The Green Economy Mirage?

Taiwan is attempting to implement the concept of a green economy through a Low Carbon Growth Plan (LCGP). However, the existing decision support tools for this measure have three key limitations: ignorance regarding the open economy; a lack of life cycle thinking; and limited categories of environmental impact. This study integrates environmentally extended, multi‐region input‐output analysis and hybrid life cycle assessment to quantify the potential environmental impact of the industrial activities and energy structure in Taiwan in 2020. Two novel indicators, environmental debts and loans, are also applied to identify the geographical shifting effects and tie environmental responsibility to the discussion. The results of this study reveal that under the existing LCGP, relative decoupling will be attained, but no significant environmental cobenefits other than those affecting climate change can be gained. Moreover, the current emission pledges cannot be fulfilled. The presence of increased environmental debt ratios reveals the geographical shifting effect of the LCGP. The main driver of the expansion of the environmental footprint can be attributed to the export of electronic components and products, which are not included in the agenda of policy discussions. As a result, three crucial policies are suggested to modify the existing LCGP: the implementation of a higher energy efficiency improvement target; rethinking the constraints on the electronics industry; and the development of a mechanism to include environmental issues in free trade agreement negotiations. With these changes, the realization of the current emission pledge and a green economy could be possible.     

The Relation between α-Helical Conformation and Amyloidogenicity

Amyloid fibrils are stable aggregates of misfolded proteins and polypeptides that are insoluble and resistant to protease activity. Abnormal formation of amyloid fibrils in vivo may lead to neurodegenerative disorders and other systemic amyloidosis, such as Alzheimer’s, Parkinson’s, and atherosclerosis. Because of their clinical importance, amyloids are under intense scientific research. It is believed that short polypeptide segments within proteins are responsible for the transformation of correctly folded proteins into parts of larger amyloid fibrils and that this transition is modulated by environmental factors, such as pH, salt concentration, interaction with the cell membrane, and interaction with metal ions. Most studies on amyloids focus on the amyloidogenic sequences. The focus of this study is on the structure of the amyloidogenic α-helical segments because the α-helical secondary structure has been recognized to be a key player in different stages of the amyloidogenesis process. We have previously shown that the α-helical conformation may be expressed by two parameters (θ and ρ) that form orthogonal coordinates based on the Ramachandran dihedrals (φ and ψ) and provide an illuminating interpretation of the α-helical conformation. By performing statistical analysis on α-helical conformations found in the Protein Data Bank, an apparent relation between α-helical conformation, as expressed by θ and ρ, and amyloidogenicity is revealed. Remarkably, random amino acid sequences, whose helical structures were obtained from the most probable dihedral angles, revealed the same dependency of amyloidogenicity, suggesting the importance of α-helical structure as opposed to sequence.     

How Many M Forms are there in the Bacteriorhodopsin Photocycle?

On capturing a quantum of light, the bacteriorhodopsin of Halobacterium halobium undergoes a photocycle involving different intermediates. The exact scheme of the photocycle and especially the number of M intermediates are subjects of debate. For a quantitative analysis of many effects connected with the photocycle, e.g. the effect of the membrane potential on the kinetics of M decay (Groma et al., 1984. Biophys. J. 45:985-992), a knowledge of the exact photocycle is needed. In the present work sophisticated measurements were made on the decay kinetics of the M forms in cell envelope vesicles, purple membrane suspension and purple membrane fragments incorporated in polyacrylamide gel. The experimental data were analyzed by fitting one, two, and three discrete exponentials. Three different real components were found in the M decay of cell envelope vesicles in 4 M NaCl. All of them exhibited a temperature-dependence obeying the Arrhenius law. Two real components were found for the purple membrane in suspension and in gel in NaCl-free medium. The third phase appeared when the gel was soaked in 4 M NaCl. As an independent means of analysis, a continuous distribution of exponentials was also fitted to the M decay kinetics in cell envelope vesicles. This calculation also resulted in three processes with distinct rates or alternatively two processes with distributed rates.     

