Soft topographic map for clustering and classification of bacteria

In this work a new method for clustering and building a topographic representation of a bacteria taxonomy is presented. The method is based on the analysis of stable parts of the genome, the so-called “housekeeping genes”. The proposed method generates topographic maps of the bacteria taxonomy, where relations among different type strains can be visually inspected and verified. Two well known DNA alignement algorithms are applied to the genomic sequences. Topographic maps are optimized to represent the similarity among the sequences according to their evolutionary distances. The experimental analysis is carried out on 147 type strains of the Gammaprotebacteria class by means of the 16S rRNA housekeeping gene. Complete sequences of the gene have been retrieved from the NCBI public database. In the experimental tests the maps show clusters of homologous type strains and present some singular cases potentially due to incorrect classification or erroneous annotations in the database.

Hydrological cycle in the Danube basin in present-day and XXII century simulations by IPCCAR4 global climate models

We present an intercomparison and verification analysis of 20 GCMs (Global Circulation Models) included in the 4th IPCC assessment report regarding their representation of the hydrological cycle on the Danube river basin for 1961–2000 and for the 2161–2200 SRESA1B scenario runs. The basin-scale properties of the hydrological cycle are computed by spatially integrating the precipitation, evaporation, and runoff fields using the Voronoi-Thiessen tessellation formalism. The span of the model- simulated mean annual water balances is of the same order of magnitude of the observed Danube discharge of the Delta; the true value is within the range simulated by the models. Some land components seem to have deficiencies since there are cases of violation of water conservation when annual means are considered. The overall performance and the degree of agreement of the GCMs are comparable to those of the RCMs (Regional Climate Models) analyzed in a previous work, in spite of the much higher resolution and common nesting of the RCMs. The reanalyses are shown to feature several inconsistencies and cannot be used as a verification benchmark for the hydrological cycle in the Danubian region. In the scenario runs, for basically all models the water balance decreases, whereas its interannual variability increases. Changes in the strength of the hydrological cycle are not consistent among models: it is confirmed that capturing the impact of climate change on the hydrological cycle is not an easy task over land areas. Moreover, in several cases we find that qualitatively different behaviors emerge among the models: the ensemble mean does not represent any sort of average model, and often it falls between the models’ clusters.

Structure and magnetic properties of an unprecedented syn-antiμ-nitrito-1κO:2κO′ bridged Mn(iii)-salen complex and its isoelectronic and isostructural formate analogue

The preparation, crystal structures and magnetic properties of two new isoelectronic and isomorphous formate-and nitrite-bridged 1D chains of Mn(III)-salen complexes, [Mn(salen)(HCOO)](n) (1) and [Mn(salen)(NO2)](n) (2), where salen is the dianion of N,N'-bis(salicylidene)-1,2-diaminoethane, are presented. The structures show that the salen ligand coordinates to the four equatorial sites of the metal ion and the formate or nitrite ions coordinate to the axial positions to bridge the Mn(III)-salen units through a syn-anti mu-1 kappa O:2 kappa O' coordination mode. Such a bridging mode is unprecedented in Mn(III) for formate and in any transition metal ion for nitrite. Variable-temperature magnetic susceptibility measurements of complexes 1 and 2 indicate the presence of ferromagnetic exchange interactions with J values of 0.0607 cm(-1) (for 1) and 0.0883 cm(-1) (for 2). The ac measurements indicate negligible frequency dependence for 1 whereas compound 2 exhibits a decrease of chi(ac)' and a concomitant increase of chi(ac)'' on elevating frequency around 2 K. This finding is an indication of slow magnetization reversal characteristic of single-chain magnets or spin-glasses. The mu-nitrito-1 kappa O:2 kappa O' bridge seems to be a potentially superior magnetic coupler to the formate bridge for the construction of single-molecule/-chain magnets as its coupling constant is greater and the chi(ac)' and chi(ac)'' show frequency dependence.

