Molecular eco-systems biology: towards an understanding of community function

Systems-biology approaches, which are driven by genome sequencing and high-throughput functional genomics data, are revolutionizing single-cell-organism biology. With the advent of various high-throughput techniques that aim to characterize complete microbial ecosystems (metagenomics, meta-transcriptomics and meta-metabolomics), we propose that the time is ripe to consider molecular systems biology at the ecosystem level (eco-systems biology). Here, we discuss the necessary data types that are required to unite molecular microbiology and ecology to develop an understanding of community function and discuss the potential shortcomings of these approaches

The impact of air pollutant and methane emission controls on tropospheric ozone and radiative forcing: CTM calculations for the period 1990-2030

To explore the relationship between tropospheric ozone and radiative forcing with changing emissions, we compiled two sets of global scenarios for the emissions of the ozone precursors methane (CH₄), carbon monoxide (CO), non-methane volatile organic compounds (NMVOC) and nitrogen oxides (NO_x) up to the year 2030 and implemented them in two global Chemistry Transport Models. The 'Current Legislation' (CLE) scenario reflects the current perspectives of individual countries on future economic development and takes the anticipated effects of presently decided emission control legislation in the individual countries into account. In addition, we developed a 'Maximum technically Feasible Reduction' (MFR) scenario that outlines the scope for emission reductions offered by full implementation of the presently available emission control technologies, while maintaining the projected levels of anthropogenic activities. Whereas the resulting projections of methane emissions lie within the range suggested by other greenhouse gas projections, the recent pollution control legislation of many Asian countries, requiring introduction of catalytic converters for vehicles, leads to significantly lower growth in emissions of the air pollutants NO_x, NMVOC and CO than was suggested by the widely used and more pessimistic IPCC (Intergovernmental Panel on Climate Change) SRES (Special Report on Emission Scenarios) scenarios (Nakicenovic et al., 2000), which made Business-as-Usual assumptions regarding emission control technology. With the TM3 and STOCHEM models we performed several long-term integrations (1990-2030) to assess global, hemispheric and regional changes in CH₄, CO, hydroxyl radicals, ozone and the radiative climate forcings resulting from these two emission scenarios. Both models reproduce broadly the observed trends in CO, and CH₄ concentrations from 1990 to 2002. <P style='line-height: 20px;'> For the 'current legislation' case, both models indicate an increase of the annual average ozone levels in the Northern Hemisphere by 5ppbv, and up to 15ppbv over the Indian sub-continent, comparing the 2020s (2020-2030) with the 1990s (1990-2000). The corresponding higher ozone and methane burdens in the atmosphere increase radiative forcing by approximately 0.2 Wm^-2. Full application of today's emissions control technologies, however, would bring down ozone below the levels experienced in the 1990s and would reduce the radiative forcing of ozone and methane to approximately -0.1 Wm^-2. This can be compared to the 0.14-0.47 Wm^-2 increase of methane and ozone radiative forcings associated with the SRES scenarios. While methane reductions lead to lower ozone burdens and to less radiative forcing, further reductions of the air pollutants NO_x and NMVOC result in lower ozone, but at the same time increase the lifetime of methane. Control of methane emissions appears an efficient option to reduce tropospheric ozone as well as radiative forcing

Protein function space: viewing the limits or limited by our view?

Given that the number of protein functions on earth is finite, the rapid expansion of biological knowledge and the concomitant exponential increase in the number of protein sequences should, at some point, enable the estimation of the limits of protein function space. The functional coverage of protein sequences can be investigated using computational methods, especially given the massive amount of data being generated by large-scale environmental sequencing (metagenomics). In completely sequenced genomes, the fraction of proteins to which at least some functional features can be assigned has recently risen to as much as approximately 85%. Although this fraction is more uncertain in metagenomics surveys, because of environmental complexities and differences in analysis protocols, our global knowledge of protein functions still appears to be considerable. However, when we consider protein families, continued sequencing seems to yield an ever-increasing number of novel families. Until we reconcile these two views, the limits of protein space will remain obscured

Influence of future air pollution mitigation strategies on total aerosol radiative forcing

