Contrasting patterns of niche partitioning between two anaerobic terminal oxidizers of organic matter

Understanding the ecological principles underlying the structure and function of microbial communities remains an important goal for microbial ecology. We examined two biogeochemically important taxa, the sulfate-reducing bacterial genus, Desulfobulbus, and the methanogenic archaeal genus, Methanosaeta, to compare and contrast niche partitioning by these two taxa that are ecologically linked as anaerobic terminal oxidizers of organic material. An observational approach utilizing functional gene pyrosequencing was combined with a community-based reciprocal incubation experiment and characterization of a novel Desulfobulbus isolate. To analyze the pyrosequencing data, we constructed a data analysis pipeline, which we validated with several control data sets. For both taxa, particular genotypes were clearly associated with certain portions of an estuarine gradient, consistent with habitat or niche partitioning. Methanosaeta genotypes were generally divided between those found almost exclusively in the marine habitat (∼30% of operational taxonomic units (OTUs)), and those which were ubiquitously distributed across all or most of the estuary (∼70% of OTUs). In contrast to this relatively monotonic distribution, for Desulfobulbus, there were many more genotypes, and their distributions represented a wide range of inferred niche widths from specialist genotypes found only at a single site, to ubiquitous or generalist genotypes found in all 10 sites examined along the full estuarine gradient. Incubation experiments clearly showed that, for both taxa, communities from opposite ends of the estuary did not come to resemble one another, regardless of the chemical environment. Growth of a Desulfobulbus isolated into pure culture indicated that the potential niche of this organism is significantly larger than the realized niche. We concluded that niche partitioning can be an important force structuring microbial populations, with biotic and abiotic components having very different effects depending on the physiology and ecology of each taxon.     

Activation of invariant NKT cells ameliorates experimental ocular autoimmunity by a mechanism involving innate IFN-gamma production and dampening of the adaptive Th1 and Th17 responses

Invariant NKT cells (iNKT cells) have been reported to play a role not only in innate immunity but also to regulate several models of autoimmunity. Furthermore, iNKT cells are necessary for the generation of the prototypic eye-related immune regulatory phenomenon, anterior chamber associated immune deviation (ACAID). In this study, we explore the role of iNKT cells in regulation of autoimmunity to retina, using a model of experimental autoimmune uveitis (EAU) in mice immunized with a uveitogenic regimen of the retinal Ag, interphotoreceptor retinoid-binding protein. Natural strain-specific variation in iNKT number or induced genetic deficiencies in iNKT did not alter baseline susceptibility to EAU. However, iNKT function seemed to correlate with susceptibility and its pharmacological enhancement in vivo by treatment with iNKT TCR ligands at the time of uveitogenic immunization reproducibly ameliorated disease scores. Use of different iNKT TCR ligands revealed dependence on the elicited cytokine profile. Surprisingly, superior protection against EAU was achieved with alpha-C-GalCer, which induces a strong IFN-gamma but only a weak IL-4 production by iNKT cells, in contrast to the ligands alpha-GalCer (both IFN-gamma and IL-4) and OCH (primarily IL-4). The protective effect of alpha-C-GalCer was associated with a reduction of adaptive Ag-specific IFN-gamma and IL-17 production and was negated by systemic neutralization of IFN-gamma. These data suggest that pharmacological activation of iNKT cells protects from EAU at least in part by a mechanism involving innate production of IFN-gamma and a consequent dampening of the Th1 as well as the Th17 effector responses.     

TLC1 RNA nucleo-cytoplasmic trafficking links telomerase biogenesis to its recruitment to telomeres

The yeast telomerase holoenzyme, which adds telomeric repeats at the chromosome ends, is composed of the TLC1 RNA and the associated proteins Est1, Est2 and Est3. To study the biogenesis of telomerase in endogenous conditions, we performed fluorescent in situ hybridization on the native TLC1 RNA. We found that the telomerase RNA colocalizes with telomeres in G1- to S-phase cells. Strains lacking any one of the Est proteins accumulate TLC1 RNA in their cytoplasm, indicating that a critical stage of telomerase biogenesis could take place outside of the nucleus. We were able to demonstrate that endogenous TLC1 RNA shuttles between the nucleus and the cytoplasm, in association with the Crm1p exportin and the nuclear importins Mtr10p-Kap122p. Furthermore, nuclear retention of the TLC1 RNA is impaired in the absence of yKu70p, Tel1p or the MRX complex, which recruit telomerase to telomeres. Altogether, our results reveal that the nucleo-cytoplasmic trafficking of the TLC1 RNA is an important step in telomere homeostasis, and link telomerase biogenesis to its recruitment to telomeres.     

Identification and characterization of FUS/TLS as a new target of ATM

ATM (ataxia-telangiectasia mutated), ATR (ATM- and Rad3-related) and DNA-PK (DNA-dependent protein kinase), important regulators of genome stability, belong to the PIKK (phosphoinositide 3-kinase-like kinase) family of protein kinases. In the present study, DNA-affinity chromatography was used to identify DNA-binding proteins phosphorylated by these kinases. This resulted in the identification of FUS (fused in sarcoma)/TLS (translocated in liposarcoma) as an in vitro target of the PIKKs. FUS is a member of the Ewing's sarcoma family of proteins that appears to play a role in regulating genome stability, since mice lacking FUS show chromosomal instability and defects in meiosis. The residues in FUS that are phosphorylated in vitro and in vivo were identified, and phospho-specific antibodies were generated to demonstrate that FUS becomes phosphorylated at Ser(42) in vivo, primarily in response to agents that cause DSBs (double-strand breaks). DSB-induced FUS phosphorylation in vivo at Ser(42) requires ATM and not DNA-PK. Although Ser(42) is retained in the oncogenic FUS-CHOP [C/EBP (CCAAT/enhancer-binding protein)-homologous protein 10] fusion generated by a t(12;16)(q13;p11) chromosomal translocation, Ser(42) in FUS-CHOP is not phosphorylated after DNA damage. These results identify FUS as a new target of the ATM-signalling pathway and strengthen the notion that FUS regulates genome stability.     

clonality V.0.4: a randomization-based program to test for heterozygosity-genet size relationships in clonal organisms

clonality V.0.4 is a program for testing heterozygosity-genet size relationships in clonal organisms using a randomization procedure. The software has been developed under the Borland Delphi developing environment and a Windows-executable version is freely downloadable from http://gemi.mpl.ird.fr/SiteSGASS/Prugnolle/ClonalityPage.html. The program compares the observed F(IS) of the population with the F(IS) expected if genets (multilocus genotypes present in multiple copies within the population) were chosen randomly from the set of different multilocus genotypes. The randomization procedure is performed with the same number of genets and the same number of repetitions per genet as what is observed in the original data set.     

The Italian verb–noun anthroponymic compounds at the Syntax / morphology interface

This paper offers an analysis of Italian anthroponymic verb–noun compounds. It is argued that the first element of these compounds historically is an imperative (2nd sg) form. Such a view not only accounts adequately for the evolutionary process at work in the original naming process; it also rightly accounts for the actual morphological make-up of these compounds. It is argued as well that anthroponymic compounds involving imperatives provided for a structural model which is still traceable in the morphological make-up of non-anthroponymic compounds, even though a reanalysis process has led to the reinterpretation of the verbal element of V–N compounds as a bare stem. Crucially, such a reanalysis will be said to have been favoured by the morphological unmarkedness of imperatives: as zero inflected stems, imperatives may serve as a base for paradigmatic restructuration. Italian Verb–noun compounds will be shown to offer an illustration of this basicness of the imperative, following a pattern of word formation which is available in other languages.