A review of measurement-based assessments of the aerosol direct radiative effect and forcing

Aerosols affect the Earth's energy budget directly by scattering and absorbing radiation and indirectly by acting as cloud condensation nuclei and, thereby, affecting cloud properties. However, large uncertainties exist in current estimates of aerosol forcing because of incomplete knowledge concerning the distribution and the physical and chemical properties of aerosols as well as aerosol-cloud interactions. In recent years, a great deal of effort has gone into improving measurements and datasets. It is thus feasible to shift the estimates of aerosol forcing from largely model-based to increasingly measurement-based. Our goal is to assess current observational capabilities and identify uncertainties in the aerosol direct forcing through comparisons of different methods with independent sources of uncertainties. Here we assess the aerosol optical depth (τ), direct radiative effect (DRE) by natural and anthropogenic aerosols, and direct climate forcing (DCF) by anthropogenic aerosols, focusing on satellite and ground-based measurements supplemented by global chemical transport model (CTM) simulations. The multi-spectral MODIS measures global distributions of aerosol optical depth (τ) on a daily scale, with a high accuracy of ±0.03±0.05τ over ocean. The annual average τ is about 0.14 over global ocean, of which about 21%±7% is contributed by human activities, as estimated by MODIS fine-mode fraction. The multi-angle MISR derives an annual average AOD of 0.23 over global land with an uncertainty of ~20% or ±0.05. These high-accuracy aerosol products and broadband flux measurements from CERES make it feasible to obtain observational constraints for the aerosol direct effect, especially over global the ocean. A number of measurement-based approaches estimate the clear-sky DRE (on solar radiation) at the top-of-atmosphere (TOA) to be about -5.5±0.2 Wm-2 (median ± standard error from various methods) over the global ocean. Accounting for thin cirrus contamination of the satellite derived aerosol field will reduce the TOA DRE to -5.0 Wm-2. Because of a lack of measurements of aerosol absorption and difficulty in characterizing land surface reflection, estimates of DRE over land and at the ocean surface are currently realized through a combination of satellite retrievals, surface measurements, and model simulations, and are less constrained. Over the oceans the surface DRE is estimated to be -8.8±0.7 Wm-2. Over land, an integration of satellite retrievals and model simulations derives a DRE of -4.9±0.7 Wm-2 and -11.8±1.9 Wm-2 at the TOA and surface, respectively. CTM simulations derive a wide range of DRE estimates that on average are smaller than the measurement-based DRE by about 30-40%, even after accounting for thin cirrus and cloud contamination. A number of issues remain. Current estimates of the aerosol direct effect over land are poorly constrained. Uncertainties of DRE estimates are also larger on regional scales than on a global scale and large discrepancies exist between different approaches. The characterization of aerosol absorption and vertical distribution remains challenging. The aerosol direct effect in the thermal infrared range and in cloudy conditions remains relatively unexplored and quite uncertain, because of a lack of global systematic aerosol vertical profile measurements. A coordinated research strategy needs to be developed for integration and assimilation of satellite measurements into models to constrain model simulations. Enhanced measurement capabilities in the next few years and high-level scientific cooperation will further advance our knowledge.

Sources, sinks, and transatlantic transport of North African dust aerosol: a multimodel analysis and comparison with remote sensing data

This study evaluates model-simulated dust aerosols over North Africa and the North Atlantic from five global models that participated in the Aerosol Comparison between Observations and Models phase II model experiments. The model results are compared with satellite aerosol optical depth (AOD) data from Moderate Resolution Imaging Spectroradiometer (MODIS), Multiangle Imaging Spectroradiometer (MISR), and Sea-viewing Wide Field-of-view Sensor, dust optical depth (DOD) derived from MODIS and MISR, AOD and coarse-mode AOD (as a proxy of DOD) from ground-based Aerosol Robotic Network Sun photometer measurements, and dust vertical distributions/centroid height from Cloud Aerosol Lidar with Orthogonal Polarization and Atmospheric Infrared Sounder satellite AOD retrievals. We examine the following quantities of AOD and DOD: (1) the magnitudes over land and over ocean in our study domain, (2) the longitudinal gradient from the dust source region over North Africa to the western North Atlantic, (3) seasonal variations at different locations, and (4) the dust vertical profile shape and the AOD centroid height (altitude above or below which half of the AOD is located). The different satellite data show consistent features in most of these aspects; however, the models display large diversity in all of them, with significant differences among the models and between models and observations. By examining dust emission, removal, and mass extinction efficiency in the five models, we also find remarkable differences among the models that all contribute to the discrepancies of model-simulated dust amount and distribution. This study highlights the challenges in simulating the dust physical and optical processes, even in the best known dust environment, and stresses the need for observable quantities to constrain the model processes.