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  • Cooperatives  (33)
  • Mineral Physics, Rheology, Heat Flow and Volcanology  (29)
  • Synthetic Biology and Assembly Cloning  (24)
  • Oxford University Press  (86)
  • MDPI
  • 2015-2019  (86)
  • 1990-1994
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  • 1
    Publication Date: 2016-07-28
    Description: Genetic engineering projects often require control over when a protein is degraded. To this end, we use a fusion between a degron and an inactivating peptide that can be added to the N-terminus of a protein. When the corresponding protease is expressed, it cleaves the peptide and the protein is degraded. Three protease:cleavage site pairs from Potyvirus are shown to be orthogonal and active in exposing degrons, releasing inhibitory domains and cleaving polyproteins. This toolbox is applied to the design of genetic circuits as a means to control regulator activity and degradation. First, we demonstrate that a gate can be constructed by constitutively expressing an inactivated repressor and having an input promoter drive the expression of the protease. It is also shown that the proteolytic release of an inhibitory domain can improve the dynamic range of a transcriptional gate (200-fold repression). Next, we design polyproteins containing multiple repressors and show that their cleavage can be used to control multiple outputs. Finally, we demonstrate that the dynamic range of an output can be improved (8-fold to 190-fold) with the addition of a protease-cleaved degron. Thus, controllable proteolysis offers a powerful tool for modulating and expanding the function of synthetic gene circuits.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 2
    Publication Date: 2016-05-05
    Description: We study a model of lava flow to determine its thermal and dynamic characteristics from thermal measurements of the lava at its surface. Mathematically this problem is reduced to solving an inverse boundary problem. Namely, using known conditions at one part of the model boundary we determine the missing condition at the remaining part of the boundary. We develop a numerical approach to the mathematical problem in the case of steady-state flow. Assuming that the temperature and the heat flow are prescribed at the upper surface of the model domain, we determine the flow characteristics in the entire model domain using a variational (adjoint) method. We have performed computations of model examples and showed that in the case of smooth input data the lava temperature and the flow velocity can be reconstructed with a high accuracy. As expected, a noise imposed on the smooth input data results in a less accurate solution, but still acceptable below some noise level. Also we analyse the influence of optimization methods on the solution convergence rate. The proposed method for reconstruction of physical parameters of lava flows can also be applied to other problems in geophysical fluid flows.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 3
    Publication Date: 2016-05-06
    Description: Studies of discrete volcanic explosions, that usually last less than 2 or 3 min, have suggested that the partitioning of seismic-acoustic energy is likely related to a range of physical mechanisms that depend on magma properties and other physical constraints such as the location of the fragmentation surface. In this paper, we explore the energy partition of a paroxysmal eruptive phase of Tungurahua volcano that lasted for over 4 hr, on 2006 July 14–15, using seismic-acoustic information recorded by stations on its flanks (near field). We find evidence of a linear scaling between seismic and acoustic energies, with time-dependent intensities, during the sustained explosive phase of the eruption. Furthermore, we argue that this scaling can be explained by two different processes: (1) the fragmentation region ultimately acts as the common source of energy producing both direct seismic waves, that travel through the volcanic edifice, and direct acoustic waves coming from a disturbed atmosphere above the summit; (2) the coupling of acoustic waves with the ground to cause seismic waves. Both processes are concurrent, however we have found that the first one is dominant for seismic records below 4 Hz. Here we use the linear scaling of intensities to construct seismic and acoustic indices, which, we argue, could be used to track an ongoing eruption. Thus, especially in strong paroxysms that can produce pyroclastic flows, the index correlation and their levels can be used as quantitative monitoring parameters to assess the volcanic hazard in real time. Additionally, we suggest from the linear scaling that the source type for both cases, seismic and acoustic, is dipolar and dominant in the near field.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 4
    Publication Date: 2015-05-03
    Description: Transformation-associated recombination (TAR) protocol allowing the selective isolation of full-length genes complete with their distal enhancer regions and entire genomic loci with sizes up to 250 kb from complex genomes in yeast S. cerevisiae has been developed more than a decade ago. However, its wide spread usage has been impeded by a low efficiency (0.5–2%) of chromosomal region capture during yeast transformants which in turn requires a time-consuming screen of hundreds of colonies. Here, we demonstrate that pre-treatment of genomic DNA with CRISPR-Cas9 nucleases to generate double-strand breaks near the targeted genomic region results in a dramatic increase in the fraction of gene-positive colonies (up to 32%). As only a dozen or less yeast transformants need to be screened to obtain a clone with the desired chromosomal region, extensive experience with yeast is no longer required. A TAR-CRISPR protocol may help to create a bank of human genes, each represented by a genomic copy containing its native regulatory elements, that would lead to a significant advance in functional, structural and comparative genomics, in diagnostics, gene replacement, generation of animal models for human diseases and has a potential for gene therapy.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 5
    Publication Date: 2015-05-10
    Description: Lying below Vatnajökull ice cap in Iceland, Bárðarbunga stratovolcano began experiencing wholesale caldera collapse in 2014 August 16, one of the largest such events recorded in the modern instrumental era. Simultaneous with this collapse is the initiation of a plate boundary rifting episode north of the caldera. Observations using the international constellation of radar satellites indicate rapid 50 cm d –1 subsidence of the glacier surface overlying the collapsing caldera and metre-scale crustal deformation in the active rift zone. Anomalous earthquakes around the rim of the caldera with highly nondouble-couple focal mechanisms provide a mechanical link to the dynamics of the collapsing magma chamber. A model of the collapse consistent with available geodetic and seismic observations suggests that the majority of the observed subsidence occurs aseismically via a deflating sill-like magma chamber.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 6
    Publication Date: 2015-05-12
    Description: The Canadian farm share for five crop-based products and seven livestock-based products from 1997 to 2010 is calculated using a supply chain IO analysis. Significant differences exist in farm shares across food commodities with higher farm shares for livestock products and lower farm shares for grain-based products. The decline in the Canadian farm share for food consumed at home is driven in large part by the food purchasing habits of consumers. This paper also addresses the hypothesis that the decline in the Canadian farm share could be partially driven by rising input costs in post-farmgate processes or rising input costs that have greater impact on downstream sectors than primary agricultural producers. Three experiments were conducted to assess the impact of an increase in the cost of corn, energy, and farm labor would have on commodity output prices, farm returns, food expenditure, and farm share. In all three cases, the overall farm share increases, albeit by a small amount, suggesting that these shocks have a larger relative impact on the prices of agricultural commodities than the prices of marketing commodities used in post-farmgate activities. A two-period comparison of these simulations shows that energy (corn and farm labour) price shocks would have had a greater (lower) impact on the farm share in 2007 than 1997.
    Keywords: Q11 - Aggregate Supply and Demand Analysis ; Prices, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 7
    Publication Date: 2015-05-12
    Description: Farm households in developing countries generally allocate a major portion of their resources to staple food production, mainly for self-consumption. Hence, many of them are more or less delinked from the market. It is well recognized, however, that market participation is crucial for farm households to ensure a flow of cash income, leading to poverty alleviation and improved livelihoods. Thus, it is meaningful to understand what factors affect farm households' decision to sell food crops, which is important for strengthening their linkages with markets. The empirical literature on impacts of market linkages has seldom focused on the determinants of market participation. Using rice farm households in Bangladesh and applying a double-hurdle model, this article demonstrates that the provision of general education and the development of agricultural infrastructure such as irrigation facilities can strengthen the market linkages of farm households by enhancing their marketable surplus through increased production. By contrast, rainfall beyond the optimum level, drought spells, and flood incidences can weaken market linkages by reducing their marketable surplus through decreased production. Specific policies such as investment in general education are drawn up based on the findings.
    Keywords: C24 - Truncated and Censored Models, D01 - Microeconomic Behavior: Underlying Principles, D13 - Household Production and Intrahousehold Allocation, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 8
    Publication Date: 2015-03-11
    Description: Deformation experiments on partially molten rocks in simple shear form melt bands at 20° to the shear plane instead of at the expected 45° principal compressive stress direction. These melt bands may play an important role in melt focusing in mid-ocean ridges. Such shallow bands are known to form for two-phase media under shear if strongly non-Newtonian power-law creep is employed for the solid phase, or anisotropy imposed. However laboratory experiments show that shallow bands occur regardless of creep mechanism, even in diffusion creep, which is nominally Newtonian. Here we propose that a couple of forms of two-phase damage allow for shallow melt bands even in diffusion creep.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 9
    Publication Date: 2015-04-21
    Description: RNA research and therapy relies primarily on synthetic RNAs. We employed recombinant RNA technology toward large-scale production of pre-miRNA agents in bacteria, but found the majority of target RNAs were not or negligibly expressed. We thus developed a novel strategy to achieve consistent high-yield biosynthesis of chimeric RNAs carrying various small RNAs (e.g. miRNAs, siRNAs and RNA aptamers), which was based upon an optimal noncoding RNA scaffold (OnRS) derived from tRNA fusion pre-miR-34a (tRNA/mir-34a). Multi-milligrams of chimeric RNAs (e.g. OnRS/miR-124, OnRS/GFP-siRNA, OnRS/Neg (scrambled RNA) and OnRS/MGA (malachite green aptamer)) were readily obtained from 1 l bacterial culture. Deep sequencing analyses revealed that mature miR-124 and target GFP-siRNA were selectively released from chimeric RNAs in human cells. Consequently, OnRS/miR-124 was active in suppressing miR-124 target gene expression and controlling cellular processes, and OnRS/GFP-siRNA was effective in knocking down GFP mRNA levels and fluorescent intensity in ES-2/GFP cells and GFP -transgenic mice. Furthermore, the OnRS/MGA sensor offered a specific strong fluorescence upon binding MG, which was utilized as label-free substrate to accurately determine serum RNase activities in pancreatic cancer patients. These results demonstrate that OnRS-based bioengineering is a common, robust and versatile strategy to assemble various types of small RNAs for broad applications.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 10
    Publication Date: 2015-12-29
    Description: This article investigates the collective choice of production standards by farmer and processor groups within a vertical food supply chain, taking into account their competition behaviours. We develop a general model to analyse the strategic motive of using standards to limit supply and shift rents between farmers and processors in the vertical chain. We find that a stringent standard can raise farmers' profit, but at the expense of processors. This is the case when the standard affects more variable costs than fixed cost of production, when the demand for the final product is inelastic, and when processors have a high degree of oligopoly power.
