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The fast decay in PEM fuel cells of a highly active, high performance, but unstable Fe/N/C catalyst like our NC_Ar + NH3 follows a chemical, not an electrochemical, demetallation mechanism for its ORR active FeN4 sites in the catalyst micropores.

The increasing demand for lignocellulosic biomass for the production of biofuels provides value to vegetative plant tissue and leads to a paradigm shift for optimizing plant architecture in bioenergy crops. Plant height (PHT) is among the most important biomass yield components and is the focus of this review, with emphasis on the energy grasses maize (Zea mays) and sorghum (Sorghum bicolor). We discuss the scientific advances in the identification of PHT quantitative trait loci (QTLs) and the understanding of pathways and genes controlling PHT, especially gibberellins and brassinosteroids. We consider pleiotropic effects of QTLs or genes affecting PHT on other agronomically important traits and, finally, we discuss strategies for applying this knowledge to the improvement of dual-purpose or dedicated bioenergy crops.

Cells respond to environmental cues by modifying protein complexes in the nucleus to produce a change in the pattern of gene expression. In this article, we review techniques that allow us to visualize these protein interactions as they occur in living cells. The cloning of genes from marine organisms that encode fluorescent proteins provides a way to tag and monitor the intracellular behavior of expressed fusion proteins. The genetic engineering of jellyfish green fluorescent protein (GFP) and the recent cloning of a sea anemone red fluorescent protein (RFP) have provided fluorescent tags that emit light at wavelengths ranging from the blue to the red spectrum. Several of these color variants can be readily distinguished by fluorescence microscopy, allowing them to be used in combination to monitor the behavior of two or more independent proteins in the same living cell. We describe the use of this approach to examine where transcription factors are assembled in the nucleus. To demonstrate that these labeled nuclear proteins are interacting, however, requires spatial resolution that exceeds the optical limit of the light microscope. This degree of spatial resolution can be achieved with the conventional light microscope using the technique of fluorescence resonance energy transfer (FRET). The application of FRET microscopy to detect the interactions between proteins labeled with the color variants of GFP and the limitations of the FRET approach are discussed. The use of different-color fluorescent proteins in combination with FRET offers the opportunity to study the complex behavior of key regulatory proteins in their natural environment within the living cell.

Abstract It is shown that the mechanism of parametric energy conversion—a non-linear phenomenon which is known to occur in all branches of physics—may play a fundamental role in energy conversion in biological structures. Parametric energy conversion means pumping of energy through the variation of an energy storing quantity (a parameter). In biological systems the energy storing parameter is the membrane itself, the structure and composition of which is varied by proceeding structure bound biochemical reactions. The principle of parametric energy conversion is introduced into a molecular kinetical model and three coupled differential equations are derived, which interconnect chemical, electrical and mechanical energy in biological structures. It is shown that they describe parametric pumping of energy. It is a particular mechanism, which is also found in the physical phenomenon of Bethenod. The mechanism is tested with the derivation and explanation of various important bioenergetical functions as special cases of parametric energy conversion, of ATP synthesis, the pumping of ions and molecules during active transport, the excitability of nerve membranes and the dynamics of oscillatory muscles. A new interpretation of the connection of structure and function in striated muscles is also derived and signal transformation in receptors discussed. It is suggested that parametric energy conversion may be the uniform basis of energy conversion in biological structures and that the path of bioenergetic evolution might have essentially followed the line marked by the characteristic properties of this flexible mechanism. The parametric hypothesis offers an elegant ordering scheme and reasonable explanation for evolution and function of a large variety of important bioenergetic mechanisms. In order to handle the intricate mechanism properly it would be necessary to give up the conventional, intuitive way of formulating and understanding biochemical mechanisms and to develop a new dimension of chemical thinking.

AbstractProtein–DNA interactions induce conformational changes in DNA such as B‐ to A‐form transitions at a local level. Such transitions are associated with a junction free energy cost at the boundary of two different conformations in a DNA molecule. In this study, we performed umbrella sampling simulations to find the free energy values of the B–A transition at the dinucleotide and trinucleotide level of DNA. Using a combination of dinucleotide and trinucleotide free energy costs obtained from simulations, we calculated the B/A junction free energy. Our study shows that the B/A junction free energy is 0.52 kcal mol−1 for the A‐philic GG step and 1.59 kcal mol−1 for the B‐philic AA step. This observation is in agreement with experimentally derived values. After excluding junction effects, we obtained an absolute free energy cost for the B‐ to A‐form conversion for all the dinucleotide steps. These absolute free energies may be used for predicting the propensity of structural transitions in DNA.

The initial biomass density had a significant effect on the growth behaviour of Leptolyngbya foveolarum HNBGU-001 in the batch culture. The test organism produced substantial amounts of biomass and lipids when allowed to grow at 40 °C and pH 8.0. The Placket-Burman design appropriately indicated the positive and negative influences of the tested nutrient factors on biomass and lipid productivities of L. foveolarum. Employing the Box-Behnken design of response surface methodology, the elevated concentrations of sulphate-S (300 mg/L) and carbonate-C (45.39 mg/L) but relatively low levels of phosphate-P (10 mg/L) and nitrate-N (375 mg/L) were identified as the optimal nutritional requirements of the test organism for the maximum lipid productivity (49.60 ± 0.70 mg/L/day) along with high lipid content (32.10 ± 0.40% dry cell weight) and biomass productivity (154.80 ± 3.60 mg/L/day). These maximized responses of biomass productivity, lipid content, and lipid productivity were respectively 2.8-, 2.4-, and 6.8-fold higher than their corresponding values under the unoptimized conditions. FAME analysis of lipids obtained from the test organism revealed some promising features for their use as algal biodiesel feedstock. Nonetheless, the test organism seems to have better potential than several other microalgae for use in biofuel production as it can give a high output of biomass as also lipids at elevated temperature prevalent in outdoor conditions of subtropical and tropical regions.

