Ashish; Conway, Matthew F.; Johnnie, Joseph; Qureshi, Tabish M.; Lige, Bao; Derrick, Anne M.; Agbo, Eddy C.; Sriram, Ganesh

    2013-01-01

    Synthetic biology enables metabolic engineering of industrial microbes to synthesize value-added molecules. In this, a major challenge is the efficient redirection of carbon to the desired metabolic pathways. Pinpointing strategies toward this goal requires an in-depth investigation of the metabolic landscape of the organism, particularly primary metabolism, to identify precursor and cofactor availability for the target compound. The potent antimalarial therapeutic artemisinin and its precursors are promising candidate molecules for production in microbial hosts. Recent advances have demonstrated the production of artemisinin precursors in engineered yeast strains as an alternative to extraction from plants. We report the application of in silico and in vivo metabolic pathway analyses to identify metabolic engineering targets to improve the yield of the direct artemisinin precursor dihydroartemisinic acid (DHA) in yeast. First, in silico extreme pathway (ExPa) analysis identified NADPH-malic enzyme and the oxidative pentose phosphate pathway (PPP) as mechanisms to meet NADPH demand for DHA synthesis. Next, we compared key DHA-synthesizing ExPas to the metabolic flux distributions obtained from in vivo 13C metabolic flux analysis of a DHA-synthesizing strain. This comparison revealed that knocking out ethanol synthesis and overexpressing glucose-6-phosphate dehydrogenase in the oxidative PPP (gene YNL241C) or the NADPH-malic enzyme ME2 (YKL029C) are vital steps toward overproducing DHA. Finally, we employed in silico flux balance analysis and minimization of metabolic adjustment on a yeast genome-scale model to identify gene knockouts for improving DHA yields. The best strategy involved knockout of an oxaloacetate transporter (YKL120W) and an aspartate aminotransferase (YKL106W), and was predicted to improve DHA yields by 70-fold. Collectively, our work elucidates multiple non-trivial metabolic engineering strategies for improving DHA yield in yeast. PMID:23898325

  11. Metabolic engineering for the microbial production of marine bioactive compounds.

    PubMed

    Mao, Xiangzhao; Liu, Zhen; Sun, Jianan; Lee, Sang Yup

    2017-03-06

    Many marine bioactive compounds have medicinal and nutritional values. These bioactive compounds have been prepared using solvent-based extraction from marine bio-resources or chemical synthesis, which are costly, inefficient with low yields, and environmentally unfriendly. Recent advances in metabolic engineering allowed to some extent more efficient production of these compounds, showing promises to meet the increasing demand of marine natural bioactive compounds. In this paper, we review the strategies and statuses of metabolic engineering applied to microbial production of marine natural bioactive compounds including terpenoids and their derivatives, omega-3 polyunsaturated fatty acids, and marine natural drugs, and provide perspectives.

  12. Advances in Metabolic Engineering of Cyanobacteria for Photosynthetic Biochemical Production

    PubMed Central

    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 diversity of bioproducts synthesized by engineered cyanobacteria, the metabolic pathways used, and the current engineering strategies used for increasing their titers. PMID:26516923

  13. Small-scale ethanol-production demonstration

    SciTech Connect

    Adcock, L.E. II; Eley, M.H.; Schroer, B.J.

    1981-09-01

    The Johnson Environmental and Energy Center with assistance from the Madison County Farm Bureau Association received a grant from the US Department of Energy to design, fabricate, and evaluate a small scale continuous ethanol plant. The scope of the study was to satisfy four specific objectives. The first objective was to design a small scale continuous distillation unit capable of producing 10 to 15 gallons per hour of 170 to 190 proof ethanol. A second objective was to economically fabricate the distillation unit. A third objective was to thoroughly evaluate the unit with emphasis on production potential, operation considerations, and energy balance. The fourth objective was to work with the Farm Bureau in identifying an organization that would place the unit in a production environment. The results of the study indicate that the distillation unit is capable of producing an average of 9 to 14 gallons per hour (based on alcohol percent in beer) of 174 proof ethanol. The energy ratio for distillation is a positive 3:1. Once the unit has reached steady state very little operator attention is required with the exception of periodically refluxing. Material cost of the plate column is approximately $5000. The unit could be built by an individual provided he is trained in welding and has the necessary shop equipment. The report also contains 7 appendices entitled: Principles of ethanol production; pump manufacturer specifications; boiler manufacturer specifications, water treatment manufacturer specifications; tank specifications; test results; and boiler efficiency data sheets. 39 figures, 112 tables.

  14. Intramolecular stable isotope distributions detect plant metabolic responses on century time scales

    NASA Astrophysics Data System (ADS)

    Schleucher, Jürgen; Ehlers, Ina; Augusti, Angela; Betson, Tatiana

    2014-05-01

    Plants respond to environmental changes on a vast range of time scales, and plant gas exchanges constitute important feedback mechanisms in the global C cycle. Responses on time scales of decades to centuries are most important for climate models, for prediction of crop productivity, and for adaptation to climate change. Unfortunately, responses on these timescale are least understood. We argue that the knowledge gap on intermediate time scales is due to a lack of adequate methods that can bridge between short-term manipulative experiments (e.g. FACE) and paleo research. Manipulative experiments in plant ecophysiology give information on metabolism on time scales up to years. However, this information cannot be linked to results from retrospective studies in paleo research, because little metabolic information can be derived from paleo archives. Stable isotopes are prominent tools in plant ecophysiology, biogeochemistry and in paleo research, but in all applications to date, isotope ratios of whole molecules are measured. However, it is well established that stable isotope abundance varies among intramolecular groups of biochemical metabolites, that is each so-called "isotopomer" has a distinct abundance. This intramolecular variation carries information on metabolic regulation, which can even be traced to individual enzymes (Schleucher et al., Plant, Cell Environ 1999). Here, we apply intramolecular isotope distributions to study the metabolic response of plants to increasing atmospheric [CO2] during the past century. Greenhouse experiments show that the deuterium abundance among the two positions in the C6H2 group of photosynthetic glucose depends on [CO2] during growth. This is observed for all plants using C3 photosynthesis, and reflects the metabolic flux ratio between photorespiration and photosynthesis. Photorespiration is a major C flux that limits assimilation in C3 plants, which encompass the overwhelming fraction of terrestrial photosynthesis and the

  15. Reconstruction of genome-scale human metabolic models using omics data.

    PubMed

    Ryu, Jae Yong; Kim, Hyun Uk; Lee, Sang Yup

    2015-08-01

    The impact of genome-scale human metabolic models on human systems biology and medical sciences is becoming greater, thanks to increasing volumes of model building platforms and publicly available omics data. The genome-scale human metabolic models started with Recon 1 in 2007, and have since been used to describe metabolic phenotypes of healthy and diseased human tissues and cells, and to predict therapeutic targets. Here we review recent trends in genome-scale human metabolic modeling, including various generic and tissue/cell type-specific human metabolic models developed to date, and methods, databases and platforms used to construct them. For generic human metabolic models, we pay attention to Recon 2 and HMR 2.0 with emphasis on data sources used to construct them. Draft and high-quality tissue/cell type-specific human metabolic models have been generated using these generic human metabolic models. Integration of tissue/cell type-specific omics data with the generic human metabolic models is the key step, and we discuss omics data and their integration methods to achieve this task. The initial version of the tissue/cell type-specific human metabolic models can further be computationally refined through gap filling, reaction directionality assignment and the subcellular localization of metabolic reactions. We review relevant tools for this model refinement procedure as well. Finally, we suggest the direction of further studies on reconstructing an improved human metabolic model.

  16. Segmented linear modeling of CHO fed‐batch culture and its application to large scale production

    PubMed Central

    Ben Yahia, Bassem; Gourevitch, Boris; Malphettes, Laetitia

    2016-01-01

    ABSTRACT We describe a systematic approach to model CHO metabolism during biopharmaceutical production across a wide range of cell culture conditions. To this end, we applied the metabolic steady state concept. We analyzed and modeled the production rates of metabolites as a function of the specific growth rate. First, the total number of metabolic steady state phases and the location of the breakpoints were determined by recursive partitioning. For this, the smoothed derivative of the metabolic rates with respect to the growth rate were used followed by hierarchical clustering of the obtained partition. We then applied a piecewise regression to the metabolic rates with the previously determined number of phases. This allowed identifying the growth rates at which the cells underwent a metabolic shift. The resulting model with piecewise linear relationships between metabolic rates and the growth rate did well describe cellular metabolism in the fed‐batch cultures. Using the model structure and parameter values from a small‐scale cell culture (2 L) training dataset, it was possible to predict metabolic rates of new fed‐batch cultures just using the experimental specific growth rates. Such prediction was successful both at the laboratory scale with 2 L bioreactors but also at the production scale of 2000 L. This type of modeling provides a flexible framework to set a solid foundation for metabolic flux analysis and mechanistic type of modeling. Biotechnol. Bioeng. 2017;114: 785–797. © 2016 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc. PMID:27869296

  17. Major evolutionary transitions of life, metabolic scaling and the number and size of mitochondria and chloroplasts.

    PubMed

    Okie, Jordan G; Smith, Val H; Martin-Cereceda, Mercedes

    2016-05-25

    We investigate the effects of trophic lifestyle and two types of major evolutionary transitions in individuality-the endosymbiotic acquisition of organelles and development of multicellularity-on organellar and cellular metabolism and allometry. We develop a quantitative framework linking the size and metabolic scaling of eukaryotic cells to the abundance, size and metabolic scaling of mitochondria and chloroplasts and analyse a newly compiled, unprecedented database representing unicellular and multicellular cells covering diverse phyla and tissues. Irrespective of cellularity, numbers and total volumes of mitochondria scale linearly with cell volume, whereas chloroplasts scale sublinearly and sizes of both organelles remain largely invariant with cell size. Our framework allows us to estimate the metabolic scaling exponents of organelles and cells. Photoautotrophic cells and organelles exhibit photosynthetic scaling exponents always less than one, whereas chemoheterotrophic cells and organelles have steeper respiratory scaling exponents close to one. Multicellularity has no discernible effect on the metabolic scaling of organelles and cells. In contrast, trophic lifestyle has a profound and uniform effect, and our results suggest that endosymbiosis fundamentally altered the metabolic scaling of free-living bacterial ancestors of mitochondria and chloroplasts, from steep ancestral scaling to a shallower scaling in their endosymbiotic descendants.

  18. A genome-scale metabolic network reconstruction of tomato (Solanum lycopersicum L.) and its application to photorespiratory metabolism.

    PubMed

    Yuan, Huili; Cheung, C Y Maurice; Poolman, Mark G; Hilbers, Peter A J; van Riel, Natal A W

    2016-01-01

    Tomato (Solanum lycopersicum L.) has been studied extensively due to its high economic value in the market, and high content in health-promoting antioxidant compounds. Tomato is also considered as an excellent model organism for studying the development and metabolism of fleshy fruits. However, the growth, yield and fruit quality of tomatoes can be affected by drought stress, a common abiotic stress for tomato. To investigate the potential metabolic response of tomato plants to drought, we reconstructed iHY3410, a genome-scale metabolic model of tomato leaf, and used this metabolic network to simulate tomato leaf metabolism. The resulting model includes 3410 genes and 2143 biochemical and transport reactions distributed across five intracellular organelles including cytosol, plastid, mitochondrion, peroxisome and vacuole. The model successfully described the known metabolic behaviour of tomato leaf under heterotrophic and phototrophic conditions. The in silico investigation of the metabolic characteristics for photorespiration and other relevant metabolic processes under drought stress suggested that: (i) the flux distributions through the mevalonate (MVA) pathway under drought were distinct from that under normal conditions; and (ii) the changes in fluxes through core metabolic pathways with varying flux ratio of RubisCO carboxylase to oxygenase may contribute to the adaptive stress response of plants. In addition, we improved on previous studies of reaction essentiality analysis for leaf metabolism by including potential alternative routes for compensating reaction knockouts. Altogether, the genome-scale model provides a sound framework for investigating tomato metabolism and gives valuable insights into the functional consequences of abiotic stresses.

  19. Genome-scale metabolic model for Lactococcus lactis MG1363 and its application to the analysis of flavor formation.

    PubMed

    Flahaut, Nicolas A L; Wiersma, Anne; van de Bunt, Bert; Martens, Dirk E; Schaap, Peter J; Sijtsma, Lolke; Dos Santos, Vitor A Martins; de Vos, Willem M

    2013-10-01

    Lactococcus lactis subsp. cremoris MG1363 is a paradigm strain for lactococci used in industrial dairy fermentations. However, despite of its importance for process development, no genome-scale metabolic model has been reported thus far. Moreover, current models for other lactococci only focus on growth and sugar degradation. A metabolic model that includes nitrogen metabolism and flavor-forming pathways is instrumental for the understanding and designing new industrial applications of these lactic acid bacteria. A genome-scale, constraint-based model of the metabolism and transport in L. lactis MG1363, accounting for 518 genes, 754 reactions, and 650 metabolites, was developed and experimentally validated. Fifty-nine reactions are directly or indirectly involved in flavor formation. Flux Balance Analysis and Flux Variability Analysis were used to investigate flux distributions within the whole metabolic network. Anaerobic carbon-limited continuous cultures were used for estimating the energetic parameters. A thorough model-driven analysis showing a highly flexible nitrogen metabolism, e.g., branched-chain amino acid catabolism which coupled with the redox balance, is pivotal for the prediction of the formation of different flavor compounds. Furthermore, the model predicted the formation of volatile sulfur compounds as a result of the fermentation. These products were subsequently identified in the experimental fermentations carried out. Thus, the genome-scale metabolic model couples the carbon and nitrogen metabolism in L. lactis MG1363 with complete known catabolic pathways leading to flavor formation. The model provided valuable insights into the metabolic networks underlying flavor formation and has the potential to contribute to new developments in dairy industries and cheese-flavor research.

  20. BHP may scale up methanol production

    SciTech Connect

    Alperowicz, N.

    1993-06-23

    Broken Hill Pty. (BHP: Melbourne) says otherwise uneconomic gas reserves in the Timor Sea off northwest Australia could be developed if the company`s plans to commercialize a novel gas-to-methanol technology prove to be viable. BHP is building an A$70-million ($50 million) research unit in Victoria using ICI`s Leading Concept Methanol gas-to-methanol process. If this unit proves viable, it could be put on a vessel and taken to Timor Sea where BHP has oil exploration and production interests. Timor gas is not economically viable because of lack of nearby markets. The 54,000-m.t./year research plant, located at Werrbee near Melbourne, is scheduled to start production in the second half of 1994, according to BHP manager Joe Evon. The plant is being built by Davy/John Brown. Provided the economic climate is right, BHP is expected to build a world-scale methanol plant offshore.

  1. Investigation on metabolism of cisplatin resistant ovarian cancer using a genome scale metabolic model and microarray data

    PubMed Central

    Motamedian, Ehsan; Ghavami, Ghazaleh; Sardari, Soroush

    2015-01-01

    Objective(s): Many cancer cells show significant resistance to drugs that kill drug sensitive cancer cells and non-tumor cells and such resistance might be a consequence of the difference in metabolism. Therefore, studying the metabolism of drug resistant cancer cells and comparison with drug sensitive and normal cell lines is the objective of this research. Material and Methods: Metabolism of cisplatin resistant and sensitive A2780 epithelial ovarian cancer cells and normal ovarian epithelium has been studied using a generic human genome-scale metabolic model and transcription data. Result: The results demonstrate that the most different metabolisms belong to resistant and normal models, and the different reactions are involved in various metabolic pathways. However, large portion of distinct reactions are related to extracellular transport for three cell lines. Capability of metabolic models to secrete lactate was investigated to find the origin of Warburg effect. Computational results introduced SLC25A10 gene, which encodes mitochondrial dicarboxylate transporter involved in exchanging of small metabolites across the mitochondrial membrane that may play key role in high growing capacity of sensitive and resistant cancer cells. The metabolic models were also used to find single and combinatorial targets that reduce the cancer cells growth. Effect of proposed target genes on growth and oxidative phosphorylation of normal cells were determined to estimate drug side-effects. Conclusion: The deletion results showed that although the cisplatin did not cause resistant cancer cells death, but it shifts the cancer cells to a more vulnerable metabolism. PMID:25945240

  2. Metabolic differences in cattle with excitable temperaments can influence productivity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Temperament can negatively affect various production traits, including live weight, ADG, DMI, conception rates, and carcass weight. Three research studies are summarized which indicate the potential influence of temperament on metabolism. In Brahman heifers, (n=12) the 6 most temperamental and 6 mos...

  3. Production of L-carnitine by secondary metabolism of bacteria

    PubMed Central

    Bernal, Vicente; Sevilla, Ángel; Cánovas, Manuel; Iborra, José L

    2007-01-01

    The increasing commercial demand for L-carnitine has led to a multiplication of efforts to improve its production with bacteria. The use of different cell environments, such as growing, resting, permeabilized, dried, osmotically stressed, freely suspended and immobilized cells, to maintain enzymes sufficiently active for L-carnitine production is discussed in the text. The different cell states of enterobacteria, such as Escherichia coli and Proteus sp., which can be used to produce L-carnitine from crotonobetaine or D-carnitine as substrate, are analyzed. Moreover, the combined application of both bioprocess and metabolic engineering has allowed a deeper understanding of the main factors controlling the production process, such as energy depletion and the alteration of the acetyl-CoA/CoA ratio which are coupled to the end of the biotransformation. Furthermore, the profiles of key central metabolic activities such as the TCA cycle, the glyoxylate shunt and the acetate metabolism are seen to be closely interrelated and affect the biotransformation efficiency. Although genetically modified strains have been obtained, new strain improvement strategies are still needed, especially in Escherichia coli as a model organism for molecular biology studies. This review aims to summarize and update the state of the art in L-carnitine production using E. coli and Proteus sp, emphasizing the importance of proper reactor design and operation strategies, together with metabolic engineering aspects and the need for feed-back between wet and in silico work to optimize this biotransformation. PMID:17910757

  4. Metabolic Design and Control for Production in Prokaryotes

    SciTech Connect

    Chhabra, Swapnil R.; Keasling, J.D.

    2010-11-10

    Prokaryotic life on earth is manifested by its diversity and omnipresence. These microbes serve as natural sources of a large variety of compounds with the potential to serve the ever growing, medicinal, chemical and transportation needs of the human population. However, commercially viable production of these compounds can be realized only through significant improvement of the native production capacity of natural isolates. The most favorable way to achieve this goal is through the genetic manipulation of metabolic pathways that direct the production of these molecules. While random mutagenesis and screening have dominated the industrial production of such compounds in the past our increased understanding of microbial physiology over the last five decades has shifted this trend towards rational approaches for metabolic design. Major drivers of this trend include recombinant DNA technology, high throughput characterization of macromolecular cellular components, quantitative modeling for metabolic engine ring, targeted combinatorial engineering and synthetic biology. In this chapter we track the evolution of microbial engineering technologies from the black box era of random mutagenesis to the science and engineering-driven era of metabolic design.

  5. A common scaling rule for abundance, energetics, and production of parasitic and free-living species

    USGS Publications Warehouse

    Hechinger, Ryan F.; Lafferty, Kevin D.; Dobson, Andy P.; Brown, James H.; Kuris, Armand M.

    2011-01-01

    The metabolic theory of ecology uses the scaling of metabolism with body size and temperature to explain the causes and consequences of species abundance. However, the theory and its empirical tests have never simultaneously examined parasites alongside free-living species. This is unfortunate because parasites represent at least half of species diversity. We show that metabolic scaling theory could not account for the abundance of parasitic or free-living species in three estuarine food webs until accounting for trophic dynamics. Analyses then revealed that the abundance of all species uniformly scaled with body mass to the - 3/4 power. This result indicates "production equivalence," where biomass production within trophic levels is invariant of body size across all species and functional groups: invertebrate or vertebrate, ectothermic or endothermic, and free-living or parasitic.

  6. A common scaling rule for abundance, energetics, and production of parasitic and free-living species.

    PubMed

    Hechinger, Ryan F; Lafferty, Kevin D; Dobson, Andy P; Brown, James H; Kuris, Armand M

    2011-07-22

    The metabolic theory of ecology uses the scaling of metabolism with body size and temperature to explain the causes and consequences of species abundance. However, the theory and its empirical tests have never simultaneously examined parasites alongside free-living species. This is unfortunate because parasites represent at least half of species diversity. We show that metabolic scaling theory could not account for the abundance of parasitic or free-living species in three estuarine food webs until accounting for trophic dynamics. Analyses then revealed that the abundance of all species uniformly scaled with body mass to the -¾ power. This result indicates "production equivalence," where biomass production within trophic levels is invariant of body size across all species and functional groups: invertebrate or vertebrate, ectothermic or endothermic, and free-living or parasitic.

  7. Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism

    PubMed Central

    Vital-Lopez, Francisco G.; Reifman, Jaques; Wallqvist, Anders

    2015-01-01

    A hallmark of Pseudomonas aeruginosa is its ability to establish biofilm-based infections that are difficult to eradicate. Biofilms are less susceptible to host inflammatory and immune responses and have higher antibiotic tolerance than free-living planktonic cells. Developing treatments against biofilms requires an understanding of bacterial biofilm-specific physiological traits. Research efforts have started to elucidate the intricate mechanisms underlying biofilm development. However, many aspects of these mechanisms are still poorly understood. Here, we addressed questions regarding biofilm metabolism using a genome-scale kinetic model of the P. aeruginosa metabolic network and gene expression profiles. Specifically, we computed metabolite concentration differences between known mutants with altered biofilm formation and the wild-type strain to predict drug targets against P. aeruginosa biofilms. We also simulated the altered metabolism driven by gene expression changes between biofilm and stationary growth-phase planktonic cultures. Our analysis suggests that the synthesis of important biofilm-related molecules, such as the quorum-sensing molecule Pseudomonas quinolone signal and the exopolysaccharide Psl, is regulated not only through the expression of genes in their own synthesis pathway, but also through the biofilm-specific expression of genes in pathways competing for precursors to these molecules. Finally, we investigated why mutants defective in anthranilate degradation have an impaired ability to form biofilms. Alternative to a previous hypothesis that this biofilm reduction is caused by a decrease in energy production, we proposed that the dysregulation of the synthesis of secondary metabolites derived from anthranilate and chorismate is what impaired the biofilms of these mutants. Notably, these insights generated through our kinetic model-based approach are not accessible from previous constraint-based model analyses of P. aeruginosa biofilm

  8. Biofilm Formation Mechanisms of Pseudomonas aeruginosa Predicted via Genome-Scale Kinetic Models of Bacterial Metabolism.

    PubMed

    Vital-Lopez, Francisco G; Reifman, Jaques; Wallqvist, Anders

    2015-10-01

    A hallmark of Pseudomonas aeruginosa is its ability to establish biofilm-based infections that are difficult to eradicate. Biofilms are less susceptible to host inflammatory and immune responses and have higher antibiotic tolerance than free-living planktonic cells. Developing treatments against biofilms requires an understanding of bacterial biofilm-specific physiological traits. Research efforts have started to elucidate the intricate mechanisms underlying biofilm development. However, many aspects of these mechanisms are still poorly understood. Here, we addressed questions regarding biofilm metabolism using a genome-scale kinetic model of the P. aeruginosa metabolic network and gene expression profiles. Specifically, we computed metabolite concentration differences between known mutants with altered biofilm formation and the wild-type strain to predict drug targets against P. aeruginosa biofilms. We also simulated the altered metabolism driven by gene expression changes between biofilm and stationary growth-phase planktonic cultures. Our analysis suggests that the synthesis of important biofilm-related molecules, such as the quorum-sensing molecule Pseudomonas quinolone signal and the exopolysaccharide Psl, is regulated not only through the expression of genes in their own synthesis pathway, but also through the biofilm-specific expression of genes in pathways competing for precursors to these molecules. Finally, we investigated why mutants defective in anthranilate degradation have an impaired ability to form biofilms. Alternative to a previous hypothesis that this biofilm reduction is caused by a decrease in energy production, we proposed that the dysregulation of the synthesis of secondary metabolites derived from anthranilate and chorismate is what impaired the biofilms of these mutants. Notably, these insights generated through our kinetic model-based approach are not accessible from previous constraint-based model analyses of P. aeruginosa biofilm

  9. TIGER: Toolbox for integrating genome-scale metabolic models, expression data, and transcriptional regulatory networks

    PubMed Central

    2011-01-01

    Background Several methods have been developed for analyzing genome-scale models of metabolism and transcriptional regulation. Many of these methods, such as Flux Balance Analysis, use constrained optimization to predict relationships between metabolic flux and the genes that encode and regulate enzyme activity. Recently, mixed integer programming has been used to encode these gene-protein-reaction (GPR) relationships into a single optimization problem, but these techniques are often of limited generality and lack a tool for automating the conversion of rules to a coupled regulatory/metabolic model. Results We present TIGER, a Toolbox for Integrating Genome-scale Metabolism, Expression, and Regulation. TIGER converts a series of generalized, Boolean or multilevel rules into a set of mixed integer inequalities. The package also includes implementations of existing algorithms to integrate high-throughput expression data with genome-scale models of metabolism and transcriptional regulation. We demonstrate how TIGER automates the coupling of a genome-scale metabolic model with GPR logic and models of transcriptional regulation, thereby serving as a platform for algorithm development and large-scale metabolic analysis. Additionally, we demonstrate how TIGER's algorithms can be used to identify inconsistencies and improve existing models of transcriptional regulation with examples from the reconstructed transcriptional regulatory network of Saccharomyces cerevisiae. Conclusion The TIGER package provides a consistent platform for algorithm development and extending existing genome-scale metabolic models with regulatory networks and high-throughput data. PMID:21943338

  10. The intraspecific scaling of metabolic rate with body mass in fishes depends on lifestyle and temperature.

    PubMed

    Killen, Shaun S; Atkinson, David; Glazier, Douglas S

    2010-02-01

    Metabolic energy fuels all biological processes, and therefore theories that explain the scaling of metabolic rate with body mass potentially have great predictive power in ecology. A new model, that could improve this predictive power, postulates that the metabolic scaling exponent (b) varies between 2/3 and 1, and is inversely related to the elevation of the intraspecific scaling relationship (metabolic level, L), which in turn varies systematically among species in response to various ecological factors. We test these predictions by examining the effects of lifestyle, swimming mode and temperature on intraspecific scaling of resting metabolic rate among 89 species of teleost fish. As predicted, b decreased as L increased with temperature, and with shifts in lifestyle from bathyal and benthic to benthopelagic to pelagic. This effect of lifestyle on b may be related to varying amounts of energetically expensive tissues associated with different capacities for swimming during predator-prey interactions.

  11. A metabolic derivation of tritium transfer coefficients in animal products.

    PubMed

    Galeriu, D; Crout, N M; Melintescu, A; Beresford, N A; Peterson, S R; Van Hees, M

    2001-12-01

    Tritium is a potentially important environmental contaminant originating from the nuclear industry, and its behaviour in the environment is controlled by that of hydrogen. Animal food products represent a potentially important source of tritium in the human diet and a number of transfer coefficient values for tritium transfer to a limited number of animal products are available. In this paper we present an approach for the derivation of tritium transfer coefficients which is based on the metabolism of hydrogen in animals. The derived transfer coefficients separately account for transfer to and from free (i.e. water) and organically bound tritium. A novel aspect of the approach is that tritium transfer can be predicted for any animal product for which the required metabolic input parameters are available. The predicted transfer coefficients are compared to available independent data. Agreement is good (R2=0.97) with the exception of the transfer coefficient for transfer from tritiated water to organically bound tritium in ruminants. This may be attributable to the particular characteristics of ruminant digestion. We show that tritium transfer coefficients will vary in response to the metabolic status of an animal (e.g. stage of lactation, diet digestibility etc.) and that the use of a single transfer coefficient from diet to animal product is inappropriate. It is possible to derive concentration ratio values from the estimated transfer coefficients which relate the concentration of tritiated water and organically bound tritium in an animal product to their respective concentrations in the animals diet. These concentration ratios are shown to be less subject to metabolic variation and may be more useful radioecological parameters than transfer coefficients. For tritiated water the concentration ratio shows little variation between animal products ranging from 0.59 to 0.82. In the case of organically bound tritium the concentration ratios vary between animal products

  12. Shift in metabolism towards ethanol production in Saccharomyces cerevisiae by addition of metabolic inhibitors

    SciTech Connect

    Hahn-Haegerdal, B.; Mattiasson, B.

    1982-01-01

    The future exploitation of fermentation processes for the production of bulk chemicals will very much depend on whether product yield and product concentration can be improved. At the present time the cost for the raw material and the product upgrading limits the competitiveness of fermentation processes in relation to petrochemical processes. Much effort is put into selecting microbial strains with higher product yields as well as improved tolerance towards increased product concentrations. This approach is rather laborious and time-consuming and the overall goal will be beneficial if it is complemented with other techniques. This investigation will describe how productivity migh be improved by addition of a specific metabolic inhibitor, sodium azide, which inhibits the cytochrome oxidase of the respiratory chain. As a model for these studies Saccaromyces cerevisiae fermenting glucose to ethanol was chosen.

  13. Altered sucrose metabolism impacts plant biomass production and flower development.

    PubMed

    Coleman, Heather D; Beamish, Leigh; Reid, Anya; Park, Ji-Young; Mansfield, Shawn D

    2010-04-01

    Nicotiana tabacum (tobacco) was transformed with three genes involved in sucrose metabolism, UDP-glucose pyrophosphorylase (UGPase, EC 2.7.7.9), sucrose synthase (SuSy, EC 2.4.1.13) and sucrose phosphate synthase (SPS, EC 2.4.1.14). Plants harbouring the single transgenes were subsequently crossed to produce double and triple transgenic lines, including: 2 x 35S::UGPase x SPS, 4CL::UGPase x SPS, 2 x 35S::SuSy x SPS, 4CL::SuSy x SPS, 2 x 35S::UGPase x SuSy x SPS, and 4CL::UGPase x SuSy x SPS. The ultimate aim of the study was to examine whether it is possible to alter cellulose production through the manipulation of sucrose metabolism genes. While altering sucrose metabolism using UGPase, SuSy and SPS does not have an end effect on cellulose production, their simultaneous overexpression resulted in enhanced primary growth as seen in an increase in height growth, in some cases over 50%. Furthermore, the pyramiding strategy of simultaneously altering the expression of multiple genes in combination resulted in increased time to reproductive bud formation as well as altered flower morphology and foliar stipule formation in 4CL lines. Upregulation of these sucrose metabolism genes appears to directly impact primary growth and therefore biomass production in tobacco.

  14. Scale Impacts in Net Ecosystem Productivity Estimations

    NASA Astrophysics Data System (ADS)

    Carvalhais, N.; Myneni, R.

    2004-12-01

    Net ecosystem production (NEP) estimations play a key role in the terrestrial carbon cycle assessment, both at regional and global scales studies. The emergence of remote sensing greatly improved NEP estimation methods and analysis domain. Yet, spatial and temporal resolution of sensors and remote sensing products often imply adjustments to NEP calculation methods. The Carnegie Ames Stanford Approach (CASA) terrestrial biogeochemical model (Potter et al., 1993; Friedlingstein et al., 1999) simulates plant and soil processes allowing the estimation of NEP through the difference between net primary productivity and soil respiration. CASA inputs include climatic data: precipitation, temperature and solar radiation; soil texture; vegetation type and percentage cover; as well as leaf area index (LAI), fraction of photosynthetically active radiation absorbed by vegetation (FPAR) and normalized difference vegetation index (NDVI). With a research interest in regional vegetation dynamics in the Iberian Peninsula (IP), estimations of NEP were compared with local measurements over a Quercus ilex and Quercus suber with perennial grassland ecosystem, representing a region characteristic land cover. The CASA calibration process aimed the tuning of efficiency scalars directly related to net primary productivity and soil respiration calculations, maximum light use efficiency (å*) and temperature effect on soil fluxes (Q10). To this end local weather station data was used as climatic inputs, with remotely sensed LAI, FPAR and NDVI products from MODIS sensor. In a first approach the NEP calculations were performed at a finer spatial and temporal resolution of 1 km and 8 days, respectively, for the periods of 2002 and 2003 (years of available NEP measurements). A confident correlation is found, although local extremes tend to differ and affect the annual balance concordance between estimations and measurements of NEP. Consequently, calibrated å* and Q10 values were used at coarser

  15. Metabolic Engineering of Microorganisms for the Production of Higher Alcohols

    PubMed Central

    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

  16. Metabolic engineering of microorganisms for the production of higher alcohols.

    PubMed

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

    2014-09-02

    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.

  17. Genome-scale modeling of human metabolism - a systems biology approach.

    PubMed

    Mardinoglu, Adil; Gatto, Francesco; Nielsen, Jens

    2013-09-01

    Altered metabolism is linked to the appearance of various human diseases and a better understanding of disease-associated metabolic changes may lead to the identification of novel prognostic biomarkers and the development of new therapies. Genome-scale metabolic models (GEMs) have been employed for studying human metabolism in a systematic manner, as well as for understanding complex human diseases. In the past decade, such metabolic models - one of the fundamental aspects of systems biology - have started contributing to the understanding of the mechanistic relationship between genotype and phenotype. In this review, we focus on the construction of the Human Metabolic Reaction database, the generation of healthy cell type- and cancer-specific GEMs using different procedures, and the potential applications of these developments in the study of human metabolism and in the identification of metabolic changes associated with various disorders. We further examine how in silico genome-scale reconstructions can be employed to simulate metabolic flux distributions and how high-throughput omics data can be analyzed in a context-dependent fashion. Insights yielded from this mechanistic modeling approach can be used for identifying new therapeutic agents and drug targets as well as for the discovery of novel biomarkers. Finally, recent advancements in genome-scale modeling and the future challenge of developing a model of whole-body metabolism are presented. The emergent contribution of GEMs to personalized and translational medicine is also discussed.

  18. Enhanced flavonoid production in Streptomyces venezuelae via metabolic engineering.

    PubMed

    Park, Sung Ryeol; Ahn, Mi Sun; Han, Ah Reum; Park, Je Won; Yoon, Yeo Joon

    2011-11-01

    Metabolic engineering of plant-specific phenylpropanoid biosynthesis has attracted an increasing amount of attention recently, owing to the vast potential of flavonoids as nutraceuticals and pharmaceuticals. Recently, we have developed a recombinant Streptomyces venezuelae as a heterologous host for the production of flavonoids. In this study, we successfully improved flavonoid production by expressing two sets of genes predicted to be involved in malonate assimilation. The introduction of matB and matC encoding for malonyl-CoA synthetase and the putative dicarboxylate carrier protein, respectively, from Streptomyces coelicolor into the recombinant S. venezuelae strains expressing flavanone and flavone biosynthetic genes resulted in enhanced production of both flavonoids.

  19. Metabolic engineering of natural product biosynthesis in actinobacteria.

    PubMed

    Bilyk, Oksana; Luzhetskyy, Andriy

    2016-12-01

    Actinomycetes are known to produce over two-thirds of all known secondary metabolites. We review here recent progress in the metabolic engineering of streptomycetes for natural product biosynthesis. Several examples of the yield improvement of polyketides (mithramycin and tylactone) and non-ribosomal peptides (balhimycin and daptomycin) demonstrate the power of precursor supply engineering. Another example is the manipulation of a regulatory network for increased production of nystatin and teicoplanin. The second part highlights new approaches in the derivatization of natural products via combination of mutasynthesis and genomic engineering.

  20. Patterns of metabolite changes identified from large-scale gene perturbations in Arabidopsis using a genome-scale metabolic network.

    PubMed

    Kim, Taehyong; Dreher, Kate; Nilo-Poyanco, Ricardo; Lee, Insuk; Fiehn, Oliver; Lange, Bernd Markus; Nikolau, Basil J; Sumner, Lloyd; Welti, Ruth; Wurtele, Eve S; Rhee, Seung Y

    2015-04-01

    Metabolomics enables quantitative evaluation of metabolic changes caused by genetic or environmental perturbations. However, little is known about how perturbing a single gene changes the metabolic system as a whole and which network and functional properties are involved in this response. To answer this question, we investigated the metabolite profiles from 136 mutants with single gene perturbations of functionally diverse Arabidopsis (Arabidopsis thaliana) genes. Fewer than 10 metabolites were changed significantly relative to the wild type in most of the mutants, indicating that the metabolic network was robust to perturbations of single metabolic genes. These changed metabolites were closer to each other in a genome-scale metabolic network than expected by chance, supporting the notion that the genetic perturbations changed the network more locally than globally. Surprisingly, the changed metabolites were close to the perturbed reactions in only 30% of the mutants of the well-characterized genes. To determine the factors that contributed to the distance between the observed metabolic changes and the perturbation site in the network, we examined nine network and functional properties of the perturbed genes. Only the isozyme number affected the distance between the perturbed reactions and changed metabolites. This study revealed patterns of metabolic changes from large-scale gene perturbations and relationships between characteristics of the perturbed genes and metabolic changes.

  1. Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis.

    PubMed

    Kotera, Masaaki; Goto, Susumu

    2016-01-01

    Metabolic pathway reconstruction presents a challenge for understanding metabolic pathways in organisms of interest. Different strategies, i.e., reference-based vs. de novo, must be used for pathway reconstruction depending on the availability of well-characterized enzymatic reactions. If at least one enzyme is already known to catalyze a reaction, its amino acid sequence can be used as a reference for identifying homologous enzymes in the genome of an organism of interest. Where there is no known enzyme able to catalyze a corresponding reaction, however, the reaction and the corresponding enzyme must be predicted de novo from chemical transformations of the putative substrate-product pair. This review summarizes studies involving reference-based and de novo metabolic pathway reconstruction and discusses the importance of the classification and structure-function relationships of enzymes.

  2. Metabolic pathway reconstruction strategies for central metabolism and natural product biosynthesis

    PubMed Central

    Kotera, Masaaki; Goto, Susumu

    2016-01-01

    Metabolic pathway reconstruction presents a challenge for understanding metabolic pathways in organisms of interest. Different strategies, i.e., reference-based vs. de novo, must be used for pathway reconstruction depending on the availability of well-characterized enzymatic reactions. If at least one enzyme is already known to catalyze a reaction, its amino acid sequence can be used as a reference for identifying homologous enzymes in the genome of an organism of interest. Where there is no known enzyme able to catalyze a corresponding reaction, however, the reaction and the corresponding enzyme must be predicted de novo from chemical transformations of the putative substrate-product pair. This review summarizes studies involving reference-based and de novo metabolic pathway reconstruction and discusses the importance of the classification and structure-function relationships of enzymes. PMID:27924274

  3. Metabolic engineering for the production of 1,3-propanediol

    SciTech Connect

    Cameron, D.C.; Tong, I.T., Skraly, F.A.

    1993-12-31

    Metabolic engineering involves the use of recombinant DNA techniques for the modification of intermediary metabolic pathways. Microorganisms have recently been engineered to produce compounds such as indigo, ethanol, fatty acids and polyhydroxyalkanoates. As a model system for research in metabolic engineering, the authors have constructed a strain of the bacterium Escherichia coli, that is able to produce 1,3-propanediol (1,3-PD) from glycerol. This strain contains the genes for the glycerol deydratase and the 1,3-PD oxidoreductase from Klebsiella pneumoniae. The authors have also investigated genetic and environmental strategies for improving the yield and productivity of 1,3-PD by the engineered organism. In addition to being a useful model system, 1,3-PD production is of current practical interest. First 1,3-PD (also known as trimethylene glycol) and 1,4-butanediol, the more readily available diols. Second, the volume of feedstock (glycerol) is expected to grow, as it is a by-product of the production of polyglycoside surfactants and biodiesel fluids.

  4. Magnesium degradation products: effects on tissue and human metabolism.

    PubMed

    Seitz, J-M; Eifler, R; Bach, Fr-W; Maier, H J

    2014-10-01

    Owing to their mechanical properties, metallic materials present a promising solution in the field of resorbable implants. The magnesium metabolism in humans differs depending on its introduction. The natural, oral administration of magnesium via, for example, food, essentially leads to an intracellular enrichment of Mg(2+) . In contrast, introducing magnesium-rich substances or implants into the tissue results in a different decomposition behavior. Here, exposing magnesium to artificial body electrolytes resulted in the formation of the following products: magnesium hydroxide, magnesium oxide, and magnesium chloride, as well as calcium and magnesium apatites. Moreover, it can be assumed that Mg(2+) , OH(-) ions, and gaseous hydrogen are also present and result from the reaction for magnesium in an aqueous environment. With the aid of physiological metabolic processes, the organism succeeds in either excreting the above mentioned products or integrating them into the natural metabolic process. Only a burst release of these products is to be considered a problem. A multitude of general tissue effects and responses from the Mg's degradation products is considered within this review, which is not targeting specific implant classes. Furthermore, common alloying elements of magnesium and their hazardous potential in vivo are taken into account.

  5. Genome-scale reconstruction and analysis of the Pseudomonas putida KT2440 metabolic network facilitates applications in biotechnology.

    PubMed

    Puchałka, Jacek; Oberhardt, Matthew A; Godinho, Miguel; Bielecka, Agata; Regenhardt, Daniela; Timmis, Kenneth N; Papin, Jason A; Martins dos Santos, Vítor A P

    2008-10-01

    A cornerstone of biotechnology is the use of microorganisms for the efficient production of chemicals and the elimination of harmful waste. Pseudomonas putida is an archetype of such microbes due to its metabolic versatility, stress resistance, amenability to genetic modifications, and vast potential for environmental and industrial applications. To address both the elucidation of the metabolic wiring in P. putida and its uses in biocatalysis, in particular for the production of non-growth-related biochemicals, we developed and present here a genome-scale constraint-based model of the metabolism of P. putida KT2440. Network reconstruction and flux balance analysis (FBA) enabled definition of the structure of the metabolic network, identification of knowledge gaps, and pin-pointing of essential metabolic functions, facilitating thereby the refinement of gene annotations. FBA and flux variability analysis were used to analyze the properties, potential, and limits of the model. These analyses allowed identification, under various conditions, of key features of metabolism such as growth yield, resource distribution, network robustness, and gene essentiality. The model was validated with data from continuous cell cultures, high-throughput phenotyping data, (13)C-measurement of internal flux distributions, and specifically generated knock-out mutants. Auxotrophy was correctly predicted in 75% of the cases. These systematic analyses revealed that the metabolic network structure is the main factor determining the accuracy of predictions, whereas biomass composition has negligible influence. Finally, we drew on the model to devise metabolic engineering strategies to improve production of polyhydroxyalkanoates, a class of biotechnologically useful compounds whose synthesis is not coupled to cell survival. The solidly validated model yields valuable insights into genotype-phenotype relationships and provides a sound framework to explore this versatile bacterium and to

  6. Shape shifting predicts ontogenetic changes in metabolic scaling in diverse aquatic invertebrates.

    PubMed

    Glazier, Douglas S; Hirst, Andrew G; Atkinson, David

    2015-03-07

    Metabolism fuels all biological activities, and thus understanding its variation is fundamentally important. Much of this variation is related to body size, which is commonly believed to follow a 3/4-power scaling law. However, during ontogeny, many kinds of animals and plants show marked shifts in metabolic scaling that deviate from 3/4-power scaling predicted by general models. Here, we show that in diverse aquatic invertebrates, ontogenetic shifts in the scaling of routine metabolic rate from near isometry (bR = scaling exponent approx. 1) to negative allometry (bR < 1), or the reverse, are associated with significant changes in body shape (indexed by bL = the scaling exponent of the relationship between body mass and body length). The observed inverse correlations between bR and bL are predicted by metabolic scaling theory that emphasizes resource/waste fluxes across external body surfaces, but contradict theory that emphasizes resource transport through internal networks. Geometric estimates of the scaling of surface area (SA) with body mass (bA) further show that ontogenetic shifts in bR and bA are positively correlated. These results support new metabolic scaling theory based on SA influences that may be applied to ontogenetic shifts in bR shown by many kinds of animals and plants.

  7. Shape shifting predicts ontogenetic changes in metabolic scaling in diverse aquatic invertebrates

    PubMed Central

    Glazier, Douglas S.; Hirst, Andrew G.; Atkinson, David

    2015-01-01

    Metabolism fuels all biological activities, and thus understanding its variation is fundamentally important. Much of this variation is related to body size, which is commonly believed to follow a 3/4-power scaling law. However, during ontogeny, many kinds of animals and plants show marked shifts in metabolic scaling that deviate from 3/4-power scaling predicted by general models. Here, we show that in diverse aquatic invertebrates, ontogenetic shifts in the scaling of routine metabolic rate from near isometry (bR = scaling exponent approx. 1) to negative allometry (bR < 1), or the reverse, are associated with significant changes in body shape (indexed by bL = the scaling exponent of the relationship between body mass and body length). The observed inverse correlations between bR and bL are predicted by metabolic scaling theory that emphasizes resource/waste fluxes across external body surfaces, but contradict theory that emphasizes resource transport through internal networks. Geometric estimates of the scaling of surface area (SA) with body mass (bA) further show that ontogenetic shifts in bR and bA are positively correlated. These results support new metabolic scaling theory based on SA influences that may be applied to ontogenetic shifts in bR shown by many kinds of animals and plants. PMID:25652833

  8. MapMaker and PathTracer for tracking carbon in genome-scale metabolic models.

    PubMed

    Tervo, Christopher J; Reed, Jennifer L

    2016-05-01

    Constraint-based reconstruction and analysis (COBRA) modeling results can be difficult to interpret given the large numbers of reactions in genome-scale models. While paths in metabolic networks can be found, existing methods are not easily combined with constraint-based approaches. To address this limitation, two tools (MapMaker and PathTracer) were developed to find paths (including cycles) between metabolites, where each step transfers carbon from reactant to product. MapMaker predicts carbon transfer maps (CTMs) between metabolites using only information on molecular formulae and reaction stoichiometry, effectively determining which reactants and products share carbon atoms. MapMaker correctly assigned CTMs for over 97% of the 2,251 reactions in an Escherichia coli metabolic model (iJO1366). Using CTMs as inputs, PathTracer finds paths between two metabolites. PathTracer was applied to iJO1366 to investigate the importance of using CTMs and COBRA constraints when enumerating paths, to find active and high flux paths in flux balance analysis (FBA) solutions, to identify paths for putrescine utilization, and to elucidate a potential CO2 fixation pathway in E. coli. These results illustrate how MapMaker and PathTracer can be used in combination with constraint-based models to identify feasible, active, and high flux paths between metabolites.

  9. Computational evaluation of Synechococcus sp. PCC 7002 metabolism for chemical production

    SciTech Connect

    Vu, Trang; Hill, Eric A.; Kucek, Leo A.; Konopka, Allan; Beliaev, Alex S.; Reed, Jennifer L.

    2013-05-24

    Cyanobacteria are ideal metabolic engineering platforms for carbon-neutral biotechnology because they directly convert CO2 to a range of valuable products. In this study, we present a computational assessment of biochemical production in Synechococcus sp. PCC 7002 (Synechococcus 7002), a fast growing cyanobacterium whose genome has been sequenced, and for which genetic modification methods have been developed. We evaluated the maximum theoretical yields (mol product per mol CO2 or mol photon) of producing various chemicals under photoautotrophic and dark conditions using a genome-scale metabolic model of Synechococcus 7002. We found that the yields were lower under dark conditions, compared to photoautotrophic conditions, due to the limited amount of energy and reductant generated from glycogen. We also examined the effects of photon and CO2 limitations on chemical production under photoautotrophic conditions. In addition, using various computational methods such as MOMA, RELATCH, and OptORF, we identified gene-knockout mutants that are predicted to improve chemical production under photoautotrophic and/or dark anoxic conditions. These computational results are useful for metabolic engineering of cyanobacteria to synthesize valueadded products.

  10. A global approach to analysis and interpretation of metabolic data for plant natural product discovery†

    PubMed Central

    Hur, Manhoi; Campbell, Alexis Ann; Almeida-de-Macedo, Marcia; Li, Ling; Ransom, Nick; Jose, Adarsh; Crispin, Matt; Nikolau, Basil J.

