Star formation efficiency in galaxy clusters

Context. The luminous material in clusters of galaxies exists in two forms: the visible galaxies and the X-ray emitting intra-cluster medium. The hot intra-cluster gas is the major observed baryonic component of clusters, about six times more massive than the stellar component. The mass contained within visible galaxies is approximately 3% of the dynamical mass. Aims. Our aim was to analyze both baryonic components, combining X-ray and optical data of a sample of five galaxy clusters (Abell 496, 1689, 2050, 2631 and 2667), within the redshift range 0.03 < z < 0.3. We determined the contribution of stars in galaxies and the intra-cluster medium to the total baryon budget. Methods. We used public XMM-Newton data to determine the gas mass and to obtain the X-ray substructures. Using the optical counterparts from SDSS or CFHT we determined the stellar contribution. Results. We examine the relative contribution of galaxies, intra-cluster light and intra-cluster medium to baryon budget in clusters through the stellar-to-gas mass ratio, estimated with recent data. We find that the stellar-to-gas mass ratio within r(500) (the radius within which the mean cluster density exceeds the critical density by a factor of 500), is anti-correlated with the ICM temperature, which range from 24% to 6% while the temperature ranges from 4.0 to 8.3 keV. This indicates that less massive cold clusters are more prolific star forming environments than massive hot clusters.

A binary engine fuelling HD 87643's complex circumstellar environment Determined using AMBER/VLTI imaging

Context. The star HD 87643, exhibiting the ""B[e] phenomenon"", has one of the most extreme infrared excesses for this object class. It harbours a large amount of both hot and cold dust, and is surrounded by an extended reflection nebula. Aims. One of our major goals was to investigate the presence of a companion in HD87643. In addition, the presence of close dusty material was tested through a combination of multi-wavelength high spatial resolution observations. Methods. We observed HD 87643 with high spatial resolution techniques, using the near-IR AMBER/VLTI interferometer with baselines ranging from 60 m to 130 m and the mid-IR MIDI/VLTI interferometer with baselines ranging from 25 m to 65 m. These observations are complemented by NACO/VLT adaptive-optics-corrected images in the K and L-bands, and ESO-2.2m optical Wide-Field Imager large-scale images in the B, V and R-bands. Results. We report the direct detection of a companion to HD 87643 by means of image synthesis using the AMBER/VLTI instrument. The presence of the companion is confirmed by the MIDI and NACO data, although with a lower confidence. The companion is separated by similar to 34 mas with a roughly north-south orientation. The period must be large (several tens of years) and hence the orbital parameters are not determined yet. Binarity with high eccentricity might be the key to interpreting the extreme characteristics of this system, namely a dusty circumstellar envelope around the primary, a compact dust nebulosity around the binary system and a complex extended nebula suggesting past violent ejections.

The merging cluster Abell 1758 revisited: multi-wavelength observations and numerical simulations

