The use of metabolomics to monitor simultaneous changes in metabolic variables following supramaximal low volume high intensity exercise

High Intensity Exercise (HIE) stimulates greater physiological remodeling when compared to workload matched low-moderate intensity exercise. This study utilized an untargeted metabolomics approach to examine the metabolic perturbations that occur following two workload matched supramaximal low volume HIE trials. In a randomized order, 7 untrained males completed two exercise protocols separated by one week; 1) HIE150%: 30 x 20s cycling at 150% VO2peak, 40s passive rest; 2) HIE300%: 30 x 10s cycling at 300% VO2peak, 50 s passive rest. Total exercise duration was 30 minutes for both trials. Blood samples were taken at rest, during and immediately following exercise and at 60 minutes post exercise. Gas chromatography-mass spectrometry (GC-MS) analysis of plasma identified 43 known metabolites of which 3 demonstrated significant fold changes (HIE300% compared to the HIE150% value) during exercise, 14 post exercise and 23 at the end of the recovery period. Significant changes in plasma metabolites relating to lipid metabolism [fatty acids: dodecanoate (p=0.042), hexadecanoate (p=0.001), octadecanoate (p=0.001)], total cholesterol (p=0.001), and glycolysis [lactate (p=0.018)] were observed following exercise and during the recovery period. The HIE300% protocol elicited greater metabolic changes relating to lipid metabolism and glycolysis when compared to HIE150% protocol. These changes were more pronounced throughout the recovery period rather than during the exercise bout itself. Data from the current study demonstrate the use of metabolomics to monitor intensity-dependent changes in multiple metabolic pathways following exercise. The small sample size indicates a need for further studies in a larger sample cohort to validate these findings.

Energy use in Indian household sector - An actor-oriented approach

Over the years, significant changes have taken place with regard to the type as well the quantity of energy used in Indian households. Many factors have contributed in bringing these changes. These include availability of energy, security of supplies, efficiency of use, cost of device, price of energy carriers, ease of use, and external factors like technological development, introduction of subsidies, and environmental considerations. The present paper presents the pattern of energy consumption in the household sector and analyses the causalities underlying the present usage patterns. It identifies specific (groups of) actors, study their specific situations, analyse the constraints and discusses opportunities for improvement. This can be referred to ``actor-oriented'' analysis in which we understand how various actors of the energy system are making the system work, and what incentives and constraints each of these actors is experiencing. It analyses actor linkages and their impact on the fuel choice mechanism. The study shows that the role of actors in household fuel choice is significant and depends on the level of factors - micro, meso and macro. It is recommended that the development interventions should include actor-oriented tools in energy planning, implementation, monitoring and evaluation. The analysis is based on the data from the national sample survey (NSS), India. This approach provides a spatial viewpoint which permits a clear assessment of the energy carrier choice by the households and the influence of various actors. The scope of the paper is motivated and limited by suggesting and formulating a powerful analytical technique to analyse the problem involving the role of actors in the Indian household sector.

A review on exploring the behavior of multi-layer composite structures under dynamic loading

This paper reviews the recent research progress on multi-layer composite structures composed of variety of materials. The utilization of multi-layer composite system is found to be common in metal structures and pavement systems. The layer of composite structure designed to encounter heavy dynamic energy should have sufficient ductility to counteract the intensity of energy. Therefore, the selection of materials and enhancement of interface bonding become crucial and both are discussed in this paper. The failure modes have also been explored in conjunction with stresses at failures and inferred solutions are also revealed. The paper attempts to reveal all technical facts on multi-layer composite structure in a broad field.