    2013-01-01

    Discovering molecular components and their functionality is key to the development of hypotheses concerning the organization and regulation of metabolic networks. The iterative experimental testing of such hypotheses is the trajectory that can ultimately enable accurate computational modelling and prediction of metabolic outcomes. This information can be particularly important for understanding the biology of natural products, whose metabolism itself is often only poorly defined. Here, we describe factors that must be in place to optimize the use of metabolomics in predictive biology. A key to achieving this vision is a collection of accurate time-resolved and spatially defined metabolite abundance data and associated metadata. One formidable challenge associated with metabolite profiling is the complexity and analytical limits associated with comprehensively determining the metabolome of an organism. Further, for metabolomics data to be efficiently used by the research community, it must be curated in publically available metabolomics databases. Such databases require clear, consistent formats, easy access to data and metadata, data download, and accessible computational tools to integrate genome system-scale datasets. Although transcriptomics and proteomics integrate the linear predictive power of the genome, the metabolome represents the nonlinear, final biochemical products of the genome, which results from the intricate system(s) that regulate genome expression. For example, the relationship of metabolomics data to the metabolic network is confounded by redundant connections between metabolites and gene-products. However, connections among metabolites are predictable through the rules of chemistry. Therefore, enhancing the ability to integrate the metabolome with anchor-points in the transcriptome and proteome will enhance the predictive power of genomics data. We detail a public database repository for metabolomics, tools and approaches for statistical

  11. A global approach to analysis and interpretation of metabolic data for plant natural product discovery.

    PubMed

    Hur, Manhoi; Campbell, Alexis Ann; Almeida-de-Macedo, Marcia; Li, Ling; Ransom, Nick; Jose, Adarsh; Crispin, Matt; Nikolau, Basil J; Wurtele, Eve Syrkin

    2013-04-01

    Discovering molecular components and their functionality is key to the development of hypotheses concerning the organization and regulation of metabolic networks. The iterative experimental testing of such hypotheses is the trajectory that can ultimately enable accurate computational modelling and prediction of metabolic outcomes. This information can be particularly important for understanding the biology of natural products, whose metabolism itself is often only poorly defined. Here, we describe factors that must be in place to optimize the use of metabolomics in predictive biology. A key to achieving this vision is a collection of accurate time-resolved and spatially defined metabolite abundance data and associated metadata. One formidable challenge associated with metabolite profiling is the complexity and analytical limits associated with comprehensively determining the metabolome of an organism. Further, for metabolomics data to be efficiently used by the research community, it must be curated in publicly available metabolomics databases. Such databases require clear, consistent formats, easy access to data and metadata, data download, and accessible computational tools to integrate genome system-scale datasets. Although transcriptomics and proteomics integrate the linear predictive power of the genome, the metabolome represents the nonlinear, final biochemical products of the genome, which results from the intricate system(s) that regulate genome expression. For example, the relationship of metabolomics data to the metabolic network is confounded by redundant connections between metabolites and gene-products. However, connections among metabolites are predictable through the rules of chemistry. Therefore, enhancing the ability to integrate the metabolome with anchor-points in the transcriptome and proteome will enhance the predictive power of genomics data. We detail a public database repository for metabolomics, tools and approaches for statistical analysis

  12. Intraspecific Scaling of the Resting and Maximum Metabolic Rates of the Crucian Carp (Carassius auratus)

    PubMed Central

    Huang, Qingda; Zhang, Yurong; Liu, Shuting; Wang, Wen; Luo, Yiping

    2013-01-01

    The question of how the scaling of metabolic rate with body mass (M) is achieved in animals is unresolved. Here, we tested the cell metabolism hypothesis and the organ size hypothesis by assessing the mass scaling of the resting metabolic rate (RMR), maximum metabolic rate (MMR), erythrocyte size, and the masses of metabolically active organs in the crucian carp (Carassius auratus). The M of the crucian carp ranged from 4.5 to 323.9 g, representing an approximately 72-fold difference. The RMR and MMR increased with M according to the allometric equations RMR = 0.212M0.776 and MMR = 0.753M0.785. The scaling exponents for RMR (br) and MMR (bm) obtained in crucian carp were close to each other. Thus, the factorial aerobic scope remained almost constant with increasing M. Although erythrocyte size was negatively correlated with both mass-specific RMR and absolute RMR adjusted to M, it and all other hematological parameters showed no significant relationship with M. These data demonstrate that the cell metabolism hypothesis does not describe metabolic scaling in the crucian carp, suggesting that erythrocyte size may not represent the general size of other cell types in this fish and the metabolic activity of cells may decrease as fish grows. The mass scaling exponents of active organs was lower than 1 while that of inactive organs was greater than 1, which suggests that the mass scaling of the RMR can be partly due to variance in the proportion of active/inactive organs in crucian carp. Furthermore, our results provide additional evidence supporting the correlation between locomotor capacity and metabolic scaling. PMID:24376588

  13. Dairy products on metabolic health: current research and clinical implications.

    PubMed

    Da Silva, Marine S; Rudkowska, Iwona

    2014-03-01

    Dairy products have been thought to have a beneficial role in the metabolic syndrome (MetS). MetS constitutes a cluster of risk factors for an increased mortality, including obesity, impaired glucose homeostasis, hypertension and atherogenic dyslipidemia. Individuals with MetS are also often in a chronic, low-grade inflammatory state. The objective of this review is to examine recent meta-analyses and clinical studies on the association between dairy products consumption and these MetS risk factors. Findings from studies demonstrate that weight loss related to dairy product intake is due to the combination of an energy-restricted diet with consumption of dairy products. Further, a limited number of studies have shown beneficial effects of dairy consumption on plasma lipids, blood pressure, glucose homeostasis or inflammatory and oxidative stress profiles. Overall, this review article suggests that adults should consume at least 2-3 servings of dairy products per day within a well-balanced diet and a healthy lifestyle for metabolic health. Yet, higher dairy product consumption may have additional beneficial effects, but more well-designed intervention studies are needed to ascertain these effects.

  14. Evaluation of endogenous acidic metabolic products associated with carbohydrate metabolism in tumor cells

    PubMed Central

    Mazzio, Elizabeth A.; Smith, Bruce

    2010-01-01

    Tumor cells have a high tolerance for acidic and hypoxic microenvironments, also producing abundant lactic acid through accelerated glycolysis in the presence or absence of O2. While the accumulation of lactate is thought to be a major contributor to the reduction of pH-circumscribing aggressive tumors, it is not known if other endogenous metabolic products contribute this acidity. Furthermore, anaerobic metabolism in cancer cells bears similarity to homo-fermentative lactic acid bacteria, however very little is known about an alternative pathway that may drive adenosine triphosphate (ATP) production independent of glycolysis. In this study, we quantify over 40 end-products (amines, acids, alcohols, aldehydes, or ketones) produced by malignant neuroblastoma under accelerated glycolysis (+glucose (GLU) supply 1–10 mM) ± mitochondrial toxin; 1-methyl-4-phenyl-pyridinium (MPP+) to abate aerobic respiration to delineate differences between anaerobic vs. aerobic cell required metabolic pathways. The data show that an acceleration of anaerobic glycolysis prompts an expected reduction in extracellular pH (pHex) from neutral to 6.7±0.006. Diverse metabolic acids associated with this drop in acidity were quantified by ionic exchange liquid chromatography (LC), showing concomitant rise in lactate (Ctrls 7.5±0.5 mM; +GLU 12.35±1.3 mM; +GLU + MPP 18.1±1.8 mM), acetate (Ctrl 0.84±0.13 mM: +GLU 1.3±0.15 mM; +GLU + MPP 2.7±0.4 mM), fumarate, and a-ketoglutarate (<10μM) while a range of other metabolic organic acids remained undetected. Amino acids quantified by o-phthalaldehyde precolumn derivatization/electrochemical detection–LC show accumulation of L-alanine (1.6±.052 mM), L-glutamate (285±9.7μM), L-asparagine (202±2.1μM), and L-aspartate (84.2±4.9μM) produced during routine metabolism, while other amino acids remain undetected. In contrast, the data show no evidence for accumulation of acetaldehyde, aldehydes, or ketones (Purpald/2

  15. Genome-Scale Metabolic Reconstructions and Theoretical Investigation of Methane Conversion in Methylomicrobium buryatense Strain 5G(B1)

    SciTech Connect

    de la Torre, Andrea; Metivier, Aisha; Chu, Frances; Laurens, Lieve M. L.; Beck, David A. C.; Pienkos, Philip T.; Lidstrom, Mary E.; Kalyuzhnaya, Marina G.

    2015-11-25

    Methane-utilizing bacteria (methanotrophs) are capable of growth on methane and are attractive systems for bio-catalysis. However, the application of natural methanotrophic strains to large-scale production of value-added chemicals/biofuels requires a number of physiological and genetic alterations. An accurate metabolic model coupled with flux balance analysis can provide a solid interpretative framework for experimental data analyses and integration.

  16. Coupled Effects of Hyporheic Flow Structure and Metabolic Pattern on Reach-scale Nutrient Uptake

    NASA Astrophysics Data System (ADS)

    Li, A.; Aubeneau, A. F.; Bolster, D.; Tank, J. L.; Packman, A. I.

    2015-12-01

    Co-injections of conservative tracers and nutrients are commonly used to assess net reach-scale nutrient transformation rates and benthic/hyporheic uptake parameters. However, little information is available on spatial metabolic patterns in the benthic and hyporheic regions. Based on observations from real systems, we used particle tracking simulations to explore the effects of localized metabolism on estimates of reach-scale nutrient uptake rates. Metabolism locally depletes nutrient concentrations relative to conservative tracers, causing their concentration profiles of injected nutrients and conservative tracers to diverge. At slow rates of hyporheic exchange relative to rates of metabolism, overall hyporheic nutrient uptake is limited by delivery from the stream, and effective reach-scale nutrient uptake parameters will be controlled by the hyporheic exchange rate. At high rates of hyporheic exchange relative to rates of metabolism, the injected tracer can propagate beyond regions of high microbial activity, which commonly occur near the streambed surface. In this case, the injected tracer may not adequately capture timescales of nutrient replenishment in the most bioactive regions. Reach-scale nutrients uptake rate increases with increasing heterogeneity in local metabolic patterns, altering the shape of breakthrough curves downstream. More observations of hyporheic rates and metabolic patterns are needed to understand how flow heterogeneity and reaction heterogeneity interact to control nutrient dynamics at reach-scale.

  17. MetaMerge: scaling up genome-scale metabolic reconstructions with application to Mycobacterium tuberculosis

    PubMed Central

    2012-01-01

    Reconstructed models of metabolic networks are widely used for studying metabolism in various organisms. Many different reconstructions of the same organism often exist concurrently, forcing researchers to choose one of them at the exclusion of the others. We describe MetaMerge, an algorithm for semi-automatically reconciling a pair of existing metabolic network reconstructions into a single metabolic network model. We use MetaMerge to combine two published metabolic networks for Mycobacterium tuberculosis into a single network, which allows many reactions that could not be active in the individual models to become active, and predicts essential genes with a higher positive predictive value. PMID:22292986

  18. Genome-Scale Metabolic Modeling in the Simulation of Field-Scale Uranium Bioremediation

    NASA Astrophysics Data System (ADS)

    Yabusaki, S.; Wilkins, M.; Fang, Y.; Williams, K. H.; Waichler, S.; Long, P. E.

    2015-12-01

    Coupled variably saturated flow and biogeochemical reactive transport modeling is used to improve understanding of the processes, properties, and conditions controlling uranium bio-immobilization in a field experiment where uranium-contaminated groundwater was amended with acetate and bicarbonate. The acetate stimulates indigenous microorganisms that catalyze metal reduction, including the conversion of aqueous U(VI) to solid-phase U(IV), which effectively removes uranium from solution. The initiation of the bicarbonate amendment prior to biostimulation was designed to promote U(VI) desorption that would increase the aqueous U(VI) available for bioreduction. The three-dimensional simulations were able to largely reproduce the timing and magnitude of the physical, chemical and biological responses to the acetate and bicarbonate amendment in the context of changing water table elevation and gradient. A time series of groundwater proteomic samples exhibited correlations between the most abundant Geobacter metallireducens proteins and the genome-scale metabolic model-predicted fluxes of intra-cellular reactions associated with each of those proteins. The desorption of U(VI) induced by the bicarbonate amendment led to initially higher rates of bioreduction compared to locations with minimal bicarbonate exposure. After bicarbonate amendment ceased, bioreduction continued at these locations whereas U(VI) sorption was the dominant removal mechanism at the bicarbonate-impacted sites.

  19. Efficient estimation of the maximum metabolic productivity of batch systems

    DOE PAGES

    St. John, Peter C.; Crowley, Michael F.; Bomble, Yannick J.

    2017-01-31

    Production of chemicals from engineered organisms in a batch culture involves an inherent trade-off between productivity, yield, and titer. Existing strategies for strain design typically focus on designing mutations that achieve the highest yield possible while maintaining growth viability. While these methods are computationally tractable, an optimum productivity could be achieved by a dynamic strategy in which the intracellular division of resources is permitted to change with time. New methods for the design and implementation of dynamic microbial processes, both computational and experimental, have therefore been explored to maximize productivity. However, solving for the optimal metabolic behavior under the assumptionmore » that all fluxes in the cell are free to vary is a challenging numerical task. Here, previous studies have therefore typically focused on simpler strategies that are more feasible to implement in practice, such as the time-dependent control of a single flux or control variable.« less

  20. Evaluating metabolic stress and plasmid stability in plasmid DNA production by Escherichia coli.

    PubMed

    Silva, Filomena; Queiroz, João A; Domingues, Fernanda C

    2012-01-01

    In the context of recombinant DNA technology, the development of feasible and high-yielding plasmid DNA production processes has regained attention as more evidence for its efficacy as vectors for gene therapy and DNA vaccination arise. When producing plasmid DNA in Escherichia coli, a number of biological restraints, triggered by plasmid maintenance and replication as well as culture conditions are responsible for limiting final biomass and product yields. This termed "metabolic burden" can also cause detrimental effects on plasmid stability and quality, since the cell machinery is no longer capable of maintaining an active metabolism towards plasmid synthesis and the stress responses elicited by plasmid maintenance can also cause increased plasmid instability. The optimization of plasmid DNA production bioprocesses is still hindered by the lack of information on the host metabolic responses as well as information on plasmid instability. Therefore, systematic and on-line approaches are required not only to characterise this "metabolic burden" and plasmid stability but also for the design of appropriate metabolic engineering and culture strategies. The monitoring tools described to date rapidly evolve from laborious, off-line and at-line monitoring to online monitoring, at a time-scale that enables researchers to solve these bioprocessing problems as they occur. This review highlights major E. coli biological alterations caused by plasmid maintenance and replication, possible causes for plasmid instability and discusses the ability of currently employed bioprocess monitoring techniques to provide information in order to circumvent metabolic burden and plasmid instability, pointing out the possible evolution of these methods towards online bioprocess monitoring.

  1. Engineering nonphosphorylative metabolism to generate lignocellulose-derived products.

    PubMed

    Tai, Yi-Shu; Xiong, Mingyong; Jambunathan, Pooja; Wang, Jingyu; Wang, Jilong; Stapleton, Cole; Zhang, Kechun

    2016-04-01

    Conversion of lignocellulosic biomass into value-added products provides important environmental and economic benefits. Here we report the engineering of an unconventional metabolism for the production of tricarboxylic acid (TCA)-cycle derivatives from D-xylose, L-arabinose and D-galacturonate. We designed a growth-based selection platform to identify several gene clusters functional in Escherichia coli that can perform this nonphosphorylative assimilation of sugars into the TCA cycle in less than six steps. To demonstrate the application of this new metabolic platform, we built artificial biosynthetic pathways to 1,4-butanediol (BDO) with a theoretical molar yield of 100%. By screening and engineering downstream pathway enzymes, 2-ketoacid decarboxylases and alcohol dehydrogenases, we constructed E. coli strains capable of producing BDO from D-xylose, L-arabinose and D-galacturonate. The titers, rates and yields were higher than those previously reported using conventional pathways. This work demonstrates the potential of nonphosphorylative metabolism for biomanufacturing with improved biosynthetic efficiencies.

  2. Enhanced hydrogen production from glucose by metabolically engineered Escherichia coli.

    PubMed

    Maeda, Toshinari; Sanchez-Torres, Viviana; Wood, Thomas K

    2007-12-01

    To utilize fermentative bacteria for producing the alternative fuel hydrogen, we performed successive rounds of P1 transduction from the Keio Escherichia coli K-12 library to introduce multiple, stable mutations into a single bacterium to direct the metabolic flux toward hydrogen production. E. coli cells convert glucose to various organic acids (such as succinate, pyruvate, lactate, formate, and acetate) to synthesize energy and hydrogen from formate by the formate hydrogen-lyase (FHL) system that consists of hydrogenase 3 and formate dehydrogenase-H. We altered the regulation of FHL by inactivating the repressor encoded by hycA and by overexpressing the activator encoded by fhlA, removed hydrogen uptake activity by deleting hyaB (hydrogenase 1) and hybC (hydrogenase 2), redirected glucose metabolism to formate by using the fdnG, fdoG, narG, focA, focB, poxB, and aceE mutations, and inactivated the succinate and lactate synthesis pathways by deleting frdC and ldhA, respectively. The best of the metabolically engineered strains, BW25113 hyaB hybC hycA fdoG frdC ldhA aceE, increased hydrogen production 4.6-fold from glucose and increased the hydrogen yield twofold from 0.65 to 1.3 mol H(2)/mol glucose (maximum, 2 mol H(2)/mol glucose).

  3. From DNA to FBA: How to Build Your Own Genome-Scale Metabolic Model

    PubMed Central

    Cuevas, Daniel A.; Edirisinghe, Janaka; Henry, Chris S.; Overbeek, Ross; O’Connell, Taylor G.; Edwards, Robert A.

    2016-01-01

    Microbiological studies are increasingly relying on in silico methods to perform exploration and rapid analysis of genomic data, and functional genomics studies are supplemented by the new perspectives that genome-scale metabolic models offer. A mathematical model consisting of a microbe’s entire metabolic map can be rapidly determined from whole-genome sequencing and annotating the genomic material encoded in its DNA. Flux-balance analysis (FBA), a linear programming technique that uses metabolic models to predict the phenotypic responses imposed by environmental elements and factors, is the leading method to simulate and manipulate cellular growth in silico. However, the process of creating an accurate model to use in FBA consists of a series of steps involving a multitude of connections between bioinformatics databases, enzyme resources, and metabolic pathways. We present the methodology and procedure to obtain a metabolic model using PyFBA, an extensible Python-based open-source software package aimed to provide a platform where functional annotations are used to build metabolic models (http://linsalrob.github.io/PyFBA). Backed by the Model SEED biochemistry database, PyFBA contains methods to reconstruct a microbe’s metabolic map, run FBA upon different media conditions, and gap-fill its metabolism. The extensibility of PyFBA facilitates novel techniques in creating accurate genome-scale metabolic models. PMID:27379044

  4. High-throughput generation, optimization and analysis of genome-scale metabolic models.

    SciTech Connect

    Henry, C. S.; DeJongh, M.; Best, A. A.; Frybarger, P. M.; Linsay, B.; Stevens, R. L.

    2010-09-01

    Genome-scale metabolic models have proven to be valuable for predicting organism phenotypes from genotypes. Yet efforts to develop new models are failing to keep pace with genome sequencing. To address this problem, we introduce the Model SEED, a web-based resource for high-throughput generation, optimization and analysis of genome-scale metabolic models. The Model SEED integrates existing methods and introduces techniques to automate nearly every step of this process, taking {approx}48 h to reconstruct a metabolic model from an assembled genome sequence. We apply this resource to generate 130 genome-scale metabolic models representing a taxonomically diverse set of bacteria. Twenty-two of the models were validated against available gene essentiality and Biolog data, with the average model accuracy determined to be 66% before optimization and 87% after optimization.

  5. Differentiating causality and correlation in allometric scaling: ant colony size drives metabolic hypometry.

    PubMed

    Waters, James S; Ochs, Alison; Fewell, Jennifer H; Harrison, Jon F

    2017-02-22

    Metabolic rates of individual animals and social insect colonies generally scale hypometrically, with mass-specific metabolic rates decreasing with increasing size. Although this allometry has wide ranging effects on social behaviour, ecology and evolution, its causes remain controversial. Because it is difficult to experimentally manipulate body size of organisms, most studies of metabolic scaling depend on correlative data, limiting their ability to determine causation. To overcome this limitation, we experimentally reduced the size of harvester ant colonies (Pogonomyrmex californicus) and quantified the consequent increase in mass-specific metabolic rates. Our results clearly demonstrate a causal relationship between colony size and hypometric changes in metabolic rate that could not be explained by changes in physical density. These findings provide evidence against prominent models arguing that the hypometric scaling of metabolic rate is primarily driven by constraints on resource delivery or surface area/volume ratios, because colonies were provided with excess food and colony size does not affect individual oxygen or nutrient transport. We found that larger colonies had lower median walking speeds and relatively more stationary ants and including walking speed as a variable in the mass-scaling allometry greatly reduced the amount of residual variation in the model, reinforcing the role of behaviour in metabolic allometry. Following the experimental size reduction, however, the proportion of stationary ants increased, demonstrating that variation in locomotory activity cannot solely explain hypometric scaling of metabolic rates in these colonies. Based on prior studies of this species, the increase in metabolic rate in size-reduced colonies could be due to increased anabolic processes associated with brood care and colony growth.

  6. Metabolic engineering strategies to bio-adipic acid production.

    PubMed

    Kruyer, Nicholas S; Peralta-Yahya, Pamela

    2017-03-30

    Adipic acid is the most industrially important dicarboxylic acid as it is a key monomer in the synthesis of nylon. Today, adipic acid is obtained via a chemical process that relies on petrochemical precursors and releases large quantities of greenhouse gases. In the last two years, significant progress has been made in engineering microbes for the production of adipic acid and its immediate precursors, muconic acid and glucaric acid. Not only have the microbial substrates expanded beyond glucose and glycerol to include lignin monomers and hemicellulose components, but the number of microbial chassis now goes further than Escherichia coli and Saccharomyces cerevisiae to include microbes proficient in aromatic degradation, cellulose secretion and degradation of multiple carbon sources. Here, we review the metabolic engineering and nascent protein engineering strategies undertaken in each of these chassis to convert different feedstocks to adipic, muconic and glucaric acid. We also highlight near term prospects and challenges for each of the metabolic routes discussed.

  7. Metabolic determinants in Listeria monocytogenes anaerobic listeriolysin O production.

    PubMed

    Wallace, Nathan; Newton, Eric; Abrams, Elizabeth; Zani, Ashley; Sun, Yvonne

    2017-03-13

    Listeria monocytogenes is a human pathogen and a facultative anaerobe. To better understand how anaerobic growth affects L. monocytogenes pathogenesis, we first showed that anaerobic growth led to decreased growth and changes in surface morphology. Moreover, compared to aerobically grown bacteria, anaerobically grown L. monocytogenes established higher level of invasion but decreased intracellular growth and actin polymerization in cultured cells. The production of listeriolysin O (LLO) was significantly lower in anaerobic cultures-a phenotype observed in wild type and isogenic mutants lacking transcriptional regulators SigB or CodY or harboring a constitutively active PrfA. To explore potential regulatory mechanisms, we established that the addition of central carbon metabolism intermediates, such as acetate, citrate, fumarate, pyruvate, lactate, and succinate, led to an increase in LLO activity in the anaerobic culture supernatant. These results highlight the regulatory role of central carbon metabolism in L. monocytogenes pathogenesis under anaerobic conditions.

  8. Evaluation of sludge reduction of three metabolic uncouplers in laboratory-scale anaerobic-anoxic-oxic process.

    PubMed

    Li, Ping; Li, Hechao; Li, Jin; Guo, Xuesong; Liu, Junxin; Xiao, Benyi

    2016-12-01

    To evaluate the sludge reduction of three metabolic uncouplers (3,3',4',5-tetrachlorosalicylanilide (TCS), 2,4-dichlorophenol (DCP), and tetrakis (hydroxymethyl) phosphonium sulfate (THPS)), we conducted continuous experiments on laboratory-scale anaerobic-anoxic-oxic processes. The three metabolic uncouplers were separately added in each oxic tank of the three systems, and a system without uncoupler addition was used as control. During the 85-day operation, sludge production and observed growth yields decreased to 38.6% and 16.98%, 43.4% and 17.55%, and 39.3% and 17.04% by the addition of TCS, DCP, and THPS, respectively. The addition of metabolic uncouplers slightly reduced the wastewater treatment efficiencies of the system (about 1.1-8.7%) and increased sludge SVIs (about 69.9-80.6%). Meanwhile, the differences among three metabolic uncouplers were little. Besides metabolic uncoupling and maintenance metabolism, which exist in the TCS- and DCP-added systems, lysis-cryptic growth also exists in the THPS-added system.

  9. Scale-down of the inactivated polio vaccine production process.

    PubMed

    Thomassen, Yvonne E; van 't Oever, Aart G; Vinke, Marian; Spiekstra, Arjen; Wijffels, René H; van der Pol, Leo A; Bakker, Wilfried A M

    2013-05-01

    The anticipated increase in the demand for inactivated polio vaccines resulting from the success in the polio eradication program requires an increase in production capacity and cost price reduction of the current inactivated polio vaccine production processes. Improvement of existing production processes is necessary as the initial process development has been done decades ago. An up-to-date lab-scale version encompassing the legacy inactivated polio vaccine production process was set-up. This lab-scale version should be representative of the large scale, meaning a scale-down model, to allow experiments for process optimization that can be readily applied. Initially the separate unit operations were scaled-down at setpoint. Subsequently, the unit operations were applied successively in a comparative manner to large-scale manufacturing. This allows the assessment of the effects of changes in one unit operation to the consecutive units at small-scale. Challenges in translating large-scale operations to lab-scale are discussed, and the concessions that needed to be made are described. The current scale-down model for cell and virus culture (2.3-L) presents a feasible model with its production scale counterpart (750-L) when operated at setpoint. Also, the current scale-down models for the DSP unit operations clarification, concentration, size exclusion chromatography, ion exchange chromatography, and inactivation are in agreement with the manufacturing scale. The small-scale units can be used separately, as well as sequentially, to study variations and critical product quality attributes in the production process. Finally, it is shown that the scale-down unit operations can be used consecutively to prepare trivalent vaccine at lab-scale with comparable characteristics to the product produced at manufacturing scale.

  10. Dissecting the energy metabolism in Mycoplasma pneumoniae through genome-scale metabolic modeling

    PubMed Central

    Wodke, Judith A H; Puchałka, Jacek; Lluch-Senar, Maria; Marcos, Josep; Yus, Eva; Godinho, Miguel; Gutiérrez-Gallego, Ricardo; dos Santos, Vitor A P Martins; Serrano, Luis; Klipp, Edda; Maier, Tobias

    2013-01-01

    Mycoplasma pneumoniae, a threatening pathogen with a minimal genome, is a model organism for bacterial systems biology for which substantial experimental information is available. With the goal of understanding the complex interactions underlying its metabolism, we analyzed and characterized the metabolic network of M. pneumoniae in great detail, integrating data from different omics analyses under a range of conditions into a constraint-based model backbone. Iterating model predictions, hypothesis generation, experimental testing, and model refinement, we accurately curated the network and quantitatively explored the energy metabolism. In contrast to other bacteria, M. pneumoniae uses most of its energy for maintenance tasks instead of growth. We show that in highly linear networks the prediction of flux distributions for different growth times allows analysis of time-dependent changes, albeit using a static model. By performing an in silico knock-out study as well as analyzing flux distributions in single and double mutant phenotypes, we demonstrated that the model accurately represents the metabolism of M. pneumoniae. The experimentally validated model provides a solid basis for understanding its metabolic regulatory mechanisms. PMID:23549481

  11. Membrane transporters in a human genome-scale metabolic knowledgebase and their implications for disease

    PubMed Central

    Sahoo, Swagatika; Aurich, Maike K.; Jonsson, Jon J.; Thiele, Ines

    2014-01-01

    Membrane transporters enable efficient cellular metabolism, aid in nutrient sensing, and have been associated with various diseases, such as obesity and cancer. Genome-scale metabolic network reconstructions capture genomic, physiological, and biochemical knowledge of a target organism, along with a detailed representation of the cellular metabolite transport mechanisms. Since the first reconstruction of human metabolism, Recon 1, published in 2007, progress has been made in the field of metabolite transport. Recently, we published an updated reconstruction, Recon 2, which significantly improved the metabolic coverage and functionality. Human metabolic reconstructions have been used to investigate the role of metabolism in disease and to predict biomarkers and drug targets. Given the importance of cellular transport systems in understanding human metabolism in health and disease, we analyzed the coverage of transport systems for various metabolite classes in Recon 2. We will review the current knowledge on transporters (i.e., their preferred substrates, transport mechanisms, metabolic relevance, and disease association for each metabolite class). We will assess missing coverage and propose modifications and additions through a transport module that is functional when combined with Recon 2. This information will be valuable for further refinements. These data will also provide starting points for further experiments by highlighting areas of incomplete knowledge. This review represents the first comprehensive overview of the transporters involved in central metabolism and their transport mechanisms, thus serving as a compendium of metabolite transporters specific for human metabolic reconstructions. PMID:24653705

  12. Metabolic engineering strategies for improving xylitol production from hemicellulosic sugars.

    PubMed

    Su, Buli; Wu, Mianbin; Lin, Jianping; Yang, Lirong

    2013-11-01

    Xylitol is a five-carbon sugar alcohol with potential for use as a sweetener. Industrially, xylitol is currently produced by chemical hydrogenation of D-xylose using Raney nickel catalysts and this requires expensive separation and purification steps as well as high pressure and temperature that lead to environmental pollution. Highly efficient biotechnological production of xylitol using microorganisms is gaining more attention and has been proposed as an alternative process. Although the biotechnological method has not yet surpassed the advantages of chemical reduction in terms of yield and cost, various strategies offer promise for the biotechnological production of xylitol. In this review, the focus is on the most recent developments of the main metabolic engineering strategies for improving the production of xylitol.

  13. Metabolic engineering towards biotechnological production of carotenoids in microorganisms.

    PubMed

    Lee, P C; Schmidt-Dannert, C

    2002-10-01

    Carotenoids are important natural pigments produced by many microorganisms and plants. Traditionally, carotenoids have been used in the feed, food and nutraceutical industries. The recent discoveries of health-related beneficial properties attributed to carotenoids have spurred great interest in the production of structurally diverse carotenoids for pharmaceutical applications. The availability of a considerable number of microbial and plant carotenoid genes that can be functionally expressed in heterologous hosts has opened ways for the production of diverse carotenoid compounds in heterologous systems. In this review, we will describe the recent progress made in metabolic engineering of non-carotenogenic microorganisms for improved carotenoid productivity. In addition, we will discuss the application of combinatorial and evolutionary strategies to carotenoid pathway engineering to broaden the diversity of carotenoid structures synthesized in recombinant hosts.

  14. Metabolic engineering for isoprenoid-based biofuel production.

    PubMed

    Gupta, P; Phulara, S C

    2015-09-01

    Sustainable economic and industrial growth is the need of the hour and it requires renewable energy resources having better performance and compatibility with existing fuel infrastructure from biological routes. Isoprenoids (C ≥ 5) can be a potential alternative due to their diverse nature and physiochemical properties similar to that of petroleum based fuels. In the past decade, extensive research has been done to utilize metabolic engineering strategies in micro-organisms primarily, (i) to overcome the limitations associated with their natural and non-natural production and (ii) to develop commercially competent microbial strain for isoprenoid-based biofuel production. This review briefly describes the engineered isoprenoid biosynthetic pathways in well-characterized microbial systems for the production of several isoprenoid-based biofuels and fuel precursors.

  15. Size matters: plasticity in metabolic scaling shows body-size may modulate responses to climate change

    PubMed Central

    Carey, Nicholas; Sigwart, Julia D.

    2014-01-01

    Variability in metabolic scaling in animals, the relationship between metabolic rate (R) and body mass (M), has been a source of debate and controversy for decades. R is proportional to Mb, the precise value of b much debated, but historically considered equal in all organisms. Recent metabolic theory, however, predicts b to vary among species with ecology and metabolic level, and may also vary within species under different abiotic conditions. Under climate change, most species will experience increased temperatures, and marine organisms will experience the additional stressor of decreased seawater pH (‘ocean acidification’). Responses to these environmental changes are modulated by myriad species-specific factors. Body-size is a fundamental biological parameter, but its modulating role is relatively unexplored. Here, we show that changes to metabolic scaling reveal asymmetric responses to stressors across body-size ranges; b is systematically decreased under increasing temperature in three grazing molluscs, indicating smaller individuals were more responsive to warming. Larger individuals were, however, more responsive to reduced seawater pH in low temperatures. These alterations to the allometry of metabolism highlight abiotic control of metabolic scaling, and indicate that responses to climate warming and ocean acidification may be modulated by body-size. PMID:25122741

  16. Size matters: plasticity in metabolic scaling shows body-size may modulate responses to climate change.

    PubMed

    Carey, Nicholas; Sigwart, Julia D

    2014-08-01

    Variability in metabolic scaling in animals, the relationship between metabolic rate ( R: ) and body mass ( M: ), has been a source of debate and controversy for decades. R: is proportional to MB: , the precise value of B: much debated, but historically considered equal in all organisms. Recent metabolic theory, however, predicts B: to vary among species with ecology and metabolic level, and may also vary within species under different abiotic conditions. Under climate change, most species will experience increased temperatures, and marine organisms will experience the additional stressor of decreased seawater pH ('ocean acidification'). Responses to these environmental changes are modulated by myriad species-specific factors. Body-size is a fundamental biological parameter, but its modulating role is relatively unexplored. Here, we show that changes to metabolic scaling reveal asymmetric responses to stressors across body-size ranges; B: is systematically decreased under increasing temperature in three grazing molluscs, indicating smaller individuals were more responsive to warming. Larger individuals were, however, more responsive to reduced seawater pH in low temperatures. These alterations to the allometry of metabolism highlight abiotic control of metabolic scaling, and indicate that responses to climate warming and ocean acidification may be modulated by body-size.

  17. Genome-scale reconstruction of the metabolic network in Yersinia pestis CO92

    NASA Astrophysics Data System (ADS)

    Navid, Ali; Almaas, Eivind

    2007-03-01

    The gram-negative bacterium Yersinia pestis is the causative agent of bubonic plague. Using publicly available genomic, biochemical and physiological data, we have developed a constraint-based flux balance model of metabolism in the CO92 strain (biovar Orientalis) of this organism. The metabolic reactions were appropriately compartmentalized, and the model accounts for the exchange of metabolites, as well as the import of nutrients and export of waste products. We have characterized the metabolic capabilities and phenotypes of this organism, after comparing the model predictions with available experimental observations to evaluate accuracy and completeness. We have also begun preliminary studies into how cellular metabolism affects virulence.

  18. Metabolic flux analyses for serine alkaline protease production.

    PubMed

    Çalik; Çalik; Takaç; Özdamar

    2000-12-01

    The intracellular metabolic fluxes through the central carbon pathways in Bacillus licheniformis in serine alkaline protease (SAP) production were calculated to predict the potential strategies for increasing the performance of the bacilli, by using two optimization approaches, i.e. the theoretical data-based (TDA) and the theoretical data-based capacity (TDC) analyses based on respectively minimum in-vivo SAP accumulation rate and maximum SAP synthesis rate assumptions, at low-, medium-, and high-oxygen transfer conditions. At all periods of low-oxygen transfer condition, in lag and early exponential periods of medium-oxygen transfer (MOT) condition, and SAP synthesis period of high-oxygen transfer (HOT) condition, the TDA and TDC analyses revealed that SAP overproduction capacity is almost equal to the observed SAP production due to the regulation effect of the oxygen transfer. In the growth and early SAP synthesis period and in SAP synthesis period at MOT condition the calculated results of the two analyses reveal that SAP synthesis rate of the microorganism can be increased 7.2 and 16.7 folds, respectively; whereas, in the growth and early SAP synthesis period at HOT condition it can be increased 12.6 folds. The diversions in the biochemical reaction network and the influence of the oxygen transfer on the performance of the bacilli were also presented. The results encourage the application of metabolic engineering for lifting the rate limitations and for improving the genetic regulations in order to increase the SAP production.

  19. A genome-scale Escherichia coli kinetic metabolic model k-ecoli457 satisfying flux data for multiple mutant strains

    PubMed Central

    Khodayari, Ali; Maranas, Costas D.

    2016-01-01

    Kinetic models of metabolism at a genome scale that faithfully recapitulate the effect of multiple genetic interventions would be transformative in our ability to reliably design novel overproducing microbial strains. Here, we introduce k-ecoli457, a genome-scale kinetic model of Escherichia coli metabolism that satisfies fluxomic data for wild-type and 25 mutant strains under different substrates and growth conditions. The k-ecoli457 model contains 457 model reactions, 337 metabolites and 295 substrate-level regulatory interactions. Parameterization is carried out using a genetic algorithm by simultaneously imposing all available fluxomic data (about 30 measured fluxes per mutant). The Pearson correlation coefficient between experimental data and predicted product yields for 320 engineered strains spanning 24 product metabolites is 0.84. This is substantially higher than that using flux balance analysis, minimization of metabolic adjustment or maximization of product yield exhibiting systematic errors with correlation coefficients of, respectively, 0.18, 0.37 and 0.47 (k-ecoli457 is available for download at http://www.maranasgroup.com). PMID:27996047

  20. A sperm-specific proteome-scale metabolic network model identifies non-glycolytic genes for energy deficiency in asthenozoospermia.

    PubMed

    Asghari, Arvand; Marashi, Sayed-Amir; Ansari-Pour, Naser

    2017-04-01

    About 15% of couples experience difficulty in conceiving a child, of which half of the cases are thought to be male-related. Asthenozoospermia, or low sperm motility, is one of the frequent types of male infertility. Although energy metabolism is suggested to be central to the etiology of asthenozoospermia, very few attempts have been made to identify its underlying metabolic pathways. Here, we reconstructed SpermNet, the first proteome-scale model of the sperm cell by using whole-proteome data and the mCADRE algorithm. The reconstructed model was then analyzed using the COBRA toolbox. Genes were knocked-out in the model to investigate their effect on ATP production. A total of 78 genes elevated ATP production rate considerably of which most encode components of oxidative phosphorylation, fatty acid oxidation, the Krebs cycle, and members of the solute carrier 25 family. Among them, we identified 11 novel genes which have previously not been associated with sperm cell energy metabolism and may thus be implicated in asthenozoospermia. We further examined the reconstructed model by in silico knock out of currently known asthenozoospermia implicated-genes that were not predicted by our model. The pathways affected by knocking out these genes were also related to energy metabolism, confirming previous findings. Therefore, our model not only predicts the known pathways, it also identifies several non-glycolytic genes for deficient energy metabolism in asthenozoospermia. Finally, this model supports the notion that metabolic pathways besides glycolysis such as oxidative phosphorylation and fatty acid oxidation are essential for sperm energy metabolism and if validated, may form a basis for fertility recovery.

  1. Genome-scale metabolic reconstruction and in silico analysis of methylotrophic yeast Pichia pastoris for strain improvement

    PubMed Central

    2010-01-01

    Background Pichia pastoris has been recognized as an effective host for recombinant protein production. A number of studies have been reported for improving this expression system. However, its physiology and cellular metabolism still remained largely uncharacterized. Thus, it is highly desirable to establish a systems biotechnological framework, in which a comprehensive in silico model of P. pastoris can be employed together with high throughput experimental data analysis, for better understanding of the methylotrophic yeast's metabolism. Results A fully compartmentalized metabolic model of P. pastoris (iPP668), composed of 1,361 reactions and 1,177 metabolites, was reconstructed based on its genome annotation and biochemical information. The constraints-based flux analysis was then used to predict achievable growth rate which is consistent with the cellular phenotype of P. pastoris observed during chemostat experiments. Subsequent in silico analysis further explored the effect of various carbon sources on cell growth, revealing sorbitol as a promising candidate for culturing recombinant P. pastoris strains producing heterologous proteins. Interestingly, methanol consumption yields a high regeneration rate of reducing equivalents which is substantial for the synthesis of valuable pharmaceutical precursors. Hence, as a case study, we examined the applicability of P. pastoris system to whole-cell biotransformation and also identified relevant metabolic engineering targets that have been experimentally verified. Conclusion The genome-scale metabolic model characterizes the cellular physiology of P. pastoris, thus allowing us to gain valuable insights into the metabolism of methylotrophic yeast and devise possible strategies for strain improvement through in silico simulations. This computational approach, combined with synthetic biology techniques, potentially forms a basis for rational analysis and design of P. pastoris metabolic network to enhance humanized

  2. Integration and Validation of the Genome-Scale Metabolic Models of Pichia pastoris: A Comprehensive Update of Protein Glycosylation Pathways, Lipid and Energy Metabolism

    PubMed Central

    Tomàs-Gamisans, Màrius; Ferrer, Pau; Albiol, Joan

    2016-01-01

    Motivation Genome-scale metabolic models (GEMs) are tools that allow predicting a phenotype from a genotype under certain environmental conditions. GEMs have been developed in the last ten years for a broad range of organisms, and are used for multiple purposes such as discovering new properties of metabolic networks, predicting new targets for metabolic engineering, as well as optimizing the cultivation conditions for biochemicals or recombinant protein production. Pichia pastoris is one of the most widely used organisms for heterologous protein expression. There are different GEMs for this methylotrophic yeast of which the most relevant and complete in the published literature are iPP668, PpaMBEL1254 and iLC915. However, these three models differ regarding certain pathways, terminology for metabolites and reactions and annotations. Moreover, GEMs for some species are typically built based on the reconstructed models of related model organisms. In these cases, some organism-specific pathways could be missing or misrepresented. Results In order to provide an updated and more comprehensive GEM for P. pastoris, we have reconstructed and validated a consensus model integrating and merging all three existing models. In this step a comprehensive review and integration of the metabolic pathways included in each one of these three versions was performed. In addition, the resulting iMT1026 model includes a new description of some metabolic processes. Particularly new information described in recently published literature is included, mainly related to fatty acid and sphingolipid metabolism, glycosylation and cell energetics. Finally the reconstructed model was tested and validated, by comparing the results of the simulations with available empirical physiological datasets results obtained from a wide range of experimental conditions, such as different carbon sources, distinct oxygen availability conditions, as well as producing of two different recombinant proteins. In

  3. Production of diacetyl by metabolically engineered Enterobacter cloacae

    PubMed Central

    Zhang, Lijie; Zhang, Yingxin; Liu, Qiuyuan; Meng, Liying; Hu, Mandong; Lv, Min; Li, Kun; Gao, Chao; Xu, Ping; Ma, Cuiqing

    2015-01-01

    Diacetyl, a high value product that can be extensively used as a food ingredient, could be produced from the non-enzymatic oxidative decarboxylation of α-acetolactate during 2,3-butanediol fermentation. In this study, the 2,3-butanediol biosynthetic pathway in Enterobacter cloacae subsp. dissolvens strain SDM, a good candidate for microbial 2,3-butanediol production, was reconstructed for diacetyl production. To enhance the accumulation of the precursor of diacetyl, the α-acetolactate decarboxylase encoding gene (budA) was knocked out in strain SDM. Subsequently, the two diacetyl reductases DR-I (gdh) and DR-II (budC) encoding genes were inactivated in strain SDM individually or in combination to decrease the reduction of diacetyl. Although the engineered strain E. cloacae SDM (ΔbudAΔbudC) was found to have a good ability for diacetyl production, more α-acetolactate than diacetyl was produced simultaneously. In order to enhance the nonenzymatic oxidative decarboxylation of α-acetolactate to diacetyl, 20 mM Fe3+ was added to the fermentation broth at the optimal time. In the end, by using the metabolically engineered strain E. cloacae SDM (ΔbudAΔbudC), diacetyl at a concentration of 1.45 g/L was obtained with a high productivity (0.13 g/(L·h)). The method developed here may be a promising process for biotechnological production of diacetyl. PMID:25761989

  4. Towards kinetic modeling of genome-scale metabolic networks without sacrificing stoichiometric, thermodynamic and physiological constraints.

    PubMed

    Chakrabarti, Anirikh; Miskovic, Ljubisa; Soh, Keng Cher; Hatzimanikatis, Vassily

    2013-09-01

    Mathematical modeling is an essential tool for the comprehensive understanding of cell metabolism and its interactions with the environmental and process conditions. Recent developments in the construction and analysis of stoichiometric models made it possible to define limits on steady-state metabolic behavior using flux balance analysis. However, detailed information on enzyme kinetics and enzyme regulation is needed to formulate kinetic models that can accurately capture the dynamic metabolic responses. The use of mechanistic enzyme kinetics is a difficult task due to uncertainty in the kinetic properties of enzymes. Therefore, the majority of recent works considered only mass action kinetics for reactions in metabolic networks. Herein, we applied the optimization and risk analysis of complex living entities (ORACLE) framework and constructed a large-scale mechanistic kinetic model of optimally grown Escherichia coli. We investigated the complex interplay between stoichiometry, thermodynamics, and kinetics in determining the flexibility and capabilities of metabolism. Our results indicate that enzyme saturation is a necessary consideration in modeling metabolic networks and it extends the feasible ranges of metabolic fluxes and metabolite concentrations. Our results further suggest that enzymes in metabolic networks have evolved to function at different saturation states to ensure greater flexibility and robustness of cellular metabolism.

  5. Slow swimming, fast strikes: effects of feeding behavior on scaling of anaerobic metabolism in epipelagic squid.

    PubMed

    Trueblood, Lloyd A; Seibel, Brad A

    2014-08-01

    Many pelagic fishes engage prey at high speeds supported by high metabolic rates and anaerobic metabolic capacity. Epipelagic squids are reported to have among the highest metabolic rates in the oceans as a result of demanding foraging strategies and the use of jet propulsion, which is inherently inefficient. This study examined enzymatic proxies of anaerobic metabolism in two species of pelagic squid, Dosidicus gigas and Doryteuthis pealeii (Lesueur 1821), over a size range of six orders of magnitude. We hypothesized that activity of the anaerobically poised enzymes would be high and increase with size as in ecologically similar fishes. In contrast, we demonstrate that anaerobic metabolic capacity in these organisms scales negatively with body mass. We explored several cephalopod-specific traits, such as the use of tentacles to capture prey, body morphology and reduced relative prey size of adult squids, that may create a diminished reliance on anaerobically fueled burst activity during prey capture in large animals.

  6. The components of crop productivity: measuring and modeling plant metabolism

    NASA Technical Reports Server (NTRS)

    Bugbee, B.

    1995-01-01

    Several investigators in the CELSS program have demonstrated that crop plants can be remarkably productive in optimal environments where plants are limited only by incident radiation. Radiation use efficiencies of 0.4 to 0.7 g biomass per mol of incident photons have been measured for crops in several laboratories. Some early published values for radiation use efficiency (1 g mol-1) were inflated due to the effect of side lighting. Sealed chambers are the basic research module for crop studies for space. Such chambers allow the measurement of radiation and CO2 fluxes, thus providing values for three determinants of plant growth: radiation absorption, photosynthetic efficiency (quantum yield), and respiration efficiency (carbon use efficiency). Continuous measurement of each of these parameters over the plant life cycle has provided a blueprint for daily growth rates, and is the basis for modeling crop productivity based on component metabolic processes. Much of what has been interpreted as low photosynthetic efficiency is really the result of reduced leaf expansion and poor radiation absorption. Measurements and models of short-term (minutes to hours) and long-term (days to weeks) plant metabolic rates have enormously improved our understanding of plant environment interactions in ground-based growth chambers and are critical to understanding plant responses to the space environment.

  7. EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model.

    PubMed

    Hädicke, Oliver; Klamt, Steffen

    2017-01-03

    Genome-scale metabolic modeling has become an invaluable tool to analyze properties and capabilities of metabolic networks and has been particularly successful for the model organism Escherichia coli. However, for several applications, smaller metabolic (core) models are needed. Using a recently introduced reduction algorithm and the latest E. coli genome-scale reconstruction iJO1366, we derived EColiCore2, a model of the central metabolism of E. coli. EColiCore2 is a subnetwork of iJO1366 and preserves predefined phenotypes including optimal growth on different substrates. The network comprises 486 metabolites and 499 reactions, is accessible for elementary-modes analysis and can, if required, be further compressed to a network with 82 reactions and 54 metabolites having an identical solution space as EColiCore2. A systematic comparison of EColiCore2 with its genome-scale parent model iJO1366 reveals that several key properties (flux ranges, reaction essentialities, production envelopes) of the central metabolism are preserved in EColiCore2 while it neglects redundancies along biosynthetic routes. We also compare calculated metabolic engineering strategies in both models and demonstrate, as a general result, how intervention strategies found in a core model allow the identification of valid strategies in a genome-scale model. Overall, EColiCore2 holds promise to become a reference model of E. coli's central metabolism.