Context. Cluster properties can be more distinctly studied in pairs of clusters, where we expect the effects of interactions to be strong. Aims. We here discuss the properties of the double cluster Abell 1758 at a redshift z similar to 0.279. These clusters show strong evidence for merging. Methods. We analyse the optical properties of the North and South cluster of Abell 1758 based on deep imaging obtained with the Canada-France-Hawaii Telescope (CFHT) archive Megaprime/Megacam camera in the g' and r' bands, covering a total region of about 1.05 x 1.16 deg(2), or 16.1 x 17.6 Mpc(2). Our X-ray analysis is based on archive XMM-Newton images. Numerical simulations were performed using an N-body algorithm to treat the dark-matter component, a semi-analytical galaxy-formation model for the evolution of the galaxies and a grid-based hydrodynamic code with a parts per million (PPM) scheme for the dynamics of the intra-cluster medium. We computed galaxy luminosity functions (GLFs) and 2D temperature and metallicity maps of the X-ray gas, which we then compared to the results of our numerical simulations. Results. The GLFs of Abell 1758 North are well fit by Schechter functions in the g' and r' bands, but with a small excess of bright galaxies, particularly in the r' band; their faint-end slopes are similar in both bands. In contrast, the GLFs of Abell 1758 South are not well fit by Schechter functions: excesses of bright galaxies are seen in both bands; the faint-end of the GLF is not very well defined in g'. The GLF computed from our numerical simulations assuming a halo mass-luminosity relation agrees with those derived from the observations. From the X-ray analysis, the most striking features are structures in the metal distribution. We found two elongated regions of high metallicity in Abell 1758 North with two peaks towards the centre. In contrast, Abell 1758 South shows a deficit of metals in its central regions. Comparing observational results to those derived from numerical simulations, we could mimic the most prominent features present in the metallicity map and propose an explanation for the dynamical history of the cluster. We found in particular that in the metal-rich elongated regions of the North cluster, winds had been more efficient than ram-pressure stripping in transporting metal-enriched gas to the outskirts. Conclusions. We confirm the merging structure of the North and South clusters, both at optical and X-ray wavelengths.

An overview of the Amazonian Aerosol Characterization Experiment 2008 (AMAZE-08)

The Amazon Basin provides an excellent environment for studying the sources, transformations, and properties of natural aerosol particles and the resulting links between biological processes and climate. With this framework in mind, the Amazonian Aerosol Characterization Experiment (AMAZE-08), carried out from 7 February to 14 March 2008 during the wet season in the central Amazon Basin, sought to understand the formation, transformations, and cloud-forming properties of fine-and coarse-mode biogenic aerosol particles, especially as related to their effects on cloud activation and regional climate. Special foci included (1) the production mechanisms of secondary organic components at a pristine continental site, including the factors regulating their temporal variability, and (2) predicting and understanding the cloud-forming properties of biogenic particles at such a site. In this overview paper, the field site and the instrumentation employed during the campaign are introduced. Observations and findings are reported, including the large-scale context for the campaign, especially as provided by satellite observations. New findings presented include: (i) a particle number-diameter distribution from 10 nm to 10 mu m that is representative of the pristine tropical rain forest and recommended for model use; (ii) the absence of substantial quantities of primary biological particles in the submicron mode as evidenced by mass spectral characterization; (iii) the large-scale production of secondary organic material; (iv) insights into the chemical and physical properties of the particles as revealed by thermodenuder-induced changes in the particle number-diameter distributions and mass spectra; and (v) comparisons of ground-based predictions and satellite-based observations of hydrometeor phase in clouds. A main finding of AMAZE-08 is the dominance of secondary organic material as particle components. The results presented here provide mechanistic insight and quantitative parameters that can serve to increase the accuracy of models of the formation, transformations, and cloud-forming properties of biogenic natural aerosol particles, especially as related to their effects on cloud activation and regional climate.

Polar organic marker compounds in atmospheric aerosols during the LBA-SMOCC 2002 biomass burning experiment in Rondonia, Brazil: sources and source processes, time series, diel variations and size distributions

