Metagenomes of Red Sea Subpopulations Challenge the Use of Marker Genes and Morphology to Assess Trichodesmium Diversity

Trichodesmium are filamentous cyanobacteria of key interest due to their ability to fix carbon and nitrogen within an oligotrophic marine environment. Their blooms consist of a dynamic assemblage of subpopulations and colony morphologies that are hypothesized to occupy unique niches. Here, we assessed the poorly studied diversity of Trichodesmium in the Red Sea, based on metagenome-assembled genomes (MAGs) and hetR gene-based phylotyping. We assembled four non-redundant MAGs from morphologically distinct Trichodesmium colonies (tufts, dense and thin puffs). Trichodesmium thiebautii (puffs) and Trichodesmium erythraeum (tufts) were the dominant species within these morphotypes. While subspecies diversity is present for both T. thiebautii and T. erythraeum, a single T. thiebautii genotype comprised both thin and dense puff morphotypes, and we hypothesize that this phenotypic variation is likely attributed to gene regulation. Additionally, we found the rare non-diazotrophic clade IV and V genotypes, related to Trichodesmium nobis and Trichodesmium miru, respectively that likely occurred as single filaments. The hetR gene phylogeny further indicated that the genotype in clade IV could represent the species Trichodesmium contortum. Importantly, we show the presence of hetR paralogs in Trichodesmium, where two copies of the hetR gene were present within T. thiebautii genomes. This may lead to the overestimation of Trichodesmium diversity as one of the copies misidentified T. thiebautii as Trichodesmium aureum. Taken together, our results highlight the importance of re-assessing Trichodesmium taxonomy while showing the ability of genomics to capture the complex diversity and distribution of Trichodesmium populations

The proteasome cap RPT5/Rpt5p subunit prevents aggregation of unfolded ricin A chain

The plant cytotoxin ricin enters mammalian cells by receptor-mediated endocytosis, undergoing retrograde transport to the endoplasmic reticulum (ER) where its catalytic A chain (RTA) is reductively separated from the holotoxin to enter the cytosol and inactivate ribosomes. The currently accepted model is that the bulk of ER-dislocated RTA is degraded by proteasomes. We show here that the proteasome has a more complex role in ricin intoxication than previously recognised, that the previously reported increase in sensitivity of mammalian cells to ricin in the presence of proteasome inhibitors simply reflects toxicity of the inhibitors themselves, and that RTA is a very poor substrate for proteasomal degradation. Denatured RTA and casein compete for a binding site on the regulatory particle of the 26S proteasome, but their fates differ. Casein is degraded, but the mammalian 26S proteasome AAA-ATPase subunit RPT5 acts as a chaperone that prevents aggregation of denatured RTA and stimulates recovery of catalytic RTA activity in vitro. Furthermore, in vivo, the ATPase activity of Rpt5p is required for maximal toxicity of RTA dislocated from the Saccharomyces cerevisiae ER. Our results implicate RPT5/Rpt5p in the triage of substrates in which either activation (folding) or inactivation (degradation) pathways may be initiated

A factor model to analyze heterogeneity in gene expression

<p>Abstract</p> <p>Background</p> <p>Microarray technology allows the simultaneous analysis of thousands of genes within a single experiment. Significance analyses of transcriptomic data ignore the gene dependence structure. This leads to correlation among test statistics which affects a strong control of the false discovery proportion. A recent method called FAMT allows capturing the gene dependence into factors in order to improve high-dimensional multiple testing procedures. In the subsequent analyses aiming at a functional characterization of the differentially expressed genes, our study shows how these factors can be used both to identify the components of expression heterogeneity and to give more insight into the underlying biological processes.</p> <p>Results</p> <p>The use of factors to characterize simple patterns of heterogeneity is first demonstrated on illustrative gene expression data sets. An expression data set primarily generated to map QTL for fatness in chickens is then analyzed. Contrarily to the analysis based on the raw data, a relevant functional information about a QTL region is revealed by factor-adjustment of the gene expressions. Additionally, the interpretation of the independent factors regarding known information about both experimental design and genes shows that some factors may have different and complex origins.</p> <p>Conclusions</p> <p>As biological information and technological biases are identified in what was before simply considered as statistical noise, analyzing heterogeneity in gene expression yields a new point of view on transcriptomic data.</p