    Keywords: L13 - Oligopoly and Other Imperfect Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 11
    Publication Date: 2016-01-09
    Description: Proteins adhere to DNA at locations and with strengths that depend on the protein conformation, the underlying DNA sequence and the ionic content of the solution. A facile technique to probe the positions and strengths of protein-DNA binding would aid in understanding these important interactions. Here, we describe a ‘DNA pulley’ for position-resolved nano-mechanical measurements of protein-DNA interactions. A molecule of DNA is tethered by one end to a glass surface, and by the other end to a magnetic bead. The DNA is stretched horizontally by a magnet, and a nanoscale knife made of silicon nitride is manipulated to contact, bend and scan along the DNA. The mechanical profile of the DNA at the contact with the knife is probed via nanometer-precision optical tracking of the magnetic bead. This system enables detection of protein bumps on the DNA and localization of their binding sites. We study theoretically the technical requirements to detect mechanical heterogeneities in the DNA itself.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 12
    Publication Date: 2016-01-09
    Description: Synthetic biology seeks to envision living cells as a matter of engineering. However, increasing evidence suggests that the genetic load imposed by the incorporation of synthetic devices in a living organism introduces a sort of unpredictability in the design process. As a result, individual part characterization is not enough to predict the behavior of designed circuits and thus, a costly trial-error process is eventually required. In this work, we provide a new theoretical framework for the predictive treatment of the genetic load. We mathematically and experimentally demonstrate that dependences among genes follow a quantitatively predictable behavior. Our theory predicts the observed reduction of the expression of a given synthetic gene when an extra genetic load is introduced in the circuit. The theory also explains that such dependence qualitatively differs when the extra load is added either by transcriptional or translational modifications. We finally show that the limitation of the cellular resources for gene expression leads to a mathematical formulation that converges to an expression analogous to the Ohm's law for electric circuits. Similitudes and divergences with this law are outlined. Our work provides a suitable framework with predictive character for the design process of complex genetic devices in synthetic biology.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 13
    Publication Date: 2016-03-31
    Description: Thinly traded agricultural commodity markets are a concern for farmers and policy markers due to the belief that prices in these settings will be highly volatile, subject to manipulation, and incapable of efficiently allocating resources. Analysis of thin agricultural markets has to date been impeded by lack of an appropriate analytical framework from which to study their behavior. In this paper we propose the modern agricultural markets (MAM) framework as an appropriate paradigm through which to view and evaluate thin markets. We argue that thinly traded markets that meet key conditions required for a MAM will generate maximum economic surplus and enable farmers to earn at least a competitive return on their investments. In the absence of these conditions, however, the concerns known as the "thin market problem" have validity. We set forth the MAM framework, interpret it in a thin-market context, and conduct several brief case studies of thin markets to illustrate use of the approach and draw some key inferences about these markets' behavior. The analysis indicates that appropriate government policies directed to thin markets are those that facilitate their convergence to MAM status, but in reality key policies under recent consideration would have the opposite effect.
    Keywords: L10 - General, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 14
    Publication Date: 2015-08-29
    Description: Progressive deformation of upper mantle rocks via dislocation creep causes their constituent crystals to take on a non-random orientation distribution (crystallographic preferred orientation or CPO) whose observable signatures include shear-wave splitting and azimuthal dependence of surface wave speeds. Comparison of these signatures with mantle flow models thus allows mantle dynamics to be unraveled on global and regional scales. However, existing self-consistent models of CPO evolution are computationally expensive when used with 3-D and/or time-dependent convection models. Here we propose a new method, called ANPAR, which is based on an analytical parametrization of the crystallographic spin predicted by the second-order (SO) self-consistent theory. Our parametrization runs 2–6  x  10 4 times faster than the SO model and fits its predictions for CPO and crystallographic spin with a variance reduction 〉99 per cent. We illustrate the ANPAR model predictions for the deformation of olivine with three dominant slip systems, (010)[100], (001)[100] and (010)[001], for three uniform deformations (uniaxial compression, pure shear and simple shear) and for a corner-flow model of a spreading mid-ocean ridge.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 15
    Publication Date: 2015-07-10
    Description: In many developing countries, supermarkets are expanding rapidly. This affects farmers’ marketing options. Previous studies have analyzed welfare effects of smallholder participation in supermarket channels from a static perspective, using cross-section data. We develop a conceptual framework and use panel data to better understand participation and impact dynamics. The analysis focuses on vegetable producers in Kenya. Participation in supermarket channels is associated with income gains. However, many farmers have dropped out of the supermarket channel due to various constraints. The initial income gains cannot be sustained when returning to the traditional market. Organizational support may be needed to avoid widening income disparities.
    Keywords: L24 - Contracting Out ; Joint Ventures ; Technology Licensing, O12 - Microeconomic Analyses of Economic Development, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 16
    Publication Date: 2015-07-11
    Description: We investigate the capability of Time Reversal Mirror (TRM) algorithm to image local acoustic sources (〈3.5 km) associated with complex, sustained volcanic eruptions. Accurate source localization for volcano infrasound (low-frequency acoustic waves) is often challenging due to pronounced volcanic topography and emergent arrivals of infrasound signals. While the accuracy of the conventional approaches (e.g. triangulation and semblance method) can be severely compromised by the complex volcanic settings, a TRM-based method may have the potential to properly image acoustic sources by the use of full waveform information and numerical modelling of the time-reversed wavefield. We apply the TRM algorithm to a pyroclastic-laden eruption (sustained for ~60 s) at Santiaguito Volcano, Guatemala, and show that an ordinary TRM operation can undergo significant reduction of its focusing power due to strong topographic propagation effects (e.g. reflection and diffraction). We propose a weighted imaging condition to compensate for complicated transmission loss of the time-reversed wavefield and demonstrate that the presented condition significantly improves the focusing quality of TRM in the presence of complex topography. The consequent TRM source images exhibit remarkable agreement with the visual observation of the eruption implying that the TRM method with a proper imaging condition can be used to localize and track acoustic sources associated with complex volcanic eruptions.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 17
    Publication Date: 2016-08-20
    Description: Light-regulated modules offer unprecedented new ways to control cellular behavior in precise spatial and temporal resolution. The availability of such tools may dramatically accelerate the progression of synthetic biology applications. Nonetheless, current optogenetic toolbox of prokaryotes has potential issues such as lack of rapid and switchable control, less portable, low dynamic expression and limited parts. To address these shortcomings, we have engineered a novel bidirectional promoter system for Escherichia coli that can be induced or repressed rapidly and reversibly using the blue light dependent DNA-binding protein EL222. We demonstrated that by modulating the dosage of light pulses or intensity we could control the level of gene expression precisely. We show that both light-inducible and repressible system can function in parallel with high spatial precision in a single cell and can be switched stably between ON- and OFF-states by repetitive pulses of blue light. In addition, the light-inducible and repressible expression kinetics were quantitatively analysed using a mathematical model. We further apply the system, for the first time, to optogenetically synchronize two receiver cells performing different logic behaviors over time using blue light as a molecular clock signal. Overall, our modular approach layers a transformative platform for next-generation light-controllable synthetic biology systems in prokaryotes.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 18
    Publication Date: 2016-08-20
    Description: Current DNA assembly methods for preparing highly purified linear subassemblies require complex and time-consuming in vitro manipulations that hinder their ability to construct megabase-sized DNAs (e.g. synthetic genomes). We have developed a new method designated ‘CasHRA ( Cas 9-facilitated H omologous R ecombination A ssembly)’ that directly uses large circular DNAs in a one-step in vivo assembly process. The large circular DNAs are co-introduced into Saccharomyces cerevisiae by protoplast fusion, and they are cleaved by RNA-guided Cas9 nuclease to release the linear DNA segments for subsequent assembly by the endogenous homologous recombination system. The CasHRA method allows efficient assembly of multiple large DNA segments in vivo ; thus, this approach should be useful in the last stage of genome construction. As a proof of concept, we combined CasHRA with an upstream assembly method (Gibson procedure of genome assembly) and successfully constructed a 1.03 Mb MGE-syn1.0 ( M inimal G enome of Escherichia coli ) that contained 449 essential genes and 267 important growth genes. We expect that CasHRA will be widely used in megabase-sized genome constructions.
    Keywords: Synthetic Biology and Assembly Cloning
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    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 19
    Publication Date: 2015-10-15
    Description: Natural regulatory networks contain many interacting components that allow for fine-tuning of switching and memory properties. Building simple bistable switches, synthetic biologists have learned the design principles of complex natural regulatory networks. However, most switches constructed so far are so simple (e.g. comprising two regulators) that they are functional only within a limited parameter range. Here, we report the construction of robust, tunable bistable switches in Escherichia coli using three heterologous protein regulators (ExsADC) that are sequestered into an inactive complex through a partner swapping mechanism. On the basis of mathematical modeling, we accurately predict and experimentally verify that the hysteretic region can be fine-tuned by controlling the interactions of the ExsADC regulatory cascade using the third member ExsC as a tuning knob. Additionally, we confirm that a dual-positive feedback switch can markedly increase the hysteretic region, compared to its single-positive feedback counterpart. The dual-positive feedback switch displays bistability over a 10 6 -fold range of inducer concentrations, to our knowledge, the largest range reported so far. This work demonstrates the successful interlocking of sequestration-based ultrasensitivity and positive feedback, a design principle that can be applied to the construction of robust, tunable, and predictable genetic programs to achieve increasingly sophisticated biological behaviors.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 20
    Publication Date: 2016-06-19
    Description: The expansion of offshore renewable energy infrastructure and the need for trans-continental shelf power transmission require the use of submarine high-voltage (HV) cables. These cables have maximum operating surface temperatures of up to 70 °C and are typically buried 1–2 m beneath the seabed, within the wide range of substrates found on the continental shelf. However, the heat flow pattern and potential effects on the sedimentary environments around such anomalously high heat sources in the near-surface sediments are poorly understood. We present temperature measurements from a 2-D laboratory experiment representing a buried submarine HV cable, and identify the thermal regimes generated within typical unconsolidated shelf sediments—coarse silt, fine sand and very coarse sand. We used a large (2 x 2.5 m 2 ) tank filled with water-saturated spherical glass beads (ballotini) and instrumented with a buried heat source and 120 thermocouples to measure the time-dependent 2-D temperature distributions. The observed and corresponding Finite Element Method simulations of the steady state heat flow regimes and normalized radial temperature distributions were assessed. Our results show that the heat transfer and thus temperature fields generated from submarine HV cables buried within a range of sediments are highly variable. Coarse silts are shown to be purely conductive, producing temperature increases of 〉10 °C up to 40 cm from the source of 60 °C above ambient; fine sands demonstrate a transition from conductive to convective heat transfer between cf. 20 and 36 °C above ambient, with 〉10 °C heat increases occurring over a metre from the source of 55 °C above ambient; and very coarse sands exhibit dominantly convective heat transfer even at very low ( cf. 7 °C) operating temperatures and reaching temperatures of up to 18 °C above ambient at a metre from the source at surface temperatures of only 18 °C. These findings are important for the surrounding near-surface environments experiencing such high temperatures and may have significant implications for chemical and physical processes operating at the grain and subgrain scale; biological activity at both microfaunal and macrofaunal levels; and indeed the operational performance of the cables themselves, as convective heat transport would increase cable current ratings, something neglected in existing standards.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 21
    Publication Date: 2016-06-03
    Description: We have investigated transcriptional interference between convergent genes in E. coli and demonstrate substantial interference for inter-promoter distances of as far as 3 kb. Interference can be elicited by both strong 70 dependent and T7 promoters. In the presented design, a strong promoter driving gene expression of a ‘forward’ gene interferes with the expression of a ‘reverse’ gene by a weak promoter. This arrangement allows inversely correlated gene expression without requiring further regulatory components. Thus, modulation of the activity of the strong promoter alters expression of both the forward and the reverse gene. We used this design to develop a dual selection system for conditional operator site binding, allowing positive selection both for binding and for non-binding to DNA. This study demonstrates the utility of this novel system using the Lac repressor as a model protein for conditional DNA binding, and spectinomycin and chloramphenicol resistance genes as positive selection markers in liquid culture. Randomized LacI libraries were created and subjected to subsequent dual selection, but mispairing IPTG and selection cues in respect to the wild-type LacI response, allowing the isolation of a LacI variant with a reversed IPTG response within three rounds of library generation and dual selection.
    Keywords: Synthetic Biology and Assembly Cloning
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    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 22
    Publication Date: 2016-08-20
    Description: This paper reviews the situation in the agricultural sector and food security in Cuba, and particularly the transformations that have (not) taken place since 1990. We compare the Cuban transition with transitions in other "transition countries" and show that Cuba does not easily fit into one of the transition patterns, and, in a way, has characteristics of "a bit of everything". To conclude, we discuss the (potential) effects of the recent policy changes and the new economic reforms that were announced.