Measurements of polar organic marker compounds were performed on aerosols that were collected at a pasture site in the Amazon basin (Rondonia, Brazil) using a high-volume dichotomous sampler (HVDS) and a Micro-Orifice Uniform Deposit Impactor (MOUDI) within the framework of the 2002 LBA-SMOCC (Large-Scale Biosphere Atmosphere Experiment in Amazonia - Smoke Aerosols, Clouds, Rainfall, and Climate: Aerosols From Biomass Burning Perturb Global and Regional Climate) campaign. The campaign spanned the late dry season (biomass burning), a transition period, and the onset of the wet season (clean conditions). In the present study a more detailed discussion is presented compared to previous reports on the behavior of selected polar marker compounds, including levoglucosan, malic acid, isoprene secondary organic aerosol (SOA) tracers and tracers for fungal spores. The tracer data are discussed taking into account new insights that recently became available into their stability and/or aerosol formation processes. During all three periods, levoglucosan was the most dominant identified organic species in the PM(2.5) size fraction of the HVDS samples. In the dry period levoglucosan reached concentrations of up to 7.5 mu g m(-3) and exhibited diel variations with a nighttime prevalence. It was closely associated with the PM mass in the size-segregated samples and was mainly present in the fine mode, except during the wet period where it peaked in the coarse mode. Isoprene SOA tracers showed an average concentration of 250 ng m(-3) during the dry period versus 157 ng m(-3) during the transition period and 52 ng m(-3) during the wet period. Malic acid and the 2-methyltetrols exhibited a different size distribution pattern, which is consistent with different aerosol formation processes (i.e., gas-to-particle partitioning in the case of malic acid and heterogeneous formation from gas-phase precursors in the case of the 2-methyltetrols). The 2-methyltetrols were mainly associated with the fine mode during all periods, while malic acid was prevalent in the fine mode only during the dry and transition periods, and dominant in the coarse mode during the wet period. The sum of the fungal spore tracers arabitol, mannitol, and erythritol in the PM(2.5) fraction of the HVDS samples during the dry, transition, and wet periods was, on average, 54 ng m(-3), 34 ng m(-3), and 27 ng m(-3), respectively, and revealed minor day/night variation. The mass size distributions of arabitol and mannitol during all periods showed similar patterns and an association with the coarse mode, consistent with their primary origin. The results show that even under the heavy smoke conditions of the dry period a natural background with contributions from bioaerosols and isoprene SOA can be revealed. The enhancement in isoprene SOA in the dry season is mainly attributed to an increased acidity of the aerosols, increased NO(x) concentrations and a decreased wet deposition.

Evaluation of the carbon content of aerosols from the burning of biomass in the Brazilian Amazon using thermal, optical and thermal-optical analysis methods

Aerosol samples were collected at a pasture site in the Amazon Basin as part of the project LBA-SMOCC-2002 (Large-Scale Biosphere-Atmosphere Experiment in Amazonia - Smoke Aerosols, Clouds, Rainfall and Climate: Aerosols from Biomass Burning Perturb Global and Regional Climate). Sampling was conducted during the late dry season, when the aerosol composition was dominated by biomass burning emissions, especially in the submicron fraction. A 13-stage Dekati low-pressure impactor (DLPI) was used to collect particles with nominal aerodynamic diameters (D(p)) ranging from 0.03 to 0.10 mu m. Gravimetric analyses of the DLPI substrates and filters were performed to obtain aerosol mass concentrations. The concentrations of total, apparent elemental, and organic carbon (TC, EC(a), and OC) were determined using thermal and thermal-optical analysis (TOA) methods. A light transmission method (LTM) was used to determine the concentration of equivalent black carbon (BC(e)) or the absorbing fraction at 880 nm for the size-resolved samples. During the dry period, due to the pervasive presence of fires in the region upwind of the sampling site, concentrations of fine aerosols (D(p) < 2.5 mu m: average 59.8 mu g m(-3)) were higher than coarse aerosols (D(p) > 2.5 mu m: 4.1 mu g m(-3)). Carbonaceous matter, estimated as the sum of the particulate organic matter (i.e., OC x 1.8) plus BC(e), comprised more than 90% to the total aerosol mass. Concentrations of EC(a) (estimated by thermal analysis with a correction for charring) and BC(e) (estimated by LTM) averaged 5.2 +/- 1.3 and 3.1 +/- 0.8 mu g m(-3), respectively. The determination of EC was improved by extracting water-soluble organic material from the samples, which reduced the average light absorption Angstrom exponent of particles in the size range of 0.1 to 1.0 mu m from >2.0 to approximately 1.2. The size-resolved BC(e) measured by the LTM showed a clear maximum between 0.4 and 0.6 mu m in diameter. The concentrations of OC and BC(e) varied diurnally during the dry period, and this variation is related to diurnal changes in boundary layer thickness and in fire frequency.