  8. EColiCore2: a reference network model of the central metabolism of Escherichia coli and relationships to its genome-scale parent model

    PubMed Central

    Hädicke, Oliver; Klamt, Steffen

    2017-01-01

    Genome-scale metabolic modeling has become an invaluable tool to analyze properties and capabilities of metabolic networks and has been particularly successful for the model organism Escherichia coli. However, for several applications, smaller metabolic (core) models are needed. Using a recently introduced reduction algorithm and the latest E. coli genome-scale reconstruction iJO1366, we derived EColiCore2, a model of the central metabolism of E. coli. EColiCore2 is a subnetwork of iJO1366 and preserves predefined phenotypes including optimal growth on different substrates. The network comprises 486 metabolites and 499 reactions, is accessible for elementary-modes analysis and can, if required, be further compressed to a network with 82 reactions and 54 metabolites having an identical solution space as EColiCore2. A systematic comparison of EColiCore2 with its genome-scale parent model iJO1366 reveals that several key properties (flux ranges, reaction essentialities, production envelopes) of the central metabolism are preserved in EColiCore2 while it neglects redundancies along biosynthetic routes. We also compare calculated metabolic engineering strategies in both models and demonstrate, as a general result, how intervention strategies found in a core model allow the identification of valid strategies in a genome-scale model. Overall, EColiCore2 holds promise to become a reference model of E. coli’s central metabolism. PMID:28045126

  9. Metabolic Engineering of Escherichia coli for Production of Mixed-Acid Fermentation End Products

    PubMed Central

    Förster, Andreas H.; Gescher, Johannes

    2014-01-01

    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 E. coli toward 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. PMID:25152889

  10. Redirecting reductant flux into hydrogen production via metabolic engineering of fermentative carbon metabolism in a cyanobacterium.

    PubMed

    McNeely, Kelsey; Xu, Yu; Bennette, Nick; Bryant, Donald A; Dismukes, G Charles

    2010-08-01

    Some aquatic microbial oxygenic photoautotrophs (AMOPs) make hydrogen (H(2)), a carbon-neutral, renewable product derived from water, in low yields during autofermentation (anaerobic metabolism) of intracellular carbohydrates previously stored during aerobic photosynthesis. We have constructed a mutant (the ldhA mutant) of the cyanobacterium Synechococcus sp. strain PCC 7002 lacking the enzyme for the NADH-dependent reduction of pyruvate to D-lactate, the major fermentative reductant sink in this AMOP. Both nuclear magnetic resonance (NMR) spectroscopy and liquid chromatography-mass spectrometry (LC-MS) metabolomic methods have shown that autofermentation by the ldhA mutant resulted in no D-lactate production and higher concentrations of excreted acetate, alanine, succinate, and hydrogen (up to 5-fold) compared to that by the wild type. The measured intracellular NAD(P)(H) concentrations demonstrated that the NAD(P)H/NAD(P)(+) ratio increased appreciably during autofermentation in the ldhA strain; we propose this to be the principal source of the observed increase in H(2) production via an NADH-dependent, bidirectional [NiFe] hydrogenase. Despite the elevated NAD(P)H/NAD(P)(+) ratio, no decrease was found in the rate of anaerobic conversion of stored carbohydrates. The measured energy conversion efficiency (ECE) from biomass (as glucose equivalents) converted to hydrogen in the ldhA mutant is 12%. Together with the unimpaired photoautotrophic growth of the ldhA mutant, these attributes reveal that metabolic engineering is an effective strategy to enhance H(2) production in AMOPs without compromising viability.

  11. High Production of 3-Hydroxypropionic Acid in Klebsiella pneumoniae by Systematic Optimization of Glycerol Metabolism

    PubMed Central

    Li, Ying; Wang, Xi; Ge, Xizhen; Tian, Pingfang

    2016-01-01

    3-Hydroxypropionic acid (3-HP) is an important platform chemical proposed by the United States Department of Energy. 3-HP can be converted to a series of bulk chemicals. Biological production of 3-HP has made great progress in recent years. However, low yield of 3-HP restricts its commercialization. In this study, systematic optimization was conducted towards high-yield production of 3-HP in Klebsiella pneumoniae. We first investigated appropriate promoters for the key enzyme (aldehyde dehydrogenase, ALDH) in 3-HP biosynthesis, and found that IPTG-inducible tac promoter enabled overexpression of an endogenous ALDH (PuuC) in K. pneumoniae. We optimized the metabolic flux and found that blocking the synthesis of lactic acid and acetic acid significantly increased the production of 3-HP. Additionally, fermentation conditions were optimized and scaled-up cultivation were investigated. The highest 3-HP titer was observed at 83.8 g/L with a high conversion ratio of 54% on substrate glycerol. Furthermore, a flux distribution model of glycerol metabolism in K. pneumoniae was proposed based on in silico analysis. To our knowledge, this is the highest 3-HP production in K. pneumoniae. This work has significantly advanced biological production of 3-HP from renewable carbon sources. PMID:27230116

  12. Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling.

    PubMed

    Gutierrez, Jahir M; Lewis, Nathan E

    2015-07-01

    Eukaryotic cell lines, including Chinese hamster ovary cells, yeast, and insect cells, are invaluable hosts for the production of many recombinant proteins. With the advent of genomic resources, one can now leverage genome-scale computational modeling of cellular pathways to rationally engineer eukaryotic host cells. Genome-scale models of metabolism include all known biochemical reactions occurring in a specific cell. By describing these mathematically and using tools such as flux balance analysis, the models can simulate cell physiology and provide targets for cell engineering that could lead to enhanced cell viability, titer, and productivity. Here we review examples in which metabolic models in eukaryotic cell cultures have been used to rationally select targets for genetic modification, improve cellular metabolic capabilities, design media supplementation, and interpret high-throughput omics data. As more comprehensive models of metabolism and other cellular processes are developed for eukaryotic cell culture, these will enable further exciting developments in cell line engineering, thus accelerating recombinant protein production and biotechnology in the years to come.

  13. Advances in the integration of transcriptional regulatory information into genome-scale metabolic models.

    PubMed

    Vivek-Ananth, R P; Samal, Areejit

    2016-09-01

    A major goal of systems biology is to build predictive computational models of cellular metabolism. Availability of complete genome sequences and wealth of legacy biochemical information has led to the reconstruction of genome-scale metabolic networks in the last 15 years for several organisms across the three domains of life. Due to paucity of information on kinetic parameters associated with metabolic reactions, the constraint-based modelling approach, flux balance analysis (FBA), has proved to be a vital alternative to investigate the capabilities of reconstructed metabolic networks. In parallel, advent of high-throughput technologies has led to the generation of massive amounts of omics data on transcriptional regulation comprising mRNA transcript levels and genome-wide binding profile of transcriptional regulators. A frontier area in metabolic systems biology has been the development of methods to integrate the available transcriptional regulatory information into constraint-based models of reconstructed metabolic networks in order to increase the predictive capabilities of computational models and understand the regulation of cellular metabolism. Here, we review the existing methods to integrate transcriptional regulatory information into constraint-based models of metabolic networks.

  14. Construction and analysis of a genome-scale metabolic network for Bacillus licheniformis WX-02.

    PubMed

    Guo, Jing; Zhang, Hong; Wang, Cheng; Chang, Ji-Wei; Chen, Ling-Ling

    2016-05-01

    We constructed the genome-scale metabolic network of Bacillus licheniformis (B. licheniformis) WX-02 by combining genomic annotation, high-throughput phenotype microarray (PM) experiments and literature-based metabolic information. The accuracy of the metabolic network was assessed by an OmniLog PM experiment. The final metabolic model iWX1009 contains 1009 genes, 1141 metabolites and 1762 reactions, and the predicted metabolic phenotypes showed an agreement rate of 76.8% with experimental PM data. In addition, key metabolic features such as growth yield, utilization of different substrates and essential genes were identified by flux balance analysis. A total of 195 essential genes were predicted from LB medium, among which 149 were verified with the experimental essential gene set of B. subtilis 168. With the removal of 5 reactions from the network, pathways for poly-γ-glutamic acid (γ-PGA) synthesis were optimized and the γ-PGA yield reached 83.8 mmol/h. Furthermore, the important metabolites and pathways related to γ-PGA synthesis and bacterium growth were comprehensively analyzed. The present study provides valuable clues for exploring the metabolisms and metabolic regulation of γ-PGA synthesis in B. licheniformis WX-02.

  15. Metabolic engineering of Bacillus subtilis for terpenoid production.

    PubMed

    Guan, Zheng; Xue, Dan; Abdallah, Ingy I; Dijkshoorn, Linda; Setroikromo, Rita; Lv, Guiyuan; Quax, Wim J

    2015-11-01

    Terpenoids are the largest group of small-molecule natural products, with more than 60,000 compounds made from isopentenyl diphosphate (IPP) and its isomer dimethylallyl diphosphate (DMAPP). As the most diverse group of small-molecule natural products, terpenoids play an important role in the pharmaceutical, food, and cosmetic industries. For decades, Escherichia coli (E. coli) and Saccharomyces cerevisiae (S. cerevisiae) were extensively studied to biosynthesize terpenoids, because they are both fully amenable to genetic modifications and have vast molecular resources. On the other hand, our literature survey (20 years) revealed that terpenoids are naturally more widespread in Bacillales. In the mid-1990s, an inherent methylerythritol phosphate (MEP) pathway was discovered in Bacillus subtilis (B. subtilis). Since B. subtilis is a generally recognized as safe (GRAS) organism and has long been used for the industrial production of proteins, attempts to biosynthesize terpenoids in this bacterium have aroused much interest in the scientific community. This review discusses metabolic engineering of B. subtilis for terpenoid production, and encountered challenges will be discussed. We will summarize some major advances and outline future directions for exploiting the potential of B. subtilis as a desired "cell factory" to produce terpenoids.

  16. Metabolic engineering of biocatalysts for carboxylic acids production

    PubMed Central

    Liu, Ping; Jarboe, Laura R.

    2012-01-01

    Fermentation of renewable feedstocks by microbes to produce sustainable fuels and chemicals has the potential to replace petrochemical-based production. For example, carboxylic acids produced by microbial fermentation can be used to generate primary building blocks of industrial chemicals by either enzymatic or chemical catalysis. In order to achieve the titer, yield and productivity values required for economically viable processes, the carboxylic acid-producing microbes need to be robust and well-performing. Traditional strain development methods based on mutagenesis have proven useful in the selection of desirable microbial behavior, such as robustness and carboxylic acid production. On the other hand, rationally-based metabolic engineering, like genetic manipulation for pathway design, has becoming increasingly important to this field and has been used for the production of several organic acids, such as succinic acid, malic acid and lactic acid. This review investigates recent works on Saccharomyces cerevisiae and Escherichia coli, as well as the strategies to improve tolerance towards these chemicals. PMID:24688671

  17. Metabolic Engineering of Oleaginous Yeasts for Fatty Alcohol Production

    SciTech Connect

    Wang, Wei; Wei, Hui; Knoshaug, Eric; Van Wychen, Stefanie; Xu, Qi; Himmel, Michael E.; Zhang, Min

    2016-04-25

    To develop pathways for advanced biological upgrading of sugars to hydrocarbons, we are seeking biological approaches to produce high carbon efficiency intermediates amenable to separations and catalytic upgrading to hydrocarbon fuels. In this study, we successfully demonstrated fatty alcohol production by oleaginous yeasts Yarrowia lipolytica and Lipomyces starkeyi by expressing a bacteria-derived fatty acyl-CoA reductase (FAR). Moreover, we find higher extracellular distribution of fatty alcohols produced by FAR-expressing L. starkeyi strain as compared to Y. lipolytica strain, which would benefit the downstream product recovery process. In both oleaginous yeasts, long chain length saturated fatty alcohols were predominant, accounting for more than 85% of the total fatty alcohols produced. To the best of our knowledge, this is the first report of fatty alcohol production in L. starkeyi. Taken together, our work demonstrates that in addition to Y. lipolytica, L. starkeyi can also serve as a platform organism for production of fatty acid-derived biofuels and bioproducts via metabolic engineering. We believe strain and process development both will significantly contribute to our goal of producing scalable and cost-effective fatty alcohols from renewable biomass.

  18. Engineering electron metabolism to increase ethanol production in Clostridium thermocellum

    DOE PAGES

    Lo, Jonathan; Olson, Daniel G.; Murphy, Sean Jean-Loup; ...

    2016-10-28

    Here, the NfnAB (NADH-dependent reduced ferredoxin:NADP+ oxidoreductase) and Rnf (Rhodobacter nitrogen fixation) complexes are thought to catalyze electron transfer between reduced ferredoxin and NAD(P)+. Efficient electron flux is critical for engineering fuel production pathways, but little is known about the relative importance of these enzymes in vivo. In this study we investigate the importance of the NfnAB and Rnf complexes in Clostridium thermocellum for growth on cellobiose and Avicel using gene deletion, enzyme assays, and fermentation product analysis. The NfnAB complex does not seem to play a major role in metabolism, since deletion of nfnAB genes had little effect onmore » the distribution of fermentation products. By contrast, the Rnf complex appears to play an important role in ethanol formation. Deletion of rnf genes resulted in a decrease in ethanol formation. Overexpression of rnf genes resulted in an increase in ethanol production of about 30%, but only in strains where the hydG hydrogenase maturation gene was also deleted.« less

  19. Engineering electron metabolism to increase ethanol production in Clostridium thermocellum

    SciTech Connect

    Lo, Jonathan; Olson, Daniel G.; Murphy, Sean Jean-Loup; Tian, Liang; Hon, Shuen; Lanahan, Anthony; Guss, Adam M.; Lynd, Lee R.

    2016-10-28

    Here, the NfnAB (NADH-dependent reduced ferredoxin:NADP+ oxidoreductase) and Rnf (Rhodobacter nitrogen fixation) complexes are thought to catalyze electron transfer between reduced ferredoxin and NAD(P)+. Efficient electron flux is critical for engineering fuel production pathways, but little is known about the relative importance of these enzymes in vivo. In this study we investigate the importance of the NfnAB and Rnf complexes in Clostridium thermocellum for growth on cellobiose and Avicel using gene deletion, enzyme assays, and fermentation product analysis. The NfnAB complex does not seem to play a major role in metabolism, since deletion of nfnAB genes had little effect on the distribution of fermentation products. By contrast, the Rnf complex appears to play an important role in ethanol formation. Deletion of rnf genes resulted in a decrease in ethanol formation. Overexpression of rnf genes resulted in an increase in ethanol production of about 30%, but only in strains where the hydG hydrogenase maturation gene was also deleted.

  20. Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

    SciTech Connect

    Tartakovsky, Guzel D.; Tartakovsky, Alexandre M.; Scheibe, Timothy D.; Fang, Yilin; Mahadevan, Radhakrishnan; Lovley, Derek R.

    2013-09-07

    Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparisonto prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model under

  1. Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

    NASA Astrophysics Data System (ADS)

    Scheibe, T. D.; Tartakovsky, G.; Tartakovsky, A. M.; Fang, Y.; Mahadevan, R.; Lovley, D. R.

    2012-12-01

    Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model

  2. Pore-scale simulation of microbial growth using a genome-scale metabolic model: Implications for Darcy-scale reactive transport

    NASA Astrophysics Data System (ADS)

    Tartakovsky, G. D.; Tartakovsky, A. M.; Scheibe, T. D.; Fang, Y.; Mahadevan, R.; Lovley, D. R.

    2013-09-01

    Recent advances in microbiology have enabled the quantitative simulation of microbial metabolism and growth based on genome-scale characterization of metabolic pathways and fluxes. We have incorporated a genome-scale metabolic model of the iron-reducing bacteria Geobacter sulfurreducens into a pore-scale simulation of microbial growth based on coupling of iron reduction to oxidation of a soluble electron donor (acetate). In our model, fluid flow and solute transport is governed by a combination of the Navier-Stokes and advection-diffusion-reaction equations. Microbial growth occurs only on the surface of soil grains where solid-phase mineral iron oxides are available. Mass fluxes of chemical species associated with microbial growth are described by the genome-scale microbial model, implemented using a constraint-based metabolic model, and provide the Robin-type boundary condition for the advection-diffusion equation at soil grain surfaces. Conventional models of microbially-mediated subsurface reactions use a lumped reaction model that does not consider individual microbial reaction pathways, and describe reactions rates using empirically-derived rate formulations such as the Monod-type kinetics. We have used our pore-scale model to explore the relationship between genome-scale metabolic models and Monod-type formulations, and to assess the manifestation of pore-scale variability (microenvironments) in terms of apparent Darcy-scale microbial reaction rates. The genome-scale model predicted lower biomass yield, and different stoichiometry for iron consumption, in comparison to prior Monod formulations based on energetics considerations. We were able to fit an equivalent Monod model, by modifying the reaction stoichiometry and biomass yield coefficient, that could effectively match results of the genome-scale simulation of microbial behaviors under excess nutrient conditions, but predictions of the fitted Monod model deviated from those of the genome-scale model

  3. A metabolite-centric view on flux distributions in genome-scale metabolic models

    PubMed Central

    2013-01-01

    Background Genome-scale metabolic models are important tools in systems biology. They permit the in-silico prediction of cellular phenotypes via mathematical optimisation procedures, most importantly flux balance analysis. Current studies on metabolic models mostly consider reaction fluxes in isolation. Based on a recently proposed metabolite-centric approach, we here describe a set of methods that enable the analysis and interpretation of flux distributions in an integrated metabolite-centric view. We demonstrate how this framework can be used for the refinement of genome-scale metabolic models. Results We applied the metabolite-centric view developed here to the most recent metabolic reconstruction of Escherichia coli. By compiling the balance sheets of a small number of currency metabolites, we were able to fully characterise the energy metabolism as predicted by the model and to identify a possibility for model refinement in NADPH metabolism. Selected branch points were examined in detail in order to demonstrate how a metabolite-centric view allows identifying functional roles of metabolites. Fructose 6-phosphate aldolase and the sedoheptulose bisphosphate bypass were identified as enzymatic reactions that can carry high fluxes in the model but are unlikely to exhibit significant activity in vivo. Performing a metabolite essentiality analysis, unconstrained import and export of iron ions could be identified as potentially problematic for the quality of model predictions. Conclusions The system-wide analysis of split ratios and branch points allows a much deeper insight into the metabolic network than reaction-centric analyses. Extending an earlier metabolite-centric approach, the methods introduced here establish an integrated metabolite-centric framework for the interpretation of flux distributions in genome-scale metabolic networks that can complement the classical reaction-centric framework. Analysing fluxes and their metabolic context simultaneously opens

  4. l-Malate Production by Metabolically Engineered Escherichia coli▿ †

    PubMed Central

    Zhang, X.; Wang, X.; Shanmugam, K. T.; Ingram, L. O.

    2011-01-01

    Escherichia coli strains (KJ060 and KJ073) that were previously developed for succinate production have now been modified for malate production. Many unexpected changes were observed during this investigation. The initial strategy of deleting fumarase isoenzymes was ineffective, and succinate continued to accumulate. Surprisingly, a mutation in fumarate reductase alone was sufficient to redirect carbon flow into malate even in the presence of fumarase. Further deletions were needed to inactivate malic enzymes (typically gluconeogenic) and prevent conversion to pyruvate. However, deletion of these genes (sfcA and maeB) resulted in the unexpected accumulation of d-lactate despite the prior deletion of mgsA and ldhA and the absence of apparent lactate dehydrogenase activity. Although the metabolic source of this d-lactate was not identified, lactate accumulation was increased by supplementation with pyruvate and decreased by the deletion of either pyruvate kinase gene (pykA or pykF) to reduce the supply of pyruvate. Many of the gene deletions adversely affected growth and cell yield in minimal medium under anaerobic conditions, and volumetric rates of malate production remained low. The final strain (XZ658) produced 163 mM malate, with a yield of 1.0 mol (mol glucose−1), half of the theoretical maximum. Using a two-stage process (aerobic cell growth and anaerobic malate production), this engineered strain produced 253 mM malate (34 g liter−1) within 72 h, with a higher yield (1.42 mol mol−1) and productivity (0.47 g liter−1 h−1). This malate yield and productivity are equal to or better than those of other known biocatalysts. PMID:21097588

  5. Metabolic engineering of higher plants and algae for isoprenoid production.

    PubMed

    Kempinski, Chase; Jiang, Zuodong; Bell, Stephen; Chappell, Joe

    2015-01-01

    Isoprenoids are a class of compounds derived from the five carbon precursors, dimethylallyl diphosphate, and isopentenyl diphosphate. These molecules present incredible natural chemical diversity, which can be valuable for humans in many aspects such as cosmetics, agriculture, and medicine. However, many terpenoids are only produced in small quantities by their natural hosts and can be difficult to generate synthetically. Therefore, much interest and effort has been directed toward capturing the genetic blueprint for their biochemistry and engineering it into alternative hosts such as plants and algae. These autotrophic organisms are attractive when compared to traditional microbial platforms because of their ability to utilize atmospheric CO2 as a carbon substrate instead of supplied carbon sources like glucose. This chapter will summarize important techniques and strategies for engineering the accumulation of isoprenoid metabolites into higher plants and algae by choosing the correct host, avoiding endogenous regulatory mechanisms, and optimizing potential flux into the target compound. Future endeavors will build on these efforts by fine-tuning product accumulation levels via the vast amount of available "-omic" data and devising metabolic engineering schemes that integrate this into a whole-organism approach. With the development of high-throughput transformation protocols and synthetic biology molecular tools, we have only begun to harness the power and utility of plant and algae metabolic engineering.

  6. Production of superoxide during the metabolism of nitrazepam.

    PubMed

    Rosen, G M; Rauckman, E J; Wilson, R L; Tschanz, C

    1984-10-01

    Nitrazepam is metabolized in both humans and rats to 7-amino-nitrazepam OFFicating that this drug is reduced to a number of metabolic intermediates including several free radical species. When rat-hepatic microsomes are incubated with NADPH in the presence of nitrazepam, its nitro anion free radical was observed under anaerobic conditions. In the presence of oxygen, this free radical reduced oxygen giving nitrazepam and superoxide. 7-Nitroxyl-nitrazepam was produced by the chemical oxidation of 7-amino-nitrazepam using m-chloroperbenzoic acid. Reaction of this reactive free radical with hepatic microsomes led to the covalent spin labelling of microsomal protein. This phenomenon was also observed by the enzymic oxidation of 7-amino-nitrazepam with hepatic microsomes, obtained from a phenobarbital-induced rat, in the presence of a NADPH-generating system. With the generation of superoxide and hydrogen peroxide (arising from the dismutation of superoxide), it is not surprising that nitrazepam-enhanced lipid peroxidation was demonstrated by monitoring the production of lipid peroxyl radicals using spin-trapping techniques.

  7. Multiscale Metabolic Modeling of C4 Plants: Connecting Nonlinear Genome-Scale Models to Leaf-Scale Metabolism in Developing Maize Leaves

    PubMed Central

    Bogart, Eli; Myers, Christopher R.

    2016-01-01

    C4 plants, such as maize, concentrate carbon dioxide in a specialized compartment surrounding the veins of their leaves to improve the efficiency of carbon dioxide assimilation. Nonlinear relationships between carbon dioxide and oxygen levels and reaction rates are key to their physiology but cannot be handled with standard techniques of constraint-based metabolic modeling. We demonstrate that incorporating these relationships as constraints on reaction rates and solving the resulting nonlinear optimization problem yields realistic predictions of the response of C4 systems to environmental and biochemical perturbations. Using a new genome-scale reconstruction of maize metabolism, we build an 18000-reaction, nonlinearly constrained model describing mesophyll and bundle sheath cells in 15 segments of the developing maize leaf, interacting via metabolite exchange, and use RNA-seq and enzyme activity measurements to predict spatial variation in metabolic state by a novel method that optimizes correlation between fluxes and expression data. Though such correlations are known to be weak in general, we suggest that developmental gradients may be particularly suited to the inference of metabolic fluxes from expression data, and we demonstrate that our method predicts fluxes that achieve high correlation with the data, successfully capture the experimentally observed base-to-tip transition between carbon-importing tissue and carbon-exporting tissue, and include a nonzero growth rate, in contrast to prior results from similar methods in other systems. PMID:26990967

  8. Metabolic engineering of Escherichia coli for the production of riboflavin

    PubMed Central

    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

  9. Metabolic model reconstruction and analysis of an artificial microbial ecosystem for vitamin C production.

    PubMed

    Ye, Chao; Zou, Wei; Xu, Nan; Liu, Liming

    2014-07-20

    An artificial microbial ecosystem (AME) consisting of Ketogulonicigenium vulgare and Bacillus megaterium is currently used in a two-step fermentation process for vitamin C production. In order to obtain a comprehensive understanding of the metabolic interactions between the two bacteria, a two-species stoichiometric metabolic model (iWZ-KV-663-BM-1055) consisting of 1718 genes, 1573 metabolites, and 1891 reactions (excluding exchange reactions) was constructed based on separate genome-scale metabolic models (GSMMs) of K. vulgare and B. megaterium. These two compartments (k and b) of iWZ-KV-663-BM-1055 shared 453 reactions and 548 metabolites. Compartment b was richer in subsystems than compartment k. In minimal media with glucose (MG), metabolite exchange between compartments was assessed by constraint-based analysis. Compartment b secreted essential amino acids, nucleic acids, vitamins and cofactors important for K. vulgare growth and biosynthesis of 2-keto-l-gulonic acid (2-KLG). Further research showed that when co-cultured with B. megaterium in l-sorbose-CSLP medium, the growth rate of K. vulgare and 2-KLG production were increased by 111.9% and 29.42%, respectively, under the constraints employed. Our study demonstrated that GSMMs and constraint-based methods can be used to decode the physiological features and inter-species interactions of AMEs used in industrial biotechnology, which will be of benefit for improving regulation and refinement in future industrial processes.

  10. CO2 production as an indicator of biofilm metabolism.

    PubMed

    Kroukamp, Otini; Wolfaardt, Gideon M

    2009-07-01

    Biofilms are important in aquatic nutrient cycling and microbial proliferation. In these structures, nutrients like carbon are channeled into the production of extracellular polymeric substances or cell division; both are vital for microbial survival and propagation. The aim of this study was to assess carbon channeling into cellular or noncellular fractions in biofilms. Growing in tubular reactors, biofilms of our model strain Pseudomonas sp. strain CT07 produced cells to the planktonic phase from the early stages of biofilm development, reaching pseudo steady state with a consistent yield of approximately 10(7) cells.cm(-2).h(-1) within 72 h. Total direct counts and image analysis showed that most of the converted carbon occurred in the noncellular fraction, with the released and sessile cells accounting for <10% and <2% of inflowing carbon, respectively. A CO(2) evolution measurement system (CEMS) that monitored CO(2) in the gas phase was developed to perform a complete carbon balance across the biofilm. The measurement system was able to determine whole-biofilm CO(2) production rates in real time and showed that gaseous CO(2) production accounted for 25% of inflowing carbon. In addition, the CEMS made it possible to measure biofilm response to changing environmental conditions; changes in temperature or inflowing carbon concentration were followed by a rapid response in biofilm metabolism and the establishment of new steady-state conditions.

  11. Metabolic modeling of mixed substrate uptake for polyhydroxyalkanoate (PHA) production.

    PubMed

    Jiang, Yang; Hebly, Marit; Kleerebezem, Robbert; Muyzer, Gerard; van Loosdrecht, Mark C M

    2011-01-01

    Polyhydroxyalkanoate (PHA) production by mixed microbial communities can be established in a two-stage process, consisting of a microbial enrichment step and a PHA accumulation step. In this study, a mathematical model was constructed for evaluating the influence of the carbon substrate composition on both steps of the PHA production process. Experiments were conducted with acetate, propionate, and acetate propionate mixtures. Microbial community analysis demonstrated that despite the changes in substrate composition the dominant microorganism was Plasticicumulans acidivorans in all experiments. A metabolic network model was established to investigate the processes observed. The model based analysis indicated that adaptation of the acetate and propionate uptake rate as a function of acetate and propionate concentrations in the substrate during cultivation occurred. The monomer composition of the PHA produced was found to be directly related to the composition of the substrate. Propionate induced mainly polyhydroxyvalerate (PHV) production whereas only polyhydroxybutyrate (PHB) was produced on acetate. Accumulation experiments with acetate-propionate mixtures yielded PHB/PHV mixtures in ratios directly related to the acetate and propionate uptake rate. The model developed can be used as a useful tool to predict the PHA composition as a function of the substrate composition for acetate-propionate mixtures.

  12. Characterization of proton production and consumption associated with microbial metabolism

    PubMed Central

    2010-01-01

    Background Production or consumption of protons in growth medium during microbial metabolism plays an important role in determining the pH of the environment. Such pH changes resulting from microbial metabolism may influence the geochemical speciation of many elements in subsurface environments. Protons produced or consumed during microbial growth were measured by determining the amount of acid or base added in a 5 L batch bioreactor equipped with pH control for different species including Escherichia coli, Geobacter sulfurreducens, and Geobacter metallireducens. Results An in silico model was used to predict the proton secretion or consumption rates and the results were compared with the data. The data was found to confirm predictions of proton consumption during aerobic growth of E. coli with acetate as the carbon source. However, in contrast to proton consumption observed during aerobic growth of E. coli with acetate, proton secretion was observed during growth of Geobacter species with acetate as the donor and Fe(III) as the extracellular electron acceptor. Conclusions In this study, we have also shown that the final pH of the medium can be either acidic or basic depending on the choice of the electron acceptor for the same electron donor. In all cases, the in silico model could predict qualitatively the proton production/consumption rates obtained from the experimental data. Therefore, measurements of pH equivalents generated or consumed during growth can help characterize the microbial physiology further and can be valuable for optimizing practical applications such as microbial fuel cells, where growth associated pH changes can limit current generation rates. PMID:20089195

  13. Both respiration and photosynthesis determine the scaling of plankton metabolism in the oligotrophic ocean

    PubMed Central

    Serret, Pablo; Robinson, Carol; Aranguren-Gassis, María; García-Martín, Enma Elena; Gist, Niki; Kitidis, Vassilis; Lozano, José; Stephens, John; Harris, Carolyn; Thomas, Rob

    2015-01-01

    Despite its importance to ocean–climate interactions, the metabolic state of the oligotrophic ocean has remained controversial for >15 years. Positions in the debate are that it is either hetero- or autotrophic, which suggests either substantial unaccounted for organic matter inputs, or that all available photosynthesis (P) estimations (including 14C) are biased. Here we show the existence of systematic differences in the metabolic state of the North (heterotrophic) and South (autotrophic) Atlantic oligotrophic gyres, resulting from differences in both P and respiration (R). The oligotrophic ocean is neither auto- nor heterotrophic, but functionally diverse. Our results show that the scaling of plankton metabolism by generalized P:R relationships that has sustained the debate is biased, and indicate that the variability of R, and not only of P, needs to be considered in regional estimations of the ocean's metabolic state. PMID:25908109

  14. Both respiration and photosynthesis determine the scaling of plankton metabolism in the oligotrophic ocean.

    PubMed

    Serret, Pablo; Robinson, Carol; Aranguren-Gassis, María; García-Martín, Enma Elena; Gist, Niki; Kitidis, Vassilis; Lozano, José; Stephens, John; Harris, Carolyn; Thomas, Rob

    2015-04-24

    Despite its importance to ocean-climate interactions, the metabolic state of the oligotrophic ocean has remained controversial for >15 years. Positions in the debate are that it is either hetero- or autotrophic, which suggests either substantial unaccounted for organic matter inputs, or that all available photosynthesis (P) estimations (including (14)C) are biased. Here we show the existence of systematic differences in the metabolic state of the North (heterotrophic) and South (autotrophic) Atlantic oligotrophic gyres, resulting from differences in both P and respiration (R). The oligotrophic ocean is neither auto- nor heterotrophic, but functionally diverse. Our results show that the scaling of plankton metabolism by generalized P:R relationships that has sustained the debate is biased, and indicate that the variability of R, and not only of P, needs to be considered in regional estimations of the ocean's metabolic state.

  15. Synechocystis sp. PCC6803 metabolic models for the enhanced production of hydrogen.

    PubMed

    Montagud, Arnau; Gamermann, Daniel; Fernández de Córdoba, Pedro; Urchueguía, Javier F

    2015-06-01

    In the present economy, difficulties to access energy sources are real drawbacks to maintain our current lifestyle. In fact, increasing interests have been gathered around efficient strategies to use energy sources that do not generate high CO2 titers. Thus, science-funding agencies have invested more resources into research on hydrogen among other biofuels as interesting energy vectors. This article reviews present energy challenges and frames it into the present fuel usage landscape. Different strategies for hydrogen production are explained and evaluated. Focus is on biological hydrogen production; fermentation and photon-fuelled hydrogen production are compared. Mathematical models in biology can be used to assess, explore and design production strategies for industrially relevant metabolites, such as biofuels. We assess the diverse construction and uses of genome-scale metabolic models of cyanobacterium Synechocystis sp. PCC6803 to efficiently obtain biofuels. This organism has been studied as a potential photon-fuelled production platform for its ability to grow from carbon dioxide, water and photons, on simple culture media. Finally, we review studies that propose production strategies to weigh this organism's viability as a biofuel production platform. Overall, the work presented in this review unveils the industrial capabilities of cyanobacterium Synechocystis sp. PCC6803 to evolve interesting metabolites as a clean biofuel production platform.

  16. Thermoneutral zone and scaling of metabolic rate on body mass in small mammals

    NASA Technical Reports Server (NTRS)

    Pace, N.; Rahlmann, D. F.

    1983-01-01

    A 4-species animal model suitable for experimental study of the effect of change in gravitational loading on the scale relationship between metabolic rate and total body mass is used to study the effect of temperature on metabolic rate in six male animals, 8-10 months of age, of each of the four species in the ambient temperature range 20-36 C. The measurements taken permitted partitioning of total body heat output into sensible heat loss by radiation, conduction and convection, and into latent heat loss by evaporation of water from the body surface. It is shown that the condition of thermoneutrality is important for metabolic scale effect studies, and that the thermoneutral zone for the species considered here is a narrow one.

  17. Advanced computational workflow for the multi-scale modeling of the bone metabolic processes.

    PubMed

    Dao, Tien Tuan

    2016-09-16

    Multi-scale modeling of the musculoskeletal system plays an essential role in the deep understanding of complex mechanisms underlying the biological phenomena and processes such as bone metabolic processes. Current multi-scale models suffer from the isolation of sub-models at each anatomical scale. The objective of this present work was to develop a new fully integrated computational workflow for simulating bone metabolic processes at multi-scale levels. Organ-level model employs multi-body dynamics to estimate body boundary and loading conditions from body kinematics. Tissue-level model uses finite element method to estimate the tissue deformation and mechanical loading under body loading conditions. Finally, cell-level model includes bone remodeling mechanism through an agent-based simulation under tissue loading. A case study on the bone remodeling process located on the human jaw was performed and presented. The developed multi-scale model of the human jaw was validated using the literature-based data at each anatomical level. Simulation outcomes fall within the literature-based ranges of values for estimated muscle force, tissue loading and cell dynamics during bone remodeling process. This study opens perspectives for accurately simulating bone metabolic processes using a fully integrated computational workflow leading to a better understanding of the musculoskeletal system function from multiple length scales as well as to provide new informative data for clinical decision support and industrial applications.

  18. Response of white peach scale to metabolic stress disinfection and disinfestation (MSDD) treatment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Metabolic stress disinfection and disinfestation (MSDD) is a postharvest treatment that combines short periods of low pressure (vacuum) and high CO2 with ethanol vapor to control pathogens and arthropod pests on commodities. The system was tested against white peach scale, Pseudaulacaspis pentagona ...

  19. Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm

    SciTech Connect

    Seaver, Samuel M.D.; Bradbury, Louis M.T.; Frelin, Océane; Zarecki, Raphy; Ruppin, Eytan; Hanson, Andrew D.; Henry, Christopher S.

    2015-03-10

    There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and possible generation of unreliable metabolic phenotype predictions. Here we introduce a new evidence-based genome-scale metabolic reconstruction of maize, with significant improvements in the quality of the gene-reaction associations included within our model. We also present a new approach for applying our model to predict active metabolic genes based on transcriptome data. This method includes a minimal set of reactions associated with low expression genes to enable activity of a maximum number of reactions associated with high expression genes. We apply this method to construct an organ-specific model for the maize leaf, and tissue specific models for maize embryo and endosperm cells. We validate our models using fluxomics data for the endosperm and embryo, demonstrating an improved capacity of our models to fit the available fluxomics data. All models are publicly available via the DOE Systems Biology Knowledgebase and PlantSEED, and our new method is generally applicable for analysis transcript profiles from any plant, paving the way for further in silico studies with a wide variety of plant genomes.

  20. Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm.

    PubMed

    Seaver, Samuel M D; Bradbury, Louis M T; Frelin, Océane; Zarecki, Raphy; Ruppin, Eytan; Hanson, Andrew D; Henry, Christopher S

    2015-01-01

    There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and possible generation of unreliable metabolic phenotype predictions. Here we introduce a new evidence-based genome-scale metabolic reconstruction of maize, with significant improvements in the quality of the gene-reaction associations included within our model. We also present a new approach for applying our model to predict active metabolic genes based on transcriptome data. This method includes a minimal set of reactions associated with low expression genes to enable activity of a maximum number of reactions associated with high expression genes. We apply this method to construct an organ-specific model for the maize leaf, and tissue specific models for maize embryo and endosperm cells. We validate our models using fluxomics data for the endosperm and embryo, demonstrating an improved capacity of our models to fit the available fluxomics data. All models are publicly available via the DOE Systems Biology Knowledgebase and PlantSEED, and our new method is generally applicable for analysis transcript profiles from any plant, paving the way for further in silico studies with a wide variety of plant genomes.

  1. Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm

    PubMed Central

    Seaver, Samuel M. D.; Bradbury, Louis M. T.; Frelin, Océane; Zarecki, Raphy; Ruppin, Eytan; Hanson, Andrew D.; Henry, Christopher S.

    2015-01-01

    There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions and possible generation of unreliable metabolic phenotype predictions. Here we introduce a new evidence-based genome-scale metabolic reconstruction of maize, with significant improvements in the quality of the gene-reaction associations included within our model. We also present a new approach for applying our model to predict active metabolic genes based on transcriptome data. This method includes a minimal set of reactions associated with low expression genes to enable activity of a maximum number of reactions associated with high expression genes. We apply this method to construct an organ-specific model for the maize leaf, and tissue specific models for maize embryo and endosperm cells. We validate our models using fluxomics data for the endosperm and embryo, demonstrating an improved capacity of our models to fit the available fluxomics data. All models are publicly available via the DOE Systems Biology Knowledgebase and PlantSEED, and our new method is generally applicable for analysis transcript profiles from any plant, paving the way for further in silico studies with a wide variety of plant genomes. PMID:25806041

  2. Improved evidence-based genome-scale metabolic models for maize leaf, embryo, and endosperm

    DOE PAGES

    Seaver, Samuel M.D.; Bradbury, Louis M.T.; Frelin, Océane; ...

    2015-03-10

    There is a growing demand for genome-scale metabolic reconstructions for plants, fueled by the need to understand the metabolic basis of crop yield and by progress in genome and transcriptome sequencing. Methods are also required to enable the interpretation of plant transcriptome data to study how cellular metabolic activity varies under different growth conditions or even within different organs, tissues, and developmental stages. Such methods depend extensively on the accuracy with which genes have been mapped to the biochemical reactions in the plant metabolic pathways. Errors in these mappings lead to metabolic reconstructions with an inflated number of reactions andmore » possible generation of unreliable metabolic phenotype predictions. Here we introduce a new evidence-based genome-scale metabolic reconstruction of maize, with significant improvements in the quality of the gene-reaction associations included within our model. We also present a new approach for applying our model to predict active metabolic genes based on transcriptome data. This method includes a minimal set of reactions associated with low expression genes to enable activity of a maximum number of reactions associated with high expression genes. We apply this method to construct an organ-specific model for the maize leaf, and tissue specific models for maize embryo and endosperm cells. We validate our models using fluxomics data for the endosperm and embryo, demonstrating an improved capacity of our models to fit the available fluxomics data. All models are publicly available via the DOE Systems Biology Knowledgebase and PlantSEED, and our new method is generally applicable for analysis transcript profiles from any plant, paving the way for further in silico studies with a wide variety of plant genomes.« less

  3. Generation of 2,000 breast cancer metabolic landscapes reveals a poor prognosis group with active serotonin production

    PubMed Central

    Leoncikas, Vytautas; Wu, Huihai; Ward, Lara T.; Kierzek, Andrzej M.; Plant, Nick J.

    2016-01-01

    A major roadblock in the effective treatment of cancers is their heterogeneity, whereby multiple molecular landscapes are classified as a single disease. To explore the contribution of cellular metabolism to cancer heterogeneity, we analyse the Metabric dataset, a landmark genomic and transcriptomic study of 2,000 individual breast tumours, in the context of the human genome-scale metabolic network. We create personalized metabolic landscapes for each tumour by exploring sets of active reactions that satisfy constraints derived from human biochemistry and maximize congruency with the Metabric transcriptome data. Classification of the personalized landscapes derived from 997 tumour samples within the Metabric discovery dataset reveals a novel poor prognosis cluster, reproducible in the 995-sample validation dataset. We experimentally follow mechanistic hypotheses resulting from the computational study and establish that active serotonin production is a major metabolic feature of the poor prognosis group. These data support the reconsideration of concomitant serotonin-specific uptake inhibitors treatment during breast cancer chemotherapy. PMID:26813959

  4. Reconstruction and analysis of the industrial strain Bacillus megaterium WSH002 genome-scale in silico metabolic model.

    PubMed

    Zou, Wei; Zhou, Maoda; Liu, Liming; Chen, Jian

    2013-04-15

    A genome-scale metabolic model of Bacillus megaterium WSH002, an industrial bacterium widely used in the vitamin C industry, was reconstructed on the basis of the genome annotation and data from the literature and biochemical databases. It comprises 1112 reactions, 993 metabolites, and 1055 genes, including 43 new annotated genes. This model was able to predict qualitatively and quantitatively the growth of B. megaterium on a range of carbon and nitrogen sources, and the results agreed well with experimental data. A gene essentiality analysis predicted a core metabolic essential gene set of 57 genes on three different media. Furthermore, constraint-based analysis revealed that B. megaterium WSH002 is capable of producing and exporting several key metabolites, which could promote the growth of Ketogulonicigenium vulgare and 2-keto-l-gulonic acid (2-KLG) production. Here, the model represents a helpful tool for understanding and exploring this important industrial organism.

  5. Metabolic modelling of full-scale enhanced biological phosphorus removal sludge.

    PubMed

    Lanham, Ana B; Oehmen, Adrian; Saunders, Aaron M; Carvalho, Gilda; Nielsen, Per H; Reis, Maria A M

    2014-12-01

    This study investigates, for the first time, the application of metabolic models incorporating polyphosphate accumulating organisms (PAOs) and glycogen accumulating organisms (GAOs) towards describing the biochemical transformations of full-scale enhanced biological phosphorus removal (EBPR) activated sludge from wastewater treatment plants (WWTPs). For this purpose, it was required to modify previous metabolic models applied to lab-scale systems by incorporating the anaerobic utilisation of the TCA cycle and the aerobic maintenance processes based on sequential utilisation of polyhydroxyalkanoates, followed by glycogen and polyphosphate. The abundance of the PAO and GAO populations quantified by fluorescence in situ hybridisation served as the initial conditions of each biomass fraction, whereby the models were able to describe accurately the experimental data. The kinetic rates were found to change among the four different WWTPs studied or even in the same plant during different seasons, either suggesting the presence of additional PAO or GAO organisms, or varying microbial activities for the same organisms. Nevertheless, these variations in kinetic rates were largely found to be proportional to the difference in acetate uptake rate, suggesting a viable means of calibrating the metabolic model. The application of the metabolic model to full-scale sludge also revealed that different Accumulibacter clades likely possess different acetate uptake mechanisms, as a correlation was observed between the energetic requirement for acetate transport across the cell membrane with the diversity of Accumulibacter present. Using the model as a predictive tool, it was shown that lower acetate concentrations in the feed as well as longer aerobic retention times favour the dominance of the TCA metabolism over glycolysis, which could explain why the anaerobic TCA pathway seems to be more relevant in full-scale WWTPs than in lab-scale systems.

  6. Biodiesel: small scale production and quality requirements.

    PubMed

    Van Gerpen, Jon

    2009-01-01

    Biodiesel is produced by reacting vegetable oils or animal fats with alcohol in the presence of an alkaline catalyst. The resulting methyl esters, which are the biodiesel fuel, are separated from the by-product glycerin, and then washed with water and dehydrated to produce fuel that must meet standardized specifications. Degraded oils containing high levels of free fatty acids can also be converted to biodiesel, but pretreatment with acid-catalyzed esterification is required. The resulting fuel is suitable for use as a neat fuel in diesel engines or blended with conventional diesel fuel.

  7. Combining Flux Balance and Energy Balance Analysis for Large-Scale Metabolic Network: Biochemical Circuit Theory for Analysis of Large-Scale Metabolic Networks

    NASA Technical Reports Server (NTRS)

    Beard, Daniel A.; Liang, Shou-Dan; Qian, Hong; Biegel, Bryan (Technical Monitor)

    2001-01-01

    Predicting behavior of large-scale biochemical metabolic networks represents one of the greatest challenges of bioinformatics and computational biology. Approaches, such as flux balance analysis (FBA), that account for the known stoichiometry of the reaction network while avoiding implementation of detailed reaction kinetics are perhaps the most promising tools for the analysis of large complex networks. As a step towards building a complete theory of biochemical circuit analysis, we introduce energy balance analysis (EBA), which compliments the FBA approach by introducing fundamental constraints based on the first and second laws of thermodynamics. Fluxes obtained with EBA are thermodynamically feasible and provide valuable insight into the activation and suppression of biochemical pathways.

  8. High-Throughput Tissue Bioenergetics Analysis Reveals Identical Metabolic Allometric Scaling for Teleost Hearts and Whole Organisms

    PubMed Central

    Jayasundara, Nishad; Kozal, Jordan S.; Arnold, Mariah C.; Chan, Sherine S. L.; Di Giulio, Richard T.

    2015-01-01

    Organismal metabolic rate, a fundamental metric in biology, demonstrates an allometric scaling relationship with body size. Fractal-like vascular distribution networks of biological systems are proposed to underlie metabolic rate allometric scaling laws from individual organisms to cells, mitochondria, and enzymes. Tissue-specific metabolic scaling is notably absent from this paradigm. In the current study, metabolic scaling relationships of hearts and brains with body size were examined by improving on a high-throughput whole-organ oxygen consumption rate (OCR) analysis method in five biomedically and environmentally relevant teleost model species. Tissue-specific metabolic scaling was compared with organismal routine metabolism (RMO2), which was measured using whole organismal respirometry. Basal heart OCR and organismal RMO2 scaled identically with body mass in a species-specific fashion across all five species tested. However, organismal maximum metabolic rates (MMO2) and pharmacologically-induced maximum cardiac metabolic rates in zebrafish Danio rerio did not show a similar relationship with body mass. Brain metabolic rates did not scale with body size. The identical allometric scaling of heart and organismal metabolic rates with body size suggests that hearts, the power generator of an organism’s vascular distribution network, might be crucial in determining teleost metabolic rate scaling under routine conditions. Furthermore, these findings indicate the possibility of measuring heart OCR utilizing the high-throughput approach presented here as a proxy for organismal metabolic rate—a useful metric in characterizing organismal fitness. In addition to heart and brain OCR, the current approach was also used to measure whole liver OCR, partition cardiac mitochondrial bioenergetic parameters using pharmacological agents, and estimate heart and brain glycolytic rates. This high-throughput whole-organ bioenergetic analysis method has important applications in

  9. High-Throughput Tissue Bioenergetics Analysis Reveals Identical Metabolic Allometric Scaling for Teleost Hearts and Whole Organisms.