    Keywords: O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, P21 - Planning, Coordination, and Reform, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 23
    Publication Date: 2015-05-21
    Description: Mobile phone coverage has expanded considerably throughout the developing world, particularly within sub-Saharan Africa. Existing evidence suggests that increased access to information technology has improved agricultural market efficiency for consumer markets and certain commodities, but there is less evidence of its impact on producer markets. Building on the work of Aker (2010) , we estimate the impact of mobile phone coverage on producer price dispersion for three commodities in Niger. Our results suggest that mobile phone coverage reduces spatial producer price dispersion by 6 percent for cowpea, a semi-perishable commodity. These effects are strongest for remote markets and during certain periods of the year. The introduction of mobile phone coverage has no effect on producer price dispersion for millet and sorghum, two staple grains that are less perishable and are commonly stored by farmers. There are no impacts of mobile phone coverage on producer price levels, but mobile phone coverage is associated with a reduction in the intra-annual price variation for cowpea.
    Keywords: O30 - General, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0258-6770
    Electronic ISSN: 1564-698X
    Topics: Economics
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  • 24
    Publication Date: 2015-05-26
    Description: We modify the behavioural postulate of self-centred inequity aversion to explain producers' reluctance to fund generic fruit and vegetable advertising as a result of experiencing negative utility when others benefit more from a public good than themselves, but positive utility when they earn more than others. We find that higher variability in returns decreases the probability of a favourable vote. Conversely, if information about payoffs is incomplete, if subjects are allowed to experience a trial run of a generic advertising programme, if returns are equal across producers, or if there is government support for the programme, the likelihood of approval rises.
    Keywords: H41 - Public Goods, M37 - Advertising, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 25
    Publication Date: 2015-04-12
    Description: We present a strategy to thoroughly investigate the effects of prominent topography on the surface tilt due to a spherical pressure source. We use Etna's topography as a case of study and, for different source positions, we compare the tilt fields calculated through (i) a 3-D boundary element method and (ii) analytical half-space solutions. We systematically determine (i) the source positions leading to the strongest tilt misfits when numerical and analytical results are compared and (ii) the surface areas where the strongest distortions in the tilt field are most likely to be observed. We also demonstrate that, under critical circumstances, in terms of respective positions of pressure source and observation points, results of inversion procedures aimed at retrieving the source parameters can be misleading, if tilt data are analysed using models that do not account for topography.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 26
    Publication Date: 2015-04-21
    Description: We describe solid-phase cloning (SPC) for high-throughput assembly of expression plasmids. Our method allows PCR products to be put directly into a liquid handler for capture and purification using paramagnetic streptavidin beads and conversion into constructs by subsequent cloning reactions. We present a robust automated protocol for restriction enzyme based SPC and its performance for the cloning of 〉60 000 unique human gene fragments into expression vectors. In addition, we report on SPC-based single-strand assembly for applications where exact control of the sequence between fragments is needed or where multiple inserts are to be assembled. In this approach, the solid support allows for head-to-tail assembly of DNA fragments based on hybridization and polymerase fill-in. The usefulness of head-to-tail SPC was demonstrated by assembly of 〉150 constructs with up to four DNA parts at an average success rate above 80%. We report on several applications for SPC and we suggest it to be particularly suitable for high-throughput efforts using laboratory workstations.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 27
    Publication Date: 2015-04-24
    Description: The agreement between shear wave velocities for the Earth's inner core observed from seismology with those derived from mineral physics is considerably worse than for any other region of the Earth. Furthermore, there is still debate as to the phase of iron present in the inner core, particularly when alloying with nickel and light elements is taken into account. To investigate the extent to which the mismatch between seismology and mineral physics is a function of either crystal structure and/or the amount of nickel present, we have used ab initio molecular dynamics simulations to calculate the elastic constants and seismic velocities ( V p and V s ) of face centred cubic (fcc) iron at Earth's inner core pressures (360 GPa) and at temperatures up to ~7000 K. We find that V p for fcc iron (fcc-Fe) is very similar to that for hexagonal close packed (hcp) iron at all temperatures. In contrast, V s for fcc-Fe is significantly higher than in hcp-Fe, with the difference increasing with increasing temperature; the difference between V s for the core (from seismology) and V s for fcc-Fe exceeds 40 per cent. These results are consistent with previous work at lower temperatures. We have also investigated the effect of 6.5 and 13 atm% Ni in fcc-Fe. We find that Ni only slightly reduces V p and V s (e.g. by 2 per cent in V s for 13 atm% Ni at 5500 K), and cannot account for the difference between the velocities observed in the core and those of pure fcc-Fe. We also tried to examine pre-melting behaviour in fcc-Fe, as reported in hcp-Fe by extending the study to very high temperatures (at which superheating may occur). However, we find that fcc-Fe spontaneously transforms to other hcp-like structures before melting; two hcp-like structures were found, both of hexagonal symmetry, which may most easily be regarded as being derived from an hcp crystal with stacking faults. That the structure did not transform to a true hcp phase is likely as a consequence of the limited size of the simulation box (108 atoms). At 360 GPa, in pure fcc-Fe, we find that the transition from fcc to the hcp-like structure occurs at 7000 K, whereas in the Ni bearing system, the transition occurs at higher temperature (7250 K). This reinforces previous work showing that fcc-Fe might transform to hcp-Fe just before melting, and that Ni tends to stabilize the fcc structure with respect to hcp.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 28
    Publication Date: 2015-04-25
    Description: Viscoelastic behaviour of materials in nature is observed in post-event deformations due to seismic or volcanic activities. In this paper, by adopting the correspondence principle, we propose an inelastic model to predict first the Laplace-domain response of a transversely isotropic viscoelastic half-space due to a shear or tensile fault of polygonal shape. The displacement and stress fields in the time domain are then obtained using an efficient and accurate algorithm for the inverse Laplace transform. Numerical examples are presented to validate the proposed solution and to show the viscoelastic displacement and stress fields due to a strike-slip, dip-slip and tensile fault of rectangular shape. The obtained results indicate that both viscoelasticity and transverse isotropy play significant roles in the viscoelastic response of the half-space due to faults, which could be used as benchmarks for the future numerical analysis of realistic post-seismic or volcanic event.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 29
    Publication Date: 2015-04-26
    Description: One of the unresolved questions concerning fault deformation is the degree and cause of localization of shear at depth beneath a fault. Geologic observations of exhumed shear zones indicate that while the motion is no longer planar, it can still be localized near the down-dip extension of the fault; however, the degree of localization is uncertain. We employ simple analytic and numerical models to investigate the structural form of distributed shear beneath a strike-slip fault, and the relative importance of the physical mechanisms that have the potential to localize a shear zone. For a purely depth dependent viscosity, = 0 exp (– z / z 0 ), we find that a shear zone develops with a half-width $\delta _w\sim \sqrt{z_0}$ for small z 0 at the base of the layer, where lengths are non-dimensionalized by the layer thickness ( d km). Including a non-linear stress–strain-rate relation ( $\dot{\epsilon }\propto \sigma ^n$ ) scales w by $1/\sqrt{n}$ , comparable to deformation length scales in thin viscous sheet calculations. We find that the primary control on the shear-zone width is the depth dependence of viscosity that arises from the temperature dependence of viscosity and the increase in temperature with depth. As this relationship is exponential, scaling relations give a dimensional half-width that scales approximately as $$ \tilde{\delta }_w\approx T_{\frac{1}{2}}\sqrt{\frac{Rd}{nQ\beta }}\text{ km}, $$ where $T_{\frac{1}{2}}$ (K) is the temperature at the midpoint of the layer, R (J mol –1 K –1 ) the gas constant, Q (J mol –1 ) the activation energy and β (K km –1 ) the geothermal gradient. This relation predicts the numerical results for the parameter range consistent with continental rheologies to within 2–5 per cent and shear-zone half-widths from 2 to 6 km. The inclusion of shear-stress heating reduces w by only an additional 5–25 per cent, depending on the initial width of the shear zone. While the width of the shear zone may not decrease significantly, local temperature increases from shear-stress heating range from 50 to 300 °C resulting in a reduction in viscosities beneath the fault of several orders of magnitude and a concomitant reduction in the stresses needed to drive the motion.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 30
    Publication Date: 2015-07-10
    Description: We argue that farm survival is influenced by neighboring farmers’ characteristics and, in particular, by the direct payments neighboring farmers receive. The article shows empirically that these interdependencies are crucial for an assessment of the effects of direct payments on farm survival. Using spatially explicit farm-level data for nearly all Norwegian farms, a spatial probit model is estimated to explain farm survival from 1999 to 2009 controlling for spatial farm interdependence. We show that ignoring spatial interdependencies between farms leads to a substantial overestimation of the effects of direct payments on farm survival. To our knowledge, this article is the first attempt to empirically analyze the importance of neighboring interdependencies for the effects of direct payments on farm survival.
    Keywords: C21 - Cross-Sectional Models ; Spatial Models ; Treatment Effect Models, C25 - Discrete Regression and Qualitative Choice Models, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 31
    Publication Date: 2015-07-09
    Description: The equation that relates pressure, temperature and volume and is described by parameters that are function of temperature at 1 bar (hereafter called thermal equation of state, TEOS), has practical computational advantages for petrological and geophysical applications over the equation that considers explicitly a thermal pressure. Some considerations that justify the use of the TEOS are discussed here. (1) The assumption that the parameters are function of temperature is perhaps better understood by looking at the Helmholtz energy function that is implicitly assumed in the case of an equation of state (EOS) derived from interatomic potentials. A test case shows that the Helmholtz energy related to the Vinet EOS and the Helmholtz energy from the Debye model are very similar. (2) The TEOS should be able to reproduce thermal expansion (α), isothermal bulk modulus ( K T ) and heat capacity ( C p and C v ) at high P , T computed from a lattice vibration model. The generalized Rydberg EOS applied to MgO is able to fit reasonably well the properties computed using Jacobs’ lattice dynamics formulation ( T range = 300–3000 K, P range = 1 bar–1500 kbar). (3) It is shown that in the case of MgO, the TEOS can be used quite successfully for extrapolation that goes beyond the P , T range of the measured/given data. Some physical constraints need to be applied to the derivation of the volume, bulk modulus and derivative of the bulk modulus with pressure at 1 bar. (4) The pressure dependence of the reference parameters in the TEOS that was inferred several decades ago is only apparent. A numerical computation demonstrates that the combined pressure effect in the terms defining the partial derivative of the reference V and K (and K') over temperature cancels out, making the reference parameters independent of pressure at any condition.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 32
    Publication Date: 2015-07-10
    Description: Existing analyses of market participation are based on a "double-hurdle" modeling approach. Such models are appropriate only when all members of the population of interest actually produce the good. In some contexts, however (e.g., smallholder farmers), many members of the population do not produce particular goods that they could produce and that their neighbors do produce. Policies influencing market participation among producers may thus also induce additional farmers to become producers. Previous double-hurdle approaches do not allow explicitly for this possibility. To address these limitations, this article presents a "triple-hurdle" approach with an initial stage that includes nonproducers. The model is used to identify the factors associated with Kenyan smallholder farmers choosing to participate in dairy production, and the role that these producers choose to play (or not) in the marketplace. In the midst of debates underway over the privatization of the parastatal Kenya Creameries Company, new knowledge about smallholder participation in dairy could be an important contribution. Results suggest the importance of rural electrification, training, and improved grazing practices. We find that expected net sales are significantly higher when farmers have access to informal private markets. We also describe a version of the ordered tobit model that includes nonproducers and is nested in our triple-hurdle model. A likelihood ratio test shows the latter to be a significantly better fit to our data. We discuss how insights gained from this study differ from the insights that would come from a double-hurdle ordered tobit that also includes nonproducers.