Signals for new spin-1 resonances in electroweak gauge boson pair production at the LHC

The mechanism of electroweak symmetry breaking ( EWSB) will be directly scrutinized soon at the CERN Large Hadron Collider. We analyze the LHC potential to look for new vector bosons associated with the EWSB sector, presenting a possible model independent approach to search for these new spin-1 resonances. We show that the analyses of the processes pp -> l(+)l(1-)E(T), l +/- jjE(T), l(1 +/-)l(+)l(-)E(T), l(+/-)jjE(T), and l(+)l(-) jj (with l, l' = e or mu and j = jet) have a large reach at the LHC and can lead to the discovery or exclusion of many EWSB scenarios such as Higgsless models.

Searching supersymmetry at the LHCb with displaced vertices

Supersymmetric theories with bilinear R-parity violation can give rise to the observed neutrino masses and mixings. One important feature of such models is that the lightest supersymmetric particle might have a sufficiently large lifetime to produce detached vertices. Working in the framework of supergravity models, we analyze the potential of the LHCb experiment to search for supersymmetric models exhibiting bilinear R-parity violation. We show that the LHCb experiment can probe a large fraction of the m(0)circle times m(1/2), being able to explore gluino masses up to 1.3 TeV. The LHCb discover potential for these kinds of models is similar to the ATLAS and CMS ones in the low luminosity phase of operation of the LHC.

Inference of gene regulatory networks from time series by Tsallis entropy

Background: The inference of gene regulatory networks (GRNs) from large-scale expression profiles is one of the most challenging problems of Systems Biology nowadays. Many techniques and models have been proposed for this task. However, it is not generally possible to recover the original topology with great accuracy, mainly due to the short time series data in face of the high complexity of the networks and the intrinsic noise of the expression measurements. In order to improve the accuracy of GRNs inference methods based on entropy (mutual information), a new criterion function is here proposed. Results: In this paper we introduce the use of generalized entropy proposed by Tsallis, for the inference of GRNs from time series expression profiles. The inference process is based on a feature selection approach and the conditional entropy is applied as criterion function. In order to assess the proposed methodology, the algorithm is applied to recover the network topology from temporal expressions generated by an artificial gene network (AGN) model as well as from the DREAM challenge. The adopted AGN is based on theoretical models of complex networks and its gene transference function is obtained from random drawing on the set of possible Boolean functions, thus creating its dynamics. On the other hand, DREAM time series data presents variation of network size and its topologies are based on real networks. The dynamics are generated by continuous differential equations with noise and perturbation. By adopting both data sources, it is possible to estimate the average quality of the inference with respect to different network topologies, transfer functions and network sizes. Conclusions: A remarkable improvement of accuracy was observed in the experimental results by reducing the number of false connections in the inferred topology by the non-Shannon entropy. The obtained best free parameter of the Tsallis entropy was on average in the range 2.5 <= q <= 3.5 (hence, subextensive entropy), which opens new perspectives for GRNs inference methods based on information theory and for investigation of the nonextensivity of such networks. The inference algorithm and criterion function proposed here were implemented and included in the DimReduction software, which is freely available at http://sourceforge.net/projects/dimreduction and http://code.google.com/p/dimreduction/.