    PubMed

    Jayasundara, Nishad; Kozal, Jordan S; Arnold, Mariah C; Chan, Sherine S L; Di Giulio, Richard T

    2015-01-01

    Organismal metabolic rate, a fundamental metric in biology, demonstrates an allometric scaling relationship with body size. Fractal-like vascular distribution networks of biological systems are proposed to underlie metabolic rate allometric scaling laws from individual organisms to cells, mitochondria, and enzymes. Tissue-specific metabolic scaling is notably absent from this paradigm. In the current study, metabolic scaling relationships of hearts and brains with body size were examined by improving on a high-throughput whole-organ oxygen consumption rate (OCR) analysis method in five biomedically and environmentally relevant teleost model species. Tissue-specific metabolic scaling was compared with organismal routine metabolism (RMO2), which was measured using whole organismal respirometry. Basal heart OCR and organismal RMO2 scaled identically with body mass in a species-specific fashion across all five species tested. However, organismal maximum metabolic rates (MMO2) and pharmacologically-induced maximum cardiac metabolic rates in zebrafish Danio rerio did not show a similar relationship with body mass. Brain metabolic rates did not scale with body size. The identical allometric scaling of heart and organismal metabolic rates with body size suggests that hearts, the power generator of an organism's vascular distribution network, might be crucial in determining teleost metabolic rate scaling under routine conditions. Furthermore, these findings indicate the possibility of measuring heart OCR utilizing the high-throughput approach presented here as a proxy for organismal metabolic rate-a useful metric in characterizing organismal fitness. In addition to heart and brain OCR, the current approach was also used to measure whole liver OCR, partition cardiac mitochondrial bioenergetic parameters using pharmacological agents, and estimate heart and brain glycolytic rates. This high-throughput whole-organ bioenergetic analysis method has important applications in

  10. Metabolic Engineering and Modeling of Metabolic Pathways to Improve Hydrogen Production by Photosynthetic Bacteria

    SciTech Connect

    Jiao, Y.; Navid, A.

    2014-12-19

    traits act as the biocatalysts of the process designed to both enhance the system efficiency of CO2 fixation and the net hydrogen production rate. Additionally we applied metabolic engineering approaches guided by computational modeling for the chosen model microorganisms to enable efficient hydrogen production.

  11. A Global-Scale Distributed Geomorphologic Product

    NASA Astrophysics Data System (ADS)

    Shen, X.; Hong, Y.; Wang, D.; Vergara, H. J.; Anagnostou, E. N.

    2015-12-01

    In response to the vital role of geomorphological analysis in natural hazards study, geomorphology, distributed hydrology and other related disciplines, we present the first global basin morphometric product of 30 characteristics, 9 archived elementary including stream order, stream number, stream length, basin relief, basin length, basin perimeter, maximal flow length, down valley length and overland flow length, and 21 derivable from these elementary morphometric characteristics. As a distributed product, characteristics of basins discharging to every grid-cell of the global earth surface are computed at 1km resolution strictly following their definitions. We introduce in this paper an efficient framework to reduce the algorithm complexity to O(N), which results in efficiency improvement in the order of 50-100 times the traditional way. We find that, spatially, 1) the relief ratio reaches its peak values along both sides of the ridges; 2) the fitness ratio of the main stream value often has a sharp decrease at the joint of large tributaries; statistically, 3) only the basin relief exhibits strong discrepancy of distribution among different continents while all others show unexpected homogeneity of distribution in spite of the size (number of cells) difference of continents; 4) the distributions of the main flow length/down valley length and basin length/basin perimeter resemble each other respectively; and 5) the distributions of the two pairs are quite different thus neither the main flow length nor down valley length should be used as substitutions of the basin length as done by some previous studies.

  12. D-lactic acid production by metabolically engineered Saccharomyces cerevisiae.

    PubMed

    Ishida, Nobuhiro; Suzuki, Tomiko; Tokuhiro, Kenro; Nagamori, Eiji; Onishi, Toru; Saitoh, Satoshi; Kitamoto, Katsuhiko; Takahashi, Haruo

    2006-02-01

    Poly D-lactic acid is an important polymer because it improves the thermostability of poly L-lactic acid by the stereo complex formation. We constructed a metabolically engineered Saccharomyces cerevisiae that produces D-lactic acid efficiently. In this recombinant, the coding region of pyruvate decarboxylase 1 (PDC1) was completely deleted, and two copies of the D-lactate dehydrogenase (D-LDH) gene from Leuconostoc mesenteroides subsp. mesenteroides strain NBRC3426 were introduced into the genome. The D-lactate production reached 61.5 g/l, the amount of glucose being transformed into D-lactic acid being 61.2% under neutralizing conditions. Additionally, the yield of free D-lactic acid was also shown to be 53.0% under non-neutralizing conditions. It was confirmed that D-lactic acid of extremely high optical purity of 99.9% or higher. Our finding obtained the possibility of a new approach for pure d-lactic acid production without a neutralizing process compared with other techniques involving lactic acid bacteria and transgenic Escherichia coli.

  13. Production of 2,3-butanediol in Saccharomyces cerevisiae by in silico aided metabolic engineering

    PubMed Central

    2012-01-01

    Background 2,3-Butanediol is a chemical compound of increasing interest due to its wide applications. It can be synthesized via mixed acid fermentation of pathogenic bacteria such as Enterobacter aerogenes and Klebsiella oxytoca. The non-pathogenic Saccharomyces cerevisiae possesses three different 2,3-butanediol biosynthetic pathways, but produces minute amount of 2,3-butanediol. Hence, we attempted to engineer S. cerevisiae strain to enhance 2,3-butanediol production. Results We first identified gene deletion strategy by performing in silico genome-scale metabolic analysis. Based on the best in silico strategy, in which disruption of alcohol dehydrogenase (ADH) pathway is required, we then constructed gene deletion mutant strains and performed batch cultivation of the strains. Deletion of three ADH genes, ADH1, ADH3 and ADH5, increased 2,3-butanediol production by 55-fold under microaerobic condition. However, overproduction of glycerol was observed in this triple deletion strain. Additional rational design to reduce glycerol production by GPD2 deletion altered the carbon fluxes back to ethanol and significantly reduced 2,3-butanediol production. Deletion of ALD6 reduced acetate production in strains lacking major ADH isozymes, but it did not favor 2,3-butanediol production. Finally, we introduced 2,3-butanediol biosynthetic pathway from Bacillus subtilis and E. aerogenes to the engineered strain and successfully increased titer and yield. Highest 2,3-butanediol titer (2.29 g·l-1) and yield (0.113 g·g-1) were achieved by Δadh1 Δadh3 Δadh5 strain under anaerobic condition. Conclusions With the aid of in silico metabolic engineering, we have successfully designed and constructed S. cerevisiae strains with improved 2,3-butanediol production. PMID:22640729

  14. Association of Lipid Accumulation Product with Cardio-Metabolic Risk Factors in Postmenopausal Women.

    PubMed

    Namazi Shabestari, Alireza; Asadi, Mojgan; Jouyandeh, Zahra; Qorbani, Mostafa; Kelishadi, Roya

    2016-06-01

    The lipid accumulation product is a novel, safe and inexpensive index of central lipid over accumulation based on waist circumference and fasting concentration of circulating triglycerides. This study was designed to investigate the ability of lipid accumulation product to predict Cardio-metabolic risk factors in postmenopausal women. In this Cross-sectional study, 264 postmenopausal women by using convenience sampling method were selected from menopause clinic in Tehran. Cardio-metabolic risk factors were measured, and lipid accumulation product (waist-58×triglycerides [nmol/L]) was calculated. Optimal cut-off point of lipid accumulation product for predicting metabolic syndrome was estimated by ROC (Receiver-operating characteristic) curve analysis. Metabolic syndrome was diagnosed in 41.2% of subjects. Optimal cut-off point of lipid accumulation product for predicting metabolic syndrome was 47.63 (sensitivity:75%; specificity:77.9%). High lipid accumulation product increases risk of all Cardio-metabolic risk factors except overweight, high Total Cholesterol, high Low Density Lipoprotein Cholesterol and high Fasting Blood Sugar in postmenopausal women. Our findings show that lipid accumulation product is associated with metabolic syndrome and some Cardio-metabolic risk factors Also lipid accumulation product may have been a useful tool for predicting cardiovascular disease and metabolic syndrome risk in postmenopausal women.

  15. Expanded bed absorption from laboratory to production scale

    SciTech Connect

    Johansson, S.; Akervall, A.; Hagel, L.

    1995-12-01

    Expanded bed adsorption is a new technique using stable homogeneous fluidization for initial recovery of a product from crude fermentation broth. The technique makes it possible to combine clarification, concentration and product capture in one unit operation. This study shows a 144 fold scale-up from laboratory to production scale. The column sizes used are 50 mm I.D. and 600 mm I.D. respectively. Residence time distribution (RTD), the response from an injected step, was used to evaluate the scale up. This reflects the hydrodynamics of the system. Adsorption kinetics was determined from a breakthrough curve of bovine serum albumine and the binding capacity was calculated. The results show that expanded bed adsorption is scaleable from laboratory to production scale with retained properties.

  16. GSMN-TB: a web-based genome-scale network model of Mycobacterium tuberculosis metabolism

    PubMed Central

    Beste, Dany JV; Hooper, Tracy; Stewart, Graham; Bonde, Bhushan; Avignone-Rossa, Claudio; Bushell, Michael E; Wheeler, Paul; Klamt, Steffen; Kierzek, Andrzej M; McFadden, Johnjoe

    2007-01-01

    Background An impediment to the rational development of novel drugs against tuberculosis (TB) is a general paucity of knowledge concerning the metabolism of Mycobacterium tuberculosis, particularly during infection. Constraint-based modeling provides a novel approach to investigating microbial metabolism but has not yet been applied to genome-scale modeling of M. tuberculosis. Results GSMN-TB, a genome-scale metabolic model of M. tuberculosis, was constructed, consisting of 849 unique reactions and 739 metabolites, and involving 726 genes. The model was calibrated by growing Mycobacterium bovis bacille Calmette Guérin in continuous culture and steady-state growth parameters were measured. Flux balance analysis was used to calculate substrate consumption rates, which were shown to correspond closely to experimentally determined values. Predictions of gene essentiality were also made by flux balance analysis simulation and were compared with global mutagenesis data for M. tuberculosis grown in vitro. A prediction accuracy of 78% was achieved. Known drug targets were predicted to be essential by the model. The model demonstrated a potential role for the enzyme isocitrate lyase during the slow growth of mycobacteria, and this hypothesis was experimentally verified. An interactive web-based version of the model is available. Conclusion The GSMN-TB model successfully simulated many of the growth properties of M. tuberculosis. The model provides a means to examine the metabolic flexibility of bacteria and predict the phenotype of mutants, and it highlights previously unexplored features of M. tuberculosis metabolism. PMID:17521419

  17. Genome-scale reconstruction of metabolic networks of Lactobacillus casei ATCC 334 and 12A.

    PubMed

    Vinay-Lara, Elena; Hamilton, Joshua J; Stahl, Buffy; Broadbent, Jeff R; Reed, Jennifer L; Steele, James L

    2014-01-01

    Lactobacillus casei strains are widely used in industry and the utility of this organism in these industrial applications is strain dependent. Hence, tools capable of predicting strain specific phenotypes would have utility in the selection of strains for specific industrial processes. Genome-scale metabolic models can be utilized to better understand genotype-phenotype relationships and to compare different organisms. To assist in the selection and development of strains with enhanced industrial utility, genome-scale models for L. casei ATCC 334, a well characterized strain, and strain 12A, a corn silage isolate, were constructed. Draft models were generated from RAST genome annotations using the Model SEED database and refined by evaluating ATP generating cycles, mass-and-charge-balances of reactions, and growth phenotypes. After the validation process was finished, we compared the metabolic networks of these two strains to identify metabolic, genetic and ortholog differences that may lead to different phenotypic behaviors. We conclude that the metabolic capabilities of the two networks are highly similar. The L. casei ATCC 334 model accounts for 1,040 reactions, 959 metabolites and 548 genes, while the L. casei 12A model accounts for 1,076 reactions, 979 metabolites and 640 genes. The developed L. casei ATCC 334 and 12A metabolic models will enable better understanding of the physiology of these organisms and be valuable tools in the development and selection of strains with enhanced utility in a variety of industrial applications.

  18. Genome –Scale Reconstruction of Metabolic Networks of Lactobacillus casei ATCC 334 and 12A

    PubMed Central

    Vinay-Lara, Elena; Hamilton, Joshua J.; Stahl, Buffy; Broadbent, Jeff R.; Reed, Jennifer L.; Steele, James L.

    2014-01-01

    Lactobacillus casei strains are widely used in industry and the utility of this organism in these industrial applications is strain dependent. Hence, tools capable of predicting strain specific phenotypes would have utility in the selection of strains for specific industrial processes. Genome-scale metabolic models can be utilized to better understand genotype-phenotype relationships and to compare different organisms. To assist in the selection and development of strains with enhanced industrial utility, genome-scale models for L. casei ATCC 334, a well characterized strain, and strain 12A, a corn silage isolate, were constructed. Draft models were generated from RAST genome annotations using the Model SEED database and refined by evaluating ATP generating cycles, mass-and-charge-balances of reactions, and growth phenotypes. After the validation process was finished, we compared the metabolic networks of these two strains to identify metabolic, genetic and ortholog differences that may lead to different phenotypic behaviors. We conclude that the metabolic capabilities of the two networks are highly similar. The L. casei ATCC 334 model accounts for 1,040 reactions, 959 metabolites and 548 genes, while the L. casei 12A model accounts for 1,076 reactions, 979 metabolites and 640 genes. The developed L. casei ATCC 334 and 12A metabolic models will enable better understanding of the physiology of these organisms and be valuable tools in the development and selection of strains with enhanced utility in a variety of industrial applications. PMID:25365062

  19. Metabolic versatility in full-scale wastewater treatment plants performing enhanced biological phosphorus removal.

    PubMed

    Lanham, Ana B; Oehmen, Adrian; Saunders, Aaron M; Carvalho, Gilda; Nielsen, Per H; Reis, Maria A M

    2013-12-01

    This study analysed the enhanced biological phosphorus removal (EBPR) microbial community and metabolic performance of five full-scale EBPR systems by using fluorescence in situ hybridisation combined with off-line batch tests fed with acetate under anaerobic-aerobic conditions. The phosphorus accumulating organisms (PAOs) in all systems were stable and showed little variability between each plant, while glycogen accumulating organisms (GAOs) were present in two of the plants. The metabolic activity of each sludge showed the frequent involvement of the anaerobic tricarboxylic acid cycle (TCA) in PAO metabolism for the anaerobic generation of reducing equivalents, in addition to the more frequently reported glycolysis pathway. Metabolic variability in the use of the two pathways was also observed, between different systems and in the same system over time. The metabolic dynamics was linked to the availability of glycogen, where a higher utilisation of the glycolysis pathway was observed in the two systems employing side-stream hydrolysis, and the TCA cycle was more active in the A(2)O systems. Full-scale plants that showed higher glycolysis activity also exhibited superior P removal performance, suggesting that promotion of the glycolysis pathway over the TCA cycle could be beneficial towards the optimisation of EBPR systems.

  20. Genome-scale metabolic modeling of a clostridial co-culture for consolidated bioprocessing.

    PubMed

    Salimi, Fahimeh; Zhuang, Kai; Mahadevan, Radhakrishnan

    2010-07-01

    An alternative consolidated bioprocessing approach is the use of a co-culture containing cellulolytic and solventogenic clostridia. It has been demonstrated that the rate of cellulose utilization in the co-culture of Clostridium acetobutylicum and Clostridium cellulolyticum is improved compared to the mono-culture of C. cellulolyticum, suggesting the presence of syntrophy between these two species. However, the metabolic interactions in the co-culture are not well understood. To understand the metabolic interactions in the co-culture, we developed a genome-scale metabolic model of C. cellulolyticum comprising of 431 genes, 621 reactions, and 603 metabolites. The C. cellulolyticum model can successfully predict the chemostat growth and byproduct secretion with cellulose as the substrate. However, a growth arrest phenomenon, which occurs in batch cultures of C. cellulolyticum at cellulose concentrations higher than 6.7 g/L, cannot be predicted by dynamic flux balance analysis due to the lack of understanding of the underlying mechanism. These genome-scale metabolic models of the pure cultures have also been integrated using a community modeling framework to develop a dynamic model of metabolic interactions in the co-culture. Co-culture simulations suggest that cellobiose inhibition cannot be the main factor that is responsible for improved cellulose utilization relative to mono-culture of C. cellulolyticum.

  1. Mathematical modeling of unicellular microalgae and cyanobacteria metabolism for biofuel production.

    PubMed

    Baroukh, Caroline; Muñoz-Tamayo, Rafael; Bernard, Olivier; Steyer, Jean-Philippe

    2015-06-01

    The conversion of microalgae lipids and cyanobacteria carbohydrates into biofuels appears to be a promising source of renewable energy. This requires a thorough understanding of their carbon metabolism, supported by mathematical models, in order to optimize biofuel production. However, unlike heterotrophic microorganisms that utilize the same substrate as sources of energy and carbon, photoautotrophic microorganisms require light for energy and CO2 as carbon source. Furthermore, they are submitted to permanent fluctuating light environments due to outdoor cultivation or mixing inducing a flashing effect. Although, modeling these nonstandard organisms is a major challenge for which classical tools are often inadequate, this step remains a prerequisite towards efficient optimization of outdoor biofuel production at an industrial scale.

  2. A general model for metabolic scaling in self-similar asymmetric networks

    PubMed Central

    Savage, Van M.; Enquist, Brian J.

    2017-01-01

    How a particular attribute of an organism changes or scales with its body size is known as an allometry. Biological allometries, such as metabolic scaling, have been hypothesized to result from selection to maximize how vascular networks fill space yet minimize internal transport distances and resistances. The West, Brown, Enquist (WBE) model argues that these two principles (space-filling and energy minimization) are (i) general principles underlying the evolution of the diversity of biological networks across plants and animals and (ii) can be used to predict how the resulting geometry of biological networks then governs their allometric scaling. Perhaps the most central biological allometry is how metabolic rate scales with body size. A core assumption of the WBE model is that networks are symmetric with respect to their geometric properties. That is, any two given branches within the same generation in the network are assumed to have identical lengths and radii. However, biological networks are rarely if ever symmetric. An open question is: Does incorporating asymmetric branching change or influence the predictions of the WBE model? We derive a general network model that relaxes the symmetric assumption and define two classes of asymmetrically bifurcating networks. We show that asymmetric branching can be incorporated into the WBE model. This asymmetric version of the WBE model results in several theoretical predictions for the structure, physiology, and metabolism of organisms, specifically in the case for the cardiovascular system. We show how network asymmetry can now be incorporated in the many allometric scaling relationships via total network volume. Most importantly, we show that the 3/4 metabolic scaling exponent from Kleiber’s Law can still be attained within many asymmetric networks. PMID:28319153

  3. A general model for metabolic scaling in self-similar asymmetric networks.

    PubMed

    Brummer, Alexander Byers; Savage, Van M; Enquist, Brian J

    2017-03-01

    How a particular attribute of an organism changes or scales with its body size is known as an allometry. Biological allometries, such as metabolic scaling, have been hypothesized to result from selection to maximize how vascular networks fill space yet minimize internal transport distances and resistances. The West, Brown, Enquist (WBE) model argues that these two principles (space-filling and energy minimization) are (i) general principles underlying the evolution of the diversity of biological networks across plants and animals and (ii) can be used to predict how the resulting geometry of biological networks then governs their allometric scaling. Perhaps the most central biological allometry is how metabolic rate scales with body size. A core assumption of the WBE model is that networks are symmetric with respect to their geometric properties. That is, any two given branches within the same generation in the network are assumed to have identical lengths and radii. However, biological networks are rarely if ever symmetric. An open question is: Does incorporating asymmetric branching change or influence the predictions of the WBE model? We derive a general network model that relaxes the symmetric assumption and define two classes of asymmetrically bifurcating networks. We show that asymmetric branching can be incorporated into the WBE model. This asymmetric version of the WBE model results in several theoretical predictions for the structure, physiology, and metabolism of organisms, specifically in the case for the cardiovascular system. We show how network asymmetry can now be incorporated in the many allometric scaling relationships via total network volume. Most importantly, we show that the 3/4 metabolic scaling exponent from Kleiber's Law can still be attained within many asymmetric networks.

  4. Intraspecific scaling in frog calls: the interplay of temperature, body size and metabolic condition.

    PubMed

    Ziegler, Lucia; Arim, Matías; Bozinovic, Francisco

    2016-07-01

    Understanding physiological and environmental determinants of strategies of reproductive allocation is a pivotal aim in biology. Because of their high metabolic cost, properties of sexual acoustic signals may correlate with body size, temperature, and an individual's energetic state. A quantitative theory of acoustic communication, based on the metabolic scaling with temperature and mass, was recently proposed, adding to the well-reported empirical patterns. It provides quantitative predictions for frequencies, call rate, and durations. Here, we analysed the mass, temperature, and body condition scaling of spectral and temporal attributes of the advertisement call of the treefrog Hypsiboas pulchellus. Mass dependence of call frequency followed metabolic expectations (f~M (-0.25), where f is frequency and M is mass) although non-metabolic allometry could also account for the observed pattern. Temporal variables scaled inversely with mass contradicting metabolic expectations (d~M (0.25), where d is duration), supporting instead empirical patterns reported to date. Temperature was positively associated with call rate and negatively with temporal variables, which is congruent with metabolic predictions. We found no significant association between temperature and frequencies, adding to the bulk of empirical evidence. Finally, a result of particular relevance was that body condition consistently determined call characteristics, in interaction with temperature or mass. Our intraspecific study highlights that even if proximate determinants of call variability are rather well understood, the mechanisms through which they operate are proving to be more complex than previously thought. The determinants of call characteristics emerge as a key topic of research in behavioural and physiological biology, with several clear points under debate which need to be analysed on theoretical and empirical grounds.

  5. Transcriptional Profiling of Hydrogen Production Metabolism of Rhodobacter capsulatus under Temperature Stress by Microarray Analysis

    PubMed Central

    Gürgan, Muazzez; Afşar Erkal, Nilüfer; Özgür, Ebru; Gündüz, Ufuk; Eroglu, Inci; Yücel, Meral

    2015-01-01

    Biohydrogen is a clean and renewable form of hydrogen, which can be produced by photosynthetic bacteria in outdoor large-scale photobioreactors using sunlight. In this study, the transcriptional response of Rhodobacter capsulatus to cold (4 °C) and heat (42 °C) stress was studied using microarrays. Bacteria were grown in 30/2 acetate/glutamate medium at 30 °C for 48 h under continuous illumination. Then, cold and heat stresses were applied for two and six hours. Growth and hydrogen production were impaired under both stress conditions. Microarray chips for R. capsulatus were custom designed by Affymetrix (GeneChip®. TR_RCH2a520699F). The numbers of significantly changed genes were 328 and 293 out of 3685 genes under cold and heat stress, respectively. Our results indicate that temperature stress greatly affects the hydrogen production metabolisms of R. capsulatus. Specifically, the expression of genes that participate in nitrogen metabolism, photosynthesis and the electron transport system were induced by cold stress, while decreased by heat stress. Heat stress also resulted in down regulation of genes related to cell envelope, transporter and binding proteins. Transcriptome analysis and physiological results were consistent with each other. The results presented here may aid clarification of the genetic mechanisms for hydrogen production in purple non-sulfur (PNS) bacteria under temperature stress. PMID:26086826

  6. Pantograph: A template-based method for genome-scale metabolic model reconstruction.

    PubMed

    Loira, Nicolas; Zhukova, Anna; Sherman, David James

    2015-04-01

    Genome-scale metabolic models are a powerful tool to study the inner workings of biological systems and to guide applications. The advent of cheap sequencing has brought the opportunity to create metabolic maps of biotechnologically interesting organisms. While this drives the development of new methods and automatic tools, network reconstruction remains a time-consuming process where extensive manual curation is required. This curation introduces specific knowledge about the modeled organism, either explicitly in the form of molecular processes, or indirectly in the form of annotations of the model elements. Paradoxically, this knowledge is usually lost when reconstruction of a different organism is started. We introduce the Pantograph method for metabolic model reconstruction. This method combines a template reaction knowledge base, orthology mappings between two organisms, and experimental phenotypic evidence, to build a genome-scale metabolic model for a target organism. Our method infers implicit knowledge from annotations in the template, and rewrites these inferences to include them in the resulting model of the target organism. The generated model is well suited for manual curation. Scripts for evaluating the model with respect to experimental data are automatically generated, to aid curators in iterative improvement. We present an implementation of the Pantograph method, as a toolbox for genome-scale model reconstruction, curation and validation. This open source package can be obtained from: http://pathtastic.gforge.inria.fr.

  7. Metabolic engineering of Arabidopsis for butanetriol production using bacterial genes.

    PubMed

    Abdel-Ghany, Salah E; Day, Irene; Heuberger, Adam L; Broeckling, Corey D; Reddy, Anireddy S N

    2013-11-01

    1,2,4-butanetriol (butanetriol) is a useful precursor for the synthesis of the energetic material butanetriol trinitrate and several pharmaceutical compounds. Bacterial synthesis of butanetriol from xylose or arabinose takes place in a pathway that requires four enzymes. To produce butanetriol in plants by expressing bacterial enzymes, we cloned native bacterial or codon optimized synthetic genes under different promoters into a binary vector and stably transformed Arabidopsis plants. Transgenic lines expressing introduced genes were analyzed for the production of butanetriol using gas chromatography coupled to mass spectrometry (GC-MS). Soil-grown transgenic plants expressing these genes produced up to 20 µg/g of butanetriol. To test if an exogenous supply of pentose sugar precursors would enhance the butanetriol level, transgenic plants were grown in a medium supplemented with either xylose or arabinose and the amount of butanetriol was quantified. Plants expressing synthetic genes in the arabinose pathway showed up to a forty-fold increase in butanetriol levels after arabinose was added to the medium. Transgenic plants expressing either bacterial or synthetic xylose pathways, or the arabinose pathway showed toxicity symptoms when xylose or arabinose was added to the medium, suggesting that a by-product in the pathway or butanetriol affected plant growth. Furthermore, the metabolite profile of plants expressing arabinose and xylose pathways was altered. Our results demonstrate that bacterial pathways that produce butanetriol can be engineered into plants to produce this chemical. This proof-of-concept study for phytoproduction of butanetriol paves the way to further manipulate metabolic pathways in plants to enhance the level of butanetriol production.

  8. A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks.

    PubMed

    Merlet, Benjamin; Paulhe, Nils; Vinson, Florence; Frainay, Clément; Chazalviel, Maxime; Poupin, Nathalie; Gloaguen, Yoann; Giacomoni, Franck; Jourdan, Fabien

    2016-01-01

    This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc) and flat file formats (SBML and Matlab files). We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics) and Glasgow Polyomics (GP) on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks. In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks. In order to achieve this goal, we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities.

  9. A Computational Solution to Automatically Map Metabolite Libraries in the Context of Genome Scale Metabolic Networks

    PubMed Central

    Merlet, Benjamin; Paulhe, Nils; Vinson, Florence; Frainay, Clément; Chazalviel, Maxime; Poupin, Nathalie; Gloaguen, Yoann; Giacomoni, Franck; Jourdan, Fabien

    2016-01-01

    This article describes a generic programmatic method for mapping chemical compound libraries on organism-specific metabolic networks from various databases (KEGG, BioCyc) and flat file formats (SBML and Matlab files). We show how this pipeline was successfully applied to decipher the coverage of chemical libraries set up by two metabolomics facilities MetaboHub (French National infrastructure for metabolomics and fluxomics) and Glasgow Polyomics (GP) on the metabolic networks available in the MetExplore web server. The present generic protocol is designed to formalize and reduce the volume of information transfer between the library and the network database. Matching of metabolites between libraries and metabolic networks is based on InChIs or InChIKeys and therefore requires that these identifiers are specified in both libraries and networks. In addition to providing covering statistics, this pipeline also allows the visualization of mapping results in the context of metabolic networks. In order to achieve this goal, we tackled issues on programmatic interaction between two servers, improvement of metabolite annotation in metabolic networks and automatic loading of a mapping in genome scale metabolic network analysis tool MetExplore. It is important to note that this mapping can also be performed on a single or a selection of organisms of interest and is thus not limited to large facilities. PMID:26909353

  10. Debottlenecking recombinant protein production in Bacillus megaterium under large-scale conditions--targeted precursor feeding designed from metabolomics.

    PubMed

    Korneli, Claudia; Bolten, Christoph Josef; Godard, Thibault; Franco-Lara, Ezequiel; Wittmann, Christoph

    2012-06-01

    In the present work the impact of large production scale was investigated for Bacillus megaterium expressing green fluorescent protein (GFP). Specifically designed scale-down studies, mimicking the intermittent and continuous nutrient supply of large- and small-scale processes, were carried out for this purpose. The recombinant strain revealed a 40% reduced GFP yield for the large-scale conditions. In line with extended carbon loss via formation of acetate and carbon dioxide, this indicated obvious limitations in the underlying metabolism of B. megaterium under the large-scale conditions. Quantitative analysis of intracellular amino acids via validated fast filtration protocols revealed that their level strongly differed between the two scenarios. During cultivation in large-scale set-up, the availability of most amino acids, serving as key building blocks of the recombinant protein, was substantially reduced. This was most pronounced for tryptophan, aspartate, histidine, glutamine, and lysine. In contrast alanine was increased, probably related to a bottleneck at the level of pyruvate which also triggered acetate overflow metabolism. The pre-cursor quantifications could then be exploited to verify the presumed bottlenecks and improve recombinant protein production under large-scale conditions. Addition of only 5 mM tryptophan, aspartate, histidine, glutamine, and lysine to the feed solution increased the GFP yield by 100%. This rational concept of driving the lab scale productivity of recombinant microorganisms under suboptimal feeding conditions emulating large scale can easily be extended to other processes and production hosts.

  11. Advanced glycation end products: possible link between metabolic syndrome and periodontal diseases.

    PubMed

    Pietropaoli, D; Monaco, A; Del Pinto, R; Cifone, M G; Marzo, G; Giannoni, M

    2012-01-01

    On a planetary scale, Metabolic Syndrome (MetS)is the third cause of inability after malnutrition and nicotinism, even higher than water shortage and sedentariness. In the USA, the prevalence is estimated at over 25 percent of the population; in Italy, it involves approximately 25 percent of men and even 27 percent of women. These are very high figures, corresponding to approximately 14 million affected individuals. The prevalence is alarming and must not be underestimated, particularly in the dental field, where more than one patient out of four sitting in a dentist chair is affected. The etiology of periodontal disease has not yet been clarified, and recently the idea to consider it as a multifactor pathology has been developed. Cofactors such as the formation of free radicals of oxygen (ROS), oxidative stress, lipid peroxidation, and formation of glycation end-products (AGEs) probably play an important role in the onset of periodontal disease. The AGEs are compounds physiologically produced by the cells. However, they accumulate and cause pro-inflammatory conditions, when the cellular clearance fails, or in hyperglycemic and oxidative states. All these conditions can be clinically summarized as Metabolic Syndrome. The purpose of this literature review is to establish a relationship between two pathologies with very high prevalence: Metabolic Syndrome and Periodontal Disorder. The literature seems to have clarified that MetS involves a pro-oxidation status, which induces AGE formation. AGEs play a very important role in the course and severity of periodontal diseases.

  12. Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease.

    PubMed

    Hyötyläinen, Tuulia; Jerby, Livnat; Petäjä, Elina M; Mattila, Ismo; Jäntti, Sirkku; Auvinen, Petri; Gastaldelli, Amalia; Yki-Järvinen, Hannele; Ruppin, Eytan; Orešič, Matej

    2016-02-03

    Non-alcoholic fatty liver disease (NAFLD) is a major risk factor leading to chronic liver disease and type 2 diabetes. Here we chart liver metabolic activity and functionality in NAFLD by integrating global transcriptomic data, from human liver biopsies, and metabolic flux data, measured across the human splanchnic vascular bed, within a genome-scale model of human metabolism. We show that an increased amount of liver fat induces mitochondrial metabolism, lipolysis, glyceroneogenesis and a switch from lactate to glycerol as substrate for gluconeogenesis, indicating an intricate balance of exacerbated opposite metabolic processes in glycemic regulation. These changes were associated with reduced metabolic adaptability on a network level in the sense that liver fat accumulation puts increasing demands on the liver to adaptively regulate metabolic responses to maintain basic liver functions. We propose that failure to meet excessive metabolic challenges coupled with reduced metabolic adaptability may lead to a vicious pathogenic cycle leading to the co-morbidities of NAFLD.

  13. Genome-scale study reveals reduced metabolic adaptability in patients with non-alcoholic fatty liver disease

    PubMed Central

    Hyötyläinen, Tuulia; Jerby, Livnat; Petäjä, Elina M.; Mattila, Ismo; Jäntti, Sirkku; Auvinen, Petri; Gastaldelli, Amalia; Yki-Järvinen, Hannele; Ruppin, Eytan; Orešič, Matej

    2016-01-01

    Non-alcoholic fatty liver disease (NAFLD) is a major risk factor leading to chronic liver disease and type 2 diabetes. Here we chart liver metabolic activity and functionality in NAFLD by integrating global transcriptomic data, from human liver biopsies, and metabolic flux data, measured across the human splanchnic vascular bed, within a genome-scale model of human metabolism. We show that an increased amount of liver fat induces mitochondrial metabolism, lipolysis, glyceroneogenesis and a switch from lactate to glycerol as substrate for gluconeogenesis, indicating an intricate balance of exacerbated opposite metabolic processes in glycemic regulation. These changes were associated with reduced metabolic adaptability on a network level in the sense that liver fat accumulation puts increasing demands on the liver to adaptively regulate metabolic responses to maintain basic liver functions. We propose that failure to meet excessive metabolic challenges coupled with reduced metabolic adaptability may lead to a vicious pathogenic cycle leading to the co-morbidities of NAFLD. PMID:26839171

  14. Metabolic engineering of Corynebacterium glutamicum aimed at alternative carbon sources and new products

    PubMed Central

    Zahoor, Ahmed; Lindner, Steffen N.; Wendisch, Volker F.

    2012-01-01

    Corynebacterium glutamicum is well known as the amino acid-producing workhorse of fermentation industry, being used for multi-million-ton scale production of glutamate and lysine for more than 60 years. However, it is only recently that extensive research has focused on engineering it beyond the scope of amino acids. Meanwhile, a variety of corynebacterial strains allows access to alternative carbon sources and/or allows production of a wide range of industrially relevant compounds. Some of these efforts set new standards in terms of titers and productivities achieved whereas others represent a proof-of-principle. These achievements manifest the position of C. glutamicum as an important industrial microorganism with capabilities far beyond the traditional amino acid production. In this review we focus on the state of the art of metabolic engineering of C. glutamicum for utilization of alternative carbon sources, (e.g. coming from wastes and unprocessed sources), and construction of C. glutamicum strains for production of new products such as diamines, organic acids and alcohols PMID:24688664

  15. Metabolic engineering of Corynebacterium glutamicum aimed at alternative carbon sources and new products.

    PubMed

    Zahoor, Ahmed; Lindner, Steffen N; Wendisch, Volker F

    2012-01-01

    Corynebacterium glutamicum is well known as the amino acid-producing workhorse of fermentation industry, being used for multi-million-ton scale production of glutamate and lysine for more than 60 years. However, it is only recently that extensive research has focused on engineering it beyond the scope of amino acids. Meanwhile, a variety of corynebacterial strains allows access to alternative carbon sources and/or allows production of a wide range of industrially relevant compounds. Some of these efforts set new standards in terms of titers and productivities achieved whereas others represent a proof-of-principle. These achievements manifest the position of C. glutamicum as an important industrial microorganism with capabilities far beyond the traditional amino acid production. In this review we focus on the state of the art of metabolic engineering of C. glutamicum for utilization of alternative carbon sources, (e.g. coming from wastes and unprocessed sources), and construction of C. glutamicum strains for production of new products such as diamines, organic acids and alcohols.

  16. Metabolic network reconstruction and genome-scale model of butanol-producing strain Clostridium beijerinckii NCIMB 8052

    PubMed Central

    2011-01-01

    Background Solventogenic clostridia offer a sustainable alternative to petroleum-based production of butanol--an important chemical feedstock and potential fuel additive or replacement. C. beijerinckii is an attractive microorganism for strain design to improve butanol production because it (i) naturally produces the highest recorded butanol concentrations as a byproduct of fermentation; and (ii) can co-ferment pentose and hexose sugars (the primary products from lignocellulosic hydrolysis). Interrogating C. beijerinckii metabolism from a systems viewpoint using constraint-based modeling allows for simulation of the global effect of genetic modifications. Results We present the first genome-scale metabolic model (iCM925) for C. beijerinckii, containing 925 genes, 938 reactions, and 881 metabolites. To build the model we employed a semi-automated procedure that integrated genome annotation information from KEGG, BioCyc, and The SEED, and utilized computational algorithms with manual curation to improve model completeness. Interestingly, we found only a 34% overlap in reactions collected from the three databases--highlighting the importance of evaluating the predictive accuracy of the resulting genome-scale model. To validate iCM925, we conducted fermentation experiments using the NCIMB 8052 strain, and evaluated the ability of the model to simulate measured substrate uptake and product production rates. Experimentally observed fermentation profiles were found to lie within the solution space of the model; however, under an optimal growth objective, additional constraints were needed to reproduce the observed profiles--suggesting the existence of selective pressures other than optimal growth. Notably, a significantly enriched fraction of actively utilized reactions in simulations--constrained to reflect experimental rates--originated from the set of reactions that overlapped between all three databases (P = 3.52 × 10-9, Fisher's exact test). Inhibition of the

  17. Do insect metabolic rates at rest and during flight scale with body mass?

    PubMed

    Niven, Jeremy E; Scharlemann, Jörn P W

    2005-09-22

    Energetically costly behaviours, such as flight, push physiological systems to their limits requiring metabolic rates (MR) that are highly elevated above the resting MR (RMR). Both RMR and MR during exercise (e.g. flight or running) in birds and mammals scale allometrically, although there is little consensus about the underlying mechanisms or the scaling relationships themselves. Even less is known about the allometric scaling of RMR and MR during exercise in insects. We analysed data on the resting and flight MR (FMR) of over 50 insect species that fly to determine whether RMR and FMR scale allometrically. RMR scaled with body mass to the power of 0.66 (M0.66), whereas FMR scaled with M1.10. Further analysis suggested that FMR scaled with two separate relationships; insects weighing less than 10mg had fourfold lower FMR than predicted from the scaling of FMR in insects weighing more than 10mg, although both groups scaled with M0.86. The scaling exponents of RMR and FMR in insects were not significantly different from those of birds and mammals, suggesting that they might be determined by similar factors. We argue that low FMR in small insects suggests these insects may be making considerable energy savings during flight, which could be extremely important for the physiology and evolution of insect flight.

  18. Genome-Scale NAD(H/+) Availability Patterns as a Differentiating Feature between Saccharomyces cerevisiae and Scheffersomyces stipitis in Relation to Fermentative Metabolism

    PubMed Central

    Acevedo, Alejandro; Aroca, German; Conejeros, Raul

    2014-01-01

    Scheffersomyces stipitis is a yeast able to ferment pentoses to ethanol, unlike Saccharomyces cerevisiae, it does not present the so-called overflow phenomenon. Metabolic features characterizing the presence or not of this phenomenon have not been fully elucidated. This work proposes that genome-scale metabolic response to variations in NAD(H/+) availability characterizes fermentative behavior in both yeasts. Thus, differentiating features in S. stipitis and S. cerevisiae were determined analyzing growth sensitivity response to changes in available reducing capacity in relation to ethanol production capacity and overall metabolic flux span. Using genome-scale constraint-based metabolic models, phenotypic phase planes and shadow price analyses, an excess of available reducing capacity for growth was found in S. cerevisiae at every metabolic phenotype where growth is limited by oxygen uptake, while in S. stipitis this was observed only for a subset of those phenotypes. Moreover, by using flux variability analysis, an increased metabolic flux span was found in S. cerevisiae at growth limited by oxygen uptake, while in S. stipitis flux span was invariant. Therefore, each yeast can be characterized by a significantly different metabolic response and flux span when growth is limited by oxygen uptake, both features suggesting a higher metabolic flexibility in S. cerevisiae. By applying an optimization-based approach on the genome-scale models, three single reaction deletions were found to generate in S. stipitis the reducing capacity availability pattern found in S. cerevisiae, two of them correspond to reactions involved in the overflow phenomenon. These results show a close relationship between the growth sensitivity response given by the metabolic network and fermentative behavior. PMID:24489927

  19. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis

    NASA Astrophysics Data System (ADS)

    De Martino, D.

    2016-02-01

    In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium. We recalculate turnover times from total fluxes by performing an energy balance analysis of the network and recurring to the fluctuation theorem. We find in many cases values one of order of magnitude lower, implying a faster picture of intermediate metabolism.

  20. Comparing Scales of Environmental Effects from Gasoline and Ethanol Production

    SciTech Connect

    Parish, Esther S; Kline, Keith L; Dale, Virginia H; Efroymson, Rebecca Ann; McBride, Allen; Johnson, Timothy L; Hilliard, Michael R; Bielicki, Dr Jeffrey M

    2013-01-01

    Understanding the environmental effects of alternative fuel production is critical to characterizing the sustainability of energy resources to inform policy and regulatory decisions. The magnitudes of these environmental effects vary according to the intensity and scale of fuel production along each step of the supply chain. We compare the scales (i.e., spatial extent and temporal duration) of ethanol and gasoline production processes and environmental effects based on a literature review, and then synthesize the scale differences on space-time diagrams. Comprehensive assessment of any fuel-production system is a moving target, and our analysis shows that decisions regarding the selection of spatial and temporal boundaries of analysis have tremendous influences on the comparisons. Effects that strongly differentiate gasoline and ethanol supply chains in terms of scale are associated with when and where energy resources are formed and how they are extracted. Although both gasoline and ethanol production may result in negative environmental effects, this study indicates that ethanol production traced through a supply chain may impact less area and result in more easily reversed effects of a shorter duration than gasoline production.

  1. Network thermodynamic curation of human and yeast genome-scale metabolic models.

    PubMed

    Martínez, Verónica S; Quek, Lake-Ee; Nielsen, Lars K

    2014-07-15

    Genome-scale models are used for an ever-widening range of applications. Although there has been much focus on specifying the stoichiometric matrix, the predictive power of genome-scale models equally depends on reaction directions. Two-thirds of reactions in the two eukaryotic reconstructions Homo sapiens Recon 1 and Yeast 5 are specified as irreversible. However, these specifications are mainly based on biochemical textbooks or on their similarity to other organisms and are rarely underpinned by detailed thermodynamic analysis. In this study, a to our knowledge new workflow combining network-embedded thermodynamic and flux variability analysis was used to evaluate existing irreversibility constraints in Recon 1 and Yeast 5 and to identify new ones. A total of 27 and 16 new irreversible reactions were identified in Recon 1 and Yeast 5, respectively, whereas only four reactions were found with directions incorrectly specified against thermodynamics (three in Yeast 5 and one in Recon 1). The workflow further identified for both models several isolated internal loops that require further curation. The framework also highlighted the need for substrate channeling (in human) and ATP hydrolysis (in yeast) for the essential reaction catalyzed by phosphoribosylaminoimidazole carboxylase in purine metabolism. Finally, the framework highlighted differences in proline metabolism between yeast (cytosolic anabolism and mitochondrial catabolism) and humans (exclusively mitochondrial metabolism). We conclude that network-embedded thermodynamics facilitates the specification and validation of irreversibility constraints in compartmentalized metabolic models, at the same time providing further insight into network properties.

  2. Genome-scale metabolic reconstruction for the insidious bacterium in aquaculture Piscirickettsia salmonis.

    PubMed

    Fuentealba, Pablo; Aros, Camila; Latorre, Yesenia; Martínez, Irene; Marshall, Sergio; Ferrer, Pau; Albiol, Joan; Altamirano, Claudia

    2017-01-01

    Piscirickettsia salmonis is a fish bacterium that causes the disease piscirickettsiosis in salmonids. This pathology is partially controlled by vaccines. The lack of knowledge has hindered its culture on laboratory and industrial scale. The study describes the metabolic phenotype of P. salmonis in culture. This study presents the first genome-scale model (iPF215) of the LF-89 strain of P. salmonis, describing the central metabolic pathway, biosynthesis and molecule degradation and transport mechanisms. The model was adjusted with experiment data, allowing the identification of the capacities that were not predicted by the automatic annotation of the genome sequences. The iPF215 model is comprised of 417 metabolites, 445 reactions and 215 genes, was used to reproduce the growth of P. salmonis (μmax 0.052±0.005h(-1)). The metabolic reconstruction of the P. salmonis LF-89 strain obtained in this research provides a baseline that describes the metabolic capacities of the bacterium and is the basis for developing improvements to its cultivation for vaccine formulation.

  3. An Experimentally-Supported Genome-Scale Metabolic Network Reconstruction for Yersinia pestis CO92

    SciTech Connect

    Charusanti, Pep; Chauhan, Sadhana; Mcateer, Kathleen; Lerman, Joshua A.; Hyduke, Daniel R.; Motin, Vladimir L.; Ansong, Charles; Adkins, Joshua N.; Palsson, Bernhard O.

    2011-10-13

    Yersinia pestis is a gram-negative bacterium that causes plague, a disease linked historically to the Black Death in Europe during the Middle Ages and to several outbreaks during the modern era. Metabolism in Y. pestis displays remarkable flexibility and robustness, allowing the bacterium to proliferate in both warm-blooded mammalian hosts and cold-blooded insect vectors such as fleas. Here we report a genome-scale reconstruction and mathematical model of metabolism for Y. pestis CO92 and supporting experimental growth and metabolite measurements. The model contains 815 genes, 678 proteins, 963 unique metabolites and 1678 reactions, accurately simulates growth on a range of carbon sources both qualitatively and quantitatively, and identifies gaps in several key biosynthetic pathways and suggests how those gaps might be filled. Furthermore, our model presents hypotheses to explain certain known nutritional requirements characteristic of this strain. Y. pestis continues to be a dangerous threat to human health during modern times. The Y. pestis genome-scale metabolic reconstruction presented here, which has been benchmarked against experimental data and correctly reproduces known phenotypes, thus provides an in silico platform with which to investigate the metabolism of this important human pathogen.

  4. Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri

    SciTech Connect

    Feist, Adam; Scholten, Johannes C.; Palsson, Bernard O.; Brockman, Fred J.; Ideker, Trey

    2006-01-31

    We present a genome-scale metabolic reconstruction for the archaeal methanogen Methanosarcina barkeri. This reconstruction represents the first large-scale, predictive model of a methanogen and an archael species. We characterize this reconstruction and compare it to those from the prokaryotic, eukaryotic, and archael domains. We further apply constraint-based methods to stimulate the metabolic fluxes and resulting phenotypes under different environmental and genetic conditions. These results are validated by comparison to experimental growth measurements and phenotypes of M. barkeri on different substrates. The predicted growth phenotypes for mutants of the methanogenic pathway were found to have a high level of agreement with experimental findings. The active reactions and pathways under selected growth conditions are presented and characterized. We also examined the efficiency of the energy-conserving reactions in the methanogenic pathway, specifically the Ech hydrogenase reaction. This work demonstrates that a reconstructed metabolic network can serve as an in silico analysis platform to predict cellular phenotypes, characterize methanogenic growth, improve the genome annotation, and further uncover the metabolic characteristics of methanogenesis.