    Keywords: C51 - Model Construction and Estimation, C81 - Methodology for Collecting, Estimating, and Organizing Microeconomic Data, O12 - Microeconomic Analyses of Economic Development, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 33
    Publication Date: 2015-07-17
    Description: The equation that relates pressure, temperature and volume and is described by parameters that are function of temperature at 1 bar (hereafter called thermal equation of state, TEOS), has practical computational advantages for petrological and geophysical applications over the equation that considers explicitly a thermal pressure. Some considerations that justify the use of the TEOS are discussed here. (1) The assumption that the parameters are function of temperature is perhaps better understood by looking at the Helmholtz energy function that is implicitly assumed in the case of an equation of state (EOS) derived from interatomic potentials. A test case shows that the Helmholtz energy related to the Vinet EOS and the Helmholtz energy from the Debye model are very similar. (2) The TEOS should be able to reproduce thermal expansion (α), isothermal bulk modulus ( K T ) and heat capacity ( C p and C v ) at high P , T computed from a lattice vibration model. The generalized Rydberg EOS applied to MgO is able to fit reasonably well the properties computed using Jacobs’ lattice dynamics formulation ( T range = 300–3000 K, P range = 1 bar–1500 kbar). (3) It is shown that in the case of MgO, the TEOS can be used quite successfully for extrapolation that goes beyond the P , T range of the measured/given data. Some physical constraints need to be applied to the derivation of the volume, bulk modulus and derivative of the bulk modulus with pressure at 1 bar. (4) The pressure dependence of the reference parameters in the TEOS that was inferred several decades ago is only apparent. A numerical computation demonstrates that the combined pressure effect in the terms defining the partial derivative of the reference V and K (and K') over temperature cancels out, making the reference parameters independent of pressure at any condition.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 34
    Publication Date: 2015-07-10
    Description: The dimensions that define a food product have expanded rapidly to include characteristics of the production process, marketing arrangements, and implications that production and consumption of the product have for the environment. Some market intermediaries have responded by requiring that their suppliers abide by restrictive production practices. We examine the economic effects of such restrictions and apply this analysis to limitations on the use of antibiotics in U.S. pork production. Results from conceptual and simulation analyses show that, in the absence of demand growth, less pork is sold due to higher costs in the restricted segment, and both pork consumers (on average) and producers are harmed. Demand growth of between 6–11% from adding new consumers who will consume the restricted (antibiotic-free) product but not the conventional product is needed to return consumer surplus to the level in the base case, and between 2–4% demand growth was required to return producer surplus to base. When restricted and conventional products are modeled using a vertical differentiation framework, results depend importantly on the ease with which consumers can switch to a seller who offers their desired product type. Significant distributional impacts among consumers are present when switching costs are prohibitive.
    Keywords: I18 - Government Policy ; Regulation ; Public Health, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 35
    Publication Date: 2015-09-12
    Description: Community Supported Agriculture (CSA) contracts allow consumers to buy claims on a farm's future production. In turn, the consumer provides working capital to the farm during the growing season. CSA contracts also provide risk management for farmers with limited access to Federal crop insurance by transferring part of the farm's risk to the consumer. We derive a theory of CSA contract pricing for the two most prevalent types of CSA contracts: yield contracts, in which consumers receive a percentage of the farm's production, and weight contracts, in which consumers receive fixed quantities. We develop a two-period model in which expected utility maximizing producers and consumers engage in CSA contracting in the first period based on anticipation of yields and spot prices in the second period. Using the model, we generate several testable hypotheses to be explored in future research. Additionally, we present an overview of the data necessary to test the propositions and potential challenges that might arise in related empirical work.
    Keywords: Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q14 - Agricultural Finance
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 36
    Publication Date: 2016-02-03
    Description: In this article, we provide an overview of the extensive literature on the impact of weather and climate on grapes and wine, with the goal of identifying how climate change is likely to affect their production. We first discuss the physical impact of weather on vine phenology (i.e., the timing of biological events such as bud break or flowering), berry composition, and yields. Then we examine the economic literature that measures the effects of temperature on wine quality, prices, costs, and profits and, based on this review, infer how climate change will affect these variables. We also describe what has been learned thus far about possible adaptation strategies for grape growers that would allow them to mitigate the economic effects of climate change. We conclude that climate change is likely to produce both winners and losers, with the winners being those located closer to the North and South Poles. There are also likely to be some substantial short-run costs as growers adapt to climate change. Nevertheless, wine making has survived through thousands of years of recorded history, a history that has included significant climate changes. ( JEL : Q13, Q18, Q54)
    Keywords: Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy, Q54 - Climate ; Natural Disasters ; Global Warming
    Print ISSN: 1750-6816
    Electronic ISSN: 1750-6824
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Political Science , Economics
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  • 37
    Publication Date: 2016-03-01
    Description: Microfluidics may revolutionize our ability to write synthetic DNA by addressing several fundamental limitations associated with generating novel genetic constructs. Here we report the first de novo synthesis and cell-free cloning of custom DNA libraries in sub-microliter reaction droplets using programmable digital microfluidics. Specifically, we developed Programmable Order Polymerization (POP), Microfluidic Combinatorial Assembly of DNA (M-CAD) and Microfluidic In-vitro Cloning (MIC) and applied them to de novo synthesis, combinatorial assembly and cell-free cloning of genes, respectively. Proof-of-concept for these methods was demonstrated by programming an autonomous microfluidic system to construct and clone libraries of yeast ribosome binding sites and bacterial Azurine, which were then retrieved in individual droplets and validated. The ability to rapidly and robustly generate designer DNA molecules in an autonomous manner should have wide application in biological research and development.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 38
    Publication Date: 2016-03-01
    Description: Recent developments in synthetic biology have positioned lactic acid bacteria (LAB) as a major class of cellular chassis for applications. To achieve the full potential of LAB, one fundamental prerequisite is the capacity for rapid engineering of complex gene networks, such as natural biosynthetic pathways and multicomponent synthetic circuits, into which cellular functions are encoded. Here, we present a synthetic biology platform for rapid construction and optimization of large-scale gene networks in LAB. The platform involves a copy-controlled shuttle for hosting target networks and two associated strategies that enable efficient genetic editing and phenotypic validation. By using a nisin biosynthesis pathway and its variants as examples, we demonstrated multiplex, continuous editing of small DNA parts, such as ribosome-binding sites, as well as efficient manipulation of large building blocks such as genes and operons. To showcase the platform, we applied it to expand the phenotypic diversity of the nisin pathway by quickly generating a library of 63 pathway variants. We further demonstrated its utility by altering the regulatory topology of the nisin pathway for constitutive bacteriocin biosynthesis. This work demonstrates the feasibility of rapid and advanced engineering of gene networks in LAB, fostering their applications in biomedicine and other areas.
    Keywords: Synthetic Biology and Assembly Cloning
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    Topics: Biology
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  • 39
    Publication Date: 2016-03-03
    Description: The presence of calcite in and near faults, as the dominant material, cement, or vein fill, indicates that the mechanical behaviour of carbonate-dominated material likely plays an important role in shallow- and mid-crustal faulting. To better understand the behaviour of calcite, under loading conditions relevant to earthquake nucleation, we sheared powdered gouge of Carrara Marble, 〉98 per cent CaCO 3 , at constant normal stresses between 1 and 100 MPa under water-saturated conditions at room temperature. We performed slide-hold-slide tests, 1–3000 s, to measure the amount of static frictional strengthening and creep relaxation, and velocity-stepping tests, 0.1–1000 μm s –1 , to evaluate frictional stability. We observe that the rates of frictional strengthening and creep relaxation decrease with increasing normal stress and diverge as shear velocity is increased from 1 to 3000 μm s –1 during slide-hold-slide experiments. We also observe complex frictional stability behaviour that depends on both normal stress and shearing velocity. At normal stresses less than 20 MPa, we observe predominantly velocity-neutral friction behaviour. Above 20 MPa, we observe strong velocity-strengthening frictional behaviour at low velocities, which then evolves towards velocity-weakening friction behaviour at high velocities. Microstructural analyses of recovered samples highlight a variety of deformation mechanisms including grain size reduction and localization, folding of calcite grains and fluid-assisted diffusion mass transfer processes promoting the development of calcite nanograins in the highly deformed portions of the experimental fault. Our combined analyses indicate that calcite fault gouge transitions from brittle to semi-brittle behaviour at high normal stress and slow sliding velocities. This transition has important implications for earthquake nucleation and propagation on faults in carbonate-dominated lithologies.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 40
    Publication Date: 2016-02-20
    Description: We study the determinants of somatic cell count (SCC) for farm milk among US dairies. We synthesise much of the work that has been done to model SCC determinants in order to identify the potential impacts of buyer-imposed penalties and incentives within the supply chain. Additionally, we estimate quantile regression for count data to measure impacts specifically for those operations with the highest SCC and to account for the statistical properties of the data. Premiums in particular have the potential to reduce SCC considerably where it is currently the highest. We draw implications for profitability in relation to SCC reduction.
    Keywords: C25 - Discrete Regression and Qualitative Choice Models, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q16 - R&D ; Agricultural Technology ; Agricultural Extension Services
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 41
    Publication Date: 2015-10-30
    Description: A knowledge of subsurface temperatures in sedimentary basins, fault zones, volcanic environments and polar ice sheets is of interest for a wide variety of geophysical applications. However, the process of drilling deep boreholes in these environments to provide access for temperature and other measurements invariably disturbs the temperature field around a newly created borehole. Although this disturbance dissipates over time, most temperature measurements are made while the temperature field is still disturbed. Thus, the measurements must be ‘corrected’ for the drilling-disturbance effect if the undisturbed temperature field is to be determined. This paper provides compact analytical solutions for the thermal drilling disturbance based on 1-D (radial) and 2-D (radial and depth) Green's functions (GFs) in cylindrical coordinates. Solutions are developed for three types of boundary conditions (BCs) at the borehole wall: (1) prescribed temperature, (2) prescribed heat flux and (3) a prescribed convective condition. The BC at the borehole wall is allowed to vary both with depth and time. Inclusion of the depth dimension in the 2-D solution allows vertical heat-transfer effects to be quantified in situations where they are potentially important, that is, near the earth's surface, at the bottom of a well and when considering finite-drilling rates. The 2-D solution also includes a radial- and time-dependent BC at the earth's surface to assess the impact of drilling-related infrastructure (drilling pads, mud pits, permanent shelters) on the subsurface temperature field. Latent-heat effects due to the melting and subsequent refreezing of interstitial ice while drilling a borehole through ice-rich permafrost can be included in the GF solution as a moving-plane heat source (or sink) located at the solid–liquid interface. Synthetic examples are provided illustrating the 1-D and 2-D GF solutions. The flexibility of the approach allows the investigation of thermal drilling effects in rock or ice for a wide variety of drilling technologies. Numerical values for the required radial GFs G R are available through the Advanced Cooperative Arctic Data and Information Service at doi:10.5065/D64F1NS6.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 42
    Publication Date: 2015-10-31
    Description: We consider how cost heterogeneity and market power affect voting power in producer referenda for mandatory agricultural marketing organisations with generic promotion programmes in the United States. We measure voting power using the Banzhaf Power Index and propose a new version of this index based on the profit-maximising theory of the firm that provides an improved estimate of voting power. Examining several types of demand shifts and voting rules, we find that both Banzhaf Power and our new measure vary considerably depending on the market structure and level of cost heterogeneity.