GPIomics: global analysis of glycosylphosphatidylinositol-anchored molecules of Trypanosoma cruzi

Glycosylphosphatidylinositol (GPI) anchoring is a common, relevant posttranslational modification of eukaryotic surface proteins. Here, we developed a fast, simple, and highly sensitive (high attomole-low femtomole range) method that uses liquid chromatography-tandem mass spectrometry (LC-MS(n)) for the first large-scale analysis of GPI-anchored molecules (i.e., the GPIome) of a eukaryote, Trypanosoma cruzi, the etiologic agent of Chagas disease. Our genome-wise prediction analysis revealed that approximately 12% of T. cruzi genes possibly encode GPI-anchored proteins. By analyzing the GPIome of T. cruzi insect-dwelling epimastigote stage using LC-MS(n), we identified 90 GPI species, of which 79 were novel. Moreover, we determined that mucins coded by the T. cruzi small mucin-like gene (TcSMUG S) family are the major GPI-anchored proteins expressed on the epimastigote cell surface. TcSMUG S mucin mature sequences are short (56-85 amino acids) and highly O-glycosylated, and contain few proteolytic sites, therefore, less likely susceptible to proteases of the midgut of the insect vector. We propose that our approach could be used for the high throughput GPIomic analysis of other lower and higher eukaryotes. Molecular Systems Biology 7 April 2009; doi:10.1038/msb.2009.13

Debris flow affecting the Cubatauo Oil Refinery, Brazil

On February 6, 1994, a large debris flow developed because of intense rains in a 800-m-high mountain range called Serra do Cubatao, the local name for the Serra do Mar, located along the coast of the state of Sao Paulo, Brazil. It affected the Presidente Bernardes Refinery, owned by Petrobras, in Cubatao. The damages amounted to about US $40 million because of the muck cleaning, repairs, and 3-week interruption of the operations. This prompted Petrobras to conduct studies, carried out by the authors, to develop protection works, which were done at a cost of approximately US $12 million. The paper describes the studies conducted on debris flow mechanics. A new criteria to define rainfall intensities that trigger debris flows is presented, as well as a correlation of slipped area with soil porosity and rain intensity. Also presented are (a) an actual grain size distribution of a deposited material, determined by laboratory and a large-scale field test, and (b) the size distribution of large boulders along the river bed. Based on theory, empirical experience and back-analysis of the events, the main parameters as the front velocity, the peak discharge and the volume of the transported sediments were determined in a rational basis for the design of the protection works. Finally, the paper describes the set of the protection works built, emphasizing their concept and function. They also included some low-cost innovative works.

Recombinant rabies virus glycoprotein synthesis in bioreactor by transfected Drosophila melanogaster S2 cells carrying a constitutive or an inducible promoter

S2 cell populations (S2AcRVGP2K and S2MtRVGP-Hy) were selected after transfection of gene expression vectors carrying the cDNA encoding the rabies virus glycoprotein (RVGP) gene under the control of the constitutive (actin) or inductive (metallothionein) promoters. These cell populations were cultivated in a 1 L bioreactor mimicking a large scale bioprocess. Cell cultures were carried out at 90 rpm and monitored/controlled for temperature (28 degrees C) and dissolved oxygen (10 or 50% air saturation). Cell growth attained similar to 1.5-3 x 10(7) cells/mL after 3-4 clays of cultivation. The constitutive synthesis of RVGP in S2AcRVGP2K cells led to values of 0.76 mu g/10(7) cells at day 4 of culture. The RVGP synthesis in S2MtRVGP-Hy cell fraction increased upon CuSO(4) induction attaining specific productivities of 1.5-2 mu g/10(7) cells at clays 4-5. RVGP values in supernatant as a result of cell lysis were always very low (<0.2 mu g/mL) indicating good integrity of cells in culture. Overall the RVGP productivity was of 1.5-3 mg/L. Our data showed an important influence of dissolved oxygen on RVGP synthesis allowing a higher and sustained productivity by S2MtRVGP-Hy cells when cultivated with a DO of 10% air saturation. The RVGP productivity in bioreactors shown here mirrors those previously observed for T-flasks and shaker bottles and allow the preparation of the large RVGP quantities required for studies of structure and function. (C) 2010 Elsevier B.V. All rights reserved.

