2,156 research outputs found

    Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale

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    Metabolic flux analysis (MFA) is considered to be the gold standard for determining the intracellular flux distribution of biological systems. The majority of work using MFA has been limited to core models of metabolism due to challenges in implementing genome-scale MFA and the undesirable trade-off between increased scope and decreased precision in flux estimations. This work presents a tunable workflow for expanding the scope of MFA to the genome-scale without trade-offs in flux precision. The genome-scale MFA model presented here, iDM2014, accounts for 537 net reactions, which includes the core pathways of traditional MFA models and also covers the additional pathways of purine, pyrimidine, isoprenoid, methionine, riboflavin, coenzyme A, and folate, as well as other biosynthetic pathways. When evaluating the iDM2014 using a set of measured intracellular intermediate and cofactor mass isotopomer distributions (MIDs), it was found that a total of 232 net fluxes of central and peripheral metabolism could be resolved in the <i>E. coli</i> network. The increase in scope was shown to cover the full biosynthetic route to an expanded set of bioproduction pathways, which should facilitate applications such as the design of more complex bioprocessing strains and aid in identifying new antimicrobials. Importantly, it was found that there was no loss in precision of core fluxes when compared to a traditional core model, and additionally there was an overall increase in precision when considering all observable reactions

    Phycomyces

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    This monographic review on a fungus is not addressed to mycologists. None of the authors has been trained or has otherwise acquired a general proficiency in mycology. They are motivated by a common interest in the performances of signal handling exhibited by the sense organs of all organisms and by the desire to attack these as yet totally obscure aspects of molecular biology by the study of a microorganism with certain desirable properties. The sporangiophore of the fungus Phycomyces is a gigantic, single-celled, erect, cylindrical, aerial hypha. It is sensitive to at least four distinct stimuli: light, gravity, stretch, and some unknown stimulus by which it avoids solid objects. These stimuli control a common output, the growth rate, producing either temporal changes in growth rate or tropic responses. We are interested in the output because it gives us information about the reception of the various signals. In the absence of external stimuli, the growth rate is controlled by internal signals keeping the network of biochemical processes in balance. The external stimuli interact with the internal signals. We wish to inquire into the early steps of this interaction. For light, for instance, the cell must have a receptor pigment as the first mediator. What kind of a molecule is this pigment? Which organelle contains it? What chemical reaction happens after a light quantum has been absorbed? And how is the information introduced by this primary photochemical event amplified in a controlled manner and processed in the next step? How do a few quanta or a few molecules trigger macroscopic responses? Will we find ourselves confronted with devices wholly distinct from anything now known in biology

    Conservation, Restoration, and Monitoring Plan for the Lower White River, Utah

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    In this report we present a conservation, restoration and monitoring plan for the lower White River, a major tributary of the Green River. The plan is intended to help guide conservation, restoration and management of the lower White River over the next several decades and is also developed as an adaptive management plan to facilitate learning. The recommended conservation and restoration actions are intended to maintain and enhance native riparian vegetation and instream habitat for native desert fishes including federally endangered Colorado Pikeminnow (Ptychocheilus lucius), federally endangered Razorback Sucker (Xyrauchen texanus), Speckled Dace (Rhinichthys osculus), Bluehead Sucker (Catostomus discobolus), Flannelmouth Sucker (C. latipinnis), and Roundtail Chub (Gila robusta). ~~Many mammals, amphibians, migratory birds, and raptors that use the riparian zone or migrate through the riverscape are also anticipated to benefit from the plan. The recommended conservation and restoration actions are based on the best available information regarding the current ecological and geomorphic conditions and restoration recovery potential. We prioritized reaches for conservation and restoration actions using expert opinion and field validation, riparian vegetation density and instream and riparian habitat condition and complexity data. We recommend an experimental design for implementation of conservation and restoration actions. Combined with monitoring, the experimental design is aimed at identifying the most successful conservation and restoration actions for maintaining complex instream habitat and a healthy native riparian community

    What determines debt structure in emerging markets: Transaction costs or public monitoring?

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    We examine the predilection for private bonds over bank financing (debt structure) for emerging markets within the frameworks of both transaction cost economics and a transparency explanation, emphasizing the distinction between public monitoring (bonds) and private monitoring (banks), as well as considering the influence of national culture on institutions. Employing several tests, including structural equation modeling, we find, among many results that in emerging markets bonds are preferred over bank loans when there is less corporate opacity and fewer foreign access restrictions, as well as in environment of greater political instability, transaction cost, and limits to legal protection. Bonds are also favored over banks in cultural environments of greater uncertainty avoidance, masculinity, long-term orientation, and indulgence and less individualism. Overall, we attribute our results to culture and institutional quality together influencing debt structure, particularly by impacting attitudes toward public monitoring. Our results will be of great interest to researchers interested in the legal, social, and cultural environments of emerging markets

    What determines debt structure in emerging markets: Transaction costs or public monitoring?

    Get PDF
    We examine the predilection for private bonds over bank financing (debt structure) for emerging markets within the frameworks of both transaction cost economics and a transparency explanation, emphasizing the distinction between public monitoring (bonds) and private monitoring (banks), as well as considering the influence of national culture on institutions. Employing several tests, including structural equation modeling, we find, among many results that in emerging markets bonds are preferred over bank loans when there is less corporate opacity and fewer foreign access restrictions, as well as in environment of greater political instability, transaction cost, and limits to legal protection. Bonds are also favored over banks in cultural environments of greater uncertainty avoidance, masculinity, long-term orientation, and indulgence and less individualism. Overall, we attribute our results to culture and institutional quality together influencing debt structure, particularly by impacting attitudes toward public monitoring. Our results will be of great interest to researchers interested in the legal, social, and cultural environments of emerging markets

    Tectonomagmatic Evolution of Southwestern Laurentia: Insights from Zircon U-Pb Geochronology and Hafnium Isotopic Composition of the Red Bluff Granite Suite, West Texas, USA

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    We provide laser ablation–multicollector–inductively coupled plasma–mass spectrometry (LA-MC-ICP-MS) and high-precision chemical abrasion–isotope dilution–thermal ionization mass spectrometry (CA-ID-TIMS) U-Pb ages and Hf isotopic compositions of zircons from the Red Bluff Granite Suite and mafic dikes in the Franklin Mountains of El Paso, Texas, USA. Granitoids exposed in the Franklin Mountains were previously divided into five magmatic stages based on cross-cutting relationships. Major and trace element compositions showed that these granitoids are ferroan, alkaline, and A2 type. Homogeneity in the whole-rock geochemistry suggests that the granite stages are genetically related and share similar petrogenetic histories. Weighted mean zircon 206Pb/238U dates from the older magmatic stage 1 alkali-feldspar quartz syenite and stage 2 alkali-feldspar granite are 1112.36 ± 0.35 and 1112.46 ± 0.37 Ma, respectively. The weighted mean εHf(t) values varying from +5.3 to +7.2 are similar to those of other regional ca. 1.1 Ga magmatic rocks throughout southwestern Laurentia. Geochemical characteristics, petrological modeling, and enriched Hf isotopic composition suggest fractional crystallization of a basaltic magma that was produced by melting of an enriched mantle reservoir. However, zircon inheritance ages of ca. 1.3 Ga and 1.26–1.15 Ga are consistent with a minor contribution from felsic crustal basement. Our data and regional geology are consistent with a post-collisional slab break-off that facilitated asthenospheric upwelling and partial melting of the enriched mantle, possibly subcontinental lithospheric mantle, extending from Llano Uplift, Texas, in the southeast to California to the northwest. Magma thus generated upon differentiation produced ferroan and A-type granitoids
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