Do males matter? The role of males in population dynamics

Models of population dynamics generally neglect the presence of males. While this assumption holds under many circumstances, behavioural ecology increasingly tells us that the presence (or absence) of males may have an impact on female fitness, and hence population sizes. Here we ask the question of whether males matter to population dynamics, operationally defined as a dependency of population growth on the relative density of males. We provide simple models, and evaluate the current empirical evidence for them, that illustrate various mechanisms of such male influence: mate searching behavior, male resource use (including effects of sexual dimorphism), sexual harassment and sexual segregation. In each case, theory predicts that males can have an effect on population densities, and in some extreme cases a positive feedback between an increasingly male-biased sex ratio and female harassment may theoretically even bring about population extinction. The results of this study, and the literature reviewed, show that the males can have a substantial effect on population dynamics, particularly so when human influences result in biased sex ratios.     

Science – or not? The status and dynamics of biotechnology

This review traces the emergence of biotechnology as a new scientific discipline since the 1980s, when it became a major economic force. Significant changes in theoretical perception, research strategies, aims, and experimental methods, mainly in genetic engineering techniques, occurred during this period. The article is based on an analysis of its scientific status over four decades: the 60s and 70s when work in the field proceeded in different disciplines with a low level of coherence and little integration, then a significant change during the 80s and 90s when common approaches and the merging of molecular biology and biochemical engineering created a new discipline. The analysis covers scientific highlights and outstanding technical progress, presenting two studies undertaken by scientific and governmental agencies in Germany and the USA, as well as results of interviews and a questionnaire dealing with the scientific status of biotechnology. Answers to the questionnaire were obtained from internationally known scientists and from young scientists with biotechnology degrees. The results collected trace the transition of biotechnology from heterogeneous specialties and approaches towards a scientific discipline of its own. A hypothesis is put forward suggesting a new common paradigm allowing for a coherent perception the of phenomena observed.     

Disturbance and stress: different meanings in ecological dynamics?

There is an increasing frequency of papers addressing disturbance and stress in ecology without clear delimitation of their meaning. Some authors use the terms disturbance and stress exclusively as impacts, while others use them for the entire process, including both causes and effects. In some studies, the disturbance is considered as a result of a temporary impact, which is positive for the ecosystem, while stress is a negative, debilitating impact. By developing and testing simple theoretical models, the authors propose to differentiate disturbance and stress by frequency. If the frequency of the event enables the variable to reach a dynamic equilibrium which might be exhibited without this event, then the event (plus its responses) is a disturbance for the system. If frequency prevents the variable’s return to similar pre-event dynamics and drives or shifts it to a new trajectory, then we are facing stress. The authors propose that changes triggered by the given stimuli can be evaluated on an absolute scale, therefore, direction of change of the variable must not be used to choose one term or the other, i.e. to choose between stress and disturbance.     

The N-Terminal Actin-Binding Tandem Calponin-Homology (CH) Domain of?Dystrophin Is in a Closed Conformation in Solution and When Bound to?F-actin

Deficiency of the vital muscle protein dystrophin triggers Duchenne/Becker muscular dystrophy, but the structure-function relationship of dystrophin is poorly understood. To date, molecular structures of three dystrophin domains have been determined, of which the N-terminal actin-binding domain (N-ABD or ABD1) is of particular interest. This domain is composed of two calponin-homology (CH) domains, which form an important class of ABDs in muscle proteins. A previously determined x-ray structure indicates that the dystrophin N-ABD is a domain-swapped dimer, with each monomer adopting an extended, open conformation in which the two CH domains do not interact. This structure is controversial because it contradicts functional studies and known structures of similar ABDs from other muscle proteins. Here, we investigated the solution conformation of the dystrophin N-ABD using a very simple and elegant technique of pyrene excimer fluorescence. Using the wild-type protein, which contains two cysteines, and the corresponding single-cysteine mutants, we show that the protein is a monomer in solution and is in a closed conformation in which the two CH domains seem to interact, as observed from the excimer fluorescence of pyrene-labeled wild-type protein. Excimer fluorescence was also observed in its actin-bound form, indicating that the dystrophin N-ABD binds to F-actin in a closed conformation. Comparison of the dystrophin N-ABD conformation with other ABDs indicates that the tandem CH domains in general may be monomeric in solution and predominantly occur in closed conformation, whereas their actin-bound conformations may differ.     