The Population Consequences of Sex and Conflict

Natural selection generally operates at the level of the individual, or more specifically at the level of the gene. As a result, individual selection does not always favour traits which benefit the population or species as a whole. The spread of an individual gene may even act to the detriment of the organism in which it finds. Thus selection at the level of the individual can affect processes at the level of the organism, group or even at the level of the species. As most behaviours ultimately affect births, deaths and the distribution of individuals, it seems inevitable that behavioural decisions will have an impact on population dynamics and population densities. Behavioural decisions can often involve costs through allocation of energy into behavioural strategies, such as the investment into armaments involved in fighting over resources or increased mortality due to injury or increased predation risk. Similarly, behaviour may act o to benefit the population, in terms of higher survival and increased fecundity. Examples include increased investment through parental care, choosing a mate based on the nuptial gifts they may supply and choosing territories in the face of competition. Investigating the impact of behaviour on population ecology may seem like a trivial task, but it is likely to have important consequences at different levels. For example, antagonistic behaviour may occasionally become so extreme that it increases the risk of extinction, and such extinction risk may have important implications for conservation. As a corollary, any such behaviour may also act as a macroevolutionary force, weeding out populations with traits which, whilst beneficial to the individuals in the short term, ultimately result in population extinction. In this thesis, I examine how behaviours, specifically conflict and competition over a resource and aspects of behaviour involved in sexual selection, can affect population densities, and what the implications are for the evolution and ecology of the populations in question. It is found that both behaviours related to individual conflict and mating strategies can have an effect at the level of the population, but that various factors, such as a feedback between selection and population densities or macroevolution caused by species extinctions, may act to limit the intensity of conflicts that we observe in nature.

Energy and cities

Any plan for decoupling growth from fossil fuel use needs to prioritise locally appropriate, integrated and multi-faceted outcomes. Such transitions can be highly complex, given the physical and institutional characteristics of existing electricity infrastructure as well as various financial, technical and practical challenges. This Chapter applies a whole systems perspective to developing decoupling solutions, reflecting on the Dutch Sustainable Technology Development Program and Townsville City (Queensland, Australia). Key aspects considered include the need for demonstrating outcomes to multiple stakeholders, using pilot projects with integrated monitoring and evaluation, fostering collaborative approaches to energy management, cultivating cultures of ‘learning by doing’, and seeking synergies across multiple agendas.

Milking Diatoms for Sustainable Energy: Biochemical Engineering versus Gasoline-Secreting Diatom Solar Panels

In the face of increasing CO2 emissions from conventional energy (gasoline), and the anticipated scarcity of Crude oil, a worldwide effort is underway for cost-effective renewable alternative energy sources. Here, we review a simple line of reasoning: (a) geologists claim that Much crude oil comes from diatoms; (b) diatoms do indeed make oil; (c) agriculturists Claim that diatoms could make 10-200 times as much oil per hectare as oil seeds; and (d) therefore, sustainable energy could be made from diatoms. In this communication, we propose ways of harvesting oil from diatoms, using biochemical engineering and also a new solar panel approach that utilizes genomically modifiable aspects of diatom biology, offering the prospect of ``milking'' diatoms for Sustainable energy by altering them to actively secrete oil products. Secretion by and milking of diatoms may provide a way around the puzzle of how to make algae that both grow quickly and have a very high oil content.

Indoor air quality and energy management through real–time sensing in commercial buildings

Rapid growth in the global population requires expansion of building stock, which in turn calls for increased energy demand. This demand varies in time and also between different buildings, yet, conventional methods are only able to provide mean energy levels per zone and are unable to capture this inhomogeneity, which is important to conserve energy. An additional challenge is that some of the attempts to conserve energy, through for example lowering of ventilation rates, have been shown to exacerbate another problem, which is unacceptable indoor air quality (IAQ). The rise of sensing technology over the past decade has shown potential to address both these issues simultaneously by providing high–resolution tempo–spatial data to systematically analyse the energy demand and its consumption as well as the impacts of measures taken to control energy consumption on IAQ. However, challenges remain in the development of affordable services for data analysis, deployment of large–scale real–time sensing network and responding through Building Energy Management Systems. This article presents the fundamental drivers behind the rise of sensing technology for the management of energy and IAQ in urban built environments, highlights major challenges for their large–scale deployment and identifies the research gaps that should be closed by future investigations.