    Keywords: D71 - Social Choice ; Clubs ; Committees ; Associations, D72 - Models of Political Processes: Rent-Seeking, Elections, Legislatures, and Voting Behavior, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 43
    Publication Date: 2015-12-02
    Description: Optimizing bio-production involves strain and process improvements performed as discrete steps. However, environment impacts genotype and a strain that is optimal under one set of conditions may not be under different conditions. We present a methodology to simultaneously vary genetic and process factors, so that both can be guided by design of experiments (DOE). Advances in DNA assembly and gene insulation facilitate this approach by accelerating multi-gene pathway construction and the statistical interpretation of screening data. This is applied to a 6-aminocaproic acid (6-ACA) pathway in Escherichia coli consisting of six heterologous enzymes. A 32-member fraction factorial library is designed that simultaneously perturbs expression and media composition. This is compared to a 64-member full factorial library just varying expression (0.64 Mb of DNA assembly). Statistical analysis of the screening data from these libraries leads to different predictions as to whether the expression of enzymes needs to increase or decrease. Therefore, if genotype and media were varied separately this would lead to a suboptimal combination. This is applied to the design of a strain and media composition that increases 6-ACA from 9 to 48 mg/l in a single optimization step. This work introduces a generalizable platform to co-optimize genetic and non-genetic factors.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 44
    Publication Date: 2016-02-03
    Description: The elastic properties of homogeneous, isotropic materials are well constrained. However, in heterogeneous and evolving materials, these essential properties are less well-explored. During sintering of volcanic ash particles by viscous processes as well as during compaction and cementation of sediments, microstructure and porosity undergo changes that affect bulk dynamic elastic properties. Here using a model system of glass particles as an analogue for initially granular rock-forming materials, we have determined porosity and P -wave velocity during densification. Using these results, we test models for the kinetics of densification and the resultant evolution of the elastic properties to derive a quantitative description of the coupling between the kinetics of isotropic densification and the evolving dynamic elastic moduli. We demonstrate the power of the resultant model on a wide range of data for non-coherent sediments as well as sedimentary and volcanic rocks. We propose that such constraints be viewed as an essential ingredient of time-dependent models for the deformation of evolving materials in volcanoes and sedimentary basins.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 45
    Publication Date: 2015-03-14
    Description: A milk scandal erupted in China in 2008 when the industrial chemical melamine was found in dairy products nationwide. While many Chinese dairy companies faced huge losses or bankruptcy as a result, one small firm, Dairy United, accelerated its development. Dairy United is one of the fastest-growing and most innovative Chinese dairy producers, one that features an unusual organizational structure and business model. Unlike most corporate and cooperative dairies that purchase cows on the market, Dairy United leases dairy cows from local farmers, giving it access to its primary asset without a large up-front investment, and letting the firm grow its dairy herds with newborn heifers. In return, farmers receive fixed payments biannually, but relinquish control rights and residual claims to the firm. Thus, Dairy United's leasing is helping transform Chinese milk production from a backyard, labor-intensive activity to a more industrialized mode of farming. The case is particularly interesting for understanding applications of agency theory in agribusiness.
    Keywords: A22 - Undergraduate, A23 - Graduate, D23 - Organizational Behavior ; Transaction Costs ; Property Rights, M10 - General, M20 - General, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 46
    Publication Date: 2015-03-14
    Description: Hoover Seeds is a fictional case study written to illustrate the challenges faced by food and agribusiness firms that are transitioning from small, entrepreneurial businesses to larger, more professionally managed enterprises. Though fictional, the competitive and financial situation of Hoover Seeds is based on realistic facts. The case introduces Dan Hoover, the Chief Executive Officer of Hoover Seeds, Inc., a small, family-owned and operated seed company in Ohio. Founded by his grandfather, Dan has worked his way up the ranks of the company and, now leading the company, has worked to expand market share. The case study details the sales, production, administration, and finances of the firm. Exhibit A includes a full set of financial statements over four years. The case also has industry context with market, customer, and competitor details.
    Keywords: Q10 - General, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 47
    Publication Date: 2015-03-14
    Description: Organic Valley is the largest organic cooperative in North America, one of two national buyers of organic milk, and one of two national organic dairy manufacturers. The cooperative's official name is Cooperative of Regional Organic Producers, and it is organized as a new generation cooperative, owned and controlled by patron-members who also transact with the business. Organic Valley has a unique policy of sustainable and stable producer pay-pricing for organic milk in the emerging organic dairy industry. This case presents challenges faced by the leadership of Organic Valley cooperative to maintain a stable and economically sustainable pay price for its farmer members. This case also introduces students to a new organizational form of cooperative, including its governance, the industry, and the market structure in which the cooperative operates. The objective of this case study is to improve student understanding of economic concepts such as theories of the imperfect market, demand and supply, and organizational design. The case also aims to help students improve their critical thinking and analytical skills by exploring the possibility of maintaining a unique sustainable and stable pricing method through the data provided. Additionally, the story introduces the economic role that organic dairy operation might play for small and medium-size dairy farmers as they attempt to maintain an economically sustainable family farm lifestyle.
    Keywords: A22 - Undergraduate, A23 - Graduate, Q01 - Sustainable Development, Q11 - Aggregate Supply and Demand Analysis ; Prices, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 48
    Publication Date: 2015-01-08
    Description: Tarim Craton is a Precambrian block situated in northwest China, just north of the Tibetan Plateau, where a large sedimentary basin with abundant hydrocarbon potential has developed. Accurate heat flow data for Tarim is vital for understanding the lithospheric evolution and hydrocarbon generation in this area; however, there were unavailable until now, due to a lack of high quality steady-state temperature logging data. Here, we report 10 new heat flow values derived from steady-state temperature logging and measured thermal conductivity data. New heat flow values range from 40.1 to 49.4 mW m –2 , with a mean of 43.1 ± 3.0 mW m –2 . In addition, radiogenic heat production from the sediments accounts for 20 per cent of the observed surface heat flow, whilst the mantle heat flow is estimated to be as low as 6–15 mW m –2 ; this indicates a dominant contribution from crustal heat, to the observed heat flow. The average heat flow and crustal temperature in the Tarim Craton are markedly lower than those in the Tibetan Plateau, whilst the calculated rheological strength of the lithosphere, beneath Tarim, is sufficiently large to resist the elevation-induced gravitational potential energy difference between Tarim and Tibet. This inherited thermal and rheological contrast, between the craton and Plateau, can be traced back to before the India–Asia collision; this accounts for the differential active deformation pattern in the Tarim Craton and adjacent areas.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 49
    Publication Date: 2016-05-14
    Description: We present a study of the seismic velocity variations that occurred in the structure before the large 2010 eruption of Merapi volcano. For the first time to our knowledge, the technique of coda wave interferometry is applied to both families of similar events (multiplets) and to correlation functions of seismic noise. About half of the seismic events recorded at the summit stations belong to one of the ten multiplets identified, including 120 similar events that occurred in the last 20 hr preceding the eruption onset. Daily noise cross-correlation functions (NCF) were calculated for the six pairs of short-period stations available. Using the stretching method, we estimate time-series of apparent velocity variation (AVV) for each multiplet and each pair of stations. No significant velocity change is detected until September 2010. From 10 October to the beginning of the eruption on 26 October, a complex pattern of AVV is observed with amplitude of up to ±1.5 per cent. Velocity decrease is first observed from families of deep events and then from shallow earthquakes. In the same period, AVV with different signs and chronologies are estimated from NCF calculated for various station pairs. The location in the horizontal plane of the velocity perturbations related with the AVV obtained from NCF is estimated by using an approach based on the radiative transfer approximation. Although their spatial resolution is limited, the resulting maps display velocity decrease in the upper part of the edifice in the period 12–25 October. After the eruption onset, the pattern of velocity perturbations is significantly modified with respect to the previous one. We interpret these velocity variations in the framework of a scenario of magmatic intrusion that integrates most observations. The perturbation of the stress field associated with the magma migration can induce both decrease and increase of the seismic velocity of rocks. Thus the detected AVVs can be considered as precursors of volcanic eruptions in andesitic volcanoes, without taking their sign into account.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 50
    Publication Date: 2016-05-19
    Description: Whether direct farmer-to-consumer outlets compete with supermarkets on produce prices remains an empirical question; marketing costs are not consistently higher in one retail channel or the other. This study compared prices of 29 fruits and vegetables across North Carolina farmers’ markets, roadside stands, and supermarkets. Larger farmers’ markets had higher prices: three fruits and one vegetable were cheaper at a direct outlet, while four vegetables were cheaper at supermarkets. Weighting item prices by consumption share attenuated differences in mean price across outlets. Direct-retail outlets are price competitive and should be considered among other tools to boost fresh fruit and vegetable intake.
    Keywords: Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 51
    Publication Date: 2016-03-19
    Description: While the cost of DNA sequencing has dropped by five orders of magnitude in the past decade, DNA synthesis remains expensive for many applications. Although DNA microarrays have decreased the cost of oligonucleotide synthesis, the use of array-synthesized oligos in practice is limited by short synthesis lengths, high synthesis error rates, low yield and the challenges of assembling long constructs from complex pools. Toward addressing these issues, we developed a protocol for multiplex pairwise assembly of oligos from array-synthesized oligonucleotide pools. To evaluate the method, we attempted to assemble up to 2271 targets ranging in length from 192–252 bases using pairs of array-synthesized oligos. Within sets of complexity ranging from 131–250 targets, we observed error-free assemblies for 90.5% of all targets. When all 2271 targets were assembled in one reaction, we observed error-free constructs for 70.6%. While the assembly method intrinsically increased accuracy to a small degree, we further increased accuracy by using a high throughput ‘Dial-Out PCR’ protocol, which combines Illumina sequencing with an in-house set of unique PCR tags to selectively amplify perfect assemblies from complex synthetic pools. This approach has broad applicability to DNA assembly and high-throughput functional screens.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 52
    Publication Date: 2016-05-06
    Description: The influx of groundwater into hot kimberlite deposits results in the reaction of water with olivine-rich rocks. The products of the reaction are serpentine and release of latent heat. The rise of temperature due to the heat release increases the rate of the reaction. Under certain conditions, this self-speeding up of the reaction can result in instabilities associated with a significantly higher final serpentinization in slightly warmer regions of the kimberlite deposit. We conduct linear stability analysis of serpentinization in an isolated volume of porous kimberlitic rocks saturated with water and an inert gas. There is a counteracting interplay between the heat release tending to destabilize the uniform distribution of parameters and the heat conduction tending to stabilize it by smoothing out temperature perturbations. We determine the critical spatial scale separating the parameters where one phenomenon dominates over another. The perturbations of longer-than-critical length grow, whereas the perturbations of shorter-than-critical length fade. The analytical results of the linear stability analysis are supported by direct numerical simulations using a full nonlinear model.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 53
    Publication Date: 2016-05-19
    Description: Regulators are proposing new position limits in U.S. commodity futures markets while the actual impact of long-only index funds on futures prices continues to be debated. Researchers have noted the data limitations—frequency and market breadth—associated with using data compiled by the U.S. Commodity Futures Trading Commission (CFTC). This research addresses these shortfalls by using daily position data for a specific long-only index fund. The empirical analysis focuses on the firm-level position data across 13 U.S. agricultural futures markets. The firm-level data are shown to be representative of the overall index fund industry. Empirical tests fail to find any evidence linking the firm's trading with market returns. However, there does appear to be a consistent negative relationship between the firm's roll transactions and changes in calendar price spreads. Notably, the direction of this impact runs contrary to the price-pressure hypothesis. The results of this study, and others, indicate that a clear verdict can be reached—new limits on speculation in agricultural futures markets are unnecessary.