A precision measurement of direct CP violation in the decay of neutral kaons into two pions

The direct CP violation parameter Re(epsilon'/epsilon) has been measured from the decay rates of neutral kaons into two pions using the NA48 detector at the CERN SPS. The 2001 running period was devoted to collecting additional data under varied conditions compared to earlier years (1997-99). The new data yield the result: Re(epsilon'/epsilon) = (13.7 +/- 3.1) times 10^{-4}. Combining this result with that published from the 1997, 98 and 99 data, an overall value of Re(epsilon'/epsilon) = (14.7 +/- 2.2) times 10^{-4} is obtained from the NA48 experiment.Comment: 19 pages, 5 figures, to be published in Physics Letters

A Spitzer Space Telescope far-infrared spectral atlas of compact sources in the Magellanic Clouds. I. The Large Magellanic Cloud

[abridged] We present 52-93 micron spectra obtained with Spitzer in the MIPS-SED mode, of a representative sample of luminous compact far-IR sources in the LMC. These include carbon stars, OH/IR AGB stars, post-AGB objects and PNe, RCrB-type star HV2671, OH/IR red supergiants WOHG064 and IRAS05280-6910, B[e] stars IRAS04530-6916, R66 and R126, Wolf-Rayet star Brey3a, Luminous Blue Variable R71, supernova remnant N49, a large number of young stellar objects, compact HII regions and molecular cores, and a background galaxy (z~0.175). We use the spectra to constrain the presence and temperature of cold dust and the excitation conditions and shocks within the neutral and ionized gas, in the circumstellar environments and interfaces with the surrounding ISM. Evolved stars, including LBV R71, lack cold dust except in some cases where we argue that this is swept-up ISM. This leads to an estimate of the duration of the prolific dust-producing phase ("superwind") of several thousand years for both RSGs and massive AGB stars, with a similar fractional mass loss experienced despite the different masses. We tentatively detect line emission from neutral oxygen in the extreme RSG WOHG064, with implications for the wind driving. In N49, the shock between the supernova ejecta and ISM is revealed by its strong [OI] 63-micron emission and possibly water vapour; we estimate that 0.2 Msun of ISM dust was swept up. Some of the compact HII regions display pronounced [OIII] 88-micron emission. The efficiency of photo-electric heating in the interfaces of ionized gas and molecular clouds is estimated at 0.1-0.3%. We confirm earlier indications of a low nitrogen content in the LMC. Evidence for solid state emission features is found in both young and evolved object; some of the YSOs are found to contain crystalline water ice.Comment: Accepted for publication in The Astronomical Journal. This paper accompanies the Summer 2009 SAGE-Spec release of 48 MIPS-SED spectra, but uses improved spectrum extraction. (Fig. 2 reduced resolution because of arXiv limit.

Earliest rock fabric formed in the Solar System preserved in a chondrule rim

Rock fabrics – the preferred orientation of grains – provide a window into the history of rock formation, deformation and compaction. Chondritic meteorites are among the oldest materials in the Solar System1 and their fabrics should record a range of processes occurring in the nebula and in asteroids, but due to abundant fine-grained material these samples have largely resisted traditional in situ fabric analysis. Here we use high resolution electron backscatter diffraction to map the orientation of sub-micrometre grains in the Allende CV carbonaceous chondrite: the matrix material that is interstitial to the mm-sized spherical chondrules that give chondrites their name, and fine-grained rims which surround those chondrules. Although Allende matrix exhibits a bulk uniaxial fabric relating to a significant compressive event in the parent asteroid, we find that fine-grained rims preserve a spherically symmetric fabric centred on the chondrule. We define a method that quantitatively relates fabric intensity to net compression, and reconstruct an initial porosity for the rims of 70-80% - a value very close to model estimates for the earliest uncompacted aggregates2,3. We conclude that the chondrule rim textures formed in a nebula setting and may therefore be the first rock fabric to have formed in the Solar System