Loop–loop interaction in an adenine-sensing riboswitch: A molecular dynamics study

Riboswitches are mRNA-based molecules capable of controlling the expression of genes. They undergo conformational changes upon ligand binding, and as a result, they inhibit or promote the expression of the associated gene. The close connection between structural rearrangement and function makes a detailed knowledge of the molecular interactions an important step to understand the riboswitch mechanism and efficiency. We have performed all-atom molecular dynamics simulations of the adenine-sensing add A-riboswitch to study the breaking of the kissing loop, one key tertiary element in the aptamer structure. We investigated the aptamer domain of the add A-riboswitch in complex with its cognate ligand and in the absence of the ligand. The opening of the hairpins was simulated using umbrella sampling using the distance between two loops as the reaction coordinate. A two-step process was observed in all the simulated systems. First, a general loss of stacking and hydrogen bond interactions is seen. The last interactions that break are the two base pairs G37-C61 and G38-C60, but the break does not affect the energy profile, indicating their pivotal role in the tertiary structure formation but not in the structure stabilization. The junction area is partially organized before the kissing loop formation and residue A24 anchors together the loop helices. Moreover, when the distance between the loops is increased, one of the hairpins showed more flexibility by changing its orientation in the structure, while the other conserved its coaxial arrangement with the rest of the structure.     

Violence Affects Physical and Mental Health Differently: The General Population Based Troms? Study

This general population-based study examined associations between violence and mental health, musculoskeletal pain, and early disability pension. The prevalence and consequences of good vs. poor adjustment (resilience vs. vulnerability) following encounters with violence were also examined. Data were based on the sixth wave of the “Tromsø Study” (N = 12,981; 65.7% response rate, 53.4% women, M-age = 57.5 years, SD-age = 12.7 years). Self-reported data on psychological (threats) and physical violence (beaten/kicked), mental health (anxiety/depression), musculoskeletal pain (MSP), and granting of disability pension (DP) were collected. Men suffered more violent events during childhood than women did, and vice versa during adulthood. Psychological violence implied poorer mental health and slightly more MSP than physical violence. The risk of MSP was highest for violence occurring during childhood in women and during the last year for men. A dose-response relationship between an increasing number of violent encounters and poorer health was observed. About 58% of individuals reported no negative impact of violence (hence, resilience group), whereas 42% considered themselves as more vulnerable following encounters with violence. Regression analyses indicated comparable mental health but slightly more MSP in the resilience group compared to the unexposed group, whereas the vulnerable group had significantly worse health overall and a higher risk of early granting of DP. Resilience is not an all-or-nothing matter, as physical ailments may characterize individuals adapting well following encounters with violence.     

The seasonal dynamics and persistence of stream macroinvertebrates in Nepal: do monsoon floods represent disturbance?

1. The monsoon causes major flood events in some Himalayan streams, but their seasonal predictability might reduce the resulting disturbance. We assessed seasonal change in the benthos of 16 streams in central Nepal over a gradient of declining rainfall and increasing altitude from 600 to 3800 m. All sites were surveyed on four occasions, two in winter (November) and two pre-monsoon (June), with additional sampling during the monsoon (August) at four low altitude sites. Invertebrate abundance, taxon richness and persistence were assessed at all sites, and density and meso-habitat distribution at the four low altitude sites only.
2. Strong seasonal variation among invertebrates was confined primarily to streams at low altitude (600–800 m) where monsoon rainfall was greatest and catchments were dominated by terraced agriculture. At these sites, a significant reduction in benthic density (on average by 77%) and taxon richness (by 20%) occurred between the winter and pre-monsoon periods, so that invertebrate numbers were already low before the monsoon. A further significant decline occurred in all meso-habitats during the monsoon, but the change in density was small in absolute terms.
3. Persistence in rank abundance was equally low at all sites, but turnover in composition was significantly lower at sites in semi-natural forest than in catchments managed for terracing or alpine pasture.
4. These data provide no evidence that monsoonal floods represent major disturbance, instead supporting the view that the ecological response might reflect an adjustment to predictable flow pattern. However, catchment land use in the Himalaya appears to be a significant source of ecosystem instability, and confounds the simple interpretation of monsoon effects.     