  5. Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom

    PubMed Central

    Broddrick, Jared; Dupont, Christopher L.; Peers, Graham; Beeri, Karen; Mayers, Joshua; Gallina, Alessandra A.; Allen, Andrew E.; Palsson, Bernhard O.; Zengler, Karsten

    2016-01-01

    Diatoms are eukaryotic microalgae that contain genes from various sources, including bacteria and the secondary endosymbiotic host. Due to this unique combination of genes, diatoms are taxonomically and functionally distinct from other algae and vascular plants and confer novel metabolic capabilities. Based on the genome annotation, we performed a genome-scale metabolic network reconstruction for the marine diatom Phaeodactylum tricornutum. Due to their endosymbiotic origin, diatoms possess a complex chloroplast structure which complicates the prediction of subcellular protein localization. Based on previous work we implemented a pipeline that exploits a series of bioinformatics tools to predict protein localization. The manually curated reconstructed metabolic network iLB1027_lipid accounts for 1,027 genes associated with 4,456 reactions and 2,172 metabolites distributed across six compartments. To constrain the genome-scale model, we determined the organism specific biomass composition in terms of lipids, carbohydrates, and proteins using Fourier transform infrared spectrometry. Our simulations indicate the presence of a yet unknown glutamine-ornithine shunt that could be used to transfer reducing equivalents generated by photosynthesis to the mitochondria. The model reflects the known biochemical composition of P. tricornutum in defined culture conditions and enables metabolic engineering strategies to improve the use of P. tricornutum for biotechnological applications. PMID:27152931

  6. Is the scaling of swim speed in sharks driven by metabolism?

    PubMed

    Jacoby, David M P; Siriwat, Penthai; Freeman, Robin; Carbone, Chris

    2015-12-01

    The movement rates of sharks are intrinsically linked to foraging ecology, predator-prey dynamics and wider ecosystem functioning in marine systems. During ram ventilation, however, shark movement rates are linked not only to ecological parameters, but also to physiology, as minimum speeds are required to provide sufficient water flow across the gills to maintain metabolism. We develop a geometric model predicting a positive scaling relationship between swim speeds in relation to body size and ultimately shark metabolism, taking into account estimates for the scaling of gill dimensions. Empirical data from 64 studies (26 species) were compiled to test our model while controlling for the influence of phylogenetic similarity between related species. Our model predictions were found to closely resemble the observed relationships from tracked sharks, providing a means to infer mobility in particularly intractable species.

  7. Is the scaling of swim speed in sharks driven by metabolism?

    PubMed Central

    Jacoby, David M. P.; Siriwat, Penthai; Freeman, Robin; Carbone, Chris

    2015-01-01

    The movement rates of sharks are intrinsically linked to foraging ecology, predator–prey dynamics and wider ecosystem functioning in marine systems. During ram ventilation, however, shark movement rates are linked not only to ecological parameters, but also to physiology, as minimum speeds are required to provide sufficient water flow across the gills to maintain metabolism. We develop a geometric model predicting a positive scaling relationship between swim speeds in relation to body size and ultimately shark metabolism, taking into account estimates for the scaling of gill dimensions. Empirical data from 64 studies (26 species) were compiled to test our model while controlling for the influence of phylogenetic similarity between related species. Our model predictions were found to closely resemble the observed relationships from tracked sharks, providing a means to infer mobility in particularly intractable species. PMID:26631246

  8. Fermentative Production of the Diamine Putrescine: System Metabolic Engineering of Corynebacterium Glutamicum

    PubMed Central

    Nguyen, Anh Q. D.; Schneider, Jens; Reddy, Gajendar Komati; Wendisch, Volker F.

    2015-01-01

    Corynebacterium glutamicum shows great potential for the production of the glutamate-derived diamine putrescine, a monomeric compound of polyamides. A genome-scale stoichiometric model of a C. glutamicum strain with reduced ornithine transcarbamoylase activity, derepressed arginine biosynthesis, and an anabolic plasmid-addiction system for heterologous expression of E. coli ornithine decarboxylase gene speC was investigated by flux balance analysis with respect to its putrescine production potential. Based on these simulations, enhancing glycolysis and anaplerosis by plasmid-borne overexpression of the genes for glyceraldehyde 3-phosphate dehydrogenase and pyruvate carboxylase as well as reducing 2-oxoglutarate dehydrogenase activity were chosen as targets for metabolic engineering. Changing the translational start codon of the chromosomal gene for 2-oxoglutarate dehydrogenase subunit E1o to the less preferred TTG and changing threonine 15 of OdhI to alanine reduced 2-oxoglutarate dehydrogenase activity about five fold and improved putrescine titers by 28%. Additional engineering steps improved further putrescine production with the largest contributions from preventing the formation of the by-product N-acetylputrescine by deletion of spermi(di)ne N-acetyltransferase gene snaA and from overexpression of the gene for a feedback-resistant N-acetylglutamate kinase variant. The resulting C. glutamicum strain NA6 obtained by systems metabolic engineering accumulated two fold more putrescine than the base strain, i.e., 58.1 ± 0.2 mM, and showed a specific productivity of 0.045 g·g−1·h−1 and a yield on glucose of 0.26 g·g−1. PMID:25919117

  9. Lipid metabolism and potentials of biofuel and high added-value oil production in red algae.

    PubMed

    Sato, Naoki; Moriyama, Takashi; Mori, Natsumi; Toyoshima, Masakazu

    2017-04-01

    Biomass production is currently explored in microalgae, macroalgae and land plants. Microalgal biofuel development has been performed mostly in green algae. In the Japanese tradition, macrophytic red algae such as Pyropia yezoensis and Gelidium crinale have been utilized as food and industrial materials. Researches on the utilization of unicellular red microalgae such as Cyanidioschyzon merolae and Porphyridium purpureum started only quite recently. Red algae have relatively large plastid genomes harboring more than 200 protein-coding genes that support the biosynthetic capacity of the plastid. Engineering the plastid genome is a unique potential of red microalgae. In addition, large-scale growth facilities of P. purpureum have been developed for industrial production of biofuels. C. merolae has been studied as a model alga for cell and molecular biological analyses with its completely determined genomes and transformation techniques. Its acidic and warm habitat makes it easy to grow this alga axenically in large scales. Its potential as a biofuel producer is recently documented under nitrogen-limited conditions. Metabolic pathways of the accumulation of starch and triacylglycerol and the enzymes involved therein are being elucidated. Engineering these regulatory mechanisms will open a possibility of exploiting the full capability of production of biofuel and high added-value oil. In the present review, we will describe the characteristics and potential of these algae as biotechnological seeds.

  10. A Genome-Scale Database and Reconstruction of Caenorhabditis elegans Metabolism.

    PubMed

    Gebauer, Juliane; Gentsch, Christoph; Mansfeld, Johannes; Schmeißer, Kathrin; Waschina, Silvio; Brandes, Susanne; Klimmasch, Lukas; Zamboni, Nicola; Zarse, Kim; Schuster, Stefan; Ristow, Michael; Schäuble, Sascha; Kaleta, Christoph

    2016-05-25

    We present a genome-scale model of Caenorhabditis elegans metabolism along with the public database ElegCyc (http://elegcyc.bioinf.uni-jena.de:1100), which represents a reference for metabolic pathways in the worm and allows for the visualization as well as analysis of omics datasets. Our model reflects the metabolic peculiarities of C. elegans that make it distinct from other higher eukaryotes and mammals, including mice and humans. We experimentally verify one of these peculiarities by showing that the lifespan-extending effect of L-tryptophan supplementation is dose dependent (hormetic). Finally, we show the utility of our model for analyzing omics datasets through predicting changes in amino acid concentrations after genetic perturbations and analyzing metabolic changes during normal aging as well as during two distinct, reactive oxygen species (ROS)-related lifespan-extending treatments. Our analyses reveal a notable similarity in metabolic adaptation between distinct lifespan-extending interventions and point to key pathways affecting lifespan in nematodes.

  11. Temporal Changes in Microbial Metabolic Characteristics in Field-Scale Biopiles Composed of Aged Oil Sludge

    PubMed Central

    Wang, Xiang; Li, Fasheng; Guo, Guanlin; Wang, Shijie; Boronin, Alexander; Wang, Qunhui

    2014-01-01

    Abstract Disposal of oil sludge, a hazardous waste, is currently a prevalent environmental issue. In this study, two field-scale biopiles were constructed to explore the temporal changes of microbial metabolic characteristics during the biotreatment of aged oil sludge. Bulking agent was mixed thoroughly with oily sludge to form a treated pile. The BIOLOG™ system was used to analyze the community level physiological parameters, including microbial metabolic activity, diversity, and variance. In comparison with the control, the community level physiological parameters of the treated pile were dramatically improved. Microbial metabolic activity of the treated pile was improved by 25.06% calculated from the maximums during the treatment. Microbial diversity index (Shannon index) ranges were improved from 1.64–3.02 (control pile) to 2.34–3.14 (treated pile). The numbers of petroleum-degrading bacteria and the total heterotrophic bacteria were correlated with the environmental temperature, and microbial metabolic characteristics in the treated pile revealed the distinctive carbon resources selection with the addition of cotton stalk. Temporal microbial metabolic characteristics, which have important effect on bioremediation, were revealed in this study. PMID:25228785

  12. Temporal Changes in Microbial Metabolic Characteristics in Field-Scale Biopiles Composed of Aged Oil Sludge.

    PubMed

    Wang, Xiang; Li, Fasheng; Guo, Guanlin; Wang, Shijie; Boronin, Alexander; Wang, Qunhui

    2014-09-01

    Disposal of oil sludge, a hazardous waste, is currently a prevalent environmental issue. In this study, two field-scale biopiles were constructed to explore the temporal changes of microbial metabolic characteristics during the biotreatment of aged oil sludge. Bulking agent was mixed thoroughly with oily sludge to form a treated pile. The BIOLOG™ system was used to analyze the community level physiological parameters, including microbial metabolic activity, diversity, and variance. In comparison with the control, the community level physiological parameters of the treated pile were dramatically improved. Microbial metabolic activity of the treated pile was improved by 25.06% calculated from the maximums during the treatment. Microbial diversity index (Shannon index) ranges were improved from 1.64-3.02 (control pile) to 2.34-3.14 (treated pile). The numbers of petroleum-degrading bacteria and the total heterotrophic bacteria were correlated with the environmental temperature, and microbial metabolic characteristics in the treated pile revealed the distinctive carbon resources selection with the addition of cotton stalk. Temporal microbial metabolic characteristics, which have important effect on bioremediation, were revealed in this study.

  13. Comparative Study of Laboratory-Scale and Prototypic Production-Scale Fuel Fabrication Processes and Product Characteristics

    SciTech Connect

    Douglas W. Marshall

    2014-10-01

    An objective of the High Temperature Gas Reactor fuel development and qualification program for the United States Department of Energy has been to qualify fuel fabricated in prototypic production-scale equipment. The quality and characteristics of the tristructural isotropic coatings on fuel kernels are influenced by the equipment scale and processing parameters. Some characteristics affecting product quality were suppressed while others have become more significant in the larger equipment. Changes to the composition and method of producing resinated graphite matrix material has eliminated the use of hazardous, flammable liquids and enabled it to be procured as a vendor-supplied feed stock. A new method of overcoating TRISO particles with the resinated graphite matrix eliminates the use of hazardous, flammable liquids, produces highly spherical particles with a narrow size distribution, and attains product yields in excess of 99%. Compact fabrication processes have been scaled-up and automated with relatively minor changes to compact quality to manual laboratory-scale processes. The impact on statistical variability of the processes and the products as equipment was scaled are discussed. The prototypic production-scale processes produce test fuels that meet fuel quality specifications.

  14. Metabolic response to air temperature and wind in day-old mallards and a standard operative temperature scale.

    PubMed

    Bakken, G S; Reynolds, P S; Kenow, K P; Korschgen, C E; Boysen, A F

    1999-01-01

    Most duckling mortality occurs during the week following hatching and is often associated with cold, windy, wet weather and scattering of the brood. We estimated the thermoregulatory demands imposed by cold, windy weather on isolated 1-d-old mallard (Anas platyrhynchos) ducklings resting in cover. We measured O2 consumption and evaporative water loss at air temperatures from 5 degrees to 25 degrees C and wind speeds of 0.1, 0.2, 0.5, and 1.0 m/s. Metabolic heat production increased as wind increased or temperature decreased but was less sensitive to wind than that of either adult passerines or small mammals. Evaporative heat loss ranged from 5% to 17% of heat production. Evaporative heat loss and the ratio of evaporative heat loss to metabolic heat production was significantly lower in rest phase. These data were used to define a standard operative temperature (Tes) scale for night or heavy overcast conditions. An increase of wind speed from 0.1 to 1 m/s decreased Tes by 3 degrees -5 degrees C.

  15. Metabolic response to air temperature and wind in day-old mallards and a standard operative temperature scale

    USGS Publications Warehouse

    Bakken, G.S.; Reynolds, P.S.; Kenow, K.P.; Korschgen, C.E.; Boysen, A.F.

    1999-01-01

    Most duckling mortality occurs during the week following hatching and is often associated with cold, windy, wet weather and scattering of the brood. We estimated the thermoregulatory demands imposed by cold, windy weather on isolated 1-d-old mallard (Anas platyrhynchos) ducklings resting in cover. We measured O-2 consumption and evaporative water loss at air temperatures from 5 degrees to 25 degrees C and wind speeds of 0.1, 0.2, 0.5, and 1.0 mis. Metabolic heat production increased as wind increased or temperature decreased but was less sensitive to wind than that of either adult passerines or small mammals. Evaporative heat loss ranged from 5% to 17% of heat production. Evaporative heal loss and the ratio of evaporative heat loss to metabolic heat production was significantly lower in rest phase. These data were used to define a standard operative temperature (T-es) scale for night or heavy overcast conditions. An increase of wind speed from 0.1 to 1 mis decreased T-es by 3 degrees-5 degrees C.

  16. An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks.

    PubMed

    Stelzer, Michael; Sun, Jibin; Kamphans, Tom; Fekete, Sándor P; Zeng, An-Ping

    2011-11-01

    The bioreaction database established by Ma and Zeng (Bioinformatics, 2003, 19, 270-277) for in silico reconstruction of genome-scale metabolic networks has been widely used. Based on more recent information in the reference databases KEGG LIGAND and Brenda, we upgrade the bioreaction database in this work by almost doubling the number of reactions from 3565 to 6851. Over 70% of the reactions have been manually updated/revised in terms of reversibility, reactant pairs, currency metabolites and error correction. For the first time, 41 spontaneous sugar mutarotation reactions are introduced into the biochemical database. The upgrade significantly improves the reconstruction of genome scale metabolic networks. Many gaps or missing biochemical links can be recovered, as exemplified with three model organisms Homo sapiens, Aspergillus niger, and Escherichia coli. The topological parameters of the constructed networks were also largely affected, however, the overall network structure remains scale-free. Furthermore, we consider the problem of computing biologically feasible shortest paths in reconstructed metabolic networks. We show that these paths are hard to compute and present solutions to find such paths in networks of small and medium size.

  17. Effects of bioactive fatty acid amide derivatives in zebrafish scale model of bone metabolism and disease.

    PubMed

    Carnovali, M; Ottria, R; Pasqualetti, S; Banfi, G; Ciuffreda, P; Mariotti, M

    2016-02-01

    The endocannabinoid system (which includes fatty acid derivatives, receptors, and metabolizing enzymes) is involved in a variety of physiological processes, including bone metabolism in which it regulates the function of osteoblasts and osteoclasts, as well as differentiation of their precursors. The zebrafish (Danio rerio) provides a useful animal model for bone research since zebrafish bones develop rapidly and are anatomically similar to mammalian bones. Putative orthologues and paralogs of endocannabinoid genes have recently been identified in zebrafish, demonstrating the presence of cannabinoid type 1 (CB1) and type 2 (CB2) receptors with affinity to endocannabinoid ligands. To identify therapeutic molecules potentially useful in bone-related diseases, we evaluated the in vivo effects of exposure to long-chain fatty acid amides in adult zebrafish. Using a well-established zebrafish scale model, we found that anandamide and N-linoleoylethanolamine are able to stimulate bone formation by increasing alkaline phosphatase activity in physiological conditions. In addition, they prevent the alteration of bone markers in a prednisolone-induced osteoporosis model in adult zebrafish scales, whereas their esterified forms do not. These data suggest that long-chain fatty acid amides are involved in regulating bone metabolism in zebrafish scales and that the CB2 receptor is a key mediator in this process.

  18. Metabolic glycoengineering bacteria for therapeutic, recombinant protein, and metabolite production applications.

    PubMed

    Saeui, Christopher T; Urias, Esteban; Liu, Lingshu; Mathew, Mohit P; Yarema, Kevin J

    2015-10-01

    Metabolic glycoengineering is a specialization of metabolic engineering that focuses on using small molecule metabolites to manipulate biosynthetic pathways responsible for oligosaccharide and glycoconjugate production. As outlined in this article, this technique has blossomed in mammalian systems over the past three decades but has made only modest progress in prokaryotes. Nevertheless, a sufficient foundation now exists to support several important applications of metabolic glycoengineering in bacteria based on methods to preferentially direct metabolic intermediates into pathways involved in lipopolysaccharide, peptidoglycan, teichoic acid, or capsule polysaccharide production. An overview of current applications and future prospects for this technology are provided in this report.

  19. Tree Morphologic Plasticity Explains Deviation from Metabolic Scaling Theory in Semi-Arid Conifer Forests, Southwestern USA

    PubMed Central

    O’Connor, Christopher D.; Lynch, Ann M.

    2016-01-01

    A significant concern about Metabolic Scaling Theory (MST) in real forests relates to consistent differences between the values of power law scaling exponents of tree primary size measures used to estimate mass and those predicted by MST. Here we consider why observed scaling exponents for diameter and height relationships deviate from MST predictions across three semi-arid conifer forests in relation to: (1) tree condition and physical form, (2) the level of inter-tree competition (e.g. open vs closed stand structure), (3) increasing tree age, and (4) differences in site productivity. Scaling exponent values derived from non-linear least-squares regression for trees in excellent condition (n = 381) were above the MST prediction at the 95% confidence level, while the exponent for trees in good condition were no different than MST (n = 926). Trees that were in fair or poor condition, characterized as diseased, leaning, or sparsely crowned had exponent values below MST predictions (n = 2,058), as did recently dead standing trees (n = 375). Exponent value of the mean-tree model that disregarded tree condition (n = 3,740) was consistent with other studies that reject MST scaling. Ostensibly, as stand density and competition increase trees exhibited greater morphological plasticity whereby the majority had characteristically fair or poor growth forms. Fitting by least-squares regression biases the mean-tree model scaling exponent toward values that are below MST idealized predictions. For 368 trees from Arizona with known establishment dates, increasing age had no significant impact on expected scaling. We further suggest height to diameter ratios below MST relate to vertical truncation caused by limitation in plant water availability. Even with environmentally imposed height limitation, proportionality between height and diameter scaling exponents were consistent with the predictions of MST. PMID:27391084

  20. Tree Morphologic Plasticity Explains Deviation from Metabolic Scaling Theory in Semi-Arid Conifer Forests, Southwestern USA.

    PubMed

    Swetnam, Tyson L; O'Connor, Christopher D; Lynch, Ann M

    2016-01-01

    A significant concern about Metabolic Scaling Theory (MST) in real forests relates to consistent differences between the values of power law scaling exponents of tree primary size measures used to estimate mass and those predicted by MST. Here we consider why observed scaling exponents for diameter and height relationships deviate from MST predictions across three semi-arid conifer forests in relation to: (1) tree condition and physical form, (2) the level of inter-tree competition (e.g. open vs closed stand structure), (3) increasing tree age, and (4) differences in site productivity. Scaling exponent values derived from non-linear least-squares regression for trees in excellent condition (n = 381) were above the MST prediction at the 95% confidence level, while the exponent for trees in good condition were no different than MST (n = 926). Trees that were in fair or poor condition, characterized as diseased, leaning, or sparsely crowned had exponent values below MST predictions (n = 2,058), as did recently dead standing trees (n = 375). Exponent value of the mean-tree model that disregarded tree condition (n = 3,740) was consistent with other studies that reject MST scaling. Ostensibly, as stand density and competition increase trees exhibited greater morphological plasticity whereby the majority had characteristically fair or poor growth forms. Fitting by least-squares regression biases the mean-tree model scaling exponent toward values that are below MST idealized predictions. For 368 trees from Arizona with known establishment dates, increasing age had no significant impact on expected scaling. We further suggest height to diameter ratios below MST relate to vertical truncation caused by limitation in plant water availability. Even with environmentally imposed height limitation, proportionality between height and diameter scaling exponents were consistent with the predictions of MST.

  1. Scaling up from traits to communities to ecosystems across broad climate gradients: Testing Metabolic Scaling Theories predictions for forests

    NASA Astrophysics Data System (ADS)

    Enquist, B. J.; Michaletz, S. T.; Buzzard, V.

    2015-12-01

    Key insights in global ecology will come from mechanistically linking pattern and process across scales. Macrosystems ecology specifically attempts to link ecological processes across spatiotemporal scales. The goal s to link the processing of energy and nutrients from cells all the way ecosystems and to understand how shifting climate influences ecosystem processes. Using new data collected from NSF funded Macrosystems project we report on new findings from forests sites across a broad temperature gradient. Our study sites span tropical, temperate, and high elevation forests we assess several key predictions and assumptions of Metabolic Scaling Theory (MST) as well as several other competing hypotheses for the role of climate, light, and plant traits on influencing forest demography and forest ecosystems. Specifically, we assess the importance of plant size, light limitation, size structure, and various climatic factors on forest growth, demography, and ecosystem functioning. We provide some of the first systematic tests of several key predictions from MST. We show that MST predictions are largely upheld and that new insights from assessing theories predictions yields new observations and findings that help modify and extend MST's predictions and applicability. We discuss how theory is critically needed to further our understanding of how to scale pattern and process in ecology - from traits to ecosystems - in order to develop a more predictive global change biology.

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

    PubMed

    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.

  3. Flux balance analysis of CHO cells before and after a metabolic switch from lactate production to consumption.

    PubMed

    Martínez, Verónica S; Dietmair, Stefanie; Quek, Lake-Ee; Hodson, Mark P; Gray, Peter; Nielsen, Lars K

    2013-02-01

    Mammalian cell cultures typically exhibit an energy inefficient phenotype characterized by the consumption of large quantities of glucose and the concomitant production of large quantities of lactate. Under certain conditions, mammalian cells can switch to a more energy efficient state during which lactate is consumed. Using a metabolic model derived from a mouse genome scale model we performed flux balance analysis of Chinese hamster ovary cells before and after a metabolic switch from lactate production (in the presence of glucose) to lactate consumption (after glucose depletion). Despite a residual degree of freedom after accounting for measurements, the calculated flux ranges and associated errors were narrow enough to enable investigation of metabolic changes across the metabolic switch. Surprisingly, the fluxes through the lower part of the TCA cycle from oxoglutarate to malate were very similar (around 60 µmol/gDW/h) for both phases. A detailed analysis of the energy metabolism showed that cells consuming lactate have an energy efficiency (total ATP produced per total C-mol substrate consumed) six times greater than lactate producing cells.

  4. Scale-down of penicillin production in Penicillium chrysogenum.

    PubMed

    de Jonge, Lodewijk P; Buijs, Nicolaas A A; ten Pierick, Angela; Deshmukh, Amit; Zhao, Zheng; Kiel, Jan A K W; Heijnen, Joseph J; van Gulik, Walter M

    2011-08-01

    In large-scale production reactors the combination of high broth viscosity and large broth volume leads to insufficient liquid-phase mixing, resulting in gradients in, for example, the concentrations of substrate and oxygen. This often leads to differences in productivity of the full-scale process compared with laboratory scale. In this scale-down study of penicillin production, the influence of substrate gradients on process performance and cell physiology was investigated by imposing an intermittent feeding regime on a laboratory-scale culture of a high yielding strain of Penicillium chrysogenum. It was found that penicillin production was reduced by a factor of two in the intermittently fed cultures relative to constant feed cultivations fed with the same amount of glucose per hour, while the biomass yield was the same. Measurement of the levels of the intermediates of the penicillin biosynthesis pathway, along with the enzyme levels, suggested that the reduction of the flux through the penicillin pathway is mainly the result of a lower influx into the pathway, possibly due to inhibitory levels of adenosine monophosphate and pyrophosphate and lower activating levels of adenosine triphosphate during the zero-substrate phase of each cycle of intermittent feeding.

  5. Comparing Scales of Environmental Effects from Gasoline and Ethanol Production

    NASA Astrophysics Data System (ADS)

    Parish, Esther S.; Kline, Keith L.; Dale, Virginia H.; Efroymson, Rebecca A.; McBride, Allen C.; Johnson, Timothy L.; Hilliard, Michael R.; Bielicki, Jeffrey M.

    2013-02-01

    Understanding the environmental effects of alternative fuel production is critical to characterizing the sustainability of energy resources to inform policy and regulatory decisions. The magnitudes of these environmental effects vary according to the intensity and scale of fuel production along each step of the supply chain. We compare the spatial extent and temporal duration of ethanol and gasoline production processes and environmental effects based on a literature review and then synthesize the scale differences on space-time diagrams. Comprehensive assessment of any fuel-production system is a moving target, and our analysis shows that decisions regarding the selection of spatial and temporal boundaries of analysis have tremendous influences on the comparisons. Effects that strongly differentiate gasoline and ethanol-supply chains in terms of scale are associated with when and where energy resources are formed and how they are extracted. Although both gasoline and ethanol production may result in negative environmental effects, this study indicates that ethanol production traced through a supply chain may impact less area and result in more easily reversed effects of a shorter duration than gasoline production.

  6. Comparing scales of environmental effects from gasoline and ethanol production.

    PubMed

    Parish, Esther S; Kline, Keith L; Dale, Virginia H; Efroymson, Rebecca A; McBride, Allen C; Johnson, Timothy L; Hilliard, Michael R; Bielicki, Jeffrey M

    2013-02-01

    Understanding the environmental effects of alternative fuel production is critical to characterizing the sustainability of energy resources to inform policy and regulatory decisions. The magnitudes of these environmental effects vary according to the intensity and scale of fuel production along each step of the supply chain. We compare the spatial extent and temporal duration of ethanol and gasoline production processes and environmental effects based on a literature review and then synthesize the scale differences on space-time diagrams. Comprehensive assessment of any fuel-production system is a moving target, and our analysis shows that decisions regarding the selection of spatial and temporal boundaries of analysis have tremendous influences on the comparisons. Effects that strongly differentiate gasoline and ethanol-supply chains in terms of scale are associated with when and where energy resources are formed and how they are extracted. Although both gasoline and ethanol production may result in negative environmental effects, this study indicates that ethanol production traced through a supply chain may impact less area and result in more easily reversed effects of a shorter duration than gasoline production.

  7. Microbial metabolic engineering for L-threonine production.

    PubMed

    Dong, Xunyan; Quinn, Peter J; Wang, Xiaoyuan

    2012-01-01

    L-threonine, one of the three major amino acids produced throughout the world, has a wide application in industry, as an additive or as a precursor for the biosynthesis of other chemicals. It is predominantly produced through microbial fermentation the efficiency of which largely depends on the quality of strains. Metabolic engineering based on a cogent understanding of the metabolic pathways of L-threonine biosynthesis and regulation provides an effective alternative to the traditional breeding for strain development. Continuing efforts have been made in revealing the mechanisms and regulation of L-threonine producing strains, as well as in metabolic engineering of suitable organisms whereby genetically-defined, industrially competitive L-threonine producing strains have been successfully constructed. This review focuses on the global metabolic and regulatory networks responsible for L-threonine biosynthesis, the molecular mechanisms of regulation, and the strategies employed in strain engineering.

  8. Systems metabolic engineering of Corynebacterium glutamicum for production of the chemical chaperone ectoine

    PubMed Central

    2013-01-01

    Background The stabilizing and function-preserving effects of ectoines have attracted considerable biotechnological interest up to industrial scale processes for their production. These rely on the release of ectoines from high-salinity-cultivated microbial producer cells upon an osmotic down-shock in rather complex processor configurations. There is growing interest in uncoupling the production of ectoines from the typical conditions required for their synthesis, and instead design strains that naturally release ectoines into the medium without the need for osmotic changes, since the use of high-salinity media in the fermentation process imposes notable constraints on the costs, design, and durability of fermenter systems. Results Here, we used a Corynebacterium glutamicum strain as a cellular chassis to establish a microbial cell factory for the biotechnological production of ectoines. The implementation of a mutant aspartokinase enzyme ensured efficient supply of L-aspartate-beta-semialdehyde, the precursor for ectoine biosynthesis. We further engineered the genome of the basic C. glutamicum strain by integrating a codon-optimized synthetic ectABCD gene cluster under expressional control of the strong and constitutive C. glutamicum tuf promoter. The resulting recombinant strain produced ectoine and excreted it into the medium; however, lysine was still found as a by-product. Subsequent inactivation of the L-lysine exporter prevented the undesired excretion of lysine while ectoine was still exported. Using the streamlined cell factory, a fed-batch process was established that allowed the production of ectoine with an overall productivity of 6.7 g L-1 day-1 under growth conditions that did not rely on the use of high-salinity media. Conclusions The present study describes the construction of a stable microbial cell factory for recombinant production of ectoine. We successfully applied metabolic engineering strategies to optimize its synthetic production in the

  9. Endogenous fructose production and metabolism in the liver contributes to the development of metabolic syndrome

    PubMed Central

    Lanaspa, Miguel A; Ishimoto, Takuji; Li, Nanxing; Cicerchi, Christina; Orlicky, David J.; Ruzicky, Philip; Rivard, Christopher; Inaba, Shinichiro; Roncal-Jimenez, Carlos A.; Bales, Elise S.; Diggle, Christine P.; Asipu, Aruna; Petrash, J. Mark; Kosugi, Tomoki; Maruyama, Shoichi; Sanchez-Lozada, Laura G.; McManaman, James L.; Bonthron, David T; Sautin, Yuri Y.; Johnson, Richard J.

    2013-01-01

    Carbohydrates with high glycemic index are proposed to promote the development of obesity, insulin resistance and fatty liver, but the mechanism by which this occurs remains unknown. High serum glucose concentrations glucose are known to induce the polyol pathway and increase fructose generation in the liver. Here we show that this hepatic, endogenously-produced fructose causes systemic metabolic changes. We demonstrate that mice unable to metabolize fructose are protected from an increase in energy intake and body weight, visceral obesity, fatty liver, elevated insulin levels and hyperleptinemia after exposure to 10% glucose for 14 weeks. In normal mice, glucose consumption is accompanied by aldose reductase and polyol pathway activation in steatotic areas. In this regard, we show that aldose reductase deficient mice were protected against glucose-induced fatty liver. We conclude that endogenous fructose generation and metabolism in the liver represents an important mechanism whereby glucose promotes the development of metabolic syndrome. PMID:24022321

  10. A state of the art of metabolic networks of unicellular microalgae and cyanobacteria for biofuel production.

    PubMed

    Baroukh, Caroline; Muñoz-Tamayo, Rafael; Steyer, Jean-Philippe; Bernard, Olivier

    2015-07-01

    The most promising and yet challenging application of microalgae and cyanobacteria is the production of renewable energy: biodiesel from microalgae triacylglycerols and bioethanol from cyanobacteria carbohydrates. A thorough understanding of microalgal and cyanobacterial metabolism is necessary to master and optimize biofuel production yields. To this end, systems biology and metabolic modeling have proven to be very efficient tools if supported by an accurate knowledge of the metabolic network. However, unlike heterotrophic microorganisms that utilize the same substrate for energy and as carbon source, microalgae and cyanobacteria require light for energy and inorganic carbon (CO2 or bicarbonate) as carbon source. This double specificity, together with the complex mechanisms of light capture, makes the representation of metabolic network nonstandard. Here, we review the existing metabolic networks of photoautotrophic microalgae and cyanobacteria. We highlight how these networks have been useful for gaining insight on photoautotrophic metabolism.

  11. Metabolism

    MedlinePlus

    Metabolism refers to all the physical and chemical processes in the body that convert or use energy, ... Tortora GJ, Derrickson BH. Metabolism. In: Tortora GJ, Derrickson ... Physiology . 14th ed. Hoboken, NJ: John Wiley & Sons; 2014:chap ...

  12. Metabolism

    MedlinePlus

    ... El metabolismo Metabolism Basics Our bodies get the energy they need from food through metabolism, the chemical ... that convert the fuel from food into the energy needed to do everything from moving to thinking ...

  13. Camelina sativa: An ideal platform for the metabolic engineering and field production of industrial lipids.

    PubMed

    Bansal, Sunil; Durrett, Timothy P

    2016-01-01

    Triacylglycerols (TAG) containing modified fatty acids with functionality beyond those found in commercially grown oil seed crops can be used as feedstocks for biofuels and bio-based materials. Over the years, advances have been made in transgenically engineering the production of various modified fatty acids in the model plant Arabidopsis thaliana. However, the inability to produce large quantities of transgenic seed has limited the functional testing of the modified oil. In contrast, the emerging oil seed crop Camelina sativa possesses important agronomic traits that recommend it as an ideal production platform for biofuels and industrial feedstocks. Camelina possesses low water and fertilizer requirements and is capable of yields comparable to other oil seed crops, particularly under stress conditions. Importantly, its relatively short growing season enables it to be grown as part of a double cropping system. In addition to these valuable agronomic features, Camelina is amenable to rapid metabolic engineering. The development of a simple and effective transformation method, combined with the availability of abundant transcriptomic and genomic data, has allowed the generation of transgenic Camelina lines capable of synthesizing high levels of unusual lipids. In some cases these levels have surpassed what was achieved in Arabidopsis. Further, the ability to use Camelina as a crop production system has allowed for the large scale growth of transgenic oil seed crops, enabling subsequent physical property testing. The application of new techniques such as genome editing will further increase the suitability of Camelina as an ideal platform for the production of biofuels and bio-materials.

  14. Improving lactate metabolism in an intensified CHO culture process: productivity and product quality considerations.

    PubMed

    Xu, Sen; Hoshan, Linda; Chen, Hao

    2016-11-01

    In this study, we discussed the development and optimization of an intensified CHO culture process, highlighting medium and control strategies to improve lactate metabolism. A few strategies, including supplementing glucose with other sugars (fructose, maltose, and galactose), controlling glucose level at <0.2 mM, and supplementing medium with copper sulfate, were found to be effective in reducing lactate accumulation. Among them, copper sulfate supplementation was found to be critical for process optimization when glucose was in excess. When copper sulfate was supplemented in the new process, two-fold increase in cell density (66.5 ± 8.4 × 10(6) cells/mL) and titer (11.9 ± 0.6 g/L) was achieved. Productivity and product quality attributes differences between batch, fed-batch, and concentrated fed-batch cultures were discussed. The importance of process and cell metabolism understanding when adapting the existing process to a new operational mode was demonstrated in the study.

  15. Exploring Hydrogenotrophic Methanogenesis: a Genome Scale Metabolic Reconstruction of Methanococcus maripaludis

    PubMed Central

    Richards, Matthew A.; Lie, Thomas J.; Zhang, Juan; Ragsdale, Stephen W.

    2016-01-01

    ABSTRACT Hydrogenotrophic methanogenesis occurs in multiple environments, ranging from the intestinal tracts of animals to anaerobic sediments and hot springs. Energy conservation in hydrogenotrophic methanogens was long a mystery; only within the last decade was it reported that net energy conservation for growth depends on electron bifurcation. In this work, we focus on Methanococcus maripaludis, a well-studied hydrogenotrophic marine methanogen. To better understand hydrogenotrophic methanogenesis and compare it with methylotrophic methanogenesis that utilizes oxidative phosphorylation rather than electron bifurcation, we have built iMR539, a genome scale metabolic reconstruction that accounts for 539 of the 1,722 protein-coding genes of M. maripaludis strain S2. Our reconstructed metabolic network uses recent literature to not only represent the central electron bifurcation reaction but also incorporate vital biosynthesis and assimilation pathways, including unique cofactor and coenzyme syntheses. We show that our model accurately predicts experimental growth and gene knockout data, with 93% accuracy and a Matthews correlation coefficient of 0.78. Furthermore, we use our metabolic network reconstruction to probe the implications of electron bifurcation by showing its essentiality, as well as investigating the infeasibility of aceticlastic methanogenesis in the network. Additionally, we demonstrate a method of applying thermodynamic constraints to a metabolic model to quickly estimate overall free-energy changes between what comes in and out of the cell. Finally, we describe a novel reconstruction-specific computational toolbox we created to improve usability. Together, our results provide a computational network for exploring hydrogenotrophic methanogenesis and confirm the importance of electron bifurcation in this process. IMPORTANCE Understanding and applying hydrogenotrophic methanogenesis is a promising avenue for developing new bioenergy technologies

  16. Protein-based biorefining: metabolic engineering for production of chemicals and fuel with regeneration of nitrogen fertilizers.

    PubMed

    Wernick, David G; Liao, James C

    2013-02-01

    Threats to stable oil supplies and concerns over environmental emissions have pushed for renewable biofuel developments to minimize dependence on fossil resources. Recent biofuel progress has moved towards fossil resource-independent carbon cycles, but environmental issues regarding use of nitrogen fertilizers have not been addressed on a global scale. The recently demonstrated conversion of waste protein biomass into advanced biofuels and renewable chemicals, while recycling nitrogen fertilizers, offers a glimpse of the efforts needed to balance the nitrogen cycle at scale. In general, the catabolism of protein into biofuels is challenging because of physiological regulation and thermodynamic limitations. This conversion became possible with metabolic engineering around ammonia assimilation, intracellular nitrogen flux, and quorum sensing. This review highlights the metabolic engineering solutions in transforming those cellular processes into driving forces for the high yield of chemical products from protein.

  17. Estimated Metabolic Heat Production of Helicopter Aircrew Members during Operations in Iraq and Afghanistan

    DTIC Science & Technology

    2012-04-01

    individual performed. Metabolic heat was estimated using a mechanical efficiency of 20% for human movement and a standardized conversion to watts (W...various activities an individual performed. Metabolic heat was estimated using a mechanical efficiency of 20% for human movement and a standardized...expenditure for that hour. To calculate metabolic heat production, a mechanical efficiency of muscular work of 20% was assumed (21, 23). Therefore

  18. Metabolic engineering of Clostridium acetobutylicum for the enhanced production of isopropanol-butanol-ethanol fuel mixture.

    PubMed

    Jang, Yu-Sin; Malaviya, Alok; Lee, Joungmin; Im, Jung Ae; Lee, Sang Yup; Lee, Julia; Eom, Moon-Ho; Cho, Jung-Hee; Seung, Do Young

    2013-01-01

    Butanol is considered as a superior biofuel, which is conventionally produced by clostridial acetone-butanol-ethanol (ABE) fermentation. Among ABE, only butanol and ethanol can be used as fuel alternatives. Coproduction of acetone thus causes lower yield of fuel alcohols. Thus, this study aimed at developing an improved Clostridium acetobutylicum strain possessing enhanced fuel alcohol production capability. For this, we previously developed a hyper ABE producing BKM19 strain was further engineered to convert acetone into isopropanol. The BKM19 strain was transformed with the plasmid pIPA100 containing the sadh (primary/secondary alcohol dehydrogenase) and hydG (putative electron transfer protein) genes from the Clostridium beijerinckii NRRL B593 cloned under the control of the thiolase promoter. The resulting BKM19 (pIPA100) strain produced 27.9 g/l isopropanol-butanol-ethanol (IBE) as a fuel alcohols with negligible amount of acetone (0.4 g/l) from 97.8 g/l glucose in lab-scale (2 l) batch fermentation. Thus, this metabolically engineered strain was able to produce 99% of total solvent produced as fuel alcohols. The scalability and stability of BKM19 (pIPA100) were evaluated at 200 l pilot-scale fermentation, which showed that the fuel alcohol yield could be improved to 0.37 g/g as compared to 0.29 g/g obtained at lab-scale fermentation, while attaining a similar titer. To the best of our knowledge, this is the highest titer of IBE achieved and the first report on the large scale fermentation of C. acetobutylicum for IBE production.

  19. A Scalable Algorithm to Explore the Gibbs Energy Landscape of Genome-Scale Metabolic Networks

    PubMed Central

    De Martino, Daniele; Figliuzzi, Matteo

    2012-01-01

    The integration of various types of genomic data into predictive models of biological networks is one of the main challenges currently faced by computational biology. Constraint-based models in particular play a key role in the attempt to obtain a quantitative understanding of cellular metabolism at genome scale. In essence, their goal is to frame the metabolic capabilities of an organism based on minimal assumptions that describe the steady states of the underlying reaction network via suitable stoichiometric constraints, specifically mass balance and energy balance (i.e. thermodynamic feasibility). The implementation of these requirements to generate viable configurations of reaction fluxes and/or to test given flux profiles for thermodynamic feasibility can however prove to be computationally intensive. We propose here a fast and scalable stoichiometry-based method to explore the Gibbs energy landscape of a biochemical network at steady state. The method is applied to the problem of reconstructing the Gibbs energy landscape underlying metabolic activity in the human red blood cell, and to that of identifying and removing thermodynamically infeasible reaction cycles in the Escherichia coli metabolic network (iAF1260). In the former case, we produce consistent predictions for chemical potentials (or log-concentrations) of intracellular metabolites; in the latter, we identify a restricted set of loops (23 in total) in the periplasmic and cytoplasmic core as the origin of thermodynamic infeasibility in a large sample () of flux configurations generated randomly and compatibly with the prior information available on reaction reversibility. PMID:22737065

  20. Why does offspring size affect performance? Integrating metabolic scaling with life-history theory

    PubMed Central

    Pettersen, Amanda K.; White, Craig R.; Marshall, Dustin J.

    2015-01-01

    Within species, larger offspring typically outperform smaller offspring. While the relationship between offspring size and performance is ubiquitous, the cause of this relationship remains elusive. By linking metabolic and life-history theory, we provide a general explanation for why larger offspring perform better than smaller offspring. Using high-throughput respirometry arrays, we link metabolic rate to offspring size in two species of marine bryozoan. We found that metabolism scales allometrically with offspring size in both species: while larger offspring use absolutely more energy than smaller offspring, larger offspring use proportionally less of their maternally derived energy throughout the dependent, non-feeding phase. The increased metabolic efficiency of larger offspring while dependent on maternal investment may explain offspring size effects—larger offspring reach nutritional independence (feed for themselves) with a higher proportion of energy relative to structure than smaller offspring. These findings offer a potentially universal explanation for why larger offspring tend to perform better than smaller offspring but studies on other taxa are needed. PMID:26559952

  1. Towards improved genome-scale metabolic network reconstructions: unification, transcript specificity and beyond

    PubMed Central

    Pfau, Thomas; Pacheco, Maria Pires; Sauter, Thomas

    2016-01-01

    Genome-scale metabolic network reconstructions provide a basis for the investigation of the metabolic properties of an organism. There are reconstructions available for multiple organisms, from prokaryotes to higher organisms and methods for the analysis of a reconstruction. One example is the use of flux balance analysis to improve the yields of a target chemical, which has been applied successfully. However, comparison of results between existing reconstructions and models presents a challenge because of the heterogeneity of the available reconstructions, for example, of standards for presenting gene-protein-reaction associations, nomenclature of metabolites and reactions or selection of protonation states. The lack of comparability for gene identifiers or model-specific reactions without annotated evidence often leads to the creation of a new model from scratch, as data cannot be properly matched otherwise. In this contribution, we propose to improve the predictive power of metabolic models by switching from gene-protein-reaction associations to transcript-isoform-reaction associations, thus taking advantage of the improvement of precision in gene expression measurements. To achieve this precision, we discuss available databases that can be used to retrieve this type of information and point at issues that can arise from their neglect. Further, we stress issues that arise from non-standardized building pipelines, like inconsistencies in protonation states. In addition, problems arising from the use of non-specific cofactors, e.g. artificial futile cycles, are discussed, and finally efforts of the metabolic modelling community to unify model reconstructions are highlighted. PMID:26615025

  2. Pulmonary diffusional screening and the scaling laws of mammalian metabolic rates

    NASA Astrophysics Data System (ADS)

    Hou, Chen; Mayo, Michael

    2011-12-01

    Theoretical considerations suggest that the mammalian metabolic rate is linearly proportional to the surface areas of mitochondria, capillary, and alveolar membranes. However, the scaling exponents of these surface areas to the mammals' body mass (approximately 0.9-1) are higher than exponents of the resting metabolic rate (RMR) to body mass (approximately 0.75), although similar to the one of exercise metabolic rate (EMR); the underlying physiological cause of this mismatch remains unclear. The analysis presented here shows that discrepancies between the scaling exponents of RMR and the relevant surface areas may originate from, at least for the system of alveolar membranes in mammalian lungs, the facts that (i) not all of the surface area is involved in the gas exchange and (ii) that larger mammals host a smaller effective surface area that participates in the material exchange rate. A result of these facts is that lung surface areas unused at rest are activated under heavy breathing conditions (e.g., exercise), wherein larger mammals support larger activated surface areas that provide a higher capability to increase the gas-exchange rate, allowing for mammals to meet, for example, the high energetic demands of foraging and predation.

  3. Pulmonary diffusional screening and the scaling laws of mammalian metabolic rates.

    PubMed

    Hou, Chen; Mayo, Michael

    2011-12-01

    Theoretical considerations suggest that the mammalian metabolic rate is linearly proportional to the surface areas of mitochondria, capillary, and alveolar membranes. However, the scaling exponents of these surface areas to the mammals' body mass (approximately 0.9-1) are higher than exponents of the resting metabolic rate (RMR) to body mass (approximately 0.75), although similar to the one of exercise metabolic rate (EMR); the underlying physiological cause of this mismatch remains unclear. The analysis presented here shows that discrepancies between the scaling exponents of RMR and the relevant surface areas may originate from, at least for the system of alveolar membranes in mammalian lungs, the facts that (i) not all of the surface area is involved in the gas exchange and (ii) that larger mammals host a smaller effective surface area that participates in the material exchange rate. A result of these facts is that lung surface areas unused at rest are activated under heavy breathing conditions (e.g., exercise), wherein larger mammals support larger activated surface areas that provide a higher capability to increase the gas-exchange rate, allowing for mammals to meet, for example, the high energetic demands of foraging and predation.

  4. The allometry of the smallest: superlinear scaling of microbial metabolic rates in the Atlantic Ocean

    PubMed Central

    García, Francisca C; García-Martín, Enma Elena; Taboada, Fernando González; Sal, Sofía; Serret, Pablo; López-Urrutia, Ángel

    2016-01-01

    Prokaryotic planktonic organisms are small in size but largely relevant in marine biogeochemical cycles. Due to their reduced size range (0.2 to 1 μm in diameter), the effects of cell size on their metabolism have been hardly considered and are usually not examined in field studies. Here, we show the results of size-fractionated experiments of marine microbial respiration rate along a latitudinal transect in the Atlantic Ocean. The scaling exponents obtained from the power relationship between respiration rate and size were significantly higher than one. This superlinearity was ubiquitous across the latitudinal transect but its value was not universal revealing a strong albeit heterogeneous effect of cell size on microbial metabolism. Our results suggest that the latitudinal differences observed are the combined result of changes in cell size and composition between functional groups within prokaryotes. Communities where the largest size fraction was dominated by prokaryotic cyanobacteria, especially Prochlorococcus, have lower allometric exponents. We hypothesize that these larger, more complex prokaryotes fall close to the evolutionary transition between prokaryotes and protists, in a range where surface area starts to constrain metabolism and, hence, are expected to follow a scaling closer to linearity. PMID:26636550

  5. 75 FR 51843 - In the Matter of Certain Large Scale Integrated Circuit Semiconductor Chips and Products...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-08-23

    ... Matter of Certain Large Scale Integrated Circuit Semiconductor Chips and Products Containing the Same... certain large scale integrated circuit semiconductor chips and products containing same by reason...

  6. Mass, phylogeny, and temperature are sufficient to explain differences in metabolic scaling across mammalian orders?

    PubMed

    Griebeler, Eva Maria; Werner, Jan

    2016-12-01

    Whether basal metabolic rate-body mass scaling relationships have a single exponent is highly discussed, and also the correct statistical model to establish relationships. Here, we aimed (1) to identify statistically best scaling models for 17 mammalian orders, Marsupialia, Eutheria and all mammals, and (2) thereby to prove whether correcting for differences in species' body temperature and their shared evolutionary history improves models and their biological interpretability. We used the large dataset from Sieg et al. (The American Naturalist174, 2009, 720) providing species' body mass (BM), basal metabolic rate (BMR) and body temperature (T). We applied different statistical approaches to identify the best scaling model for each taxon: ordinary least squares regression analysis (OLS) and phylogenetically informed analysis (PGLS), both without and with controlling for T. Under each approach, we tested linear equations (log-log-transformed data) estimating scaling exponents and normalization constants, and such with a variable normalization constant and a fixed exponent of either ⅔ or ¾, and also a curvature. Only under temperature correction, an additional variable coefficient modeled the influence of T on BMR. Except for Pholidata and Carnivora, in all taxa studied linear models were clearly supported over a curvature by AICc. They indicated no single exponent at the level of orders or at higher taxonomic levels. The majority of all best models corrected for phylogeny, whereas only half of them included T. When correcting for T, the mathematically expected correlation between the exponent (b) and the normalization constant (a) in the standard scaling model y = a x(b) was removed, but the normalization constant and temperature coefficient still correlated strongly. In six taxa, T and BM correlated positively or negatively. All this hampers a disentangling of the effect of BM, T and other factors on BMR, and an interpretation of linear BMR-BM scaling

  7. Reach-scale spatial and temporal variations in whole-stream metabolism estimates within a lowland river in California

    NASA Astrophysics Data System (ADS)

    Villamizar, S. R.; Pai, H.; Butler, C. A.; Barnes, P.; Harmon, T. C.