Gravitational Microlensing and the Galactic Halo

By means of extensive galactic modeling we study the implications of the more than eighty microlensing events that have now been observed for the composition of the dark halo of the Galaxy, as well as for other properties of the Galaxy. We take the Galaxy to be comprised of luminous and dark disk components, a bulge, and a dark halo consisting of both MACHOs and cold dark matter with each component being described by several observationally motivated parameters. We pare down an initial model space of millions of galactic models to viable models, those which are consistent with the observational data, including rotation curve, local projected mass density, and microlensing rates toward the LMC and bulge. On the basis of a conservative, minimal set of observational constraints an all-MACHO halo cannot yet be excluded, although in most viable models of the Galaxy the halo MACHO fraction is between 0\% and 30\%, consistent with expectations for a universe whose primary component is cold dark matter. An all-MACHO halo is required to be light, and when data on the local escape velocity and satellite-galaxy proper motions, which probe the extent of the dark halo, are taken into account, models which have a high MACHO mass fraction are ruled out. We also explore the possibility that there are no MACHOs in the halo. Finally, we point out several important tests that could definitively exclude an all-MACHO e.g., optical depth for microlensing which is less than $1.5\times 10^{-7}$ toward the LMC or greater than $3\times 10^{-6}$ toward the bulge.Comment: 19 pages, 13 multipart figures are available at ftp://astro.uchicago.edu/ftp/pub/astro/gyuk

Lineage Analysis of Circulating Trypanosoma cruzi Parasites and Their Association with Clinical Forms of Chagas Disease in Bolivia

Around 30–50% of Trypanosoma cruzi infections in Latin America cause chronic Chagas disease 10–30 years after the primary infection due to lack of effective treatment. The major clinical complications associated with chronic Chagas disease are cardiac myositis (leading to cardiac failure), and autonomous neuroplexus degeneration of the digestive tract that can cause megacolon or megaesophagus. Therefore, there are three major clinical forms of Chagas disease; cardiac, digestive and indeterminate (asymptomatic). The parasites, which can infect humans as well as other mammals, are transmitted by species of triatomines commonly found in the Americas. The parasite is divided in at least six discrete typing units: TcI, TcIIa–e. In humans, the TcI is mainly observed in Central America and northern parts of South America while the TcIIb/d/e is confined mainly to the southern cone of Latin America. We determined which DTU were prevalent in chronic patients in Bolivia, where the three clinical forms and several DTUs of the parasites are present, in order to determine whether there was a link between a particular parasite DTU and a particular clinical outcome. We found a vast majority of TcIId but its kDNA polymorphism showed no association with any of the clinical manifestations of chronic Chagas

On the origin and evolution of the material in 67P/Churyumov-Gerasimenko

International audiencePrimitive objects like comets hold important information on the material that formed our solar system. Several comets have been visited by spacecraft and many more have been observed through Earth- and space-based telescopes. Still our understanding remains limited. Molecular abundances in comets have been shown to be similar to interstellar ices and thus indicate that common processes and conditions were involved in their formation. The samples returned by the Stardust mission to comet Wild 2 showed that the bulk refractory material was processed by high temperatures in the vicinity of the early sun. The recent Rosetta mission acquired a wealth of new data on the composition of comet 67P/Churyumov-Gerasimenko (hereafter 67P/C-G) and complemented earlier observations of other comets. The isotopic, elemental, and molecular abundances of the volatile, semi-volatile, and refractory phases brought many new insights into the origin and processing of the incorporated material. The emerging picture after Rosetta is that at least part of the volatile material was formed before the solar system and that cometary nuclei agglomerated over a wide range of heliocentric distances, different from where they are found today. Deviations from bulk solar system abundances indicate that the material was not fully homogenized at the location of comet formation, despite the radial mixing implied by the Stardust results. Post-formation evolution of the material might play an important role, which further complicates the picture. This paper discusses these major findings of the Rosetta mission with respect to the origin of the material and puts them in the context of what we know from other comets and solar system objects