We apply different aerosol and aerosol precursor emission scenarios reflecting possible future control strategies for air pollution in the ECHAM5-HAM model, and simulate the resulting effect on the Earth's radiation budget. We use two opposing future mitigation strategies for the year 2030: one in which emission reduction legislation decided in countries throughout the world are effectively implemented (current legislation; CLE 2030) and one in which all technical options for emission reductions are being implemented independent of their cost (maximum feasible reduction; MFR 2030). We consider the direct, semi-direct and indirect radiative effects of aerosols. The total anthropogenic aerosol radiative forcing defined as the difference in the top-of-the-atmosphere radiation between 2000 and pre-industrial times amounts to -2.00 W/m2. In the future this negative global annual mean aerosol radiative forcing will only slightly change (+0.02 W/m2) under the "current legislation" scenario. Regionally, the effects are much larger: e.g. over Eastern Europe radiative forcing would increase by +1.50 W/m2 because of successful aerosol reduction policies, whereas over South Asia it would decrease by -1.10 W/m2 because of further growth of emissions. A "maximum feasible reduction" of aerosols and their precursors would lead to an increase of the global annual mean aerosol radiative forcing by +1.13 W/m2. Hence, in the latter case, the present day negative anthropogenic aerosol forcing could be more than halved by 2030 because of aerosol reduction policies and climate change thereafter will be to a larger extent be controlled by greenhouse gas emissions. We combined these two opposing future mitigation strategies for a number of experiments focusing on different sectors and regions. In addition, we performed sensitivity studies to estimate the importance of future changes in oxidant concentrations and the importance of the aerosol microphysical coupling within the range of expected future changes. For changes in oxidant concentrations caused by future air pollution mitigation, we do not find a significant effect for the global annual mean radiative aerosol forcing. In the extreme case of only abating SO2 or carbonaceous emissions to a maximum feasible extent, we find deviations from additivity for the radiative forcing over anthropogenic source regions up to 10% compared to an experiment abating both at the same time

Imaging dielectric relaxation in nanostructured polymers by frequency modulation electrostatic force microscopy

We have developed a method for imaging the temperature-frequency dependence of the dynamics of nanostructured polymer films with spatial resolution. This method provides images with dielectric compositional contrast well decoupled from topography. Using frequency-modulation electrostatic-force-microscopy, we probe the local frequency-dependent (0.1–100 Hz) dielectric response through measurement of the amplitude and phase of the force gradient in response to an oscillating applied electric field. When the phase is imaged at fixed frequency, it reveals the spatial variation in dielectric losses, i.e., the spatial variation in molecular/dipolar dynamics, with 40 nm lateral resolution. This is demonstrated by using as a model system; a phase separated polystyrene/polyvinyl-acetate (PVAc) blend. We show that nanoscale dynamic domains of PVAc are clearly identifiable in phase images as those which light-up in a band of temperature, reflecting the variations in the molecular/dipolar dynamics approaching the glass transition temperature of PVAc

Physical aerosol properties and their relation to air mass origin at Monte Cimone (Italy) during the first MINATROC campaign

Aerosol physical properties were measured at the Monte Cimone Observatory (Italy) from 1 June till 6 July 2000. The measurement site is located in the transition zone between the continental boundary layer and the free troposphere (FT), at the border between the Mediterranean area and Central Europe, and is exposed to a variety of air masses. Sub-&mu;m number size distributions, aerosol hygroscopicity near 90% RH, refractory size distribution at 270&deg;C and equivalent black carbon mass were continuously measured. Number size distributions and hygroscopic properties indicate that the site is exposed to aged continental air masses, however during daytime it is also affected by upslope winds. The mixing of this transported polluted boundary layer air masses with relatively clean FT air leads to frequent nucleation events around local noon. <P style='line-height: 20px;'> Night-time size distributions, including fine and coarse fractions for each air mass episode, have been parameterized by a 3-modal lognormal distribution. Number and volume concentrations in the sub-&mu;m modes are strongly affected by the air mass origin, with highest levels in NW-European air masses, versus very clean, free tropospheric air coming from the N-European sector. During a brief but distinct dust episode, the coarse mode is clearly enhanced. <P style='line-height: 20px;'> The observed hygroscopic behavior of the aerosol is consistent with the chemical composition described by Putaud et al.&nbsp;(2004), but no closure between known chemical composition and measured hygroscopicity could be made because the hygroscopic properties of the water-soluble organic matter (WSOM) are not known. The data suggest that WSOM is slightly-to-moderately hygroscopic (hygroscopic growth factor GF at 90% relative humidity between 1.05 and 1.51), and that this property may well depend on the air mass origin and history. <P style='line-height: 20px;'> External mixing of aerosol particles is observed in all air masses through the occurrence of two hygroscopicity modes (average GF of 1.22 and 1.37, respectively). However, the presence of 'less' hygroscopic particles has mostly such a low occurrence rate that the average growth factor distribution for each air mass sector actually appears as a single mode. This is not the case for the dust episode, where the external mixing between less hygroscopic and more hygroscopic particles is very prominent, and indicating clearly the occurrence of a dust accumulation mode, extending down to 50 nm particles, along with an anthropogenic pollution mode. <P style='line-height: 20px;'> The presented physical measurements finally allow us to provide a partitioning of the sub-&mu;m aerosol in four non-overlapping fractions (soluble/volatile, non-soluble/volatile, refractory/non-black carbon, black carbon) which can be associated with separate groups of chemical compounds determined with chemical-analytical techniques (ions, non-water soluble organic matter, dust, elemental carbon). All air masses except the free-tropospheric N-European and Dust episodes show a similar composition within the uncertainty of the data (53%, 37%, 5% and 5% respectively for the four defined fractions). Compared to these sectors, the dust episode shows a clearly enhanced refractory-non-BC fraction (17%), attributed to dust in the accumulation mode, whereas for the very clean N-EUR sector, the total refractory fraction is 25%, of which 13% non-BC and 12% BC

Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases

While metagenomic sequencing has become the tool of preference to study host-associated microbial communities, downstream analyses and clinical interpretation of microbiome data remains challenging due to the sparsity and compositionality of sequence matrices. Here, we evaluate both computational and experimental approaches proposed to mitigate the impact of these outstanding issues. Generating fecal metagenomes drawn from simulated microbial communities, we benchmark the performance of thirteen commonly used analytical approaches in terms of diversity estimation, identification of taxon-taxon associations, and assessment of taxon-metadata correlations under the challenge of varying microbial ecosystem loads. We find quantitative approaches including experimental procedures to incorporate microbial load variation in downstream analyses to perform significantly better than computational strategies designed to mitigate data compositionality and sparsity, not only improving the identification of true positive associations, but also reducing false positive detection. When analyzing simulated scenarios of low microbial load dysbiosis as observed in inflammatory pathologies, quantitative methods correcting for sampling depth show higher precision compared to uncorrected scaling. Overall, our findings advocate for a wider adoption of experimental quantitative approaches in microbiome research, yet also suggest preferred transformations for specific cases where determination of microbial load of samples is not feasible

The human gut microbiome: from association to modulation

Our understanding of the human gut microbiome continues to evolve at a rapid pace, but practical application of thisknowledge is still in its infancy. This review discusses the type of studies that will be essential for translating microbiome research into targeted modulations with dedicated benefits for the human host

Back-translation for discovering distant protein homologies

Frameshift mutations in protein-coding DNA sequences produce a drastic change in the resulting protein sequence, which prevents classic protein alignment methods from revealing the proteins' common origin. Moreover, when a large number of substitutions are additionally involved in the divergence, the homology detection becomes difficult even at the DNA level. To cope with this situation, we propose a novel method to infer distant homology relations of two proteins, that accounts for frameshift and point mutations that may have affected the coding sequences. We design a dynamic programming alignment algorithm over memory-efficient graph representations of the complete set of putative DNA sequences of each protein, with the goal of determining the two putative DNA sequences which have the best scoring alignment under a powerful scoring system designed to reflect the most probable evolutionary process. This allows us to uncover evolutionary information that is not captured by traditional alignment methods, which is confirmed by biologically significant examples.Comment: The 9th International Workshop in Algorithms in Bioinformatics (WABI), Philadelphia : \'Etats-Unis d'Am\'erique (2009

Local mapping of dissipative vortex motion

We explore, with unprecedented single vortex resolution, the dissipation and motion of vortices in a superconducting ribbon under the influence of an external alternating magnetic field. This is achieved by combing the phase sensitive character of ac-susceptibility, allowing to distinguish between the inductive-and dissipative response, with the local power of scanning Hall probe microscopy. Whereas the induced reversible screening currents contribute only inductively, the vortices do leave a fingerprint in the out-of-phase component. The observed large phase-lag demonstrates the dissipation of vortices at timescales comparable to the period of the driving force (i.e. 13 ms). These results indicate the presence of slow microscopic loss mechanisms mediated by thermally activated hopping transport of vortices between metastable states.Comment: 5 pages, 2 figure