    Keywords: D84 - Expectations ; Speculations, G12 - Asset Pricing ; Trading volume ; Bond Interest Rates, G13 - Contingent Pricing ; Futures Pricing, G14 - Information and Market Efficiency ; Event Studies, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q41 - Demand and Supply
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 54
    Publication Date: 2016-05-22
    Description: Inelastic deformation can either occur with dilatancy or compaction, implying differences in porosity changes, failure and petrophysical properties. In this study, the roles of water as a pore fluid, and of temperature, on the deformation and failure of a micritic limestone (white Tavel limestone, porosity 14.7 per cent) were investigated under triaxial stresses. For each sample, a hydrostatic load was applied up to the desired confining pressure (from 0 up to 85 MPa) at either room temperature or at 70 °C. Two pore fluid conditions were investigated at room temperature: dry and water saturated. The samples were deformed up to failure at a constant strain rate of ~10 –5 s –1 . The experiments were coupled with ultrasonic wave velocity surveys to monitor crack densities. The linear trend between the axial crack density and the relative volumetric strain beyond the onset of dilatancy suggests that cracks propagate at constant aspect ratio. The decrease of ultrasonic wave velocities beyond the onset of inelastic compaction in the semi-brittle regime indicates the ongoing interplay of shear-enhanced compaction and crack development. Water has a weakening effect on the onset of dilatancy in the brittle regime, but no measurable influence on the peak strength. Temperature lowers the confining pressure at which the brittle–semi-brittle transition is observed but does not change the stress states at the onset of inelastic compaction and at the post-yield onset of dilatancy.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 55
    Publication Date: 2016-03-31
    Description: This case study examines the challenges of implementing a vaguely defined concept called sustainability in a large organization that also has a cooperative structure. Stakeholder theory is described and applied to a multinational dairy firm. The case firm, Land O'Lakes, must balance the needs of multiple constituencies: the general public, employees, cooperative members, external funding organizations, and the management team. One challenge is to define sustainability for the entire dairy industry. The case discusses the strategies used by firms in developing a sustainability response where the tradeoffs between different strategies are between credibility and autonomy and using an industry rather than a firm-level response.
    Keywords: L15 - Information and Product Quality ; Standardization and Compatibility, L66 - Food ; Beverages ; Cosmetics ; Tobacco ; Wine and Spirits, M14 - Corporate Culture ; Social Responsibility, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 56
    Publication Date: 2016-02-10
    Description: We investigate storage in the presence of backwardation and the existence of the Working curve for Chicago Board of Trade corn, soybeans, and wheat markets and the Kansas City Board of Trade wheat market using 1990–2010 data. Two spread measures—the futures-spot and futures-futures—are matched with deliverable stocks on the first Friday of delivery. To account for grade and location aggregation issues, the futures-spot spreads are measured using the lowest spot bid and highest futures price. Storage in the presence of backwardation is pervasive both in terms of the percentage of observations and the magnitude of the stockholdings. The Working curve emerges most clearly in KCBT wheat and soybeans. Convenience yield is also supported by the negligible holdings of delivery shipping certificates in backwardations. Overall, the results show that the Working curve does indeed still work today. When evaluating policy proposals to deal with heightened price volatility in agricultural markets it is important that models incorporate this well-established relationship.
    Keywords: G13 - Contingent Pricing ; Futures Pricing, Q11 - Aggregate Supply and Demand Analysis ; Prices, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 57
    Publication Date: 2016-02-12
    Description: Remote sensing thermal data of active lava flows allow the evaluation of effusion rates. This is made possible by a simple formula relating the lava effusion rate to the heat flux radiated per unit time from the surface of the flow. Due to the assumptions of the model, this formula implies that heat flux, surface temperature and lava temperature vary as a function of the flow thickness. These relationships, never verified or validated before, have been used by several authors as a proof of the weakness of the model. Here, multispectral infrared and visible imaging spectrometer (MIVIS) high spatial resolution (5–10 m) thermal data acquired during Etna's 2001 eruption were used to investigate downflow heat flux variations in the lava flow emitted from a vent located at 2100 m a.s.l. A high correlation between the downflow heat flux and the lava flow thickness (measured from a pre-existing digital elevation model) was found. Topography beneath the flow appears to play an important role both in lava emplacement mechanisms and flow dynamics. MIVIS-derived downflow effusion rates are consistent with the law of conservation of mass assessing the reliability of remote sensing techniques.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 58
    Publication Date: 2016-09-03
    Description: Libraries of well-characterised components regulating gene expression levels are essential to many synthetic biology applications. While widely available for the Gram-negative model bacterium Escherichia coli , such libraries are lacking for the Gram-positive model Bacillus subtilis , a key organism for basic research and biotechnological applications. Here, we engineered a genetic toolbox comprising libraries of promoters, Ribosome Binding Sites (RBS), and protein degradation tags to precisely tune gene expression in B. subtilis . We first designed a modular Expression Operating Unit (EOU) facilitating parts assembly and modifications and providing a standard genetic context for gene circuits implementation. We then selected native, constitutive promoters of B. subtilis and efficient RBS sequences from which we engineered three promoters and three RBS sequence libraries exhibiting ~14 000-fold dynamic range in gene expression levels. We also designed a collection of SsrA proteolysis tags of variable strength. Finally, by using fluorescence fluctuation methods coupled with two-photon microscopy, we quantified the absolute concentration of GFP in a subset of strains from the library. Our complete promoters and RBS sequences library comprising over 135 constructs enables tuning of GFP concentration over five orders of magnitude, from 0.05 to 700 μM. This toolbox of regulatory components will support many research and engineering applications in B. subtilis .
    Keywords: Synthetic Biology and Assembly Cloning
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    Topics: Biology
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  • 59
    Publication Date: 2016-12-07
    Description: The Agricultural Act of 2014 replaced dairy product price supports and countercyclical income support payments with the Margin Protection Program for Dairy Producers. Using farm-level data, producer decisions and aggregate policy costs under a variety of risk environments and policy design alternatives are simulated. Fixed premium rates may result in budget outlays that are substantially higher than for equivalent variable-rate insurance subsidized at levels observed in revenue-based crop insurance policies. Due to the absence of adjusted gross income or production eligibility constraints, a significant portion of benefits may accrue to a small share of large dairy farms.
    Keywords: Q11 - Aggregate Supply and Demand Analysis ; Prices, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 60
    Publication Date: 2016-12-22
    Description: We performed complex conductivity measurements on 28 core samples from the hole drilled for the Humu'ula Groundwater Research Project (Hawai'i Island, HI, USA). The complex conductivity measurements were performed at 4 different pore water conductivities (0.07, 0.5, 1.0 or 2.0, and 10 S m –1 prepared with NaCl) over the frequency range 1 mHz to 45 kHz at 22 ± 1 °C. The in-phase conductivity data are plotted against the pore water conductivity to determine, sample by sample, the intrinsic formation factor and the surface conductivity. The intrinsic formation factor is related to porosity by Archie's law with an average value of the cementation exponent m of 2.45, indicating that only a small fraction of the connected pore space controls the transport properties. Both the surface and quadrature conductivities are found to be linearly related to the cation exchange capacity of the material, which was measured with the cobalt hexamine chloride method. Surface and quadrature conductivities are found to be proportional to each other like for sedimentary siliclastic rocks. A Stern layer polarization model is used to explain these experimental results. Despite the fact that the samples contain some magnetite (up to 5 per cent wt.), we were not able to identify the effect of this mineral on the complex conductivity spectra. These results are very encouraging in showing that galvanometric induced polarization measurements can be used in volcanic areas to separate the bulk from the surface conductivity and therefore to define some alteration attributes. Such a goal cannot be achieved with resistivity alone.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 61
    Publication Date: 2016-12-22
    Description: We investigate the relationship between complex conductivity spectra and both permeability and pore mean size and distribution of 22 core samples (21 volcanic rocks and 1 clayey sandstone). The volcanic core samples were extracted from a wellbore drilled for the Humu‘ula Groundwater Research Project in the Humu‘ula saddle region between Mauna Kea and Mauna Loa volcanoes (Hawaii). The quadrature conductivity spectra of volcanic rocks exhibit a subtle, but generally detectable, relaxation frequency in the range 0.3 Hz to 45 kHz similar to the relaxation frequency observed for clayey sandstones. We find a fair relationship between this relaxation frequency and the pore size determined by mercury porosimetry. Combined with the intrinsic formation factor of the core samples, the relaxation frequency can be used as an indicator of the permeability of the material. The predicted values of the permeability are grossly consistent with the permeability values to air (in the range 0.001–100 mD) within two orders of magnitude. The measured permeability values are highly correlated to the peak of the pore size distribution determined from mercury porosimetry divided by the intrinsic formation factor. By fitting the complex conductivity spectra with the pore size distribution, we obtain the normalized chargeability of the core samples, which is, in turn, highly correlated to the measured cation exchange capacity.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
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    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 62
    Publication Date: 2016-11-10
    Description: The Puyehue-Cordón Caulle Volcanic Complex (PCCVC) is one of the best examples of tectonic control on volcanism at the Southern Volcanic Zone of the Andes (southern Chile). The PCCVC comprises several volcanic centres that erupted dominantly SiO 2 -rich magmas at the intersection of the trench-parallel Liquiñe-Ofqui Fault Zone (LOFZ) and an inherited NW–SE basement structure. The PCCVC began an explosive and later effusive eruption on 2011 June 4 causing decimetre- to metre-scale surface deformation that was observed by a series of Envisat ASAR satellite scenes. We modelled this data and complemented it with time-series of two continuous GPS stations and seismicity recorded by a local network. Deformation during the first 3 days of the eruption can be modelled either by two point sources aligned with the NW–SE Cordón Caulle graben or by a closing dyke with a significant component of left-lateral motion along the graben. These models are discussed with respect to their implications on the estimated rheology and the eruption mechanism. GPS observations near the volcanic complex reveal an additional, more localised effect related to the LOFZ in the south of the complex. Coeruptive deformation at the main geological structures of the PCCVC is further supported by relocated seismicity, which is concentrated along the Cordón Caulle graben and to the western side of the LOFZ.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
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    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 63
    Publication Date: 2015-08-18
    Description: Synthetic biology has significantly advanced the rational design of trigger-inducible gene switches that program cellular behavior in a reliable and predictable manner. Capitalizing on genetic componentry, including the repressor PmeR and its cognate operator O PmeR , that has evolved in Pseudomonas syringae pathovar tomato DC3000 to sense and resist plant-defence metabolites of the paraben class, we have designed a set of inducible and repressible mammalian transcription-control devices that could dose-dependently fine-tune transgene expression in mammalian cells and mice in response to paraben derivatives. With an over 60-years track record as licensed preservatives in the cosmetics industry, paraben derivatives have become a commonplace ingredient of most skin-care products including shower gels, cleansing toners and hand creams. As parabens can rapidly reach the bloodstream of mice following topical application, we used this feature to percutaneously program transgene expression of subcutaneous designer cell implants using off-the-shelf commercial paraben-containing skin-care cosmetics. The combination of non-invasive, transdermal and orthogonal trigger-inducible remote control of transgene expression may provide novel opportunities for dynamic interventions in future gene and cell-based therapies.