Free energy calculations of glycosaminoglycan - Protein interactions

Glycosaminoglycans (GAGs) are complex highly charged linear polysaccharides that have a variety of roles in biological processes. We report the first use of molecular dynamics (MD) free energy calculations using the MM/PBSA method to investigate the binding of GAGs to protein molecules, namely the platelet endothelial cell adhesion molecule 1 (PECAM-1) and annexin A2. Calculations of the free energy of the binding of heparin fragments of different sizes reveal the existence of a region of low GAG-binding affinity in domains 5-6 of PECAM-1 and a region of high affinity in domains 2-3, consistent with experimental data and ligand-protein docking studies. A conformational hinge movement between domains 2 and 3 was observed, which allows the binding of heparin fragments of increasing size (pentasaccharides to octasaccharides) with an increasingly higher binding affinity. Similar simulations of the binding of a heparin fragment to annexin A2 reveal the optimization of electrostatic and hydrogen bonding interactions with the protein and protein-bound calcium ions. In general, these free energy calculations reveal that the binding of heparin to protein surfaces is dominated by strong electrostatic interactions for longer fragments, with equally important contributions from van der Waals interactions and vibrational entropy changes, against a large unfavorable desolvation penalty due to the high charge density of these molecules.

Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein

The c-Fos–c-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.

Calculations of the free energy of interaction of the c-Fos−c-Jun coiled coil: Effects of the solvation model and the inclusion of polarization effects

The leucine zipper region of activator protein-1 (AP-1) comprises the c-Jun and c-Fos proteins and constitutes a well-known coiled coil protein−protein interaction motif. We have used molecular dynamics (MD) simulations in conjunction with the molecular mechanics/Poisson−Boltzmann generalized-Born surface area [MM/PB(GB)SA] methods to predict the free energy of interaction of these proteins. In particular, the influence of the choice of solvation model, protein force field, and water potential on the stability and dynamic properties of the c-Fos−c-Jun complex were investigated. Use of the AMBER polarizable force field ff02 in combination with the polarizable POL3 water potential was found to result in increased stability of the c-Fos−c-Jun complex. MM/PB(GB)SA calculations revealed that MD simulations using the POL3 water potential give the lowest predicted free energies of interaction compared to other nonpolarizable water potentials. In addition, the calculated absolute free energy of binding was predicted to be closest to the experimental value using the MM/GBSA method with independent MD simulation trajectories using the POL3 water potential and the polarizable ff02 force field, while all other binding affinities were overestimated.

Legume pastures can reduce N2O emissions intensity in subtropical cereal cropping systems

Alternative sources of N are required to bolster subtropical cereal production without increasing N2O emissions from these agro-ecosystems. The reintroduction of legumes in cereal cropping systems is a possible strategy to reduce synthetic N inputs but elevated N2O losses have sometimes been observed after the incorporation of legume residues. However, the magnitude of these losses is highly dependent on local conditions and very little data are available for subtropical regions. The aim of this study was to assess whether, under subtropical conditions, the N mineralised from legume residues can substantially decrease the synthetic N input required by the subsequent cereal crop and reduce overall N2O emissions during the cereal cropping phase. Using a fully automated measuring system, N2O emissions were monitored in a cereal crop (sorghum) following a legume pasture and compared to the same crop in rotation with a grass pasture. Each crop rotation included a nil and a fertilised treatment to assess the N availability of the residues. The incorporation of legumes provided enough readily available N to effectively support crop development but the low labile C left by these residues is likely to have limited denitrification and therefore N2O emissions. As a result, N2O emissions intensities (kg N2O-N yield−1 ha−1) were considerably lower in the legume histories than in the grass. Overall, these findings indicate that the C supplied by the crop residue can be more important than the soil NO3− content in stimulating denitrification and that introducing a legume pasture in a subtropical cereal cropping system is a sustainable practice from both environmental and agronomic perspectives.

