86 research outputs found

    Improved Farmer\u27s Capasity Model of Private Forest Management: Studies in Ranggang Village, South Kalimantan

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    Farmer\u27s capacity is one of the important factors that determine the success of private forest management. However, the farmer\u27s capacity level in several places is still low so that potentially to inhibiting successful of private forests management practices. This study aims to analyze the factors that affect farmer\u27s capacity level of private forests management practices, and to formulate improved farmer\u27s capacity model of private forests management in Ranggang Village, South Kalimantan. The data was analyzed by Structural Equation Model (SEM) with the help of SmartPls 2.0 M3. Results showed (1) learning experience level directly affect to farmer\u27s capacity while farmer\u27s characteristics, external support, social and cultural environment supporting, the role of extension, and information availability indirectly affect to farmer\u27s capacity of private forests management in Ranggang Village, and (2) improved farmer\u27s capacity model can be done by improving the farmer\u27s learning experience through intensive, scheduled, and suistainable education, training and extension with stakeholders support

    Correlation between Oncogenic Mutations and Parameter Sensitivity of the Apoptosis Pathway Model

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    <div><p>One of the major breakthroughs in oncogenesis research in recent years is the discovery that, in most patients, oncogenic mutations are concentrated in a few core biological functional pathways. This discovery indicates that oncogenic mechanisms are highly related to the dynamics of biologic regulatory networks, which govern the behaviour of functional pathways. Here, we propose that oncogenic mutations found in different biological functional pathways are closely related to parameter sensitivity of the corresponding networks. To test this hypothesis, we focus on the DNA damage-induced apoptotic pathwayβ€”the most important safeguard against oncogenesis. We first built the regulatory network that governs the apoptosis pathway, and then translated the network into dynamics equations. Using sensitivity analysis of the network parameters and comparing the results with cancer gene mutation spectra, we found that parameters that significantly affect the bifurcation point correspond to high-frequency oncogenic mutations. This result shows that the position of the bifurcation point is a better measure of the functionality of a biological network than gene expression levels of certain key proteins. It further demonstrates the suitability of applying systems-level analysis to biological networks as opposed to studying genes or proteins in isolation.</p></div

    Robust network topologies for generating oscillations with temperature-independent periods

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    <div><p>Nearly all living systems feature a temperature-independent oscillation period in circadian clocks. This ubiquitous property occurs at the system level and is rooted in the network architecture of the clock machinery. To investigate the mechanism of this prominent property of the circadian clock and provide general guidance for generating robust genetic oscillators with temperature-compensated oscillations, we theoretically explored the design principle and core network topologies preferred by oscillations with a temperature-independent period. By enumerating all topologies of genetic regulatory circuits with three genes, we obtained four network motifs, namely, a delayed negative feedback oscillator, repressilator, activator-inhibitor oscillator and substrate-depletion oscillator; hybrids of these motifs constitute the vast majority of target network topologies. These motifs are biased in their capacities for achieving oscillations and the temperature sensitivity of the period. The delayed negative feedback oscillator and repressilator are more robust for oscillations, whereas the activator-inhibitor and substrate-depletion oscillators are superior for maintaining a temperature-independent oscillation period. These results suggest that thermally robust oscillation can be more plausibly achieved by hybridizing these two categories of network motifs. Antagonistic balance and temperature insulation mechanisms for achieving temperature compensation are typically found in these topologies with temperature robustness. In the temperature insulation approach, the oscillation period relies on very few parameters, and these parameters are influenced only slightly by temperature. This approach prevents the temperature from affecting the oscillation period and generates circadian rhythms that are robust against environmental perturbations.</p></div

    Core interactions in circadian clocks across species.

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    <p>Core interactions in circadian clocks across species.</p

    Bifurcation diagram for nuclear p53 and caspase3 for apoptosis.

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    <p>(A) The bifurcation diagram for nuclear p53 using DNA damage as the control parameter. (B) The bifurcation diagram for caspase3 using DNA damage as the control parameter (black dots). (C) Comparison of bifurcation point with an increase in the parameter kf5. Black, without increase; green, 1.9-fold increase; red, 4.2-fold increase.</p

    Ranking of the Q-values.

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    <p>Q-values for all two-node networks (A) and all three networks (B), both showing exponential-like dependence on the ranking.</p

    Parameter sensitivity analysis.

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    <p>(A) The change of the saddle-node bifurcation point in response to a 20% increase or decrease in each parameter of the apoptosis pathway. (B) The change in the steady-state concentration of caspase3 in response to a 20% increase or decrease in each parameter of the apoptosis pathway.</p

    Screening for networks with DoRA function.

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    <p>For each network with two nodes and three nodes, 10,000 random sets of parameters were assigned. The corresponding kinetic equations were solved numerically to obtain the dose-response curves. Linear correlation coefficients were calculated subsequently from the relationship between the responses of the output node and the input node. The number of parameter sets that render good linear output-input dependence (Q-value) measures the ability for the corresponding network to achieve dose-response alignment.</p

    The correspondence between parameter sensitivities and the cancer gene mutation spectrum.

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    <p>(A) The correspondence between parameters linked to sensitivity of the bifurcation point (yellow bar) or caspase3 (blue bar) and high-frequency mutation genes. (B) The correspondence between insensitive parameters and low-frequency mutation genes. (C) The inconsistency between parameter sensitivity and gene mutation frequency. The numbers in the frame indicate the number of occurrences in the mutation spectrum of the gene that relates to the corresponding parameters.</p

    Comparison of parameters linked to sensitivity of caspase3 levels and gene mutations.

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    <p>The numbers in the frame indicate the number of occurrences in the mutation spectrum of the gene relating to the corresponding parameters. Magenta bar, change in the steady-state concentration of caspase3; Green bar, change in the critical point of bifurcation. gpre-casp, the basal generation rate of pre-caspase; dcaspase, the degradation rate of caspase3.</p
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