Abstract We evaluated three Integrated Assessment Models (IAMs: IGSM, MERGE, MiniCAM) by: (i) comparing their global Primary Energy year-2000 initializations and projections for 2010 and 2015 to historical data; (ii) mapping their CO2 emissions projections against observations; and (iii) examining model-output diagnostics. The IAMs underestimated historical primary energy consumption and initial/projected CO2 emissions in both reference and stabilization scenarios (particularly for combustion fuels) but overestimated usage of non-biomass renewables, causing underestimates of future CO2 emissions that, for the stabilization scenarios, are wildly optimistic. Mitigation technology breakdowns in the policy scenarios vary enormously across IAMs, suggesting that confidence in their projections might be misplaced, or that options for mitigation have greater scope than is supposed. Most increases in carbon-free technologies in the stabilization scenarios are already captured in the reference cases. Energy-conversion efficiencies in electricity generation improve over time, but, (except for gas-powered generation in IGSM), efficiencies in the policy scenarios are less than in the reference. Electrification results diverge widely: IGSM has little change over the 21st century, while MiniCAM and MERGE have major electrification increases in their policy scenarios. We suggest: 1) comprehensive model output suitable for secondary analysis should be more readily available; 2) directly comparable reference and policy-driven mitigation scenarios are essential for assessing mitigation measures; 3) model validation using historical, source-specific energy data is crucial for assessing model credibility; 4) separation of mitigation contributions into no-policy and policy-driven amounts is needed to assess the effectiveness of mitigation policies; and 5) detailed inter-model comparisons can provide important insights into model credibility.

Schrödinger [Schrödinger, E., 1944. What is Life? Cambridge University Press, Cambridge] marvelled at how the organism is able to use metabolic energy to maintain and even increase its organisation, which could not be understood in terms of classical statistical thermodynamics. Ho [Ho, M.W., 1993. The Rainbow and the Worm, The Physics of Organisms, World Scientific, Singapore; Ho, M.W., 1998a. The Rainbow and the Worm, The Physics of Organisms, 2nd (enlarged) ed., reprinted 1999, 2001, 2003 (available online from ISIS website www.i-sis.org.uk)] outlined a novel "thermodynamics of organised complexity" based on a nested dynamical structure that enables the organism to maintain its organisation and simultaneously achieve non-equilibrium and equilibrium energy transfer at maximum efficiency. This thermodynamic model of the organism is reminiscent of the dynamical structure of steady state ecosystems identified by Ulanowicz [Ulanowicz, R.E., 1983. Identifying the structure of cycling in ecosystems. Math. Biosci. 65, 210-237; Ulanowicz, R.E., 2003. Some steps towards a central theory of ecosystem dynamics. Comput. Biol. Chem. 27, 523-530]. The healthy organism excels in maintaining its organisation and keeping away from thermodynamic equilibrium--death by another name--and in reproducing and providing for future generations. In those respects, it is the ideal sustainable system. We propose therefore to explore the common features between organisms and ecosystems, to see how far we can analyse sustainable systems in agriculture, ecology and economics as organisms, and to extract indicators of the system's health or sustainability. We find that looking at sustainable systems as organisms provides fresh insights on sustainability, and offers diagnostic criteria for sustainability that reflect the system's health. In the case of ecosystems, those diagnostic criteria of health translate into properties such as biodiversity and productivity, the richness of cycles, the efficiency of energy use and minimum dissipation. In the case of economic systems, they translate into space-time differentiation or organised heterogeneity, local autonomy and sufficiency at appropriate levels, reciprocity and equality of exchange, and most of all, balancing the exploitation of natural resources--real input into the system--against the ability of the ecosystem to regenerate itself.

The waste and by-products of the soybean industry could be an economic source of nutrients to satisfy the high nutritional demands for the cultivation of lactic acid bacteria. The aims of this work were to maximize the biomass production of Lacticaseibacillus paracasei 90 (L90) in three culture media formulated from an effluent derived from soy protein concentrate production and to assess the effects these media have on the enzymatic activity of L90, together with their influence on its fermentation profile in milk. The presence of essential minerals and fermentable carbohydrates (sucrose, raffinose, and stachyose) in the effluent was verified. L90 reached high levels of microbiological counts (∼ 9 log cfu mL-1) and dry weight (> 1 g L-1) on the three optimized media. Enzymatic activities (lactate dehydrogenase and β-galactosidase) of L90, and its metabolism of lactose and citric acid, as well as lactic acid and pyruvic acid production in milk, were modified depending on the growth media. The ability of the L90 to produce the key flavour compounds (diacetyl and acetoin) was maintained or improved by growing in the optimized media in comparison with MRS.