Conformation of the circular dumbbell d〈pCGC-TT-GCG-TT〉: Structure determination and molecular dynamics

Summary The circular DNA decamer 5-dpCGC-TT-GCG-TT-3 was studied in solution by means of NMR spectroscopy and molecular dynamics in H₂O. At a temperature of 269 K, a 50/50 mixture of two dumbbell structures (denoted L2L2 and L2L4) is present. The L2L2 form contains three Watson-Crick C-G base pairs and two two-residue loops in opposite parts of the molecule. On raising the temperature from 269 K to 314 K, the L2L4 conformer becomes increasingly dominant (95% at 314 K). This conformer has a partially disrupted G(anti)-C(syn) closing base pair in the 5-GTTC-3 loop with only one remaining (solvent-accessible) hydrogen bond between NH of the cytosine dC(1) and O6 of the guanine dG(8). The opposite 5-CTTG-3 loop remains stable. The two conformers occur in slow equilibrium (rate constant 2–20 s^–1). Structure determination of the L2L2 and L2L4 forms was performed with the aid of a full relaxation matrix approach (IRMA) in combination with restrained MD. Torsional information was obtained from coupling constants. Coupling constant analysis (³J_HH, ³J_HP, ³J_CP) gave detailed information about the local geometry around backbone torsion angles , , and , revealing a relatively high flexibility of the 5-GTTC-3 loop. The values of the coupling constants are virtually temperature-independent. Weakly constrained molecular dynamics in solvent was used to sample the conformational space of the dumbbell. The relaxation matrices from the MD simulation were averaged over r^–3 to predict dynamic NOE volumes. In order to account for the 1:1 conformational mixture of L2L2 and L2L4 present at 271 K, we also included S² factors and r^–6 averaging of the r^–3-averaged relaxation matrices. On matrix averaging, the agreement of NOE volumes with experiment improved significantly for protons located in the thermodynamically less stable 5-GTTC-3 loop. The difference in stability of the 5-CTTG-3 and 5-GTTC-3 loops is mainly caused by differences in the number of potential hydrogen bonds in the minor groove and differences in stacking overlap of the base pairs closing the minihairpin loops. The syn conformation for dC(1), favored at high temperature, is stabilized by solvation in the major groove. However, the conformational properties of the dC(1) base, as deduced from R-factor analysis and MD simulations, include a large flexibility about torsion angle .     

Is soil carbon disappearing? The dynamics of soil organic carbon in Java

Research in the soil of the tropics mostly has demonstrated the decline of soil organic carbon (SOC) after conversion of primary forest to plantation and cultivated lands. This paper illustrates the dynamics of SOC on the island of Java, Indonesia, from 1930 to 2010. We used 2002 soil profile observations containing organic carbon (C) analysis in the topsoil, which were collected by the Indonesian Center for Agricultural Land Resources Research & Development from 1923 to 2007. Results show the obvious decline of SOC values from around 2% in 1930–1940 to 0.8% in 1960–1970. However, there has been an increase of SOC content since 1970, with a median level of 1.1% in the year 2000. Our analysis suggests that the human influence and agricultural practices on SOC in Java have been a stronger influence than the environmental factors. SOC for the top 10 cm has shown a net accumulation rate of 0.2–0.3 Mg C ha^?1 yr^?1 during the period 1990–2000. These findings give rise to optimism for increased soil C sequestration in the tropics.     

Is there chaos in plankton dynamics?

A controversial issue in ecosystem modeling is whether the irregularfluctuations that one observes in nature are due solely to randomenvironmental factors or whether, at least partially, a deterministicmechanism is responsible for the unpredictable behavior. Thissecond alternative is called deterministic chaos and the issuein this paper is to decide if actual plankton time series canvindicate the hypothesis of chaotic dynamics. The near-neighborforecasting method is a recent technique for detecting determinismin a time series and we apply it to measurements of phytoplanktonand zooplankton biomass obtained at a single station in theMiddle Atlantic Bight. Although the results do not concludethe presence of chaos, they do give some support to the ideathat deterministic non-linear trophic dynamics may account forat least some of the variability that is seen in the data, particularlyin terms of inferring zooplankton oscillations from those ofphytoplankton.     

Protein dynamics and enzyme catalysis: the ghost in the machine?

One of the most controversial questions in enzymology today is whether protein dynamics are significant in enzyme catalysis. A particular issue in these debates is the unusual temperature-dependence of some kinetic isotope effects for enzyme-catalysed reactions. In the present paper, we review our recent model [Glowacki, Harvey and Mulholland (2012) Nat. Chem. 4, 169-176] that is capable of reproducing intriguing temperature-dependences of enzyme reactions involving significant quantum tunnelling. This model relies on treating multiple conformations of the enzyme-substrate complex. The results show that direct 'driving' motions of proteins are not necessary to explain experimental observations, and show that enzyme reactivity can be understood and accounted for in the framework of transition state theory.     

The scaling of colony size with nest volume in termites: a role in population dynamics?

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