Stereochemical studies on cyclic peptides: Detailed energy minimization studies on hydrogen bonded all-trans cyclic pentapeptide backbones

Conformational studies have been carried out on hydrogenbonded all-trans cyclic pentapeptide backbone. Application of a combination of grid search and energy minimization on this system has resulted in obtaining 23 minimum energy conformations, which are characterized by unique patterns of hydrogen bonding comprising of β- and γ-turns. A study of the minimum energy conformationsvis-a-vis non-planar deviation of the peptide units reveals that non-planarity is an inherent feature in many cases. A study on conformational clustering of minimum energy conformations shows that the minimum energy conformations fall into 6 distinct conformational families. Preliminary comparison with available X-ray structures of cyclic pentapeptide indicates that only some of the minimum energy conformations have formed crystal structures. The set of minimum energy conformations worked out in the present study can form a consolidated database of prototypes for hydrogen bonded backbone and be useful for modelling cyclic pentapeptides both synthetic and bioactive in nature.

Low carbon fuels and commodity chemicals from waste gases – systematic approach to understand energy metabolism in a model acetogen

Gas fermentation using acetogenic bacteria offers a promising route for the sustainable production of low carbon fuels and commodity chemicals from abundant, inexpensive C1 feedstocks including industrial waste gases, syngas, reformed methane or methanol. Clostridium autoethanogenum is a model gas fermenting acetogen that produces fuel ethanol and 2,3-butanediol, a precursor for nylon and rubber. Acetogens have already been used in large scale industrial fermentations, they are ubiquitous and known to play a prominent role in the global carbon cycle. Still, they are considered to live on the thermodynamic edge of life and potential energy constraints when growing on C1 gases pose a major challange for the commercial production of fuels and chemicals. We have developed a systematic platform to investigate acetogenic energy metabolism, exemplified here by experiments contrasting heterotrophic and autotrophic metabolism. The platform is built from complete omics technologies, augmented with genetic tools and complemented by a manually curated genome-scale mathematical model. Together the tools enable the design and development of new, energy efficient pathways and strains for the production of chemicals and advanced fuels via C1 gas fermentation. As a proof-of-platform, we investigated heterotrophic growth on fructose versus autotrophic growth on gas that demonstrate the role of the Rnf complex and Nfn complex in maintaining growth using the Wood–Ljungdahl pathway. Pyruvate carboxykinase was found to control the rate-limiting step of gluconeogenesis and a new specialized glyceraldehyde-3-phosphate dehydrogenase was identified that potentially enhances anabolic capacity by reducing the amount of ATP consumed by gluconeogenesis. The results have been confirmed by the construction of mutant strains.

Intensity Oscillation in the Corona as Observed during the Total Solar Eclipse of 29 March 2006

We obtained the images of the eastern part of the solar corona in the Fe xiv 530.3 nm (green) and Fe x 637.4 nm (red) coronal emission lines during the total solar eclipse of 29 March 2006 at Manavgat, Antalya, Turkey. The images were obtained using a 35 cm Meade telescope equipped with a Peltier-cooled 2k x 2k CCD and 0.3 nm pass-band interference filters at the rates of 2.95 s (exposure times of 100 ms) and 2.0 s (exposure times of 300 ms) in the Fe xiv and Fe x emission lines,respectively. The analysis of the data indicates intensity variations at some locations with period of strongest power around 27 s for the green line and 20 s for the red line. These results confirm earlier findings of variations in the continuum intensity with periods in the range of 5 to 56 s by Singh et al. (Solar Phys. 170, 235, 1997). The wavelet analysis has been used to identify significant intensity oscillations at all pixels within our field of view. Significant oscillations with high probability estimates were detected for some locations only. These locations seem to follow the boundary of an active region and in the neighborhood, rather than within the loops themselves. These intensity oscillations may be caused by fast magneto-sonic waves in the solar corona and partly account for heating of the plasma in the corona.