Repeated fed-batch cultivation of Arthrospira (Spirulina) platensis using urea as nitrogen source

Arthospira (Spirulina) platensis (Nordstedt) Gomont was autotrophically cultivated for biomass production in repeated fed-batch process using urea as nitrogen source, with the aim of making large-scale production easier, increasing cell productivity and then reducing the production costs. It was investigated the influence or the ratio of renewed volume to total volume (R), the Urea feeding time (t(f)) and the number of successive repealed fed-batch cycles on the maximum cell concentration (X(m)), cell productivity (P(x)), nitrogen-to-cell conversion yield (Y(x/n)), maximum specific growth rate (mu(m)) and protein content of, dry biomass. The experimental results demonstrated chat R=0.80 and t(f) = 6d were the best cultivation conditions, being able to simultaneously ensure, throughout the three fed-batch cycles, the highest average values of three of the five responses (X(m) = 2101 +/- 113 mg L(-1), P(x) = 219 +/- 13 mg L(-1) d(-1) and Y(x/n) = 10.3 +/- 0.8,g g(-1)). (C) 2008 Elsevier B.V. All rights reserved.

New transposons to generate GFP protein fusions in Candida albicans

Transposon elements are important tools for gene function analysis, for example they can be used to easily create genome-wide collections of insertion mutants. Transposons may also carry sequences coding for an epitope or fluorescent marker useful for protein expression and localization analysis. We have developed three new Tn5-based transposons that incorporate a GFP (green fluorescent protein) coding sequence to generate fusion proteins in the important fungal pathogen Candida albicans. Each transposon also contains the URA3 and Kan(R) genes for yeast and bacterial selection, respectively. After in vitro transposition, the insertional allele is transferred to the chromosomal locus by homologous recombination. Transposons Tn5-CaGFP and Tn5-CaGFP-URA3:FLIP can generate C-terminal truncated GFP fusions. A URA3 flipper recycling cassette was incorporated into the transposon Th5-CaGFP-UFRA3:FLIP. After the induction of Flip recombinase to excise the marker, the heterozygous strain is transformed again in order to obtain a GFP-tagged homozygous strains. In the Tn5-CaGFP-FL transposon the markers are flanked by a rare-cutting enzyme. After in vitro transposition into a plasmid-borne target gene, the markers are eliminated by restriction digestion and religation, resulting in a construct coding for full-length GFP-fusion proteins. This transposon can generate plasmid libraries of GFP insertions in proteins where N- or C-terminal tagging may alter localization. We tested our transposon system by mutagenizing the essential septin CDC3 gene. The results indicate that the Cdc3 C-terminal extension is important for correct septin filament assembly. The transposons described here provide a new system to obtain global gene expression and protein localization data in C. albicans. (c) 2008 Elsevier B.V. All rights reserved.

Gene Expression Profiles Stratified according to Type 1 Diabetes Mellitus Susceptibility Regions

The MHC region (6p21) aggregates the major genes that contribute to susceptibility to type 1 diabetes (T1D). Three additional relevant susceptibility regions mapped on chromosomes 1p13 (PTPN22), 2q33 (CTLA-4), and 11p15 (insulin) have also been described by linkage studies. To evaluate the contribution of these susceptibility regions and the chromosomes that house these regions, we performed a large-scale differential gene expression on lymphomononuclear cells of recently diagnosed T1D patients, pinpointing relevant modulated genes clustered in these regions and their respective chromosomes. A total of 4608 cDNAs from the IMAGE library were spotted onto glass slides using robotic technology. Statistical analysis was carried out using the SAM program, and data regarding gene location and biological function were obtained at the SOURCE, NCBI, and FATIGO programs. Three induced genes were observed spanning around the MHC region (6p21-6p23), and seven modulated genes (5 repressed and 2 repressed) were seen spanning around the 6q21-24 region. Additional modulated genes were observed in and around the 1p13, 2q33, and 11p15 regions. Overall, modulated genes in these regions were primarily associated with cellular metabolism, transcription factors and signaling transduction. The differential gene expression characterization may identify new genes potentially involved with diabetes pathogenesis.