    Keywords: Synthetic Biology and Assembly Cloning
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    Topics: Biology
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  • 64
    Publication Date: 2015-08-18
    Description: Effector-triggered immunity (ETI) is activated when plant disease resistance (R) proteins recognize the presence of pathogen effector proteins delivered into host cells. The ETI response generally encompasses a defensive ‘hypersensitive response’ (HR) that involves programmed cell death at the site of pathogen recognition. While many R protein and effector protein pairs are known to trigger HR, other components of the ETI signaling pathway remain elusive. Effector genes regulated by inducible promoters cause background HR due to leaky protein expression, preventing the generation of relevant transgenic plant lines. By employing the HyP5SM suicide exon, we have developed a strategy to tightly regulate effector proteins such that HR is chemically inducible and non-leaky. This alternative splicing-based gene regulation system was shown to successfully control Bs2/AvrBs2-dependent and RPP1/ATR151-dependent HR in Nicotiana benthamiana and Nicotiana tabacum , respectively. It was also used to generate viable and healthy transgenic Arabidopsis thaliana plants that inducibly initiate HR. Beyond enabling studies on the ETI pathway, our regulatory strategy is generally applicable to reduce or eliminate undesired background expression of transgenes.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 65
    Publication Date: 2015-07-25
    Description: We have developed a method for assembling genetic pathways for expression in Saccharomyces cerevisiae . Our pathway assembly method, called VEGAS (Versatile genetic assembly system), exploits the native capacity of S. cerevisiae to perform homologous recombination and efficiently join sequences with terminal homology. In the VEGAS workflow, terminal homology between adjacent pathway genes and the assembly vector is encoded by ‘VEGAS adapter’ (VA) sequences, which are orthogonal in sequence with respect to the yeast genome. Prior to pathway assembly by VEGAS in S. cerevisiae , each gene is assigned an appropriate pair of VAs and assembled using a previously described technique called yeast Golden Gate (yGG). Here we describe the application of yGG specifically to building transcription units for VEGAS assembly as well as the VEGAS methodology. We demonstrate the assembly of four-, five- and six-gene pathways by VEGAS to generate S. cerevisiae cells synthesizing β-carotene and violacein. Moreover, we demonstrate the capacity of yGG coupled to VEGAS for combinatorial assembly.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 66
    Publication Date: 2015-07-25
    Description: It is a routine task in metabolic engineering to introduce multicomponent pathways into a heterologous host for production of metabolites. However, this process sometimes may take weeks to months due to the lack of standardized genetic tools. Here, we present a method for the design and construction of biological parts based on the native genes and regulatory elements in Saccharomyces cerevisiae . We have developed highly efficient protocols (termed YeastFab Assembly) to synthesize these genetic elements as standardized biological parts, which can be used to assemble transcriptional units in a single-tube reaction. In addition, standardized characterization assays are developed using reporter constructs to calibrate the function of promoters. Furthermore, the assembled transcription units can be either assayed individually or applied to construct multi-gene metabolic pathways, which targets a genomic locus or a receiving plasmid effectively, through a simple in vitro reaction. Finally, using β-carotene biosynthesis pathway as an example, we demonstrate that our method allows us not only to construct and test a metabolic pathway in several days, but also to optimize the production through combinatorial assembly of a pathway using hundreds of regulatory biological parts.
    Keywords: Synthetic Biology and Assembly Cloning
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  • 67
    Publication Date: 2015-07-25
    Description: Targeted sequence enrichment enables better identification of genetic variation by providing increased sequencing coverage for genomic regions of interest. Here, we report the development of a new target enrichment technology that is highly differentiated from other approaches currently in use. Our method, MESA (Microfluidic droplet Enrichment for Sequence Analysis), isolates genomic DNA fragments in microfluidic droplets and performs TaqMan PCR reactions to identify droplets containing a desired target sequence. The TaqMan positive droplets are subsequently recovered via dielectrophoretic sorting, and the TaqMan amplicons are removed enzymatically prior to sequencing. We demonstrated the utility of this approach by generating an average 31.6-fold sequence enrichment across 250 kb of targeted genomic DNA from five unique genomic loci. Significantly, this enrichment enabled a more comprehensive identification of genetic polymorphisms within the targeted loci. MESA requires low amounts of input DNA, minimal prior locus sequence information and enriches the target region without PCR bias or artifacts. These features make it well suited for the study of genetic variation in a number of research and diagnostic applications.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 68
    Publication Date: 2015-07-29
    Description: Models describing the development of collective reputation have focused on the impact of past performance measures, but ignore the role of various marketing efforts for food and beverage products that highlight appellation information. We designed a laboratory experiment and used auction data to estimate consumer response to information tying US wine regions to famous wine production regions in France, a phenomenon we define as reputation tapping. Results show that reputation tapping increases bids for the wines produced in burgeoning US wine regions. Our findings also suggest that full protection of geographical indications may require monitoring of activities beyond those by individual firms.
    Keywords: C91 - Laboratory, Individual Behavior, L14 - Transactional Relationships ; Contracts and Reputation ; Networks, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 69
    Publication Date: 2015-10-31
    Description: Many cooperatives and related organisations use revenue pooling wherein products across multiple quality levels are commingled. Recent work showed that pooling ensures farmers against risks due to stochastic product quality and counteracts farmers' tendency to overproduce high-quality product. We extend their analysis to incorporate farmers who are heterogeneous in ability to produce high-quality products. We show that the revenue-pooling benefits of cooperation may be sufficient to cause high-quality producers to join a cooperative and pool revenues, at least partially, with lower-quality producers. We explore the producer and market characteristics conducive to the emergence of stable revenue-pooling cooperatives.
    Keywords: P13 - Cooperative Enterprises, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 70
    Publication Date: 2015-10-31
    Description: What causes firms to behave the way they do when they face different investment opportunities? We argue that both people and processes are behind the decision-making of project implementation. Member and professional CEOs of cooperatives differ regarding their managerial vision towards upstream and downstream projects. Cooperatives with member CEOs are upstream focused and it is reflected by the cascading effect of negative vision bias towards downstream projects. When downstream activities become more important, cooperatives need to replace the member CEOs with professional CEOs. However, a cooperative with a professional CEO may still be in a disadvantageous position if the member-dominated Board of Directors' negative bias towards downstream projects is too strong, which may result in an investor owned firm being the efficient governance structure.
    Keywords: D21 - Firm Behavior, L23 - Organization of Production, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 71
    Publication Date: 2015-11-05
    Description: In this study, equations are developed that predict for synthetic sedimentary rocks (clastics, carbonates and evapourates) thermal properties comprising thermal conductivity, specific heat capacity and thermal diffusivity. The rock groups are composed of mineral assemblages with variable contents of 15 major rock-forming minerals and porosities of 0–30 per cent. Petrophysical properties and their well-logging-tool-characteristic readings were assigned to these rock-forming minerals and to pore-filling fluids. Relationships are explored between each thermal property and other petrophysical properties (density, sonic interval transit time, hydrogen index, volume fraction of shale and photoelectric absorption index) using multivariate statistics. The application of these relations allows computing continuous borehole profiles for each rock thermal property. The uncertainties in the prediction of each property vary depending on the selected well-log combination. Best prediction is in the range of 2–8 per cent for the specific heat capacity, of 5–10 per cent for the thermal conductivity, and of 8–15 for the thermal diffusivity, respectively. Well-log derived thermal conductivity is validated by laboratory data measured on cores from deep boreholes of the Danish Basin, the North German Basin, and the Molasse Basin. Additional validation of thermal conductivity was performed by comparing predicted and measured temperature logs. The maximum deviation between these logs is 〈3 °C. The thermal-conductivity calculation allowed an evaluation of the depth range in which the palaeoclimatic effect on the subsurface temperature field can be observed in the North German Basin. This effect reduces the surface heat-flow density by 25 mW m –2 .
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 72
    Publication Date: 2016-01-02
    Description: Coal fires are severe hazards to environment, health and safety throughout the world. Efficient and economical extinguishing of these fires requires that the extent of the subsurface coal fires should be delineated. Electrical and electromagnetic methods have been used to detect coal fires in recent years. However, the resistivity change of coal-bearing rocks at high temperature is rarely investigated. The resistivity characteristics of coal fires at different temperatures and depths are seldomly researched as well. In this paper, we present the results of measurements of several coal-bearing rocks’ resistivity and permeability under high temperature. Two major causes for the change in resistivity with increasing temperature are recognized, there are the increase of charge carriers and thermal fracturing, of which the first one is probably the dominant cause. A set of 2-D simulations is carried out to compare the relation of resolution and efficiency of coal fires detection to temperature and depth when adopting the electrical resistance tomography. The simulation results show that the resolution and efficiency decrease with the decrease of temperature and the increase of depth. Finally, the electrical resistance tomography is used to delineate coal fires in the Anjialing Open Pit Mine. Most low-resistivity regions are verified as coal-fire areas according to the long-term monitoring of borehole temperature. The results indicate that the electrical resistance tomography can be used as a tool for the detection of coal fires.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 73
    Publication Date: 2017-01-05
    Description: Commodity-equity return co-movements rose dramatically during the Great Recession. This development took place following what has been dubbed the "financialization" of commodity markets. We first document changes since 1995 in the relative importance of financial institutions’ activity in agricultural futures markets. We then use a structural vector autoregression (VAR) model to ascertain the role of that activity in explaining correlations between weekly grain, livestock, and equity returns from 1995–2015. We provide robust evidence that, accounting for shocks that are idiosyncratic to agricultural markets, world business cycle shocks have a substantial and long-lasting impact on the latter’s co-movements with financial markets. In contrast, changes in the intensity of financial speculation have an impact on cross-market return linkages that is shorter-lived and not statistically significant in all model specifications.
    Keywords: G12 - Asset Pricing ; Trading volume ; Bond Interest Rates, G13 - Contingent Pricing ; Futures Pricing, Q11 - Aggregate Supply and Demand Analysis ; Prices, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 74
    Publication Date: 2016-10-21
    Description: Accurate information on thermal conductivity and thermal diffusivity of materials is of central importance in relation to geoscience and engineering problems involving the transfer of heat. Several methods, including the classical divided bar technique, are available for laboratory measurements of thermal conductivity, but much fewer for thermal diffusivity. We have generalized the divided bar technique to the transient case in which thermal conductivity, volumetric heat capacity and thereby also thermal diffusivity are measured simultaneously. As the density of samples is easily determined independently, specific heat capacity can also be determined. The finite element formulation provides a flexible forward solution for heat transfer across the bar, and thermal properties are estimated by inverse Monte Carlo modelling. This methodology enables a proper quantification of experimental uncertainties on measured thermal properties and information on their origin. The developed methodology was applied to various materials, including a standard ceramic material and different rock samples, and measuring results were compared with results applying traditional steady-state divided bar and an independent line-source method. All measurements show highly consistent results and with excellent reproducibility and high accuracy. For conductivity the obtained uncertainty is typically 1–3 per cent, and for diffusivity uncertainty may be reduced to about 3–5 per cent. The main uncertainty originates from the presence of thermal contact resistance associated with the internal interfaces in the bar. These are not resolved during inversion and it is imperative that they are minimized. The proposed procedure is simple and may quite easily be implemented to the many steady-state divided bar systems in operation. A thermally controlled bath, as applied here, may not be needed. Simpler systems, such as applying temperature-controlled water directly from a tap, may also be applied.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 75
    Publication Date: 2016-10-08
    Description: A whole-cell biosensor utilizing a transcription factor (TF) is an effective tool for sensitive and selective detection of specialty chemicals or anthropogenic molecules, but requires access to an expanded repertoire of TFs. Using homology modeling and ligand docking for binding pocket identification, assisted by conservative mutations in the pocket, we engineered a novel specificity in an Acinetobacter TF, PobR, to ‘sense’ a chemical p-nitrophenol (pNP) and measured the response via a fluorescent protein reporter expressed from a PobR promoter. Out of 10 7 variants of PobR, four were active when dosed with pNP, with two mutants showing a specificity switch from the native effector 4-hydroxybenzoate (4HB). One of the mutants, pNPmut1 was then used to create a smart microbial cell responding to pNP production from hydrolysis of an insecticide, paraoxon, in a coupled assay involving phosphotriesterase (PTE) enzyme expressed from a separate promoter. We show the fluorescence of the cells correlated with the catalytic efficiency of the PTE variant expressed in each cell. High selectivity between similar molecules (4HB versus pNP), high sensitivity for pNP detection (~2 μM) and agreement of apo- and holo-structures of PobR scaffold with predetermined computational models are other significant results presented in this work.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 76
    Publication Date: 2017-01-05
    Description: This article considers changes in the perception and avoidance behavior of food risks over time. In Japan, consumers’ concerns about the risks of radiation exposure via food consumption rose rapidly after the accident at the Fukushima Daiichi Nuclear Power Station in 2011. We conducted choice experiment surveys three months, seven months, and eleven months after the Fukushima accident and simulated the conditional means of willingness to pay (WTP) for avoiding radiation exposure via food consumption in each survey period. The results show that although the characteristics of changes in averting behaviors vary depending on the type of food, the heterogeneity in WTP values for avoiding food risk tends to reduce (broaden) when their magnitude decreases (increases).