    2009-12-01

    Stationary and distributed estimates of river metabolism developed during a 4-day period within a lowland section of the Merced River in California, allowed us to identify spatial and temporal variations in the estimates not related to the River Continuum Concept but to local factors. The estimates of whole-stream metabolism (Primary Production/Community Respiration, or P/R ratios) were obtained using a one-station approach at both a stationary sampling point, and at an array of 11 points along a 23-m river cross section using a robotic Networked Info-Mechanical System (NIMS). An in-river meteorological station, distributed self-logging light sensors, and digital time-stamped imagery were used to assess spatiotemporal photosynthetically active radiation (PAR) availability. Temporally, PAR was found to be the limiting factor during the last day of analysis, explaining the variation in estimated P/R ratios (0.79, 0.77, 0.76 and 0.56 for days one through four, respectively). Spatially, the distribution of metabolism estimates found along the river cross section, with P/R ratios ranging from 0.51 to 0.94, may be attributed to (1) the variable availability of PAR due to both the influence of the riparian vegetation and the daily radiation and shade patterns; and (2) a heterogeneous distribution of the respiration rates within the cross section (on a volumetric basis, respiration rates were three-fold higher in the shallow zone than in the deep zone of the cross section). A comparison of the results obtained with the two approaches (stationary and distributed) suggests that only one sampling point within the cross section may not be sufficient to characterize reach-scale processes related to stream metabolism in the context of habitat quality, groundwater-surface water exchanges, and other spatiotemporally complex issues.

  8. The genome-scale metabolic model iIN800 of Saccharomyces cerevisiae and its validation: a scaffold to query lipid metabolism

    PubMed Central

    Nookaew, Intawat; Jewett, Michael C; Meechai, Asawin; Thammarongtham, Chinae; Laoteng, Kobkul; Cheevadhanarak, Supapon; Nielsen, Jens; Bhumiratana, Sakarindr

    2008-01-01

    Background Up to now, there have been three published versions of a yeast genome-scale metabolic model: iFF708, iND750 and iLL672. All three models, however, lack a detailed description of lipid metabolism and thus are unable to be used as integrated scaffolds for gaining insights into lipid metabolism from multilevel omic measurement technologies (e.g. genome-wide mRNA levels). To overcome this limitation, we reconstructed a new version of the Saccharomyces cerevisiae genome-scale model, iIN800 that includes a more rigorous and detailed description of lipid metabolism. Results The reconstructed metabolic model comprises 1446 reactions and 1013 metabolites. Beyond incorporating new reactions involved in lipid metabolism, we also present new biomass equations that improve the predictive power of flux balance analysis simulations. Predictions of both growth capability and large scale in silico single gene deletions by iIN800 were consistent with experimental data. In addition, 13C-labeling experiments validated the new biomass equations and calculated intracellular fluxes. To demonstrate the applicability of iIN800, we show that the model can be used as a scaffold to reveal the regulatory importance of lipid metabolism precursors and intermediates that would have been missed in previous models from transcriptome datasets. Conclusion Performing integrated analyses using iIN800 as a network scaffold is shown to be a valuable tool for elucidating the behavior of complex metabolic networks, particularly for identifying regulatory targets in lipid metabolism that can be used for industrial applications or for understanding lipid disease states. PMID:18687109

  9. Shaping Component Leads for Small-Scale Production

    NASA Technical Reports Server (NTRS)

    Jan, Lawrence

    1987-01-01

    Simple tool makes it easy to bend leads of electronic components quickly and uniformly for assembly on circuit board. Useful in small-scale production of electronic circuits; saves labor but avoids cost of complicated machinery. Made in range of sizes to accommodate components in variety of dimensions.

  10. Recent developments in cosmogenic nuclide production rate scaling

    NASA Astrophysics Data System (ADS)

    Lifton, N. A.

    2013-12-01

    A new cosmogenic nuclide production rate scaling model based on analytical fits to Monte Carlo simulations of atmospheric cosmic ray flux spectra (both of which agree well with measured spectra) enables identification and quantification of the biases in previously published models (Lifton, N., Sato, T., Dunai, T., in review, Earth and Planet. Sci. Lett.). Scaling predictions derived from the new model (termed LSD) suggest two potential sources of bias in the previous models: different energy responses of the secondary neutron detectors used in developing the models, and different geomagnetic parameterizations. In addition, the particle flux spectra generated by the LSD model allow one to generate nuclide-specific scaling factors that reflect the influences of the flux energy distribution and the relevant excitation functions (probability of nuclide production in a given nuclear reaction as a function of energy). Resulting scaling factors indicate 3He shows the strongest positive deviation from the flux-based scaling, while 14C exhibits a negative deviation. These results are consistent with previous studies showing an increasing 3He/10Be ratio with altitude in the Himalayas, but with a much lower magnitude for the effect. Furthermore, the new model provides a flexible framework for exploring the implications of future advances in model inputs. For example, the effects of recently updated paleomagnetic models (e.g. Korte et al., 2011, Earth and Planet Sci. Lett. 312, 497-505) on scaling predictions will also be presented.

  11. On the depth and scale of metabolic rate variation: scaling of oxygen consumption rates and enzymatic activity in the Class Cephalopoda (Mollusca).

    PubMed

    Seibel, Brad A

    2007-01-01

    Recent ecological theory depends, for predictive power, on the apparent similarity of metabolic rates within broad taxonomic or functional groups of organisms (e.g. invertebrates or ectotherms). Such metabolic commonality is challenged here, as I demonstrate more than 200-fold variation in metabolic rates independent of body mass and temperature in a single class of animals, the Cephalopoda, over seven orders of magnitude size range. I further demonstrate wide variation in the slopes of metabolic scaling curves. The observed variation in metabolism reflects differential selection among species for locomotory capacity rather than mass or temperature constraints. Such selection is highest among epipelagic squids (Lolignidae and Ommastrephidae) that, as adults, have temperature-corrected metabolic rates higher than mammals of similar size.

  12. Use of genome-scale metabolic models in evolutionary systems biology.

    PubMed

    Papp, Balázs; Szappanos, Balázs; Notebaart, Richard A

    2011-01-01

    One of the major aims of the nascent field of evolutionary systems biology is to test evolutionary hypotheses that are not only realistic from a population genetic point of view but also detailed in terms of molecular biology mechanisms. By providing a mapping between genotype and phenotype for hundreds of genes, genome-scale systems biology models of metabolic networks have already provided valuable insights into the evolution of metabolic gene contents and phenotypes of yeast and other microbial species. Here we review the recent use of these computational models to predict the fitness effect of mutations, genetic interactions, evolutionary outcomes, and to decipher the mechanisms of mutational robustness. While these studies have demonstrated that even simplified models of biochemical reaction networks can be highly informative for evolutionary analyses, they have also revealed the weakness of this modeling framework to quantitatively predict mutational effects, a challenge that needs to be addressed for future progress in evolutionary systems biology.

  13. Supply-Side Constraints Are Insufficient to Explain the Ontogenetic Scaling of Metabolic Rate in the Tobacco Hornworm, Manduca sexta

    PubMed Central

    Callier, Viviane; Nijhout, H. Frederik

    2012-01-01

    Explanations for the hypoallometric scaling of metabolic rate through ontogeny generally fall into two categories: supply-side constraints on delivery of oxygen, or decreased mass-specific intrinsic demand for oxygen. In many animals, supply and demand increase together as the body grows, thus making it impossible to tease apart the relative contributions of changing supply and demand to the observed scaling of metabolic rate. In larval insects, the large components of the tracheal system are set in size at each molt, but then remain constant in size until the next molt. Larvae of Manduca sexta increase up to ten-fold in mass between molts, leading to increased oxygen need without a concomitant increase in supply. At the molt, the tracheal system is shed and replaced with a new, larger one. Due to this discontinuous growth of the tracheal system, insect larvae present an ideal system in which to examine the relative contributions of supply and demand of oxygen to the ontogenetic scaling of metabolic rate. We observed that the metabolic rate at the beginning of successive instars scales hypoallometrically. This decrease in specific intrinsic demand could be due to a decrease in the proportion of highly metabolically active tissues (the midgut) or to a decrease in mitochondrial activity in individual cells. We found that decreased intrinsic demand, mediated by a decrease in the proportion of highly metabolically active tissues in the fifth instar, along with a decrease in the specific mitochondrial activity, contribute to the hypoallometric scaling of metabolic rate. PMID:23029018

  14. Supply-side constraints are insufficient to explain the ontogenetic scaling of metabolic rate in the tobacco Hornworm, Manduca sexta.

    PubMed

    Callier, Viviane; Nijhout, H Frederik

    2012-01-01

    Explanations for the hypoallometric scaling of metabolic rate through ontogeny generally fall into two categories: supply-side constraints on delivery of oxygen, or decreased mass-specific intrinsic demand for oxygen. In many animals, supply and demand increase together as the body grows, thus making it impossible to tease apart the relative contributions of changing supply and demand to the observed scaling of metabolic rate. In larval insects, the large components of the tracheal system are set in size at each molt, but then remain constant in size until the next molt. Larvae of Manduca sexta increase up to ten-fold in mass between molts, leading to increased oxygen need without a concomitant increase in supply. At the molt, the tracheal system is shed and replaced with a new, larger one. Due to this discontinuous growth of the tracheal system, insect larvae present an ideal system in which to examine the relative contributions of supply and demand of oxygen to the ontogenetic scaling of metabolic rate. We observed that the metabolic rate at the beginning of successive instars scales hypoallometrically. This decrease in specific intrinsic demand could be due to a decrease in the proportion of highly metabolically active tissues (the midgut) or to a decrease in mitochondrial activity in individual cells. We found that decreased intrinsic demand, mediated by a decrease in the proportion of highly metabolically active tissues in the fifth instar, along with a decrease in the specific mitochondrial activity, contribute to the hypoallometric scaling of metabolic rate.

  15. Urban Scaling and the Production Function for Cities

    PubMed Central

    Lobo, José; Bettencourt, Luís M. A.; Strumsky, Deborah; West, Geoffrey B.

    2013-01-01

    The factors that account for the differences in the economic productivity of urban areas have remained difficult to measure and identify unambiguously. Here we show that a microscopic derivation of urban scaling relations for economic quantities vs. population, obtained from the consideration of social and infrastructural properties common to all cities, implies an effective model of economic output in the form of a Cobb-Douglas type production function. As a result we derive a new expression for the Total Factor Productivity (TFP) of urban areas, which is the standard measure of economic productivity per unit of aggregate production factors (labor and capital). Using these results we empirically demonstrate that there is a systematic dependence of urban productivity on city population size, resulting from the mismatch between the size dependence of wages and labor, so that in contemporary US cities productivity increases by about 11% with each doubling of their population. Moreover, deviations from the average scale dependence of economic output, capturing the effect of local factors, including history and other local contingencies, also manifest surprising regularities. Although, productivity is maximized by the combination of high wages and low labor input, high productivity cities show invariably high wages and high levels of employment relative to their size expectation. Conversely, low productivity cities show both low wages and employment. These results shed new light on the microscopic processes that underlie urban economic productivity, explain the emergence of effective aggregate urban economic output models in terms of labor and capital inputs and may inform the development of economic theory related to growth. PMID:23544042

  16. Integrating Kinetic Model of E. coli with Genome Scale Metabolic Fluxes Overcomes Its Open System Problem and Reveals Bistability in Central Metabolism

    PubMed Central

    Mannan, Ahmad A.; Toya, Yoshihiro; Shimizu, Kazuyuki; McFadden, Johnjoe; Kierzek, Andrzej M.; Rocco, Andrea

    2015-01-01

    An understanding of the dynamics of the metabolic profile of a bacterial cell is sought from a dynamical systems analysis of kinetic models. This modelling formalism relies on a deterministic mathematical description of enzyme kinetics and their metabolite regulation. However, it is severely impeded by the lack of available kinetic information, limiting the size of the system that can be modelled. Furthermore, the subsystem of the metabolic network whose dynamics can be modelled is faced with three problems: how to parameterize the model with mostly incomplete steady state data, how to close what is now an inherently open system, and how to account for the impact on growth. In this study we address these challenges of kinetic modelling by capitalizing on multi-‘omics’ steady state data and a genome-scale metabolic network model. We use these to generate parameters that integrate knowledge embedded in the genome-scale metabolic network model, into the most comprehensive kinetic model of the central carbon metabolism of E. coli realized to date. As an application, we performed a dynamical systems analysis of the resulting enriched model. This revealed bistability of the central carbon metabolism and thus its potential to express two distinct metabolic states. Furthermore, since our model-informing technique ensures both stable states are constrained by the same thermodynamically feasible steady state growth rate, the ensuing bistability represents a temporal coexistence of the two states, and by extension, reveals the emergence of a phenotypically heterogeneous population. PMID:26469081

  17. A numerical scale to assess the outcomes of metabolic/bariatric surgery (NOMS)

    PubMed Central

    Michalik, Maciej; Buchwald, Henry

    2015-01-01

    Introduction Absent today is a simple numerical system of outcomes assessment that recognizes that bariatric surgery is metabolic surgery and incorporates weight loss, hypertension control, and type 2 diabetes control. Aim To introduce a simple, new Numerical Scale to Assess the Outcomes of Metabolic Surgery (NOMS). Material and methods For the stratification of weight outcomes, we used the percentage excess weight loss (%EWL); for hypertension, the systolic blood pressure (SBP) and diastolic blood pressure (DBP) combined with medication usage; and for type 2 diabetes, the hemoglobin A1c (HbA1c) value combined with medication usage. Results Utilizing the guidelines of the American Diabetes Association, the Working Group of the European Society of Hypertension, the European Society of Cardiology, and the American College of Cardiology/American Heart Association, we propose for %EWL: W1 ≥ 50, W2 > 25 and < 50, and W3 ≤ 25; for hypertension H1 SBP/DPB < 140/90 mm Hg on no medication, H2 SBP/DBP ≥ 140/90 mm Hg with improvement of SBP or possible reduction of antihypertensive medication, and H3 no change or SBP higher than before surgery; for diabetes mellitus D1 HbA1c ≤ 7% and no medication, D2 HbA1c > 7% with a decrease of the HbA1c level or possible reduction of medication, D3 no change in HbA1c or HbA1c higher than before surgery. Designations of H0 and D0 are given if hypertension or diabetes was not present before surgery. Patient examples for numerical scores are provided. Conclusions The introduction of our numerical scale (NOMS) can be of benefit in metabolic/bariatric outcomes assessment; communications among metabolic/bariatric surgery centers, physicians, and patients; and for more precise reporting in the evidence-based literature. PMID:26649080

  18. Extreme Scaling of Production Visualization Software on Diverse Architectures

    SciTech Connect

    Childs, Henry; Pugmire, David; Ahern, Sean; Whitlock, Brad; Howison, Mark; Weber, Gunther; Bethel, E. Wes

    2009-12-22

    We present the results of a series of experiments studying how visualization software scales to massive data sets. Although several paradigms exist for processing large data, we focus on pure parallelism, the dominant approach for production software. These experiments utilized multiple visualization algorithms and were run on multiple architectures. Two types of experiments were performed. For the first, we examined performance at massive scale: 16,000 or more cores and one trillion or more cells. For the second, we studied weak scaling performance. These experiments were performed on the largest data set sizes published to date in visualization literature, and the findings on scaling characteristics and bottlenecks contribute to understanding of how pure parallelism will perform at high levels of concurrency and with very large data sets.

  19. Toward glycerol biorefinery: metabolic engineering for the production of biofuels and chemicals from glycerol.

    PubMed

    Chen, Zhen; Liu, Dehua

    2016-01-01

    As an inevitable by-product of the biofuel industry, glycerol is becoming an attractive feedstock for biorefinery due to its abundance, low price and high degree of reduction. Converting crude glycerol into value-added products is important to increase the economic viability of the biofuel industry. Metabolic engineering of industrial strains to improve its performance and to enlarge the product spectrum of glycerol biotransformation process is highly important toward glycerol biorefinery. This review focuses on recent metabolic engineering efforts as well as challenges involved in the utilization of glycerol as feedstock for the production of fuels and chemicals, especially for the production of diols, organic acids and biofuels.

  20. Batch and semi-continuous microalgal TAG production in lab-scale and outdoor photobioreactors.

    PubMed

    Benvenuti, Giulia; Bosma, Rouke; Ji, Fang; Lamers, Packo; Barbosa, Maria J; Wijffels, René H

    2016-01-01

    Microalgal triglycerides (TAGs) represent a sustainable feedstock for food, chemical and biofuel industries. The operational strategy (batch, semi-continuous, continuous cultivations) has an impact on the TAG productivity. In this study, semi-continuous (i.e. with fixed harvesting frequency) and batch cultivations were compared on TAG production both at lab-scale and in outdoor cultivations. At lab-scale, the semi-continuous TAG productivity was highest for a cycle time of 2 days (SC1; 0.21 g L(-1) day(-1)) and similar to the maximum obtained with the batch (optimal harvest time; 0.23 g L(-1) day(-1)). Although TAG content was lower for SC1 (22 %) than for the batch (35 %), higher biomass productivities were obtained with SC1. Outdoors, semi-continuous cultivations were subjected to a lower degree of stress (i.e. higher amount of nitrogen present in the system relative to the given irradiance) compared to lab-scale. This yielded low and similar TAG contents (10-13 %) in the different semi-continuous runs that were outdone by the batch on both TAG content (15-25 %) and productivity (batch, 0.97-2.46 g m(-2) day(-1); semi-continuous, 0.35-0.85 g m(-2) day(-1)). The lab-scale experiments showed that semi-continuous strategies, besides leading to similar TAG productivities compared to the batch, could make TAG production cost effective by valorising also non-TAG compounds. However, optimization of outdoor semi-continuous cultivations is still required. For instance, the nitrogen supply and the harvest frequency should be adjusted on the total irradiance. Additionally, future research should focus on recovery metabolism upon nitrogen resupply.

  1. Biological hydrogen production by dark fermentation: challenges and prospects towards scaled-up production.

    PubMed

    RenNanqi; GuoWanqian; LiuBingfeng; CaoGuangli; DingJie

    2011-06-01

    Among different technologies of hydrogen production, bio-hydrogen production exhibits perhaps the greatest potential to replace fossil fuels. Based on recent research on dark fermentative hydrogen production, this article reviews the following aspects towards scaled-up application of this technology: bioreactor development and parameter optimization, process modeling and simulation, exploitation of cheaper raw materials and combining dark-fermentation with photo-fermentation. Bioreactors are necessary for dark-fermentation hydrogen production, so the design of reactor type and optimization of parameters are essential. Process modeling and simulation can help engineers design and optimize large-scale systems and operations. Use of cheaper raw materials will surely accelerate the pace of scaled-up production of biological hydrogen. And finally, combining dark-fermentation with photo-fermentation holds considerable promise, and has successfully achieved maximum overall hydrogen yield from a single substrate. Future development of bio-hydrogen production will also be discussed.

  2. Genome-Scale Reconstruction and Analysis of the Metabolic Network in the Hyperthermophilic Archaeon Sulfolobus Solfataricus

    PubMed Central

    Ulas, Thomas; Riemer, S. Alexander; Zaparty, Melanie; Siebers, Bettina; Schomburg, Dietmar

    2012-01-01

    We describe the reconstruction of a genome-scale metabolic model of the crenarchaeon Sulfolobus solfataricus, a hyperthermoacidophilic microorganism. It grows in terrestrial volcanic hot springs with growth occurring at pH 2–4 (optimum 3.5) and a temperature of 75–80°C (optimum 80°C). The genome of Sulfolobus solfataricus P2 contains 2,992,245 bp on a single circular chromosome and encodes 2,977 proteins and a number of RNAs. The network comprises 718 metabolic and 58 transport/exchange reactions and 705 unique metabolites, based on the annotated genome and available biochemical data. Using the model in conjunction with constraint-based methods, we simulated the metabolic fluxes induced by different environmental and genetic conditions. The predictions were compared to experimental measurements and phenotypes of S. solfataricus. Furthermore, the performance of the network for 35 different carbon sources known for S. solfataricus from the literature was simulated. Comparing the growth on different carbon sources revealed that glycerol is the carbon source with the highest biomass flux per imported carbon atom (75% higher than glucose). Experimental data was also used to fit the model to phenotypic observations. In addition to the commonly known heterotrophic growth of S. solfataricus, the crenarchaeon is also able to grow autotrophically using the hydroxypropionate-hydroxybutyrate cycle for bicarbonate fixation. We integrated this pathway into our model and compared bicarbonate fixation with growth on glucose as sole carbon source. Finally, we tested the robustness of the metabolism with respect to gene deletions using the method of Minimization of Metabolic Adjustment (MOMA), which predicted that 18% of all possible single gene deletions would be lethal for the organism. PMID:22952675

  3. Uniform Sampling of Steady States in Metabolic Networks: Heterogeneous Scales and Rounding

    PubMed Central

    De Martino, Daniele; Mori, Matteo; Parisi, Valerio

    2015-01-01

    The uniform sampling of convex polytopes is an interesting computational problem with many applications in inference from linear constraints, but the performances of sampling algorithms can be affected by ill-conditioning. This is the case of inferring the feasible steady states in models of metabolic networks, since they can show heterogeneous time scales. In this work we focus on rounding procedures based on building an ellipsoid that closely matches the sampling space, that can be used to define an efficient hit-and-run (HR) Markov Chain Monte Carlo. In this way the uniformity of the sampling of the convex space of interest is rigorously guaranteed, at odds with non markovian methods. We analyze and compare three rounding methods in order to sample the feasible steady states of metabolic networks of three models of growing size up to genomic scale. The first is based on principal component analysis (PCA), the second on linear programming (LP) and finally we employ the Lovazs ellipsoid method (LEM). Our results show that a rounding procedure dramatically improves the performances of the HR in these inference problems and suggest that a combination of LEM or LP with a subsequent PCA perform the best. We finally compare the distributions of the HR with that of two heuristics based on the Artificially Centered hit-and-run (ACHR), gpSampler and optGpSampler. They show a good agreement with the results of the HR for the small network, while on genome scale models present inconsistencies. PMID:25849140

  4. Thermocline deepening boosts ecosystem metabolism: evidence from a large-scale lake enclosure experiment simulating a summer storm.

    PubMed

    Giling, Darren P; Nejstgaard, Jens C; Berger, Stella A; Grossart, Hans-Peter; Kirillin, Georgiy; Penske, Armin; Lentz, Maren; Casper, Peter; Sareyka, Jörg; Gessner, Mark O

    2017-04-01

    Extreme weather events can pervasively influence ecosystems. Observations in lakes indicate that severe storms in particular can have pronounced ecosystem-scale consequences, but the underlying mechanisms have not been rigorously assessed in experiments. One major effect of storms on lakes is the redistribution of mineral resources and plankton communities as a result of abrupt thermocline deepening. We aimed at elucidating the importance of this effect by mimicking in replicated large enclosures (each 9 m in diameter, ca. 20 m deep, ca. 1300 m(3) in volume) a mixing event caused by a severe natural storm that was previously observed in a deep clear-water lake. Metabolic rates were derived from diel changes in vertical profiles of dissolved oxygen concentrations using a Bayesian modelling approach, based on high-frequency measurements. Experimental thermocline deepening stimulated daily gross primary production (GPP) in surface waters by an average of 63% for >4 weeks even though thermal stratification re-established within 5 days. Ecosystem respiration (ER) was tightly coupled to GPP, exceeding that in control enclosures by 53% over the same period. As GPP responded more strongly than ER, net ecosystem productivity (NEP) of the entire water column was also increased. These protracted increases in ecosystem metabolism and autotrophy were driven by a proliferation of inedible filamentous cyanobacteria released from light and nutrient limitation after they were entrained from below the thermocline into the surface water. Thus, thermocline deepening by a single severe storm can induce prolonged responses of lake ecosystem metabolism independent of other storm-induced effects, such as inputs of terrestrial materials by increased catchment run-off. This highlights that future shifts in frequency, severity or timing of storms are an important component of climate change, whose impacts on lake thermal structure will superimpose upon climate trends to influence algal

  5. Deviation from symmetrically self-similar branching in trees predicts altered hydraulics, mechanics, light interception and metabolic scaling.

    PubMed

    Smith, Duncan D; Sperry, John S; Enquist, Brian J; Savage, Van M; McCulloh, Katherine A; Bentley, Lisa P

    2014-01-01

    The West, Brown, Enquist (WBE) model derives symmetrically self-similar branching to predict metabolic scaling from hydraulic conductance, K, (a metabolism proxy) and tree mass (or volume, V). The original prediction was Kα V(0.75). We ask whether trees differ from WBE symmetry and if it matters for plant function and scaling. We measure tree branching and model how architecture influences K, V, mechanical stability, light interception and metabolic scaling. We quantified branching architecture by measuring the path fraction, Pf : mean/maximum trunk-to-twig pathlength. WBE symmetry produces the maximum, Pf = 1.0. We explored tree morphospace using a probability-based numerical model constrained only by biomechanical principles. Real tree Pf ranged from 0.930 (nearly symmetric) to 0.357 (very asymmetric). At each modeled tree size, a reduction in Pf led to: increased K; decreased V; increased mechanical stability; and decreased light absorption. When Pf was ontogenetically constant, strong asymmetry only slightly steepened metabolic scaling. The Pf ontogeny of real trees, however, was 'U' shaped, resulting in size-dependent metabolic scaling that exceeded 0.75 in small trees before falling below 0.65. Architectural diversity appears to matter considerably for whole-tree hydraulics, mechanics, photosynthesis and potentially metabolic scaling. Optimal architectures likely exist that maximize carbon gain per structural investment.

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

    PubMed

    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.

  7. Scale-up and kinetic modeling for bioethanol production.

    PubMed

    Imamoglu, Esra; Sukan, Fazilet Vardar

    2013-09-01

    Bioethanol was produced from acidic hydrolysate of rice hulls using recombinant Escherichia coli KO11. Two different issues (scale-up and kinetic modeling) were evaluated simultaneously and concomitantly for bioethanol production. During the step-wise scale-up process from 100 mL shaken flask to 10 L stirred-tank bioreactor, the constant Reynolds number and the constant impeller tip speed were evaluated as scale-up methodologies under laboratory conditions. It was determined that the volumetric bioethanol productivity was 88% higher in 10 L bioreactor in comparison to the value of 0.21 g L(-1) h(-1) in shaken flask. The modified Monod and Luedeking-Piret models provided an accurate approach for the modeling of the experimental data. Ethanol concentration reached the maximum level of 29.03 g/L, which was 5% higher than the value of model prediction in 10 L bioreactor. The findings of this research could contribute to the industrial scale productions especially from lignocellulosic raw materials.

  8. Metabolic engineering for microbial production of aromatic amino acids and derived compounds.

    PubMed

    Bongaerts, J; Krämer, M; Müller, U; Raeven, L; Wubbolts, M

    2001-10-01

    Metabolic engineering to design and construct microorganisms suitable for the production of aromatic amino acids and derivatives thereof requires control of a complicated network of metabolic reactions that partly act in parallel and frequently are in rapid equilibrium. Engineering the regulatory circuits, the uptake of carbon, the glycolytic pathway, the pentose phosphate pathway, and the common aromatic amino acid pathway as well as amino acid importers and exporters that have all been targeted to effect higher productivities of these compounds are discussed.

  9. Full-scale validation of a model of algal productivity.

    PubMed

    Béchet, Quentin; Shilton, Andy; Guieysse, Benoit

    2014-12-02

    While modeling algal productivity outdoors is crucial to assess the economic and environmental performance of full-scale cultivation, most of the models hitherto developed for this purpose have not been validated under fully relevant conditions, especially with regard to temperature variations. The objective of this study was to independently validate a model of algal biomass productivity accounting for both light and temperature and constructed using parameters experimentally derived using short-term indoor experiments. To do this, the accuracy of a model developed for Chlorella vulgaris was assessed against data collected from photobioreactors operated outdoor (New Zealand) over different seasons, years, and operating conditions (temperature-control/no temperature-control, batch, and fed-batch regimes). The model accurately predicted experimental productivities under all conditions tested, yielding an overall accuracy of ±8.4% over 148 days of cultivation. For the purpose of assessing the feasibility of full-scale algal cultivation, the use of the productivity model was therefore shown to markedly reduce uncertainty in cost of biofuel production while also eliminating uncertainties in water demand, a critical element of environmental impact assessments. Simulations at five climatic locations demonstrated that temperature-control in outdoor photobioreactors would require tremendous amounts of energy without considerable increase of algal biomass. Prior assessments neglecting the impact of temperature variations on algal productivity in photobioreactors may therefore be erroneous.

  10. Capturing the response of Clostridium acetobutylicum to chemical stressors using a regulated genome-scale metabolic model

    DOE PAGES

    Dash, Satyakam; Mueller, Thomas J.; Venkataramanan, Keerthi P.; ...

    2014-10-14

    Clostridia are anaerobic Gram-positive Firmicutes containing broad and flexible systems for substrate utilization, which have been used successfully to produce a range of industrial compounds. Clostridium acetobutylicum has been used to produce butanol on an industrial scale through acetone-butanol-ethanol (ABE) fermentation. A genome-scale metabolic (GSM) model is a powerful tool for understanding the metabolic capacities of an organism and developing metabolic engineering strategies for strain development. The integration of stress related specific transcriptomics information with the GSM model provides opportunities for elucidating the focal points of regulation.

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

    PubMed Central

    Nambou, Komi; Jian, Xingxing; Zhang, Xinkai; Wei, Liujing; Lou, Jiajia; Madzak, Catherine; Hua, Qiang

    2015-01-01

    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. PMID:26703753

  12. Industrialization of lipid nanoparticles: From laboratory-scale to large-scale production line.

    PubMed

    Hu, Caibiao; Qian, Airui; Wang, Qiang; Xu, Feng; He, Yi; Xu, Jing; Xia, Yongchang; Xia, Qiang

    2016-12-01

    This work aimed at developing a large-scale modular production line, which referred to coenzyme Q10 loaded-NLC as well as its continuous and scalable emulsification and homogenization process. The production line exhibited good control over the emulsification and homogenization process and enabled the particle size of NLC below 210nm at a throughput of 25kg/h (for lipid solution at a flow rate of 0.4kg/min). Among the several process parameters investigated, the size of the NLC was mainly influenced by the pre-emulsification temperature, homogenization pressure and homogenization. Suitable emulsification temperature (70°C), homogenization pressure (600, 800bar), and homogenization cycle (3, 4cycles) resulted in relatively smaller particles. These results proved that coenzyme Q10, a model active, had been successfully loaded into the NLC. Meanwhile, the large-scale production line can be effectively applied for continuous and modular production of NLC. The line had modern networking features-essential in the Internet age-and a modular design that was easily modified and upgraded. In addition, the long-term stability over 6month was monitored at 30°C and at 40°C to assess a potential effect of the laboratory scale and large scale on stability. All batches at room temperature and below were stable, and only a negligible increase in size was observed.

  13. Metabolic changes during B cell differentiation for the production of intestinal IgA antibody.

    PubMed

    Kunisawa, Jun

    2017-04-01

    To sustain the bio-energetic demands of growth, proliferation, and effector functions, the metabolism of immune cells changes dramatically in response to immunologic stimuli. In this review, I focus on B cell metabolism, especially regarding the production of intestinal IgA antibody. Accumulating evidence has implicated not only host-derived factors (e.g., cytokines) but also gut environmental factors, including the possible involvement of commensal bacteria and diet, in the control of B cell metabolism during intestinal IgA antibody production. These findings yield new insights into the regulation of immunosurveillance and homeostasis in the gut.

  14. Mass-Specific Metabolic Rate Influences Sperm Performance through Energy Production in Mammals.

    PubMed

    Tourmente, Maximiliano; Roldan, Eduardo R S

    2015-01-01

    Mass-specific metabolic rate, the rate at which organisms consume energy per gram of body weight, is negatively associated with body size in metazoans. As a consequence, small species have higher cellular metabolic rates and are able to process resources at a faster rate than large species. Since mass-specific metabolic rate has been shown to constrain evolution of sperm traits, and most of the metabolic activity of sperm cells relates to ATP production for sperm motility, we hypothesized that mass-specific metabolic rate could influence sperm energetic metabolism at the cellular level if sperm cells maintain the metabolic rate of organisms that generate them. We compared data on sperm straight-line velocity, mass-specific metabolic rate, and sperm ATP content from 40 mammalian species and found that the mass-specific metabolic rate positively influences sperm swimming velocity by (a) an indirect effect of sperm as the result of an increased sperm length, and (b) a direct effect independent of sperm length. In addition, our analyses show that species with higher mass-specific metabolic rate have higher ATP content per sperm and higher concentration of ATP per μm of sperm length, which are positively associated with sperm velocity. In conclusion, our results suggest that species with high mass-specific metabolic rate have been able to evolve both long and fast sperm. Moreover, independently of its effect on the production of larger sperm, the mass-specific metabolic rate is able to influence sperm velocity by increasing sperm ATP content in mammals.

  15. Invariant features of metabolic networks: a data analysis application on scaling properties of biochemical pathways

    NASA Astrophysics Data System (ADS)

    Giuliani, Alessandro; Zbilut, Joseph P.; Conti, Filippo; Manetti, Cesare; Miccheli, Alfredo

    2004-06-01

    The network metaphor is currently one of the most common general paradigms in biological sciences: this paradigm spans different scales of definition going from gene regulation to protein-protein interaction studies and metabolic regulation networks. Generally, the networks are defined by the nature of the connected elements (nodes) and their relative relations (edges). In this paper we demonstrate how the same biochemical regulation network can assume different shapes in terms of both constituting elements and intervening relations while remaining recognizable as a specific entity. This behaviour can be explained by the general scaling properties of biological networks and points to regulation pathways as emergent features of biochemical systems posited at a different hierarchical level with respect to the intervening metabolites.

  16. Genome-scale reconstruction of the metabolic network in Yersinia pestis, strain 91001

    SciTech Connect

    Navid, A; Almaas, E

    2009-01-13

    The gram-negative bacterium Yersinia pestis, the aetiological agent of bubonic plague, is one the deadliest pathogens known to man. Despite its historical reputation, plague is a modern disease which annually afflicts thousands of people. Public safety considerations greatly limit clinical experimentation on this organism and thus development of theoretical tools to analyze the capabilities of this pathogen is of utmost importance. Here, we report the first genome-scale metabolic model of Yersinia pestis biovar Mediaevalis based both on its recently annotated genome, and physiological and biochemical data from literature. Our model demonstrates excellent agreement with Y. pestis known metabolic needs and capabilities. Since Y. pestis is a meiotrophic organism, we have developed CryptFind, a systematic approach to identify all candidate cryptic genes responsible for known and theoretical meiotrophic phenomena. In addition to uncovering every known cryptic gene for Y. pestis, our analysis of the rhamnose fermentation pathway suggests that betB is the responsible cryptic gene. Despite all of our medical advances, we still do not have a vaccine for bubonic plague. Recent discoveries of antibiotic resistant strains of Yersinia pestis coupled with the threat of plague being used as a bioterrorism weapon compel us to develop new tools for studying the physiology of this deadly pathogen. Using our theoretical model, we can study the cell's phenotypic behavior under different circumstances and identify metabolic weaknesses which may be harnessed for the development of therapeutics. Additionally, the automatic identification of cryptic genes expands the usage of genomic data for pharmaceutical purposes.

  17. Identifying anti-growth factors for human cancer cell lines through genome-scale metabolic modeling

    PubMed Central

    Ghaffari, Pouyan; Mardinoglu, Adil; Asplund, Anna; Shoaie, Saeed; Kampf, Caroline; Uhlen, Mathias; Nielsen, Jens

    2015-01-01

    Human cancer cell lines are used as important model systems to study molecular mechanisms associated with tumor growth, hereunder how genomic and biological heterogeneity found in primary tumors affect cellular phenotypes. We reconstructed Genome scale metabolic models (GEMs) for eleven cell lines based on RNA-Seq data and validated the functionality of these models with data from metabolite profiling. We used cell line-specific GEMs to analyze the differences in the metabolism of cancer cell lines, and to explore the heterogeneous expression of the metabolic subsystems. Furthermore, we predicted 85 antimetabolites that can inhibit growth of, or even kill, any of the cell lines, while at the same time not being toxic for 83 different healthy human cell types. 60 of these antimetabolites were found to inhibit growth in all cell lines. Finally, we experimentally validated one of the predicted antimetabolites using two cell lines with different phenotypic origins, and found that it is effective in inhibiting the growth of these cell lines. Using immunohistochemistry, we also showed high or moderate expression levels of proteins targeted by the validated antimetabolite. Identified anti-growth factors for inhibition of cell growth may provide leads for the development of efficient cancer treatment strategies. PMID:25640694

  18. Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data.

    PubMed

    Gu, Deqing; Jian, Xingxing; Zhang, Cheng; Hua, Qiang

    2016-06-08

    Genome-scale metabolic network models (GEMs) have played important roles in the design of genetically engineered strains and helped biologists to decipher metabolism. However, due to the complex gene-reaction relationships that exist in model systems, most algorithms have limited capabilities with respect to directly predicting accurate genetic design for metabolic engineering. In particular, methods that predict reaction knockout strategies leading to overproduction are often impractical in terms of gene manipulations. Recently, we proposed a method named LTM (logical transformation of model) to simplify the gene-reaction associations by introducing intermediate pseudo reactions, which makes it possible to generate genetic design. Here, we propose an alternative method to relieve researchers from deciphering complex gene-reactions by adding pseudo gene controlling reactions. In comparison to LTM, this new method introduces fewer pseudo reactions and generates a much smaller model system named as gModel. We showed that gModel allows two seldom reported applications: identification of minimal genomes and design of minimal cell factories within a modified OptKnock framework. In addition, gModel could be used to integrate expression data directly and improve the performance of the E-Fmin method for predicting fluxes. In conclusion, the model transformation procedure will facilitate genetic research based on GEMs, extending their applications.

  19. Small scale production of biofuels: a feasibility assessment

    SciTech Connect

    Geyler, J.

    1980-01-01

    Current public policy fails to adequately address one of the most exigent concerns of the agricultural producer: the cost and availability of energy. Specifically, they are interested in energy production alternatives that are feasible and economic for implementation by smaller agricultural producers. After a extended review of much of the available popular and technical literature, as well as conducting interviews with numerous individuals knowledgeable in the field of alternative energy production, the Roosevelt-Custer Regional Council for Development has prepared this preliminary feasibility assessment on the small scale production of biofuels in North Dakota. The production of energy from renewable sources is not chimerical; it is reality. Currently, North Dakotan's rely on energy produced from agricultural products to run their automobiles and to heat their homes, as well as to dry the crops on which much of the North Dakota economy depends. Over the next 20 years, this reliance on renewable energy sources is expected to triple. Unfortunately, most of the processes currently used to produce these biofuels are not adaptable for use by the smaller producer/consumer. Today, economics simply preclude the small scale production of biofuels. A deplorable consequence of this lag between demand and technical feasibility is the appearance of the quick-buck consultant. These individuals have not limited their activities to North Dakota but, in fact, they have appeared over the length and breadth of this Nation. This report then is an assessment of the feasibility of producing biofuels in North Dakota by the small scale producer. Specific types of biofuels to be critiqued are: alcohol; vegetable oils; biogas/methane; and biomass briquettes.

  20. Small scale production of biofuels: a feasibility assessment

    SciTech Connect

    Geyler, J.

    1980-01-01

    Current public policy fails to adequately address one of the most exigent concerns of the agricultural producer: the cost and availability of energy. Specifically, they are interested in energy production alternatives that are feasible and economic for implementation by smaller agricultural producers. After an extended review of much of the available popular and technical literature, as well as conducting interviews with numerous individuals knowledgeable in the field of alternative energy production, the Roosevelt-Custer Regional Council for Development has prepared this preliminary feasibility assessment on the small scale production of biofuels in North Dakota. The production of energy from renewable sources is not commerical; it is reality. Currently, North Dakotan's rely on energy produced from agricultural products to run their automobiles and to heat their homes, as well as to dry the crops on which much of the North Dakota economy depends. Over the next 20 years, this reliance on renewable energy sources is expected to triple. Unfortunately, most of the processes currently used to produce these biofuels are not adaptable for use by the smaller producer/consumer. Today, economics simply preclude the small scale production of biofuels. A deplorable consequence of this lag between demand and technical feasibility is the appearance of the quick-buck consultant. These individuals have not limited their activities to North Dakota but, in fact, they have appeared over the length and breadth of this nation. This report then is an assessment of the feasibility of producing biofuels in North Dakota by the small scale producer. Specific types of biofuels to be critiqued are: alcohol; vegetable oils; biogas/methane; and biomass briquettes.

  1. Interannual Variation in Phytoplankton Primary Production at a Global Scale

    NASA Technical Reports Server (NTRS)

    Rousseaux, Cecile Severine; Gregg, Watson W.

    2013-01-01

    We used the NASA Ocean Biogeochemical Model (NOBM) combined with remote sensing data via assimilation to evaluate the contribution of four phytoplankton groups to the total primary production. First, we assessed the contribution of each phytoplankton groups to the total primary production at a global scale for the period 1998-2011. Globally, diatoms contributed the most to the total phytoplankton production ((is)approximately 50%, the equivalent of 20 PgC·y1). Coccolithophores and chlorophytes each contributed approximately 20% ((is) approximately 7 PgC·y1) of the total primary production and cyanobacteria represented about 10% ((is) approximately 4 PgC·y1) of the total primary production. Primary production by diatoms was highest in the high latitudes ((is) greater than 40 deg) and in major upwelling systems (Equatorial Pacific and Benguela system). We then assessed interannual variability of this group-specific primary production over the period 1998-2011. Globally the annual relative contribution of each phytoplankton groups to the total primary production varied by maximum 4% (1-2 PgC·y1). We assessed the effects of climate variability on group-specific primary production using global (i.e., Multivariate El Niño Index, MEI) and "regional" climate indices (e.g., Southern Annular Mode (SAM), Pacific Decadal Oscillation (PDO) and North Atlantic Oscillation (NAO)). Most interannual variability occurred in the Equatorial Pacific and was associated with climate variability as indicated by significant correlation (p (is) less than 0.05) between the MEI and the group-specific primary production from all groups except coccolithophores. In the Atlantic, climate variability as indicated by NAO was significantly correlated to the primary production of 2 out of the 4 groups in the North Central Atlantic (diatoms/cyanobacteria) and in the North Atlantic (chlorophytes and coccolithophores). We found that climate variability as indicated by SAM had only a limited effect

  2. Metabolic engineering of Escherichia coli for 1-butanol production.

    PubMed

    Atsumi, Shota; Cann, Anthony F; Connor, Michael R; Shen, Claire R; Smith, Kevin M; Brynildsen, Mark P; Chou, Katherine J Y; Hanai, Taizo; Liao, James C

    2008-11-01

    Compared to ethanol, butanol offers many advantages as a substitute for gasoline because of higher energy content and higher hydrophobicity. Typically, 1-butanol is produced by Clostridium in a mixed-product fermentation. To facilitate strain improvement for specificity and productivity, we engineered a synthetic pathway in Escherichia coli and demonstrated the production of 1-butanol from this non-native user-friendly host. Alternative genes and competing pathway deletions were evaluated for 1-butanol production. Results show promise for using E. coli for 1-butanol production.

  3. Improving fatty acids production by engineering dynamic pathway regulation and metabolic control

    PubMed Central

    Xu, Peng; Li, Lingyun; Zhang, Fuming; Stephanopoulos, Gregory; Koffas, Mattheos

    2014-01-01

    Global energy demand and environmental concerns have stimulated increasing efforts to produce carbon-neutral fuels directly from renewable resources. Microbially derived aliphatic hydrocarbons, the petroleum-replica fuels, have emerged as promising alternatives to meet this goal. However, engineering metabolic pathways with high productivity and yield requires dynamic redistribution of cellular resources and optimal control of pathway expression. Here we report a genetically encoded metabolic switch that enables dynamic regulation of fatty acids (FA) biosynthesis in Escherichia coli. The engineered strains were able to dynamically compensate the critical enzymes involved in the supply and consumption of malonyl-CoA and efficiently redirect carbon flux toward FA biosynthesis. Implementation of this metabolic control resulted in an oscillatory malonyl-CoA pattern and a balanced metabolism between cell growth and product formation, yielding 15.7- and 2.1-fold improvement in FA titer compared with the wild-type strain and the strain carrying the uncontrolled metabolic pathway. This study provides a new paradigm in metabolic engineering to control and optimize metabolic pathways facilitating the high-yield production of other malonyl-CoA–derived compounds. PMID:25049420

  4. Improved Triacylglycerol Production in Acinetobacter baylyi ADP1 by Metabolic Engineering

    PubMed Central

    2011-01-01

    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. PMID:21592360

  5. Multi-scale modeling of Arabidopsis thaliana response to different CO2 conditions: From gene expression to metabolic flux.

    PubMed

    Liu, Lin; Shen, Fangzhou; Xin, Changpeng; Wang, Zhuo

    2016-01-01

    Multi-scale investigation from gene transcript level to metabolic activity is important to uncover plant response to environment perturbation. Here we integrated a genome-scale constraint-based metabolic model with transcriptome data to explore Arabidopsis thaliana response to both elevated and low CO2 conditions. The four condition-specific models from low to high CO2 concentrations show differences in active reaction sets, enriched pathways for increased/decreased fluxes, and putative post-transcriptional regulation, which indicates that condition-specific models are necessary to reflect physiological metabolic states. The simulated CO2 fixation flux at different CO2 concentrations is consistent with the measured Assimilation-CO2intercellular curve. Interestingly, we found that reactions in primary metabolism are affected most significantly by CO2 perturbation, whereas secondary metabolic reactions are not influenced a lot. The changes predicted in key pathways are consistent with existing knowledge. Another interesting point is that Arabidopsis is required to make stronger adjustment on metabolism to adapt to the more severe low CO2 stress than elevated CO2 . The challenges of identifying post-transcriptional regulation could also be addressed by the integrative model. In conclusion, this innovative application of multi-scale modeling in plants demonstrates potential to uncover the mechanisms of metabolic response to different conditions.

  6. Systematic Analysis of Conservation Relations in Escherichia coli Genome-Scale Metabolic Network Reveals Novel Growth Media

    PubMed Central

    Imieliński, Marcin; Belta, Calin; Rubin, Harvey; Halász, Ádam

    2006-01-01

    A biochemical species is called producible in a constraints-based metabolic model if a feasible steady-state flux configuration exists that sustains its nonzero concentration during growth. Extreme semipositive conservation relations (ESCRs) are the simplest semipositive linear combinations of species concentrations that are invariant to all metabolic flux configurations. In this article, we outline a fundamental relationship between the ESCRs of a metabolic network and the producibility of a biochemical species under a nutrient media. We exploit this relationship in an algorithm that systematically enumerates all minimal nutrient sets that render an objective species weakly producible (i.e., producible in the absence of thermodynamic constraints) through a simple traversal of ESCRs. We apply our results to a recent genome scale model of Escherichia coli metabolism, in which we traverse the 51 anhydrous ESCRs of the metabolic network to determine all 928 minimal aqueous nutrient media that render biomass weakly producible. Applying irreversibility constraints, we find 287 of these 928 nutrient sets to be thermodynamically feasible. We also find that an additional 365 of these nutrient sets are thermodynamically feasible in the presence of oxygen. Since biomass producibility is commonly used as a surrogate for growth in genome scale metabolic models, our results represent testable hypotheses of alternate growth media derived from in silico analysis of the E. coli genome scale metabolic network. PMID:16461408

  7. Urban Economies Resource Productivity and Decoupling: Metabolism Trends of 1996-2011 in Sweden, Stockholm, and Gothenburg.