    Keywords: Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy, Q51 - Valuation of Environmental Effects
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 77
    Publication Date: 2016-10-08
    Description: Advances in synthetic biology and our understanding of the rules of promoter architecture have led to the development of diverse synthetic constitutive and inducible promoters in eukaryotes and prokaryotes. However, the design of promoters inducible by specific endogenous or environmental conditions is still rarely undertaken. In this study, we engineered and characterized a set of strong, synthetic promoters for budding yeast Saccharomyces cerevisiae that are inducible under acidic conditions (pH ≤ 3). Using available expression and transcription factor binding data, literature on transcriptional regulation, and known rules of promoter architecture we improved the low-pH performance of the YGP1 promoter by modifying transcription factor binding sites in its upstream activation sequence. The engineering strategy outlined for the YGP1 promoter was subsequently applied to create a response to low pH in the unrelated CCW14 promoter. We applied our best promoter variants to low-pH fermentations, enabling ten-fold increased production of lactic acid compared to titres obtained with the commonly used, native TEF1 promoter. Our findings outline and validate a general strategy to iteratively design and engineer synthetic yeast promoters inducible to environmental conditions or stresses of interest.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 78
    Publication Date: 2016-12-01
    Description: Sensory photoreceptors have enabled non-invasive and spatiotemporal control of numerous biological processes. Photoreceptor engineering has expanded the repertoire beyond natural receptors, but to date no generally applicable strategy exists towards constructing light-regulated protein actuators of arbitrary function. We hence explored whether the homodimeric Rhodobacter sphaeroides light-oxygen-voltage (LOV) domain ( Rs LOV) that dissociates upon blue-light exposure can confer light sensitivity onto effector proteins, via a mechanism of light-induced functional site release. We chose the RNA-guided programmable DNA endonuclease Cas9 as proof-of-principle effector, and constructed a comprehensive library of Rs LOV inserted throughout the Cas9 protein. Screening with a high-throughput assay based on transcriptional repression in Escherichia coli yielded paRC9, a moderately light-activatable variant. As domain insertion can lead to protein destabilization, we also screened the library for temperature-sensitive variants and isolated tsRC9, a variant with robust activity at 29°C but negligible activity at 37°C. Biochemical assays confirmed temperature-dependent DNA cleavage and binding for tsRC9, but indicated that the light sensitivity of paRC9 is specific to the cellular setting. Using tsRC9, the first temperature-sensitive Cas9 variant, we demonstrate temperature-dependent transcriptional control over ectopic and endogenous genetic loci. Taken together, Rs LOV can confer light sensitivity onto an unrelated effector; unexpectedly, the same LOV domain can also impart strong temperature sensitivity.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 79
    Publication Date: 2017-01-10
    Description: Despite the extensive use of  Saccharomyces cerevisiae  as a platform for synthetic biology, strain engineering remains slow and laborious. Here, we employ CRISPR/Cas9 technology to build a cloning-free toolkit that addresses commonly encountered obstacles in metabolic engineering, including chromosomal integration locus and promoter selection, as well as protein localization and solubility. The toolkit includes 23 Cas9-sgRNA plasmids, 37 promoters of various strengths and temporal expression profiles, and 10 protein-localization, degradation and solubility tags. We facilitated the use of these parts via a web-based tool, that automates the generation of DNA fragments for integration. Our system builds upon existing gene editing methods in the thoroughness with which the parts are standardized and characterized, the types and number of parts available and the ease with which our methodology can be used to perform genetic edits in yeast. We demonstrated the applicability of this toolkit by optimizing the expression of a challenging but industrially important enzyme, taxadiene synthase (TXS). This approach enabled us to diagnose an issue with TXS solubility, the resolution of which yielded a 25-fold improvement in taxadiene production.
    Keywords: Synthetic Biology and Assembly Cloning
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 80
    Publication Date: 2015-03-18
    Description: It is important to know the electrokinetic properties of crustal rocks for interpreting the conductivity mechanisms and seismoelectric phenomena during earthquakes and seismoelectric well logging. In this study, electrokinetic experiments are conducted using a special core-holder by employing an AC lock-in technique. A series of experiments are conducted on 10 sandstone samples to measure the streaming potentials and streaming currents, and the experiments on each sample are done at six different salinities. The streaming potential coefficient and streaming current coefficient are calculated from the measured streaming potentials and streaming currents. The experimental results show that streaming potential coefficient and streaming current coefficient decrease as the salinity increases. The dependence of these two coefficients on permeability and pore radius are analysed and compared with previous works. At low salinities, the streaming potential coefficient and streaming current coefficient increase with the increasing permeability and pore radius. At high salinities, the streaming potential coefficient (streaming current coefficient) almost share a same value for 10 different samples. This conclusion indicates that the differences of rock parameters can only be well recognized at lower salinities, and the electrokinetic signals are invalid at high salinities, which offers a restrictive condition for using the amplitude of electrokinetic signals to estimate rock parameters. The zeta-potential have also been estimated through combined measurements of streaming potential and streaming current. The surface conductivity and its contribution to electrokinetic effects are determined from a comparison of zeta-potentials by two different methods, and then the validation of the Helmholz–Smoluchowski equation for a capillary tube is tested in rocks. We also compare our date with theoretical and experimental works, and set up an expression about the relationship between zeta potential and salinity, which fits the experimental data well.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 81
    Publication Date: 2015-02-06
    Description: We analyse the effects of geographical indication labelling on quality choices and welfare in a vertical differentiation framework with two attributes of goods, gustatory quality and geographical origin. We investigate two extreme cases of the protected designation of origin (PDO) label: a denomination standard, which guarantees only the origin of the product without any requirement on production specifications, and a minimum quality requirement, which guarantees both the origin and the quality of the product. We find that as long the PDO good is the high-quality good, binding production specifications on the quality level adversely affect the PDO producer(s).
    Keywords: D21 - Firm Behavior, L13 - Oligopoly and Other Imperfect Markets, L15 - Information and Product Quality ; Standardization and Compatibility, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 82
    Publication Date: 2015-02-28
    Description: A mixed effects model is used to estimate intercepts, price and expenditure elasticities for vegetables, meat and fish in different cohorts. Results from Wald tests reveal that intercepts for fish are higher for older cohorts than for younger cohorts, and expenditure elasticities for meat are higher for older cohorts than for younger cohorts. The implication is that over time, when younger cohorts replace older cohorts, the total expenditure share for fish is likely to decrease contributing to a negative trend in fish consumption. For meat, the total expenditure elasticity is likely to decrease.
    Keywords: D12 - Consumer Economics: Empirical Analysis, J10 - General, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 83
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    Oxford University Press
    Publication Date: 2015-02-28
    Description: Pricing and selling strategies in the retail sector are hotly debated in policy circles. This article analyses the impact of sales below cost on the negotiation outcomes in intermediate goods markets. Assuming that consumers have a sufficiently strong preference for one-stop shopping, we model below-cost pricing as the result of a profit-maximising cross-subsidisation strategy of a multi-product retailer. We find that below-cost pricing improves the supplier's bargaining position vis-à-vis the retailer. Correspondingly, the supplier of the loss-leader benefits from the retailer's below-cost pricing strategy, though the retailer is better off under a ban of sales below cost. These results disprove the often expressed fear that retailers use sales at a loss to squeeze wholesale prices.
    Keywords: L22 - Firm Organization and Market Structure, L42 - Vertical Restraints ; Resale Price Maintenance ; Quantity Discounts, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 84
    Publication Date: 2015-02-28
    Description: This article investigates member deliveries in agricultural marketing cooperatives. Since cooperatives depend on members’ contributions to achieve efficiency in processing and marketing, side-selling by members poses a threat to the economic viability of cooperatives in the long run. We develop a model for the farmers’ marketing decision that relates farm size to the share of produce delivered to the cooperative. Based on survey data from cooperatively organised coffee farmers in Costa Rica, we find that the share delivered to cooperatives decreases with farm size, albeit at a decreasing rate. The empirical results thus confirm the theoretical model prediction of a u-shaped relationship between farm size and member deliveries.
    Keywords: Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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  • 85
    Publication Date: 2015-03-04
    Description: We used ab initio molecular dynamics to calculate the elastic constants of MgSiO 3 , FeSiO 3 and (Fe 0.5 Mg 0.5 )SiO 3 perovskite under lower-most mantle conditions (136 GPa, 2000–4000 K). At 0 K, V p and V s for FeSiO 3 perovskite are 12 and 18 per cent lower, respectively than those for MgSiO 3 , in agreement with previous work. The difference in velocity, however, increases with temperature for high spin (but not low spin) states and at 4000 K, V p and V s for the end-member FeSiO 3 are, respectively, 19 and 34 per cent lower than those of MgSiO 3 . We find that (dln V s /dln V p ) T,P of Fe x Mg 1- x O 3 remains below 2 for all relevant iron concentrations and lower than the value of 3 seen in most ultralow velocity zones (ULVZ). Moreover, we are unable to match simultaneously the observed density increase and shear wave velocity reduction shown by ULVZs by increasing the ferrous iron content in perovskite except for the largest density increases and the smallest shear wave decreases observed in ULVZs. Assuming that current seismic estimates of ULVZ properties are accurate, our results suggest that ferrous iron enrichment alone cannot explain ULVZs.
    Keywords: Mineral Physics, Rheology, Heat Flow and Volcanology
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 86
    Publication Date: 2015-02-11
    Description: We analyze the inclusiveness and effectiveness of agricultural cooperatives in Rwanda. We estimate mean income and poverty effects of cooperative membership using propensity score matching techniques. We analyze heterogeneous treatment effects across farmers by analyzing how estimated treatment effects vary over farm and farmer characteristics and over the estimated propensity score. We find that cooperative membership in general increases income and reduces poverty and that these effects are largest for larger farms and in more remote areas. We find evidence of a negative selection because impact is largest for farmers with the lowest propensity to be a cooperative member .
    Keywords: I32 - Measurement and Analysis of Poverty, J54 - Producer Cooperatives ; Labor Managed Firms, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness
    Print ISSN: 2040-5790
    Electronic ISSN: 2040-5804
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
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