    PubMed

    Kalmykova, Yuliya; Rosado, Leonardo; Patrício, João

    2015-07-21

    Resource productivity and evidence of economic decoupling were investigated on the basis of the time series in 1996-2011 of material flow analysis for Sweden, Stockholm, and Gothenburg. In the three cases, absolute reductions in CO2 emissions by about 20% were observed, energy consumption per capita decreased, while gross domestic product (GDP) per capita grew. The energy consumption of the residential and public sectors decreased drastically, while the transport energy consumption is still growing steadily. Decoupling of the economy as a whole (i.e., including materials) is not yet happening at any scale. The domestic material consumption (DMC) continues to increase, in parallel with the GDP. The rate of increase for DMC is slower than that for GDP in both Stockholm and Sweden as a whole (i.e., relative decoupling). The metabolism of the cities does not replicate the national metabolism, and the two cities each have their own distinct metabolism profiles. As a consequence, policy implications for each of the case studies were suggested. In general, because of the necessarily different roles of the two cities in the national economy, generic resource productivity benchmarks, such as CO2 per capita, should be avoided in favor of sectorial benchmarks, such as industry, transport, or residential CO2 per capita. In addition, the share of the city impacts caused by the provision of a service for the rest of the country, such as a port, could be allocated to the national economy.

  8. Pilot scale production of cellulolytic enzymes by Trichoderma reesei

    SciTech Connect

    Warzywoda, M.; Chevron, F.; Ferre, V.; Pourquie, J.

    1983-01-01

    The French substitute fuels program aims at the substitution of part of gasoline by methanol. In order to avoid phase separation of the gasoline-methanol blend, a cosolvant has to be added; one of the most efficient cosolvants is the mixture of acetone and butanol produced by anaerobic acetone-butanol fermentation. The Institut Francais du Petrole is thus implementing a research and development program on the production of acetone butanol from biomass, either sugar crops (fodder beets and Jerusalem artichoke) or lignocellulosic (corn stover and wheat straw). Production of sugars from lignocellulosics is a major part of this program. The enzymatic hydrolysis route, based on Trichoderma reesei cellulolytic enzymes, has been chosen since it does not cause any degradation of C/sub 5/ sugars which are good substrates of the acetone butanol fermentation. Efficient and cheap large-scale production of cellulolytic enzymes is thus a key step in this process. This paper reports on production of cellulases by Trichoderma reesei in a 3-m/sup 3/ pilot fermentor under conditions which should facilitate the scaling-up of the process. 7 references, 2 figures, 2 tables.

  9. NEON Data Products: Enabling Continental-Scale Ecological Science

    NASA Astrophysics Data System (ADS)

    Berukoff, S. J.

    2011-12-01

    The National Ecological Observatory Network (NEON) is a NSF-funded major research and facilities initiative under development, designed to address how climate change, land use change, and invasive species affect ecological science on a continental scale. The standardization of measurement methodologies, engineering practice, and data organization across NEON's sixty sites fosters the creation of ecological data products. These data products are community-approved and Observatory-vetted, and cover the breadth of NEON collection activities, including measurements of physical variables such as air, water, and soil temperature and chemistry, observations and analyses of species and habitats, and airborne spectral and LiDAR remote sensing. Together, these low-level (fundamental measurement and observation data)and high-level (integrative, continental-scale assessments) will be useful for scientists, students, educators, policymakers, and the general public. Here, we discuss the development status of NEON's data product suites, describing how they are constructed and vetted, and provide an example of how one current effort will provide several foundational data products. Further, we discuss and solicit feedback for how stakeholder communities can contribute to their veracity and validation.

  10. Scale-by-scale energy transfer in the production region of a fractal grid

    NASA Astrophysics Data System (ADS)

    Gomes Fernandes, Rafael; Ganapathisubramani, Bharathram; Vassilicos, Christos

    2013-11-01

    An experimental study of turbulence generated by low-blockage space-filling fractal square grids was performed using time-resolved Particle Image Velocimetry in a water tunnel. Scale-by-scale energy transfer is computed using the transport equation of the second order structure function for inhomogeneous flows. The balance of each of the equation terms is presented. In some particular locations in the production region, the map of the radial divergence of the energy flux shows an upward energy transfer in the direction of the mean flow and downwards in the perpendicular direction. In these locations, the energy spectra already exhibits a well-defined -5/3 power law over more than one decade; and the third order structure function of the velocity component parallel to the mean flow, evaluated in that direction at the centerline, has a positive sign throughout the range of scales dominated by the -5/3 scaling. Any velocity derivative checks of small-scale isotropy available to us indicate that the small-scales are indeed isotropic in these locations.

  11. Establishment, in silico analysis, and experimental verification of a large-scale metabolic network of the xanthan producing Xanthomonas campestris pv. campestris strain B100.

    PubMed

    Schatschneider, Sarah; Persicke, Marcus; Watt, Steven Alexander; Hublik, Gerd; Pühler, Alfred; Niehaus, Karsten; Vorhölter, Frank-Jörg

    2013-08-20

    The γ-proteobacterium Xanthomonas campestris pv. campestris (Xcc) B100 synthesizes the polysaccharide xanthan, a commercially important viscosifier. Since the complete genome of Xcc B100 is available, systems biology tools were applied to obtain a deeper understanding of the metabolism involved in xanthan biosynthesis. A large-scale metabolic network was reconstructed and manually curated. The reconstructed network included 352 genes, 437 biochemical reactions, 10 transport reactions, and 338 internal metabolites. To use this network for flux balance analysis, the biomass composition of Xcc B100 was determined. The comprehensive model obtained was applied for in silico analyses to predict biomass generation and gene essentiality. Predictions were extensively validated by analyzing batch culture performance and by carbon balancing including xanthan production. Single gene deletion mutants causing deficiencies in the central carbohydrate metabolism were constructed to enforce major flux redistributions. The impact of xanthan production was studied in vivo and in silico, comparing the physiology of a gumD mutant, negative in xanthan production, with the original strain. The results indicate a redistribution of resources from xanthan to biomass, rather than a reduction in carbon uptake. With this high quality metabolic model, both systems biology analyses and synthetic biology reengineering of Xcc gained an important tool.

  12. Lipid and fatty acid metabolism in Ralstonia eutropha: relevance for the biotechnological production of value-added products.

    PubMed

    Riedel, Sebastian L; Lu, Jingnan; Stahl, Ulf; Brigham, Christopher J

    2014-02-01

    Lipid and fatty acid metabolism has been well studied in model microbial organisms like Escherichia coli and Bacillus subtilis. The major precursor of fatty acid biosynthesis is also the major product of fatty acid degradation (β-oxidation), acetyl-CoA, which is a key metabolite for all organisms. Controlling carbon flux to fatty acid biosynthesis and from β-oxidation allows for the biosynthesis of natural products of biotechnological importance. Ralstonia eutropha can utilize acetyl-CoA from fatty acid metabolism to produce intracellular polyhydroxyalkanoate (PHA). R. eutropha can also be engineered to utilize fatty acid metabolism intermediates to produce different PHA precursors. Metabolism of lipids and fatty acids can be rerouted to convert carbon into other value-added compounds like biofuels. This review discusses the lipid and fatty acid metabolic pathways in R. eutropha and how they can be used to construct reagents for the biosynthesis of products of industrial importance. Specifically, how the use of lipids or fatty acids as the sole carbon source in R. eutropha cultures adds value to these biotechnological products will be discussed here.

  13. Determining the Products of Inertia for Small Scale UAVs

    NASA Technical Reports Server (NTRS)

    Lorenzetti, Joseph S.; Banuelos, Leonel C.; Clarke, Robert; Murillo, Oscar J.; Bowers, Albion H.

    2017-01-01

    Moments of inertia and products of inertia often need to be determined for aircraft. As complex bodies, their mass properties need to be determined experimentally for best accuracy. While several moment of inertia experimental techniques have been developed, there are few to determine the products of inertia. Products of inertia can be easily determined mathematically if the angle between the aircraft x body axis and principal x axis is known. This method finds the principal inclination angle by mathematically correlating the measured moments of inertia about a range of axes of the aircraft. This correlation uses a least squares error minimization of a mathematical model that describes the ellipse of inertia in the aircraft's x-z axes plane. Results from a test conducted on a small scale UAV (Unmanned Aerial Vehicle) at NASA Armstrong Flight Research Center is also presented, which is an example of the intended application of this technique.

  14. Scale incidence on production pipes of Cerro Prieto geothermal wells

    SciTech Connect

    Mercado, S.; Hurtado, R. ); Bermejo, F.; Terrazas, B.; Hernandez, L. . Coordinadora Ejecutiva de Cerro Prieto)

    1989-01-01

    Scaling of geothermal wells in the Cerro Prieto field is a problem that has been experienced since the plant start-up, but has been diminished by selection of the main productive strata (avoiding the mixing of water from different temperature layers) and using orifice restrictions at the wellhead discharge. This last technique works in some new wells with a wellhead pressure of 120 bars. One hundred fifty wells have been drilled with the deepest production well being 3650 m. The drilling for exploration and production wells continues at the present time. Around one hundred million tons of a water-steam mixture is extracted every year; 40% is separated steam which is used in three geothermoelectric power stations having a total of 620 MWe of installed capacity.

  15. Alternative Bioenergy: Small Scale Pellet Production from Forest Residues

    NASA Astrophysics Data System (ADS)

    Cochran, Audra S.

    Forests can readily supply feedstock for alternative bioenergy production. Feedstock removal has the potential to benefit forest health and provide ecosystem services, while also generating profit for landowners, contractors and forest managers. However, many landowners are faced with the challenge of managing forest residuals to meet slash compliances and fire regulations. Currently, most residuals are burned or left on site to decompose. Every year, the north-central Idaho region produces over 16 million dry tons of unutilized forest residues. In a time where alternative energy sources are growing in demand, new approaches to utilize these residuals for bioenergy production are being examined. One approach is a portable, small-scale wood pellet mill that can be taken directly to the logging site. Utilizing forest residues for pellet production reduces residue burning and its potential negative impacts on air quality. This presentation focuses on the quality of wood pellets manufactured by a portable wood pellet mill utilizing various forms of forest residuals.

  16. A 9-pool metabolic structured kinetic model describing days to seconds dynamics of growth and product formation by Penicillium chrysogenum.

    PubMed

    Tang, Wenjun; Deshmukh, Amit T; Haringa, Cees; Wang, Guan; van Gulik, Walter; van Winden, Wouter; Reuss, Matthias; Heijnen, Joseph J; Xia, Jianye; Chu, Ju; Noorman, Henk J

    2017-03-21

    A powerful approach for the optimization of industrial bioprocesses is to perform detailed simulations integrating large scale computational fluid dynamics (CFD) and cellular reaction dynamics (CRD). However, complex metabolic kinetic models containing a large number of equations pose formidable challenges in CFD-CRD coupling and computation time afterward. This necessitates to formulate a relatively simple but yet representative model structure. Such a kinetic model should be able to reproduce metabolic responses for short-term (mixing time scale of tens of seconds) and long-term (fed-batch cultivation of hours/days) dynamics in industrial bioprocesses. In this paper, we used Penicillium chrysogenum as a model system and developed a metabolically structured kinetic model for growth and production. By lumping the most important intracellular metabolites in 5 pools and 4 intracellular enzyme pools, linked by 10 reactions, we succeeded in maintaining the model structure relatively simple, while providing informative insight into the state of the organism. The performance of this 9-pool model was validated with a periodic glucose feast-famine cycle experiment at the minute time scale. Comparison of this model and a reported black box model for this strain shows the necessity of employing a structured model under feast-famine conditions. This proposed model provides deeper insight into the in vivo kinetics and, most importantly, can be straightforwardly integrated into a computational fluid dynamic framework for simulating complete fermentation performance and cell population dynamics in large scale and small scale fermentors. This article is protected by copyright. All rights reserved.

  17. A Newton Cooperative Genetic Algorithm Method for In Silico Optimization of Metabolic Pathway Production

    PubMed Central

    Mohamad, Mohd Saberi; Abdullah, Afnizanfaizal

    2015-01-01

    This paper presents an in silico optimization method of metabolic pathway production. The metabolic pathway can be represented by a mathematical model known as the generalized mass action model, which leads to a complex nonlinear equations system. The optimization process becomes difficult when steady state and the constraints of the components in the metabolic pathway are involved. To deal with this situation, this paper presents an in silico optimization method, namely the Newton Cooperative Genetic Algorithm (NCGA). The NCGA used Newton method in dealing with the metabolic pathway, and then integrated genetic algorithm and cooperative co-evolutionary algorithm. The proposed method was experimentally applied on the benchmark metabolic pathways, and the results showed that the NCGA achieved better results compared to the existing methods. PMID:25961295

  18. Metabolic differences in temperamental Brahman cattle can affect productivity

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Many factors may adversely affect the growth and productivity of livestock. These include stressors associated with management practices, such as weaning, handling relative to transportation, and vaccination, that can modulate growth through the production of stress-related hormones (i.e., cortisol,...

  19. L-malate production by metabolically engineered escherichia coli

    SciTech Connect

    Zhang, Xueli; Wang, Xuan; Shanmugam, Keelnatham T.; Ingram, Lonnie O'Neal

    2015-11-17

    A process for the production of malic acid in commercially significant quantities from the carbon compounds by genetically modified bacterial strains (GMBS; also referred to as biocatalysts or genetically modified microorganisms) is disclosed. Microorganisms suitable for the production of malic acid can be cultured in one or two-step processes as disclosed herein.

  20. Metabolism

    MedlinePlus

    ... and intestines. Several of the hormones of the endocrine system are involved in controlling the rate and direction ... For Kids For Parents MORE ON THIS TOPIC Endocrine System What Can I Do About My High Metabolism? ...

  1. Metabolism

    MedlinePlus

    ... symptoms. Metabolic diseases and conditions include: Hyperthyroidism (pronounced: hi-per-THIGH-roy-dih-zum). Hyperthyroidism is caused ... or through surgery or radiation treatments. Hypothyroidism (pronounced: hi-po-THIGH-roy-dih-zum). Hypothyroidism is caused ...

  2. Redirecting metabolic flux in Saccharomyces cerevisiae through regulation of cofactors in UMP production.

    PubMed

    Chen, Yong; Liu, Qingguo; Chen, Xiaochun; Wu, Jinglan; Guo, Ting; Zhu, Chenjie; Ying, Hanjie

    2015-04-01

    Although it is generally known that cofactors play a major role in the production of different fermentation products, their role has not been thoroughly and systematically studied. To understand the impact of cofactors on physiological functions, a systematic approach was applied, which involved redox state analysis, energy charge analysis, and metabolite analysis. Using uridine 5'-monophosphate metabolism in Saccharomyces cerevisiae as a model, we demonstrated that regulation of intracellular the ratio of NADPH to NADP(+) not only redistributed the carbon flux between the glycolytic and pentose phosphate pathways, but also regulated the redox state of NAD(H), resulting in a significant change of ATP, and a significantly altered spectrum of metabolic products.

  3. Sustainable source of omega-3 eicosapentaenoic acid from metabolically engineered Yarrowia lipolytica: from fundamental research to commercial production.

    PubMed

    Xie, Dongming; Jackson, Ethel N; Zhu, Quinn

    2015-02-01

    The omega-3 fatty acids, cis-5, 8, 11, 14, and 17-eicosapentaenoic acid (C20:5; EPA) and cis-4, 7, 10, 13, 16, and 19-docosahexaenoic acid (C22:6; DHA), have wide-ranging benefits in improving heart health, immune function, mental health, and infant cognitive development. Currently, the major source for EPA and DHA is from fish oil, and a minor source of DHA is from microalgae. With the increased demand for EPA and DHA, DuPont has developed a clean and sustainable source of the omega-3 fatty acid EPA through fermentation using metabolically engineered strains of Yarrowia lipolytica. In this mini-review, we will focus on DuPont's technology for EPA production. Specifically, EPA biosynthetic and supporting pathways have been introduced into the oleaginous yeast to synthesize and accumulate EPA under fermentation conditions. This Yarrowia platform can also produce tailored omega-3 (EPA, DHA) and/or omega-6 (ARA, GLA) fatty acid mixtures in the cellular lipid profiles. Fundamental research such as metabolic engineering for strain construction, high-throughput screening for strain selection, fermentation process development, and process scale-up were all needed to achieve the high levels of EPA titer, rate, and yield required for commercial application. Here, we summarize how we have combined the fundamental bioscience and the industrial engineering skills to achieve large-scale production of Yarrowia biomass containing high amounts of EPA, which led to two commercial products, New Harvest™ EPA oil and Verlasso® salmon.

  4. Pathways of trans,trans-muconaldehyde metabolism in mouse liver cytosol: reversibility of monoreductive metabolism and formation of end products.

    PubMed

    Zhang, Z; Kline, S A; Kirley, T A; Goldstein, B D; Witz, G

    1993-01-01

    The metabolism of trans,trans-muconaldehyde (MUC), a hematotoxic agent which is a presumed in vivo metabolite of benzene, was studied in mouse liver cytosol. MUC was incubated for 30 min at 37 degrees C with mouse liver cytosol (from CD-1 mice) supplemented with NAD+ and the products were analyzed by reverse phase HPLC. Two products were detected in addition to the previously identified acid-aldehyde 6-oxo-trans,trans-2,4-hexadienoic acid (COOH-M-CHO) and the diacid trans,trans-muconic acid (COOH-M-COOH). Based on the molecular weight (112) obtained by thermo-spray LC-mass spectrometry and the absorbance maximum (269 nm), one of the products was identified as the aldehyde-alcohol 6-hydroxy-trans,trans-2,4-hexadienal (CHO-M-OH). The second product was identified as 6-hydroxy-trans,trans-2,4-hexadienoic acid (COOH-M-OH) by coelution with authentic standard, the fragmentation pattern obtained by electron impact mass spectrometry and the absorbance maximum (258 nm). Time course and concentration dependency studies indicate that COOH-M-OH and COOH-M-COOH are end products of MUC metabolism while CHO-M-OH, and COOH-M-CHO, the initially formed mono-reduction and mono-oxidation products, respectively, are the intermediates leading to these end products. The metabolite COOH-M-OH is formed mainly by oxidation of CHO-M-OH and to a much lesser extent by reduction of CHO-M-COOH, whereas COOH-M-COOH is formed solely by oxidation of COOH-M-CHO. The reduction of MUC to CHO-M-OH is reversible, whereas oxidation to COOH-M-CHO is not. The compound CHO-M-OH is not only oxidized to COOH-M-OH by oxidation of the aldehyde functional group, but is also converted back to MUC by oxidation of the alcohol functional group.

  5. Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum.

    PubMed

    Thompson, R Adam; Layton, Donovan S; Guss, Adam M; Olson, Daniel G; Lynd, Lee R; Trinh, Cong T

    2015-11-01

    Clostridium thermocellum is an anaerobic, Gram-positive, thermophilic bacterium that has generated great interest due to its ability to ferment lignocellulosic biomass to ethanol. However, ethanol production is low due to the complex and poorly understood branched metabolism of C. thermocellum, and in some cases overflow metabolism as well. In this work, we developed a predictive stoichiometric metabolic model for C. thermocellum which incorporates the current state of understanding, with particular attention to cofactor specificity in the atypical glycolytic enzymes and the complex energy, redox, and fermentative pathways with the goal of aiding metabolic engineering efforts. We validated the model's capability to encompass experimentally observed phenotypes for the parent strain and derived mutants designed for significant perturbation of redox and energy pathways. Metabolic flux distributions revealed significant alterations in key metabolic branch points (e.g., phosphoenol pyruvate, pyruvate, acetyl-CoA, and cofactor nodes) in engineered strains for channeling electron and carbon fluxes for enhanced ethanol synthesis, with the best performing strain doubling ethanol yield and titer compared to the parent strain. In silico predictions of a redox-imbalanced genotype incapable of growth were confirmed in vivo, and a mutant strain was used as a platform to probe redox bottlenecks in the central metabolism that hinder efficient ethanol production. The results highlight the robustness of the redox metabolism of C. thermocellum and the necessity of streamlined electron flux from reduced ferredoxin to NAD(P)H for high ethanol production. The model was further used to design a metabolic engineering strategy to phenotypically constrain C. thermocellum to achieve high ethanol yields while requiring minimal genetic manipulations. The model can be applied to design C. thermocellum as a platform microbe for consolidated bioprocessing to produce ethanol and other reduced

  6. Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum

    SciTech Connect

    Thompson, R. Adam; Layton, Donovan S.; Guss, Adam M.; Olson, Daniel G.; Lynd, Lee R.; Trinh, Cong T.

    2015-10-21

    Clostridium thermocellum is an anaerobic, Gram-positive, thermophilic bacterium that has generated great interest due to its ability to ferment lignocellulosic biomass to ethanol. However, ethanol production is low due to the complex and poorly understood branched metabolism of C. thermocellum, and in some cases overflow metabolism as well. In this work, we developed a predictive stoichiometric metabolic model for C. thermocellum which incorporates the current state of understanding, with particular attention to cofactor specificity in the atypical glycolytic enzymes and the complex energy, redox, and fermentative pathways with the goal of aiding metabolic engineering efforts. We validated the model s capability to encompass experimentally observed phenotypes for the parent strain and derived mutants designed for significant perturbation of redox and energy pathways. Metabolic flux distributions revealed significant alterations in key metabolic branch points (e.g., phosphoenol pyruvate, pyruvate, acetyl-CoA, and cofactor nodes) in engineered strains for channeling electron and carbon fluxes for enhanced ethanol synthesis, with the best performing strain doubling ethanol yield and titer compared to the parent strain. In silico predictions of a redox-imbalanced genotype incapable of growth were confirmed in vivo, and a mutant strain was used as a platform to probe redox bottlenecks in the central metabolism that hinder efficient ethanol production. The results highlight the robustness of the redox metabolism of C. thermocellum and the necessity of streamlined electron flux from reduced ferredoxin to NAD(P)H for high ethanol production. The model was further used to design a metabolic engineering strategy to phenotypically constrain C. thermocellum to achieve high ethanol yields while requiring minimal genetic manipulations. Furthermore, the model can be applied to design C. thermocellum as a platform microbe for

  7. Elucidating central metabolic redox obstacles hindering ethanol production in Clostridium thermocellum

    DOE PAGES

    Thompson, R. Adam; Layton, Donovan S.; Guss, Adam M.; ...

    2015-10-21

    Clostridium thermocellum is an anaerobic, Gram-positive, thermophilic bacterium that has generated great interest due to its ability to ferment lignocellulosic biomass to ethanol. However, ethanol production is low due to the complex and poorly understood branched metabolism of C. thermocellum, and in some cases overflow metabolism as well. In this work, we developed a predictive stoichiometric metabolic model for C. thermocellum which incorporates the current state of understanding, with particular attention to cofactor specificity in the atypical glycolytic enzymes and the complex energy, redox, and fermentative pathways with the goal of aiding metabolic engineering efforts. We validated the model smore » capability to encompass experimentally observed phenotypes for the parent strain and derived mutants designed for significant perturbation of redox and energy pathways. Metabolic flux distributions revealed significant alterations in key metabolic branch points (e.g., phosphoenol pyruvate, pyruvate, acetyl-CoA, and cofactor nodes) in engineered strains for channeling electron and carbon fluxes for enhanced ethanol synthesis, with the best performing strain doubling ethanol yield and titer compared to the parent strain. In silico predictions of a redox-imbalanced genotype incapable of growth were confirmed in vivo, and a mutant strain was used as a platform to probe redox bottlenecks in the central metabolism that hinder efficient ethanol production. The results highlight the robustness of the redox metabolism of C. thermocellum and the necessity of streamlined electron flux from reduced ferredoxin to NAD(P)H for high ethanol production. The model was further used to design a metabolic engineering strategy to phenotypically constrain C. thermocellum to achieve high ethanol yields while requiring minimal genetic manipulations. Furthermore, the model can be applied to design C. thermocellum as a platform microbe for consolidated bioprocessing to produce ethanol

  8. Fermentative production of branched chain amino acids: a focus on metabolic engineering.

    PubMed

    Park, Jin Hwan; Lee, Sang Yup

    2010-01-01

    The branched chain amino acids (BCAAs), L-valine, L-leucine, and L-isoleucine, have recently been attracting much attention as their potential to be applied in various fields, including animal feed additive, cosmetics, and pharmaceuticals, increased. Strategies for developing microbial strains efficiently producing BCAAs are now in transition toward systems metabolic engineering from random mutagenesis. The metabolism and regulatory circuits of BCAA biosynthesis need to be thoroughly understood for designing system-wide metabolic engineering strategies. Here we review the current knowledge on BCAAs including their biosynthetic pathways, regulations, and export and transport systems. Recent advances in the development of BCAA production strains are also reviewed with a particular focus on L-valine production strain. At the end, the general strategies for developing BCAA overproducers by systems metabolic engineering are suggested.

  9. Piezotolerance as a metabolic engineering tool for the biosynthesis of natural products.

    PubMed

    Wright, Phillip C; Westacott, Robin E; Burja, Adam M

    2003-07-01

    Thermodynamically, high-pressure (>10's of MPa) has a potentially vastly superior effect on reactions and their rates within metabolic processes than temperature. Thus, it might be expected that changes in the pressure experienced by living organisms would have effects on the products of their metabolism. To examine the potential for modification of metabolic pathways based on thermodynamic principles we have performed simple molecular dynamics simulations, in vacuo and in aquo on the metabolites synthesized by recombinant polyketide synthases (PKS). We were able to determine, in this in silico study, the volume changes associated with each reaction step along the parallel PKS pathways. Results indicate the importance of explicitly including the solvent in the simulations. Furthermore, the addition of solvent and high pressure reveals that high pressure may have a beneficial effect on certain pathways over others. Thus, the future looks bright for pressure driven novel secondary metabolite discoveries, and their sustained and efficient production via metabolic engineering.

  10. Reduced metabolic rate and oxygen radicals production in stored insect sperm.

    PubMed

    Ribou, Anne-Cécile; Reinhardt, Klaus

    2012-06-07

    Females of internally fertilizing species can significantly extend sperm lifespan and functionality during sperm storage. The mechanisms for such delayed cellular senescence remain unknown. Here, we apply current hypotheses of cellular senescence developed for diploid cells to sperm cells, and empirically test opposing predictions on the relationship between sperm metabolic rate and oxygen radical production in an insect model, the cricket Gryllus bimaculatus. Using time-resolved microfluorimetry, we found a negative correlation between metabolic rate (proportion of protein-bound NAD[P]H) and in situ intracellular oxygen radicals production in freshly ejaculated sperm. In contrast, sperm stored by females for periods of 1 h to 26 days showed a positive correlation between metabolic rate and oxygen radicals production. At the same time, stored sperm showed a 37 per cent reduced metabolic rate, and 42 per cent reduced reactive oxygen species (ROS) production, compared with freshly ejaculated sperm. Rank differences between males in ROS production and metabolic rate observed in ejaculated sperm did not predict rank differences in stored sperm. Our method of simultaneously measuring ROS production and metabolic rate of the same sample has the advantage of providing data that are independent of sperm density and any extracellular antioxidants that are proteins. Our method also excludes effects owing to accumulated hydrogen peroxide. Our results unify aspects of competing theories of cellular ageing and suggest that reducing metabolic rate may be an important means of extending stored sperm lifespan and functionality in crickets. Our data also provide a possible explanation for why traits of ejaculates sampled from the male may be rather poor predictors of paternity in sexual selection studies and likelihood of pregnancy in reproductive medicine.

  11. Thiosulfate as a metabolic product: the bacterial fermentation of taurine.

    PubMed

    Denger, K; Laue, H; Cook, A M

    1997-10-01

    Thiosulfate (S2O32-) is a natural product that is widely utilized in natural ecosystems as an electron sink or as an electron donor. However, the major biological source(s) of this thiosulfate is unknown. We present the first report that taurine (2-aminoethanesulfonate), the major mammalian solute, is subject to fermentation. This bacterial fermentation was found to be catalyzed by a new isolate, strain GKNTAU, a strictly anaerobic, gram-positive, motile rod that formed subterminal spores. Thiosulfate was a quantitative fermentation product. The other fermentation products were ammonia and acetate, and all could be formed by cell-free extracts.

  12. Scaling of basal metabolic rate with body mass and temperature in mammals.

    PubMed

    Clarke, Andrew; Rothery, Peter; Isaac, Nick J B

    2010-05-01

    1. We present a statistical analysis of the scaling of resting (basal) metabolic rate, BMR, with body mass, B(m) and body temperature, T(b), in mammals. 2. Whilst the majority of the variance in ln BMR is explained by ln B(m), the T(b) term is statistically significant. The best fit model was quadratic, indicating that the scaling of ln BMR with ln B(m) varies with body size; the value of any scaling exponent estimated for a sample of mammals will therefore depend on the size distribution of species in the study. This effect can account for much of the variation in scaling exponents reported in the literature for mammals. 3. In all models, inclusion of T(b) reduced the strength of scaling with ln B(m). The model including T(b) suggests that birds and mammals have a similar underlying thermal dependence of BMR, equivalent to a Q(10) of 2.9 across the range of T(b) values 32-42 degrees C. 4. There was significant heterogeneity in both the mass scaling exponent and mean BMR across mammalian orders, with a tendency for orders dominated by larger taxa to have steeper scaling exponents. This heterogeneity was particularly marked across orders with smaller mean B(m) and the taxonomic composition of the sample will thus also affect the observed scaling exponent. After correcting for the effects of ln B(m) and T(b), Soricomorpha, Didelphimorphia and Artiodactyla had the highest BMR of those orders represented by more than 10 species in the data set. 5. Inclusion of T(b) in the model removed the effect of diet category evident from a model in ln B(m) alone and widely reported in the literature; this was caused by a strong interaction between diet category and T(b) in mammals. 6. Inclusion of mean ambient temperature, T(a), in the model indicated a significant inverse relationship between ln BMR and T(a), complicated by an interaction between T(a) and T(b). All other things being equal, a polar mammal living at -10 degrees C has a body temperature approximately 2.7 degrees C

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

    PubMed Central

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

    2014-01-01

    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. PMID:24481660

  14. Glucose metabolic flux distribution of Lactobacillus amylophilus during lactic acid production using kitchen waste saccharified solution.

    PubMed

    Liu, Jianguo; Wang, Qunhui; Zou, Hui; Liu, Yingying; Wang, Juan; Gan, Kemin; Xiang, Juan

    2013-11-01

    The (13) C isotope tracer method was used to investigate the glucose metabolic flux distribution and regulation in Lactobacillus amylophilus to improve lactic acid production using kitchen waste saccharified solution (KWSS). The results demonstrate that L. amylophilus is a homofermentative bacterium. In synthetic medium, 60.6% of the glucose entered the Embden-Meyerhof-Parnas (EMP) to produce lactic acid, whereas 36.4% of the glucose entered the pentose phosphate metabolic pathway (HMP). After solid-liquid separation of the KWSS, the addition of Fe(3+) during fermentation enhanced the NADPH production efficiency and increased the NADH content. The flux to the EMP was also effectively increased. Compared with the control (60.6% flux to EMP without Fe(3+) addition), the flux to the EMP with the addition of Fe(3+) (74.3%) increased by 23.8%. In the subsequent pyruvate metabolism, Fe(3+) also increased lactate dehydrogenase activity, and inhibited alcohol dehydrogenase, pyruvate dehydrogenase and pyruvate carboxylase, thereby increasing the lactic acid production to 9.03 g l(-1) , an increase of 8% compared with the control. All other organic acid by-products were lower than in the control. However, the addition of Zn(2+) showed an opposite effect, decreasing the lactic acid production. In conclusion it is feasible and effective means using GC-MS, isotope experiment and MATLAB software to integrate research the metabolic flux distribution of lactic acid bacteria, and the results provide the theoretical foundation for similar metabolic flux distribution.

  15. Time scaling of tree rings cell production in Siberia

    NASA Astrophysics Data System (ADS)

    Popkova, Margarita; Babushkina, Elena; Tychkov, Ivan; Shishov, Vladimir; Vaganov, Eugene

    2016-04-01

    It is assumed that an annual tree-ring growth is adequately determined by a linear function of local or regional precipitation and temperature with a set of coefficients that are temporally invariant. But often that relations are non-linear. The process-based tree-ring VS-model can be used to resolve the critical processes linking climate variables to tree-ring formation. This work describes a new block of VS-model which allows to estimate a cell production in tree rings and transfer it into time scale based on the simulated integral growth rates of the model. In the algorithm of time identification for cell production we used a integral growth rates simulated by the VS-model for each growing season. The obtained detailed approach with a calculation of the time of each cell formation improves significantly the date accuracy of new cell formation in growing season. As a result for each cell in the tree-ring we estimate the temporal moment of the cell production corresponded to the seasonal growth rate in the same time scale. The approach was applied and tested for the cell measurements obtained for Scots pine (Pinus sylvestris) for the period 1964-2013 in Malaya Minusa river (Khakassia, South Siberia). The work was supported by the Russian Science Foundation (RSF # 14-14-00219)

  16. Metabolic Flux Elucidation for Large-Scale Models Using 13C Labeled Isotopes

    PubMed Central

    Suthers, Patrick F.; Burgard, Anthony P.; Dasika, Madhukar S.; Nowroozi, Farnaz; Van Dien, Stephen; Keasling, Jay D.; Maranas, Costas D.

    2007-01-01

    A key consideration in metabolic engineering is the determination of fluxes of the metabolites within the cell. This determination provides an unambiguous description of metabolism before and/or after engineering interventions. Here, we present a computational framework that combines a constraint-based modeling framework with isotopic label tracing on a large-scale. When cells are fed a growth substrate with certain carbon positions labeled with 13C, the distribution of this label in the intracellular metabolites can be calculated based on the known biochemistry of the participating pathways. Most labeling studies focus on skeletal representations of central metabolism and ignore many flux routes that could contribute to the observed isotopic labeling patterns. In contrast, our approach investigates the importance of carrying out isotopic labeling studies using a more comprehensive reaction network consisting of 350 fluxes and 184 metabolites in Escherichia coli including global metabolite balances on cofactors such as ATP, NADH, and NADPH. The proposed procedure is demonstrated on an E. coli strain engineered to produce amorphadiene, a precursor to the anti-malarial drug artemisinin. The cells were grown in continuous culture on glucose containing 20% [U-13C]glucose; the measurements are made using GC-MS performed on 13 amino acids extracted from the cells. We identify flux distributions for which the calculated labeling patterns agree well with the measurements alluding to the accuracy of the network reconstruction. Furthermore, we explore the robustness of the flux calculations to variability in the experimental MS measurements, as well as highlight the key experimental measurements necessary for flux determination. Finally, we discuss the effect of reducing the model, as well as shed light onto the customization of the developed computational framework to other systems. PMID:17632026

  17. Bottom-up Metabolic Reconstruction of Arabidopsis and Its Application to Determining the Metabolic Costs of Enzyme Production[W

    PubMed Central

    Arnold, Anne; Nikoloski, Zoran

    2014-01-01

    Large-scale modeling of plant metabolism provides the possibility to compare and contrast different cellular and environmental scenarios with the ultimate aim of identifying the components underlying the respective plant behavior. The existing models of Arabidopsis (Arabidopsis thaliana) are top-down assembled, whereby the starting point is the annotated genome, in particular, the metabolic genes. Hence, dead-end metabolites and blocked reactions can arise that are subsequently addressed by using gap-filling algorithms in combination with species-unspecific genes. Here, we present a bottom-up-assembled, large-scale model that relies solely on Arabidopsis-specific annotations and results in the inclusion of only manually curated reactions. While the existing models are largely condition unspecific by employing a single biomass reaction, we provide three biomass compositions that pertain to realistic and frequently examined scenarios: carbon-limiting, nitrogen-limiting, and optimal growth conditions. The comparative analysis indicates that the proposed Arabidopsis core model exhibits comparable efficiency in carbon utilization and flexibility to the existing network alternatives. Moreover, the model is utilized to quantify the energy demand of amino acid and enzyme de novo synthesis in photoautotrophic growth conditions. Illustrated by the case of the most abundant protein in the world, Rubisco, we determine its synthesis cost in terms of ATP requirements. This, in turn, allows us to explore the tradeoff between protein synthesis and growth in Arabidopsis. Altogether, the model provides a solid basis for completely species-specific integration of high-throughput data, such as gene expression levels, and for condition-specific investigations of in silico metabolic engineering strategies. PMID:24808102

  18. Metabolic Engineering of the Actinomycete Amycolatopsis sp. Strain ATCC 39116 towards Enhanced Production of Natural Vanillin

    PubMed Central

    Fleige, Christian; Meyer, Florian

    2016-01-01

    ABSTRACT The Gram-positive bacterium Amycolatopsis sp. ATCC 39116 is used for the fermentative production of natural vanillin from ferulic acid on an industrial scale. The strain is known for its outstanding tolerance to this toxic product. In order to improve the productivity of the fermentation process, the strain's metabolism was engineered for higher final concentrations and molar yields. Degradation of vanillin could be decreased by more than 90% through deletion of the vdh gene, which codes for the central vanillin catabolism enzyme, vanillin dehydrogenase. This mutation resulted in improvement of the final concentration of vanillin by more than 2.2 g/liter, with a molar yield of 80.9%. Further improvement was achieved with constitutive expression of the vanillin anabolism genes ech and fcs, coding for the enzymes feruloyl-coenzyme A (CoA) synthetase (fcs) and enoyl-CoA hydratase/aldolase (ech). The transcription of both genes was shown to be induced by ferulic acid, which explains the unwanted adaptation phase in the fermentation process before vanillin was efficiently produced by the wild-type cells. Through the constitutive and enhanced expression of the two genes, the adaptation phase was eliminated and a final vanillin concentration of 19.3 g/liter, with a molar yield of 94.9%, was obtained. Moreover, an even higher final vanillin concentration of 22.3 g/liter was achieved, at the expense of a lower molar yield, by using an improved feeding strategy. This is the highest reported vanillin concentration reached in microbial fermentation processes without extraction of the product. Furthermore, the vanillin was produced almost without by-products, with a molar yield that nearly approached the theoretical maximum. IMPORTANCE Much effort has been put into optimization of the biotechnological production of natural vanillin. The demand for this compound is growing due to increased consumer concerns regarding chemically produced food additives. Since this

  19. Revisiting the chlorophyll biosynthesis pathway using genome scale metabolic model of Oryza sativa japonica

    PubMed Central

    Chatterjee, Ankita; Kundu, Sudip

    2015-01-01

    Chlorophyll is one of the most important pigments present in green plants and rice is one of the major food crops consumed worldwide. We curated the existing genome scale metabolic model (GSM) of rice leaf by incorporating new compartment, reactions and transporters. We used this modified GSM to elucidate how the chlorophyll is synthesized in a leaf through a series of bio-chemical reactions spanned over different organelles using inorganic macronutrients and light energy. We predicted the essential reactions and the associated genes of chlorophyll synthesis and validated against the existing experimental evidences. Further, ammonia is known to be the preferred source of nitrogen in rice paddy fields. The ammonia entering into the plant is assimilated in the root and leaf. The focus of the present work is centered on rice leaf metabolism. We studied the relative importance of ammonia transporters through the chloroplast and the cytosol and their interlink with other intracellular transporters. Ammonia assimilation in the leaves takes place by the enzyme glutamine synthetase (GS) which is present in the cytosol (GS1) and chloroplast (GS2). Our results provided possible explanation why GS2 mutants show normal growth under minimum photorespiration and appear chlorotic when exposed to air. PMID:26443104

  20. Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

    NASA Astrophysics Data System (ADS)

    Ma, Ding; Yang, Laurence; Fleming, Ronan M. T.; Thiele, Ines; Palsson, Bernhard O.; Saunders, Michael A.

    2017-01-01

    Constraint-Based Reconstruction and Analysis (COBRA) is currently the only methodology that permits integrated modeling of Metabolism and macromolecular Expression (ME) at genome-scale. Linear optimization computes steady-state flux solutions to ME models, but flux values are spread over many orders of magnitude. Data values also have greatly varying magnitudes. Standard double-precision solvers may return inaccurate solutions or report that no solution exists. Exact simplex solvers based on rational arithmetic require a near-optimal warm start to be practical on large problems (current ME models have 70,000 constraints and variables and will grow larger). We have developed a quadruple-precision version of our linear and nonlinear optimizer MINOS, and a solution procedure (DQQ) involving Double and Quad MINOS that achieves reliability and efficiency for ME models and other challenging problems tested here. DQQ will enable extensive use of large linear and nonlinear models in systems biology and other applications involving multiscale data.

  1. The fractal architecture of cytoplasmic organization: scaling, kinetics and emergence in metabolic networks.

    PubMed

    Aon, Miguel Antonio; O'Rourke, Brian; Cortassa, Sonia

    2004-01-01

    In this work, we highlight the links between fractals and scaling in cells and explore the kinetic consequences for biochemical reactions operating in fractal media. Based on the proposal that the cytoskeletal architecture is organized as a percolation lattice, with clusters emerging as fractal forms, the analysis of kinetics in percolation clusters is especially emphasized. A key consequence of this spatiotemporal cytoplasmic organization is that enzyme reactions following Michaelis-Menten or allosteric type kinetics exhibit higher rates in fractal media (for short times and at lower substrate concentrations) at the percolation threshold than in Euclidean media. As a result, considerably faster and higher amplification of enzymatic activity is obtained. Finally, we describe some of the properties bestowed by cytoskeletal organization and dynamics on metabolic networks.

  2. Biome-specific scaling of ocean productivity, temperature, and carbon export efficiency

    NASA Astrophysics Data System (ADS)

    Britten, Gregory L.; Primeau, François W.

    2016-05-01

    Mass conservation and metabolic theory place constraints on how marine export production (EP) scales with net primary productivity (NPP) and sea surface temperature (SST); however, little is empirically known about how these relationships vary across ecologically distinct ocean biomes. Here we compiled in situ observations of EP, NPP, and SST and used statistical model selection theory to demonstrate significant biome-specific scaling relationships among these variables. Multiple statistically similar models yield a threefold variation in the globally integrated carbon flux (~4-12 Pg C yr-1) when applied to climatological satellite-derived NPP and SST. Simulated NPP and SST input variables from a 4×CO2 climate model experiment further show that biome-specific scaling alters the predicted response of EP to simulated increases of atmospheric CO2. These results highlight the need to better understand distinct pathways of carbon export across unique ecological biomes and may help guide proposed efforts for in situ observations of the ocean carbon cycle.

  3. Biobased production of alkanes and alkenes through metabolic engineering of microorganisms.

    PubMed

    Kang, Min-Kyoung; Nielsen, Jens

    2016-08-26

    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 and possible solutions to accomplish industrial level production of these chemicals by microbial fermentation.

  4. Metabolic engineering for production of biorenewable fuels and chemicals: contributions of synthetic biology.

    PubMed

    Jarboe, Laura R; Zhang, Xueli; Wang, Xuan; Moore, Jonathan C; Shanmugam, K T; Ingram, Lonnie O

    2010-01-01

    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.

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

    PubMed Central

    Jarboe, Laura R.; Zhang, Xueli; Wang, Xuan; Moore, Jonathan C.; Shanmugam, K. T.; Ingram, Lonnie O.

    2010-01-01

    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. PMID:20414363

  6. Combinatorial metabolic engineering of Saccharomyces cerevisiae for terminal alkene production.

    PubMed

    Chen, Binbin; Lee, Dong-Yup; Chang, Matthew Wook

    2015-09-01

    Biological production of terminal alkenes has garnered a significant interest due to their industrial applications such as lubricants, detergents and fuels. Here, we engineered the yeast Saccharomyces cerevisiae to produce terminal alkenes via a one-step fatty acid decarboxylation pathway and improved the alkene production using combinatorial engineering strategies. In brief, we first characterized eight fatty acid decarboxylases to enable and enhance alkene production. We then increased the production titer 7-fold by improving the availability of the precursor fatty acids. We additionally increased the titer about 5-fold through genetic cofactor engineering and gene expression tuning in rich medium. Lastly, we further improved the titer 1.8-fold to 3.7 mg/L by optimizing the culturing conditions in bioreactors. This study represents the first report of terminal alkene biosynthesis in S. cerevisiae, and the abovementioned combinatorial engineering approaches collectively increased the titer 67.4-fold. We envision that these approaches could provide insights into devising engineering strategies to improve the production of fatty acid-derived biochemicals in S. cerevisiae.

  7. Metabolic engineering of Saccharomyces cerevisiae for production of ginsenosides.

    PubMed

    Dai, Zhubo; Liu, Yi; Zhang, Xianan; Shi, Mingyu; Wang, Beibei; Wang, Dong; Huang, Luqi; Zhang, Xueli

    2013-11-01

    Ginsenosides are the primary bioactive components of ginseng, which is a popular medicinal herb and exhibits diverse pharmacological activities. Protopanaxadiol is the aglycon of several dammarane-type ginsenosides, which also has anticancer activity. For microbial production of protopanaxadiol, dammarenediol-II synthase and protopanaxadiol synthase genes of Panax ginseng, together with a NADPH-cytochrome P450 reductase gene of Arabidopsis thaliana, were introduced into Saccharomyces cerevisiae, resulting in production of 0.05 mg/g DCW protopanaxadiol. Increasing squalene and 2,3-oxidosqualene supplies through overexpressing truncated 3-hydroxyl-3-methylglutaryl-CoA reductase, farnesyl diphosphate synthase, squalene synthase and 2,3-oxidosqualene synthase genes, together with increasing protopanaxadiol synthase activity through codon optimization, led to 262-fold increase of protopanaxadiol production. Finally, using two-phase extractive fermentation resulted in production of 8.40 mg/g DCW protopanaxadiol (1189 mg/L), together with 10.94 mg/g DCW dammarenediol-II (1548 mg/L). The yeast strains engineered in this work can serve as the basis for creating an alternative way for production of ginsenosides in place of extraction from plant sources.

  8. Metabolic engineering of acetaldehyde production by Streptococcus thermophilus.

    PubMed

    Chaves, A C S D; Fernandez, M; Lerayer, A L S; Mierau, I; Kleerebezem, M; Hugenholtz, J

    2002-11-01

    The process of acetaldehyde formation by the yogurt bacterium Streptococcus thermophilus is described in this paper. Attention was focused on one specific reaction for acetaldehyde formation catalyzed by serine hydroxymethyltransferase (SHMT), encoded by the glyA gene. In S. thermophilus, SHMT also possesses threonine aldolase (TA) activity, the interconversion of threonine into glycine and acetaldehyde. In this work, several wild-type S. thermophilus strains were screened for acetaldehyde production in the presence and absence of L-threonine. Supplementation of the growth medium with L-threonine led to an increase in acetaldehyde production. Furthermore, acetaldehyde formation during fermentation could be correlated to the TA activity of SHMT. To study the physiological role of SHMT, a glyA mutant was constructed by gene disruption. Inactivation of glyA resulted in a severe reduction in TA activity and complete loss of acetaldehyde formation during fermentation. Subsequently, an S. thermophilus strain was constructed in which the glyA gene was cloned under the control of a strong promoter (P(LacA)). When this strain was used for fermentation, an increase in TA activity and in acetaldehyde and folic acid production was observed. These results show that, in S. thermophilus, SHMT, displaying TA activity, constitutes the main pathway for acetaldehyde formation under our experimental conditions. These findings can be used to control and improve acetaldehyde production in fermented (dairy) products with S. thermophilus as starter culture.

  9. The temporal scale research of MODIS albedo product authenticity verification

    NASA Astrophysics Data System (ADS)

    Cao, Yongxing; Xue, Zhihang; Cheng, Hui; Xiong, Yajv; Chen, Yunping; Tong, Ling

    2016-06-01

    This study introduces a method that normalizes the inversed ETM+ albedo to the local solar noon albedo for the temporal scale of the MODIS albedo validation. Firstly, the statistical relation model between the surface albedo and the solar elevation angle was set up, and then deducing relationship between ETM+ albedo and the solar elevation angle, so the ETM+ albedo at local solar noon could be got. Secondly, the ground measurement albedo at the local solar noon was used to assess the inversed ETM+ albedo and the normalized albedo. The experiment results show that the method can effectively improve the accuracy of product certification.

  10. Metabolic engineering of Thermoanaerobacterium saccharolyticum for n-butanol production

    SciTech Connect

    Bhandiwad, Ashwini; Shaw, A Joe; Guss, Adam M; Guseva, Anna; Lynd, Lee R

    2014-01-01

    The thermophilic anaerobe Thermoanaerobacterium saccharolyticum JW/SL-YS485 was investigated as a host for n-butanol production. A systematic approach was taken to demonstrate functionality of heterologous components of the clostridial n-butanol pathway via gene expression and enzymatic activity assays in this organism. Subsequently, integration of the entire pathway in the wild-type strain resulted in n-butanol production of 0.85 g/L from 10 g/L xylose, corresponding to 21% of the theoretical maximum yield. We were unable to integrate the n-butanol pathway in strains lacking the ability to produce acetate, despite the theoretical overall redox neutrality of n-butanol formation. However, integration of the n-butanol pathway in lactate deficient strains resulted in n-butanol production of 1.05 g/L from 10 g/L xylose, corresponding to 26% of the theoretical maximum.

  11. Secondary metabolism in simulated microgravity: beta-lactam production by Streptomyces clavuligerus

    NASA Technical Reports Server (NTRS)

    Fang, A.; Pierson, D. L.; Mishra, S. K.; Koenig, D. W.; Demain, A. L.

    1997-01-01

    Rotating bioreactors designed at NASA's Johnson Space Center were used to simulate a microgravity environment in which to study secondary metabolism. The system examined was beta-lactam antibiotic production by Streptomyces clavuligerus. Both growth and beta-lactam production occurred in simulated microgravity. Stimulatory effects of phosphate and L-lysine, previously detected in normal gravity, also occurred in simulated microgravity. The degree of beta-lactam antibiotic production was markedly inhibited by simulated microgravity.

  12. Multi-scale exploration of the technical, economic, and environmental dimensions of bio-based chemical production.

    PubMed

    Zhuang, Kai H; Herrgård, Markus J

    2015-09-01

    In recent years, bio-based chemicals have gained traction as a sustainable alternative to petrochemicals. However, despite rapid advances in metabolic engineering and synthetic biology, there remain significant economic and environmental challenges. In order to maximize the impact of research investment in a new bio-based chemical industry, there is a need for assessing the technological, economic, and environmental potentials of combinations of biomass feedstocks, biochemical products, bioprocess technologies, and metabolic engineering approaches in the early phase of development of cell factories. To address this issue, we have developed a comprehensive Multi-scale framework for modeling Sustainable Industrial Chemicals production (MuSIC), which integrates modeling approaches for cellular metabolism, bioreactor design, upstream/downstream processes and economic impact assessment. We demonstrate the use of the MuSIC framework in a case study where two major polymer precursors (1,3-propanediol and 3-hydroxypropionic acid) are produced from two biomass feedstocks (corn-based glucose and soy-based glycerol) through 66 proposed biosynthetic pathways in two host organisms (Escherichia coli and Saccharomyces cerevisiae). The MuSIC framework allows exploration of tradeoffs and interactions between economy-scale objectives (e.g. profit maximization, emission minimization), constraints (e.g. land-use constraints) and process- and cell-scale technology choices (e.g. strain design or oxygenation conditions). We demonstrate that economy-scale assessment can be used to guide specific strain design decisions in metabolic engineering, and that these design decisions can be affected by non-intuitive dependencies across multiple scales.

  13. Streamlining workflow and automation to accelerate laboratory scale protein production.

    PubMed

    Konczal, Jennifer; Gray, Christopher H

    2017-03-19

    Protein production facilities are often required to produce diverse arrays of proteins for demanding methodologies including crystallography, NMR, ITC and other reagent intensive techniques. It is common for these teams to find themselves a bottleneck in the pipeline of ambitious projects. This pressure to deliver has resulted in the evolution of many novel methods to increase capacity and throughput at all stages in the pipeline for generation of recombinant proteins. This review aims to describe current and emerging options to accelerate the success of protein production in Escherichia coli. We emphasize technologies that have been evaluated and implemented in our laboratory, including innovative molecular biology and expression vectors, small-scale expression screening strategies and the automation of parallel and multidimensional chromatography.

  14. A metabolic and body-size scaling framework for parasite within-host abundance, biomass, and energy flux.

    PubMed

    Hechinger, Ryan F

    2013-08-01

    Energetics may provide a useful currency for studying the ecology of parasite assemblages within individual hosts. Parasite assemblages may also provide powerful models to study general principles of ecological energetics. Yet there has been little ecological research on parasite-host energetics, probably due to methodological difficulties. However, the scaling relationships of individual metabolic rate with body or cell size and temperature may permit us to tackle the energetics of parasite assemblages in hosts. This article offers the foundations and initial testing of a metabolic theory of ecology (MTE) framework for parasites in hosts. I first provide equations to estimate energetic flux through observed parasite assemblages. I then develop metabolic scaling theory for parasite abundance, energetics, and biomass in individual hosts. In contrast to previous efforts, the theory factors in both host and parasite metabolic scaling, how parasites use host space, and whether energy or space dictates carrying capacity. Empirical tests indicate that host energetic flux can set parasite carrying capacity, which decreases as predicted considering the scaling of host and parasite metabolic rates. The theory and results also highlight that the phenomenon of "energetic equivalence" is not an assumption of MTE but a possible outcome contingent on how species partition resources. Hence, applying MTE to parasites can lend mechanistic, quantitative, predictive insight into the nature of parasitism and can inform general ecological theory.

  15. Microbial isoprenoid production: an example of green chemistry through metabolic engineering.

    PubMed

    Maury, Jérôme; Asadollahi, Mohammad A; Møller, Kasper; Clark, Anthony; Nielsen, Jens

    2005-01-01

    Saving energy, cost efficiency, producing less waste, improving the biodegradability of products, potential for producing novel and complex molecules with improved properties, and reducing the dependency on fossil fuels as raw materials are the main advantages of using biotechnological processes to produce chemicals. Such processes are often referred to as green chemistry or white biotechnology. Metabolic engineering, which permits the rational design of cell factories using directed genetic modifications, is an indispensable strategy for expanding green chemistry. In this chapter, the benefits of using metabolic engineering approaches for the development of green chemistry are illustrated by the recent advances in microbial production of isoprenoids, a diverse and important group of natural compounds with numerous existing and potential commercial applications. Accumulated knowledge on the metabolic pathways leading to the synthesis of the principal precursors of isoprenoids is reviewed, and recent investigations into isoprenoid production using engineered cell factories are described.

  16. Studies on xylitol production by metabolic pathway engineered Debaryomyces hansenii.

    PubMed

    Pal, Suksham; Choudhary, Vikas; Kumar, Anil; Biswas, Dipanwita; Mondal, Alok K; Sahoo, Debendra K

    2013-11-01

    Debaryomyces hansenii is one of the most promising natural xylitol producers. As the conversion of xylitol to xylulose mediated by NAD(+) cofactor dependent xylitol dehydrogenase (XDH) reduces its xylitol yield, xylitol dehydrogenase gene (DhXDH)-disrupted mutant of D. hansenii having potential for xylose assimilating pathway stopping at xylitol, was used to study the effects of co-substrates, xylose and oxygen availability on xylitol production. Compared to low cell growth and xylitol production in cultivation medium containing xylose as the only substrate, XDH disrupted mutants grown on glycerol as co-substrate accumulated 2.5-fold increased xylitol concentration over those cells grown on glucose as co-substrate. The oxygen availability, in terms of volumetric oxygen transfer coefficient, kLa (23.86-87.96 h(-1)), affected both xylitol productivity and yield, though the effect is more pronounced on the former. The addition of extra xylose at different phases of xylitol fermentation did not enhance xylitol productivity under experimental conditions.

  17. Acetone production with metabolically engineered strains of Acetobacterium woodii.

    PubMed

    Hoffmeister, Sabrina; Gerdom, Marzena; Bengelsdorf, Frank R; Linder, Sonja; Flüchter, Sebastian; Öztürk, Hatice; Blümke, Wilfried; May, Antje; Fischer, Ralf-Jörg; Bahl, Hubert; Dürre, Peter

    2016-07-01

    Expected depletion of oil and fossil resources urges the development of new alternative routes for the production of bulk chemicals and fuels beyond petroleum resources. In this study, the clostridial acetone pathway was used for the formation of acetone in the acetogenic bacterium Acetobacterium woodii. The acetone production operon (APO) containing the genes thlA (encoding thiolase A), ctfA/ctfB (encoding CoA transferase), and adc (encoding acetoacetate decarboxylase) from Clostridium acetobutylicum were cloned under the control of the thlA promoter into four vectors having different replicons for Gram-positives (pIP404, pBP1, pCB102, and pCD6). Stable replication was observed for all constructs. A. woodii [pJIR_actthlA] achieved the maximal acetone concentration under autotrophic conditions (15.2±3.4mM). Promoter sequences of the genes ackA from A. woodii and pta-ack from C. ljungdahlii were determined by primer extension (PEX) and cloned upstream of the APO. The highest acetone production in recombinant A. woodii cells was achieved using the promoters PthlA and Ppta-ack. Batch fermentations using A. woodii [pMTL84151_actthlA] in a bioreactor revealed that acetate concentration had an effect on the acetone production, due to the high Km value of the CoA transferase. In order to establish consistent acetate concentration within the bioreactor and to increase biomass, a continuous fermentation process for A. woodii was developed. Thus, acetone productivity of the strain A. woodii [pMTL84151_actthlA] was increased from 1.2mgL(-1)h(-1) in bottle fermentation to 26.4mgL(-1)h(-1) in continuous gas fermentation.

  18. A Genome-Scale Modeling Approach to Study Inborn Errors of Liver Metabolism: Toward an In Silico Patient

    PubMed Central

    Pagliarini, Roberto

    2013-01-01

    Abstract Inborn errors of metabolism (IEM) are genetic diseases caused by mutations in enzymes or transporters affecting specific metabolic reactions that cause a block in the physiological metabolic fluxes. Therapeutic treatment can be achieved either by decreasing the metabolic flux upstream of the block or by increasing the flux downstream of the block. The identification of upstream and downstream fluxes however is not trivial, since metabolic reactions are intertwined in a complex network. To overcome this problem, we propose an innovative computational workflow to model the alteration of metabolism caused by IEM and predict the metabolites and reactions that are affected by the mutation. Our workflow exploits a recent genome-scale metabolic network model of hepatocyte metabolism to identify metabolites accumulating in hepatocytes due to single gene mutations in IEM via an innovative “differential flux analysis.” We simulated 38 IEMs in the liver, and in about half of the cases, our workflow correctly identified the metabolites known to accumulate in the blood and urine of IEM patients. PMID:23464878

  19. Manufacturing Ultra-Precision Meso-scale Products by Coining

    SciTech Connect

    Seugling, R M; Davis, P J; Rickens, K; Osmer, J; Brinksmeier, E

    2010-02-18

    A method for replicating ultra-precision, meso-scale features onto a near-net-shape metallic blank has been demonstrated. The 'coining' technology can be used to imprint a wide range of features and/or profiles into two opposing surfaces. The instrumented system provides the ability to measure and control the product thickness and total thickness variation (TTV). The coining mechanism relies on kinematic principles to accurately and efficiently produce ultra-precision work pieces without the production of by products such as machining chips, or grinding swarf while preserving surface finish, material structure and overall form. Coining has been developed as a niche process for manufacturing difficult to machine, millimeter size components made from materials that may present hazardous conditions. In the case described in this paper a refractory metal part, tantalum (Ta) was produced with 4 {micro}m peak to valley 50 {micro}m special wavelength sine wave coined into the surface of 50 {micro}m blank. This technique shows promise for use on ductile materials that cannot be precision machined with conventional single crystal diamond tooling and/or has strict requirements on subsurface damage, surface impurities and grain structure. As a production process, it can be used to reduce manufacturing costs where large numbers of ultra-precision, repetitive designs are required and produce parts out of hazardous materials without generating added waste.

  20. Metabolic engineering of Zymomonas mobilis for 2,3-butanediol production from lignocellulosic biomass sugars

    DOE PAGES

    Yang, Shihui; Mohagheghi, Ali; Franden, Mary Ann; ...

    2016-09-02

    To develop pathways for advanced biofuel production, and to understand the impact of host metabolism and environmental conditions on heterologous pathway engineering for economic advanced biofuels production from biomass, we seek to redirect the carbon flow of the model ethanologen Zymomonas mobilis to produce desirable hydrocarbon intermediate 2,3-butanediol (2,3-BDO). 2,3-BDO is a bulk chemical building block, and can be upgraded in high yields to gasoline, diesel, and jet fuel. 2,3-BDO biosynthesis pathways from various bacterial species were examined, which include three genes encoding acetolactate synthase, acetolactate decarboxylase, and butanediol dehydrogenase. Bioinformatics analysis was carried out to pinpoint potential bottlenecks formore » high 2,3-BDO production. Different combinations of 2,3-BDO biosynthesis metabolic pathways using genes from different bacterial species have been constructed. Our results demonstrated that carbon flux can be deviated from ethanol production into 2,3-BDO biosynthesis, and all three heterologous genes are essential to efficiently redirect pyruvate from ethanol production for high 2,3-BDO production in Z. mobilis. The down-selection of best gene combinations up to now enabled Z. mobilis to reach the 2,3-BDO production of more than 10 g/L from glucose and xylose, as well as mixed C6/C5 sugar streams derived from the deacetylation and mechanical refining process. In conclusion, this study confirms the value of integrating bioinformatics analysis and systems biology data during metabolic engineering endeavors, provides guidance for value-added chemical production in Z. mobilis, and reveals the interactions between host metabolism, oxygen levels, and a heterologous 2,3-BDO biosynthesis pathway. Taken together, this work provides guidance for future metabolic engineering efforts aimed at boosting 2,3-BDO titer anaerobically.« less

  1. Towards large scale production and separation of carbon nanotubes

    NASA Astrophysics Data System (ADS)

    Alvarez, Noe T.

    Since their discovery, carbon nanotubes (CNTs) have boosted the research and applications of nanotechnology; however, many applications of CNTs are inaccessible because they depend upon large-scale CNT production and separations. Type, chirality and diameter control of CNTs determine many of their physical properties, and such control is still not accesible. This thesis studies the fundamentals for scalable selective reactions of HiPCo CNTs as well as the early phase of routes to an inexpensive approach for large-scale CNT production. In the growth part, this thesis covers a complete wet-chemistry process of catalyst and catalyst support deposition for growth of vertically aligned (VA) CNTs. A wet-chemistry preparation process has significant importance for CNT synthesis through chemical vapor deposition (CVD). CVD is by far, the most suitable and inexpensive process for large-scale CNT production when compared to other common processes such as laser ablation and arc discharge. However, its potential has been limited by low-yielding and difficult preparation processes of catalyst and its support, therefore its competitiveness has been reduced. The wet-chemistry process takes advantage of current nanoparticle technology to deposit the catalyst and the catalyst support as a thin film of nanoparticles, making the protocol simple compared to electron beam evaporation and sputtering processes. In the CNT selective reactions part, this thesis studies UV irradiation of individually dispersed HiPCo CNTs that generates auto-selective reactions in the liquid phase with good control over their diameter and chirality. This technique is ideal for large-scale and continuous-process of separations of CNTs by diameter and type. Additionally, an innovative simple catalyst deposition through abrasion is demonstrated. Simple friction between the catalyst and the substrates deposit a high enough density of metal catalyst particles for successful CNT growth. This simple approach has

  2. Multi-omic profiling -of EPO-producing Chinese hamster ovary cell panel reveals metabolic adaptation to heterologous protein production.

    PubMed

    Ley, Daniel; Seresht, Ali Kazemi; Engmark, Mikael; Magdenoska, Olivera; Nielsen, Kristian Fog; Kildegaard, Helene Faustrup; Andersen, Mikael Rørdam

    2015-11-01

    Chinese hamster ovary (CHO) cells are the preferred production host for many therapeutic proteins. The production of heterologous proteins in CHO cells imposes a burden on the host cell metabolism and impact cellular physiology on a global scale. In this work, a multi-omics approach was applied to study the production of erythropoietin (EPO) in a panel of CHO-K1 cells under growth-limited and unlimited conditions in batch and chemostat cultures. Physiological characterization of the EPO-producing cells included global transcriptome analysis, targeted metabolome analysis, including intracellular pools of glycolytic intermediates, NAD(P)H/NAD(P)(+) , adenine nucleotide phosphates (ANP), and extracellular concentrations of sugars, organic acids, and amino acids. Potential impact of EPO expression on the protein secretory pathway was assessed at multiple stages using quantitative PCR (qPCR), reverse transcription PCR (qRT-PCR), Western blots (WB), and global gene expression analysis to assess EPO gene copy numbers, EPO gene expression, intracellular EPO retention, and differentially expressed genes functionally related to secretory protein processing, respectively. We found no evidence supporting the existence of production bottlenecks in energy metabolism (i.e., glycolytic metabolites, NAD(P)H/NAD(P)(+) and ANPs) in batch culture or in the secretory protein production pathway (i.e., gene dosage, transcription and post-translational processing of EPO) in chemostat culture at specific productivities up to 5 pg/cell/day. Time-course analysis of high- and low-producing clones in chemostat culture revealed rapid adaptation of transcription levels of amino acid catabolic genes in favor of EPO production within nine generations. Interestingly, the adaptation was followed by an increase in specific EPO productivity.

  3. Metabolic constituents of grapevine and grape-derived products

    PubMed Central

    Ali, Kashif; Maltese, Federica; Verpoorte, Robert

    2009-01-01

    The numerous uses of the grapevine fruit, especially for wine and beverages, have made it one of the most important plants worldwide. The phytochemistry of grapevine is rich in a wide range of compounds. Many of them are renowned for their numerous medicinal uses. The production of grapevine metabolites is highly conditioned by many factors like environment or pathogen attack. Some grapevine phytoalexins have gained a great deal of attention due to their antimicrobial activities, being also involved in the induction of resistance in grapevine against those pathogens. Meanwhile grapevine biotechnology is still evolving, thanks to the technological advance of modern science, and biotechnologists are making huge efforts to produce grapevine cultivars of desired characteristics. In this paper, important metabolites from grapevine and grape derived products like wine will be reviewed with their health promoting effects and their role against certain stress factors in grapevine physiology. PMID:20835385

  4. Application of (13)C flux analysis to identify high-productivity CHO metabolic phenotypes.

    PubMed

    Templeton, Neil; Smith, Kevin D; McAtee-Pereira, Allison G; Dorai, Haimanti; Betenbaugh, Michael J; Lang, Steven E; Young, Jamey D

    2017-01-23

    Industrial bioprocesses place high demands on the energy metabolism of host cells to meet biosynthetic requirements for maximal protein expression. Identifying metabolic phenotypes that promote high expression is therefore a major goal of the biotech industry. We conducted a series of (13)C flux analysis studies to examine the metabolic response to IgG expression during early stationary phase of CHO cell cultures grown in 3L fed-batch bioreactors. We examined eight clones expressing four different IgGs and compared with three non-expressing host-cell controls. Some clones were genetically manipulated to be apoptosis-resistant by expressing Bcl-2Δ, which correlated with increased IgG production and elevated glucose metabolism. The metabolic phenotypes of the non-expressing, IgG-expressing, and Bcl-2Δ/IgG-expressing clones were fully segregated by hierarchical clustering analysis. Lactate consumption and citric acid cycle fluxes were most strongly associated with specific IgG productivity. These studies indicate that enhanced oxidative metabolism is a characteristic of high-producing CHO cell lines.

  5. Jasmonates during senescence: signals or products of metabolism?

    PubMed

    Seltmann, Martin A; Hussels, Wiebke; Berger, Susanne

    2010-11-01

    Jasmonic acid and derivatives are oxylipin signaling compounds derived from linolenic acid. Jasmonates accumulate during natural and dark-induced senescence but the increase in these compounds is not essential for the initiation or progression of these senescence processes. Here we report that during natural and dark-induced senescence the increase in jasmonate levels does not trigger jasmonate signaling. Furthermore we provide evidence that jasmonate production might result from membrane turnover during dark-induced senescence.

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

    PubMed

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

    2008-12-01

    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.

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

    SciTech Connect

    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.

  8. Metabolically engineered Saccharomyces cerevisiae for branched-chain ester productions.

    PubMed

    Yuan, Jifeng; Mishra, Pranjul; Ching, Chi Bun

    2016-12-10

    Medium branched-chain esters can be used not only as a biofuel but are also useful chemicals with various industrial applications. The development of economically feasible and environment friendly bio-based fuels requires efficient cell factories capable of producing desired products in high yield. Herein, we sought to use a number of strategies to engineer Saccharomyces cerevisiae for high-level production of branched-chain esters. Mitochondrion-based expression of ATF1 gene in a base strain with an overexpressed valine biosynthetic pathway together with expression of mitochondrion-relocalized α-ketoacid decarboxylase (encoded by ARO10) and alcohol dehydrogenase (encoded by ADH7) not only produced isobutyl acetate, but also 3-methyl-1-butyl acetate and 2-methyl-1-butyl acetate. Further segmentation of the downstream esterification step into the cytosol to utilize the cytosolic acetyl-CoA pool for acetyltransferase (ATF)-mediated condensation enabled an additional fold improvement of ester productions. The best titre attained in the present study is 260.2mg/L isobutyl acetate, 296.1mg/L 3-methyl-1-butyl acetate and 289.6mg/L 2-methyl-1-butyl acetate.

  9. Quantitative assessment of thermodynamic constraints on the solution space of genome-scale metabolic models.

    PubMed

    Hamilton, Joshua J; Dwivedi, Vivek; Reed, Jennifer L

    2013-07-16

    Constraint-based methods provide powerful computational techniques to allow understanding and prediction of cellular behavior. These methods rely on physiochemical constraints to eliminate infeasible behaviors from the space of available behaviors. One such constraint is thermodynamic feasibility, the requirement that intracellular flux distributions obey the laws of thermodynamics. The past decade has seen several constraint-based methods that interpret this constraint in different ways, including those that are limited to small networks, rely on predefined reaction directions, and/or neglect the relationship between reaction free energies and metabolite concentrations. In this work, we utilize one such approach, thermodynamics-based metabolic flux analysis (TMFA), to make genome-scale, quantitative predictions about metabolite concentrations and reaction free energies in the absence of prior knowledge of reaction directions, while accounting for uncertainties in thermodynamic estimates. We applied TMFA to a genome-scale network reconstruction of Escherichia coli and examined the effect of thermodynamic constraints on the flux space. We also assessed the predictive performance of TMFA against gene essentiality and quantitative metabolomics data, under both aerobic and anaerobic, and optimal and suboptimal growth conditions. Based on these results, we propose that TMFA is a useful tool for validating phenotypes and generating hypotheses, and that additional types of data and constraints can improve predictions of metabolite concentrations.

  10. Metabolism of pharmaceutical and personal care products by carrot cell cultures.

    PubMed

    Wu, Xiaoqin; Fu, Qiuguo; Gan, Jay

    2016-04-01

    With the increasing use of treated wastewater and biosolids in agriculture, residues of pharmaceutical and personal care products (PPCPs) in these reused resources may contaminate food produce via plant uptake, constituting a route for human exposure. Although various PPCPs have been reported to be taken up by plants in laboratories or under field conditions, at present little information is available on their metabolism in plants. In this study, we applied carrot cell cultures to investigate the plant metabolism of PPCPs. Five phase I metabolites of carbamazepine were identified and the potential metabolism pathways of carbamazepine were proposed. We also used the carrot cell cultures as a rapid screening tool to initially assess the metabolism potentials of 18 PPCPs. Eleven PPCPs, including acetaminophen, caffeine, meprobamate, primidone, atenolol, trimethoprim, DEET, carbamazepine, dilantin, diazepam, and triclocarban, were found to be recalcitrant to metabolism. The other 7 PPCPs, including triclosan, naproxen, diclofenac, ibuprofen, gemfibrozil, sulfamethoxazole, and atorvastatin, displayed rapid metabolism, with 0.4-47.3% remaining in the culture at the end of the experiment. Further investigation using glycosidase hydrolysis showed that 1.3-20.6% of initially spiked naproxen, diclofenac, ibuprofen, and gemfibrozil were transformed into glycoside conjugates. Results from this study showed that plant cell cultures may be a useful tool for initially exploring the potential metabolites of PPCPs in plants as well as for rapidly screening the metabolism potentials of a variety of PPCPs or other emerging contaminants, and therefore may be used for prioritizing compounds for further comprehensive evaluations.

  11. Identification of candidate network hubs involved in metabolic adjustments of rice under drought stress by integrating transcriptome data and genome-scale metabolic network.

    PubMed

    Mohanty, Bijayalaxmi; Kitazumi, Ai; Cheung, C Y Maurice; Lakshmanan, Meiyappan; de los Reyes, Benildo G; Jang, In-Cheol; Lee, Dong-Yup

    2016-01-01

    In this study, we have integrated a rice genome-scale metabolic network and the transcriptome of a drought-tolerant rice line, DK151, to identify the major transcriptional regulators involved in metabolic adjustments necessary for adaptation to drought. This was achieved by examining the differential expressions of transcription factors and metabolic genes in leaf, root and young panicle of rice plants subjected to drought stress during tillering, booting and panicle elongation stages. Critical transcription factors such as AP2/ERF, bZIP, MYB and NAC that control the important nodes in the gene regulatory pathway were identified through correlative analysis of the patterns of spatio-temporal expression and cis-element enrichment. We showed that many of the candidate transcription factors involved in metabolic adjustments were previously linked to phenotypic variation for drought tolerance. This approach represents the first attempt to integrate models of transcriptional regulation and metabolic pathways for the identification of candidate regulatory genes for targeted selection in rice breeding.

  12. Metabolic trade-offs between biomass synthesis and photosynthate export at different light intensities in a genome–scale metabolic model of rice

    PubMed Central

    Poolman, Mark G.; Kundu, Sudip; Shaw, Rahul; Fell, David A.

    2014-01-01

    Previously we have used a genome scale model of rice metabolism to describe how metabolism reconfigures at different light intensities in an expanding leaf of rice. Although this established that the metabolism of the leaf was adequately represented, in the model, the scenario was not that of the typical function of the leaf—to provide material for the rest of the plant. Here we extend our analysis to explore the transition to a source leaf as export of photosynthate increases at the expense of making leaf biomass precursors, again as a function of light intensity. In particular we investigate whether, when the leaf is making a smaller range of compounds for export to the phloem, the same changes occur in the interactions between mitochondrial and chloroplast metabolism as seen in biomass synthesis for growth when light intensity increases. Our results show that the same changes occur qualitatively, though there are slight quantitative differences reflecting differences in the energy and redox requirements for the different metabolic outputs. PMID:25506349

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

    SciTech Connect

    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

  14. Oxygen-controlled biosurfactant production in a bench scale bioreactor.

    PubMed

    Kronemberger, Frederico de Araujo; Santa Anna, Lidia Maria Melo; Fernandes, Ana Carolina Loureiro Brito; Menezes, Reginaldo Ramos de; Borges, Cristiano Piacsek; Freire, Denise Maria Guimarães

    2008-03-01

    Rhamnolipids have been pointed out as promising biosurfactants. The most studied microorganisms for the aerobic production of these molecules are the bacteria of the genus Pseudomonas. The aim of this work was to produce a rhamnolipid-type biosurfactant in a bench-scale bioreactor by one strain of Pseudomonas aeruginosa isolated from oil environments. To study the microorganism growth and production dependency on oxygen, a nondispersive oxygenation device was developed, and a programmable logic controller (PLC) was used to set the dissolved oxygen (DO) concentration. Using the data stored in a computer and the predetermined characteristics of the oxygenation device, it was possible to evaluate the oxygen uptake rate (OUR) and the specific OUR (SOUR) of this microorganism. These rates, obtained for some different DO concentrations, were then compared to the bacterial growth, to the carbon source consumption, and to the rhamnolipid and other virulence factors production. The SOUR presented an initial value of about 60.0 mgO(2)/g(DW) h. Then, when the exponential growth phase begins, there is a rise in this rate. After that, the SOUR reduces to about 20.0 mgO(2)/g(DW) h. The carbon source consumption is linear during the whole process.

  15. Production of recombinant proteins in microalgae at pilot greenhouse scale.

    PubMed

    Gimpel, Javier A; Hyun, James S; Schoepp, Nathan G; Mayfield, Stephen P

    2015-02-01

    Recombinant protein production in microalgae chloroplasts can provide correctly folded proteins in significant quantities and potentially inexpensive costs compared to other heterologous protein production platforms. The best results have been achieved by using the psbA promoter and 5' untranslated region (UTR) to drive the expression of heterologous genes in a psbA-deficient, non-photosynthetic, algal host. Unfortunately, using such a strategy makes the system unviable for large scale cultivation using natural sunlight for photosynthetic growth. In this study we characterized eight different combinations of 5' regulatory regions and psbA coding sequences for their ability to restore photosynthesis in a psbA-deficient Chlamydomonas reinhardtii, while maintaining robust accumulation of a commercially viable recombinant protein driven by the psbA promoter/5'UTR. The recombinant protein corresponded to bovine Milk Amyloid A (MAA), which is present in milk colostrum and could be used to prevent infectious diarrhea in mammals. This approach allowed us to identify photosynthetic strains that achieved constitutive production of MAA when grown photosynthetically in 100 L bags in a greenhouse. Under these conditions, the maximum MAA expression achieved was 1.86% of total protein, which corresponded to 3.28 mg/L of culture medium. Within our knowledge, this is the first report of a recombinant protein being produced this way in microalgae.

  16. Oxygen-controlled Biosurfactant Production in a Bench Scale Bioreactor

    NASA Astrophysics Data System (ADS)

    de Kronemberger, Frederico Araujo; Anna, Lidia Maria Melo Santa; Fernandes, Ana Carolina Loureiro Brito; de Menezes, Reginaldo Ramos; Borges, Cristiano Piacsek; Freire, Denise Maria Guimarães

    Rhamnolipids have been pointed out as promising biosurfactants. The most studied microorganisms for the aerobic production of these molecules are the bacteria of the genus Pseudomonas. The aim of this work was to produce a rhamnolipid-type biosurfactant in a bench-scale bioreactor by one strain of Pseudomonas aeruginosa isolated from oil environments. To study the microorganism growth and production dependency on oxygen, a nondispersive oxygenation device was developed, and a programmable logic controller (PLC) was used to set the dissolved oxygen (DO) concentration. Using the data stored in a computer and the predetermined characteristics of the oxygenation device, it was possible to evaluate the oxygen uptake rate (OUR) and the specific OUR (SOUR) of this microorganism. These rates, obtained for some different DO concentrations, were then compared to the bacterial growth, to the carbon source consumption, and to the rhamnolipid and other virulence factors production. The SOUR presented an initial value of about 60.0 mg02/gdw h. Then, when the exponential growth phase begins, there is a rise in this rate. After that, the SOUR reduces to about 20.0 mg02/gdw h. The carbon source consumption is linear during the whole process.

  17. Enhancement of L-lactic acid production in Lactobacillus casei from Jerusalem artichoke tubers by kinetic optimization and citrate metabolism.

    PubMed

    Ge, Xiang-Yang; Qian, He; Zhang, Wei-Guo

    2010-01-01

    Efficient L-lactic acid production from Jerusalem artichoke tubers by Lactobacillus casei G-02 using simultaneous saccharification and fermentation (SSF) in fed-batch culture is demonstrated. The kinetic analysis in the SSF signified that the inulinase activity was subjected to product inhibition, while the fermentation activity of G-02 was subjected to substrate inhibition. It was also found that the intracellularly NOX activity was enhanced by the citrate metabolism, which increased the carbon flux of Embden-Meyerhof-Parnas (EMP) pathway dramatically, and resulted more ATP production. As a result, when the SSF was carried out at 40 degrees after the initial hydrolysis of 1 h with supplemented sodium citrate of 10g/L, L-lactic acid concentration of 141.5 g/L was obtained in 30 h with a volumetric productivity of 4.7 g/L/h. The conversion efficiency and product yield were 93.6% of the theoretical lactic acid yield and 52.4 g lactic acid/100 g Jerusalem artichoke flour, respectively. Such a high concentration of lactic acid with high productivity from Jerusalem artichoke has not been reported previously, and hence G-02 could be a potential candidate for economical production of L-lactic acid from Jerusalem artichoke at a commercial scale.

  18. Analysis of Genetic Variation and Potential Applications in Genome-Scale Metabolic Modeling

    PubMed Central

    Cardoso, João G. R.; Andersen, Mikael Rørdam; Herrgård, Markus J.; Sonnenschein, Nikolaus

    2015-01-01

    Genetic variation is the motor of evolution and allows organisms to overcome the environmental challenges they encounter. It can be both beneficial and harmful in the process of engineering cell factories for the production of proteins and chemicals. Throughout the history of biotechnology, there have been efforts to exploit genetic variation in our favor to create strains with favorable phenotypes. Genetic variation can either be present in natural populations or it can be artificially created by mutagenesis and selection or adaptive laboratory evolution. On the other hand, unintended genetic variation during a long term production process may lead to significant economic losses and it is important to understand how to control this type of variation. With the emergence of next-generation sequencing technologies, genetic variation in microbial strains can now be determined on an unprecedented scale and resolution by re-sequencing thousands of strains systematically. In this article, we review challenges in the integration and analysis of large-scale re-sequencing data, present an extensive overview of bioinformatics methods for predicting the effects of genetic variants on protein function, and discuss approaches for interfacing existing bioinformatics approaches with genome-scale models of cellular processes in order to predict effects of sequence variation on cellular phenotypes. PMID:25763369

  19. Metabolic engineering of Nicotiana benthamiana for the increased production of taxadiene.

    PubMed

    Hasan, Md Mohidul; Kim, Hyun-Soon; Jeon, Jae-Heung; Kim, Sung Hong; Moon, BoKyung; Song, Jai-Young; Shim, Sang Hee; Baek, Kwang-Hyun

    2014-06-01

    We report the production of taxadiene by transformation of N. benthamiana with a taxadiene synthase gene. The production was significantly increased by an elicitor treatment or metabolic pathway shunting. Paclitaxel (Taxol(®)) was first isolated from the bark of the pacific yew tree as an anticancer agent and has been used extensively to treat various types of cancer. Taxadiene, the first committed product of paclitaxel synthesis is cyclized from geranylgeranyl diphosphate (GGPP), and further complex hydroxylation and acylation processes of the unique taxane core skeleton produce paclitaxel. To accomplish de novo production of taxadiene, we transformed Nicotiana benthamiana with a taxadiene synthase (TS) gene. The introduced TS gene under the transcriptional control of the CaMV 35S promoter was constitutively expressed in N. benthamiana, and the de novo production of taxadiene was confirmed by mass spectroscopy profiling. Transformed N. benthamiana homozygous lines produced 11-27 μg taxadiene/g of dry weight. The highest taxadiene production line TSS-8 was further treated with an elicitor, methyl jasmonate, and metabolic pathway shunting by suppression of the phytoene synthase gene expression which resulted in accumulation of increased taxadiene accumulation by 1.4- or 1.9-fold, respectively. In summary, we report that the production of taxadiene in N. benthamiana was possible by the ectopic expression of the TS gene, and higher accumulation of taxadiene could be achieved by elicitor treatment or metabolic pathway shunting of the terpenoid pathway.

  20. Metabolic engineering of Corynebacterium crenatium for enhancing production of higher alcohols

    PubMed Central

    Su, Haifeng; Lin, Jiafu; Wang, GuangWei

    2016-01-01

    Biosynthesis approaches for the production of higher alcohols as a source of alternative fossil fuels have garnered increasing interest recently. However, there is little information available in the literature about using undirected whole-cell mutagenesis (UWCM) in vivo to improve higher alcohols production. In this study, for the first time, we approached this question from two aspects: first preferentially improving the capacity of expression host, and subsequently optimizing metabolic pathways using multiple genetic mutations to shift metabolic flux toward the biosynthetic pathway of target products to convert intermediate 2-keto acid compounds into diversified C4~C5 higher alcohols using UWCM in vivo, with the aim of improving the production. The results demonstrated the production of higher alcohols including isobutanol, 2-methyl-1-butanol, 3-methyl-1-butanol from glucose and duckweed under simultaneous saccharification and fermentation (SSF) scheme were higher based on the two aspects compared with only the use of wild-type stain as expression host. These findings showed that the improvement via UWCM in vivo in the two aspects for expression host and metabolic flux can facilitate the increase of higher alcohols production before using gene editing technology. Our work demonstrates that a multi-faceted approach for the engineering of novel synthetic pathways in microorganisms for improving biofuel production is feasible. PMID:27996038

  1. Metabolic engineering of Corynebacterium crenatium for enhancing production of higher alcohols

    NASA Astrophysics Data System (ADS)

    Su, Haifeng; Lin, Jiafu; Wang, Guangwei

    2016-12-01

    Biosynthesis approaches for the production of higher alcohols as a source of alternative fossil fuels have garnered increasing interest recently. However, there is little information available in the literature about using undirected whole-cell mutagenesis (UWCM) in vivo to improve higher alcohols production. In this study, for the first time, we approached this question from two aspects: first preferentially improving the capacity of expression host, and subsequently optimizing metabolic pathways using multiple genetic mutations to shift metabolic flux toward the biosynthetic pathway of target products to convert intermediate 2-keto acid compounds into diversified C4~C5 higher alcohols using UWCM in vivo, with the aim of improving the production. The results demonstrated the production of higher alcohols including isobutanol, 2-methyl-1-butanol, 3-methyl-1-butanol from glucose and duckweed under simultaneous saccharification and fermentation (SSF) scheme were higher based on the two aspects compared with only the use of wild-type stain as expression host. These findings showed that the improvement via UWCM in vivo in the two aspects for expression host and metabolic flux can facilitate the increase of higher alcohols production before using gene editing technology. Our work demonstrates that a multi-faceted approach for the engineering of novel synthetic pathways in microorganisms for improving biofuel production is feasible.

  2. Recent trends in metabolic engineering of microorganisms for the production of advanced biofuels.

    PubMed

    Cheon, Seungwoo; Kim, Hye Mi; Gustavsson, Martin; Lee, Sang Yup

    2016-12-01

    As climate change has become one of the major global risks, our heavy dependence on petroleum-derived fuels has received much public attention. To solve such problems, production of sustainable fuels has been intensively studied over the past years. Thanks to recent advances in synthetic biology and metabolic engineering technologies, bio-based platforms for advanced biofuels production have been developed using various microorganisms. The strategies for production of advanced biofuels have converged upon four major metabolic routes: the 2-ketoacid pathway, the fatty acid synthesis (FAS) pathway, the isoprenoid pathway, and the reverse β-oxidation pathway. Additionally, the polyketide synthesis pathway has recently been attracting interest as a promising alternative biofuel production route. In this article, recent trends in advanced biofuels production are reviewed by categorizing them into three types of advanced biofuels: alcohols, biodiesel and jet fuel, and gasoline. Focus is given on the strategies of employing synthetic biology and metabolic engineering for the development of microbial strains producing advanced fuels. Finally, the prospects for future advances needed to achieve much more efficient bio-based production of advanced biofuels are discussed, focusing on designing advanced biofuel production pathways coupled with screening, modifying, and creating novel enzymes.

  3. A refined genome-scale reconstruction of Chlamydomonas metabolism provides a platform for systems-level analyses

    PubMed Central

    Imam, Saheed; Schäuble, Sascha; Valenzuela, Jacob; de Lomana, Adrián López García; Carter, Warren; Price, Nathan D.; Baliga, Nitin S.

    2015-01-01

    Summary Microalgae have reemerged as organisms of prime biotechnological interest due to their ability to synthesize a suite of valuable chemicals. To harness the capabilities of these organisms, we need a comprehensive systems-level understanding of their metabolism, which can be fundamentally achieved through large-scale mechanistic models of metabolism. In this study, we present a revised and significantly improved genome-scale metabolic model for the widely-studied microalga, Chlamydomonas reinhardtii. The model, iCre1355, represents a major advance over previous models, both in content and predictive power. iCre1355 encompasses a broad range of metabolic functions encoded across the nuclear, chloroplast and mitochondrial genomes accounting for 1355 genes (1460 transcripts), 2394 and 1133 metabolites. We found improved performance over the previous metabolic model based on comparisons of predictive accuracy across 306 phenotypes (from 81 mutants), lipid yield analysis and growth rates derived from chemostat-grown cells (under 3 conditions). Measurement of macronutrient uptake revealed carbon and phosphate to be good predictors of growth rate, while nitrogen consumption appeared to be in excess. We analyzed high-resolution time series transcriptomics data using iCre1355 to uncover dynamic pathway-level changes that occur in response to nitrogen starvation and changes in light intensity. This approach enabled accurate prediction of growth rates, the cessation of growth and accumulation of triacylglycerols during nitrogen starvation, and the temporal response of different growth-associated pathways to increased light intensity. Thus, iCre1355 represents an experimentally-validated genome-scale reconstruction of C. reinhardtii metabolism that should serve as a useful resource for studying the metabolic processes of this and related microalgae. PMID:26485611

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

    PubMed

    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.

  5. Synthetic Spider Silk Production on a Laboratory Scale

    PubMed Central

    Hsia, Yang; Gnesa, Eric; Pacheco, Ryan; Kohler, Kristin; Jeffery, Felicia; Vierra, Craig

    2012-01-01

    As society progresses and resources become scarcer, it is becoming increasingly important to cultivate new technologies that engineer next generation biomaterials with high performance properties. The development of these new structural materials must be rapid, cost-efficient and involve processing methodologies and products that are environmentally friendly and sustainable. Spiders spin a multitude of different fiber types with diverse mechanical properties, offering a rich source of next generation engineering materials for biomimicry that rival the best manmade and natural materials. Since the collection of large quantities of natural spider silk is impractical, synthetic silk production has the ability to provide scientists with access to an unlimited supply of threads. Therefore, if the spinning process can be streamlined and perfected, artificial spider fibers have the potential use for a broad range of applications ranging from body armor, surgical sutures, ropes and cables, tires, strings for musical instruments, and composites for aviation and aerospace technology. In order to advance the synthetic silk production process and to yield fibers that display low variance in their material properties from spin to spin, we developed a wet-spinning protocol that integrates expression of recombinant spider silk proteins in bacteria, purification and concentration of the proteins, followed by fiber extrusion and a mechanical post-spin treatment. This is the first visual representation that reveals a step-by-step process to spin and analyze artificial silk fibers on a laboratory scale. It also provides details to minimize the introduction of variability among fibers spun from the same spinning dope. Collectively, these methods will propel the process of artificial silk production, leading to higher quality fibers that surpass natural spider silks. PMID:22847722

  6. Synthetic spider silk production on a laboratory scale.

    PubMed

    Hsia, Yang; Gnesa, Eric; Pacheco, Ryan; Kohler, Kristin; Jeffery, Felicia; Vierra, Craig

    2012-07-18

    As society progresses and resources become scarcer, it is becoming increasingly important to cultivate new technologies that engineer next generation biomaterials with high performance properties. The development of these new structural materials must be rapid, cost-efficient and involve processing methodologies and products that are environmentally friendly and sustainable. Spiders spin a multitude of different fiber types with diverse mechanical properties, offering a rich source of next generation engineering materials for biomimicry that rival the best manmade and natural materials. Since the collection of large quantities of natural spider silk is impractical, synthetic silk production has the ability to provide scientists with access to an unlimited supply of threads. Therefore, if the spinning process can be streamlined and perfected, artificial spider fibers have the potential use for a broad range of applications ranging from body armor, surgical sutures, ropes and cables, tires, strings for musical instruments, and composites for aviation and aerospace technology. In order to advance the synthetic silk production process and to yield fibers that display low variance in their material properties from spin to spin, we developed a wet-spinning protocol that integrates expression of recombinant spider silk proteins in bacteria, purification and concentration of the proteins, followed by fiber extrusion and a mechanical post-spin treatment. This is the first visual representation that reveals a step-by-step process to spin and analyze artificial silk fibers on a laboratory scale. It also provides details to minimize the introduction of variability among fibers spun from the same spinning dope. Collectively, these methods will propel the process of artificial silk production, leading to higher quality fibers that surpass natural spider silks.

  7. Intentionally reduced intestinal integrity causes inflammation and negatively affects metabolism and productivity in lactating Holstein cows

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Study objectives were to evaluate the effects of intentionally reduced intestinal barrier function on productivity, metabolism, and inflammatory indices in otherwise healthy dairy cows. Fourteen lactating Holstein cows (parity 2.6 ± 0.3; 117 ± 18 days in milk) were enrolled in two experimental perio...

  8. Production of xylitol by a Coniochaeta ligniaria strain tolerant of inhibitors and defective in xylose metabolism

    Technology Transfer Automated Retrieval System (TEKTRAN)

    In conversion of biomass to fuels or chemicals, inhibitory compounds arising from physical-chemical pretreatment of the feedstock can interfere with fermentation of the sugars to product. Fungal strain Coniochaeta ligniaria NRRL30616, metabolizes the furan aldehydes furfural and 5-hydroxymethylfurfu...

  9. Engineering microaerobic metabolism of E. coli for 1,2-propanediol production.

    PubMed

    Jain, Rachit; Huang, Jin; Yuan, Qipeng; Yan, Yajun

    2015-07-01

    Establishment of novel metabolic pathways for biosynthesis of chemicals, fuels and pharmaceuticals has been demonstrated in Escherichia coli due to its ease of genetic manipulation and adaptability to varying oxygen levels. E. coli growing under microaerobic condition is known to exhibit features of both aerobic and anaerobic metabolism. In this work, we attempt to engineer this metabolism for production of 1,2-propanediol. We first redirect the carbon flux by disrupting carbon-competing pathways to increase the production of 1,2-propanediol microaerobically from 0.25 to 0.85 g/L. We then disrupt the first committed step of E. coli's ubiquinone biosynthesis pathway (ubiC) to prevent the oxidation of NADH in microaerobic conditions. Coupling this strategy with carbon flux redirection leads to enhanced production of 1,2-propanediol at 1.2 g/L. This work demonstrates the production of non-native reduced chemicals in E. coli by engineering its microaerobic metabolism.

  10. Plasma graviton production in TeV-scale gravity

    NASA Astrophysics Data System (ADS)

    Melkumova, E. Yu

    2010-11-01

    We develop the theory of interaction of classical plasma with Kaluza-Klein (KK) gravitons in the ADD model of TeV-scale gravity. Plasma is described within the kinetic approach as the system of charged particles and Maxwell field both confined on the brane. Interaction with multidimensional gravity living in the bulk with n compact extra dimensions is introduced within the linearized theory. The KK gravitons emission rates are computed taking into account plasma collective effects through the two-point correlation functions of the fluctuations of the plasma energy-momentum tensor. Apart from known mechanisms (such as bremsstrahlung and gravi-Primakoff effect) we find essentially collective channels such as the coalescence of plasma waves into gravitons which may be manifest in turbulent plasmas. Our results indicate that commonly used rates of the KK gravitons production in stars and supernovae may be underestimated.

  11. Production Scale-Up or Activated Carbons for Ultracapacitors

    SciTech Connect

    Dr. Steven D. Dietz

    2007-01-10

    Transportation use accounts for 67% of the petroleum consumption in the US. Electric and hybrid vehicles are promising technologies for decreasing our dependence on petroleum, and this is the objective of the FreedomCAR & Vehicle Technologies Program. Inexpensive and efficient energy storage devices are needed for electric and hybrid vehicle to be economically viable, and ultracapacitors are a leading energy storage technology being investigated by the FreedomCAR program. The most important parameter in determining the power and energy density of a carbon-based ultracapacitor is the amount of surface area accessible to the electrolyte, which is primarily determined by the pore size distribution. The major problems with current carbons are that their pore size distribution is not optimized for liquid electrolytes and the best carbons are very expensive. TDA Research, Inc. (TDA) has developed methods to prepare porous carbons with tunable pore size distributions from inexpensive carbohydrate based precursors. The use of low-cost feedstocks and processing steps greatly lowers the production costs. During this project with the assistance of Maxwell Technologies, we found that an impurity was limiting the performance of our carbon and the major impurity found was sulfur. A new carbon with low sulfur content was made and found that the performance of the carbon was greatly improved. We also scaled-up the process to pre-