Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data

The Photo-Activatable Ribonucleoside-enhanced CrossLinking and ImmunoPrecipitation (PAR-CLIP) method was recently developed for global identification of RNAs interacting with proteins. The strength of this versatile method results from induction of specific T to C transitions at sites of interaction. However, current analytical tools do not distinguish between non-experimentally and experimentally induced transitions. Furthermore, geometric properties at potential binding sites are not taken into account. To surmount these shortcomings, we developed a two-step algorithm consisting of a non-parametric two-component mixture model and a wavelet-based peak calling procedure. Our algorithm can reduce the number of false positives up to 24% thereby identifying high confidence interaction sites. We successfully employed this approach in conjunction with a modified PAR-CLIP protocol to study the functional role of nuclear Moloney leukemia virus 10, a putative RNA helicase interacting with Argonaute2 and Polycomb. Our method, available as the R package wavClusteR, is generally applicable to any substitution-based inference problem in genomics.     

Metagenomic Analysis from the Interior of a Speleothem in Tjuv-Ante's Cave,Northern Sweden

Speleothems are secondary mineral deposits normally formed by water supersaturated with calcium carbonate percolating into underground caves, and are often associated with low-nutrient and mostly non-phototrophic conditions. Tjuv-Ante’s cave is a shallow-depth cave formed by the action of waves, with granite and dolerite as major components, and opal-A and calcite as part of the speleothems, making it a rare kind of cave. We generated two DNA shotgun sequencing metagenomic datasets from the interior of a speleothem from Tjuv-Ante’s cave representing areas of old and relatively recent speleothem formation. We used these datasets to perform i) an evaluation of the use of these speleothems as past biodiversity archives, ii) functional and taxonomic profiling of the speleothem’s different formation periods, and iii) taxonomic comparison of the metagenomic results to previous microscopic analyses from a nearby speleothem of the same cave. Our analyses confirm the abundance of Actinobacteria and fungi as previously reported by microscopic analyses on this cave, however we also discovered a larger biodiversity. Interestingly, we identified photosynthetic genes, as well as genes related to iron and sulphur metabolism, suggesting the presence of chemoautotrophs. Furthermore, we identified taxa and functions related to biomineralization. However, we could not confidently establish the use of this type of speleothems as biological paleoarchives due to the potential leaching from the outside of the cave and the DNA damage that we propose has been caused by the fungal chemical etching.     

Resistance to actinomycin D and to vincristine induced in a SEWA mouse tumor cell line with concomitant appearance of double minutes and a low molecular weight protein

By increasing stepwise the drug concentration of the medium, we have induced, in a cell line of the murine SEWA tumor, resistance to actinomycin D (AMD) and vincristine (VCR) 30-50 times above the normal. In both types of resistant cells, we have revealed, by two-dimensional gel electrophoresis, a protein (MW 21K , pI 5) not found in control cells. Large fractions of the resistant cells contained double minutes (DM). In AMD-resistant cells, correlation was demonstrated between number of DM and degree of resistance. Back in AMD-free medium, resistant cells lost both the DM and the 21K protein. Cross-resistance prevailed between AMD and VCR. Cells resistant to AMD and VCR showed erratic resistance to methotrexate (MTX), but no significant resistance existed in the reverse direction.     

Riochemical and physiological effects in farmed Baltic salmon fed lipids containing xenobiotics extracted from Baltic herring

During a 2-year experimental period female baltic salmon (Salmo salar) were fed pellets impregnated with oil extracted from Baltic herring (Clupea harengus). This extract contained lipid-soluble xenobiotics present in Baltic herring, which constitute a major part of the natural diet of Baltic salmon. The fish were examined at the time of ovulation in November each year. After 2 years of feeding, the load of polychlorinated dibenzo-paradioxins and furans in the exposed group was about twice that in the control group, but still low compared with concentrations in feral Baltic salmon. In spite of the relatively low exposure level, several vital biochemical functions were disturbed in the treated fish. Organic skeletal variables were affected indicating that the bone metabolism had been altered. Furthermore, the activities of enzymes involved in steroid biosynthesis were affected, which could lead to disturbances in reproductive functions. Splenocytes from exposed fish sampled in November 1990 showed a reduced mitogenic response, indicating that their immune system was suppressed. Feeding the salmon with pollutant-impregnated pellets also resulted in an induction of the hepatic ethoxyresorufin-O-deethylase (EROD) activity after only 6 weeks of exposure. Likewise, morphological abnormalities, i.e. hypertrophic hepatocytes and various stages of hepatic degeneration, were already apparent after 6 weeks of exposure. However, no EROD induction or morphological responses were recorded at the second and third sampling event, i.e. after one and 2 years of exposure, respectively. this could indicate that some physiological functions may adapt to a restricted xenobiotic load.     

Sphagnum divinum (sp. nov.) and S. medium Limpr. and their relationship to S. magellanicum Brid.

Sphagnum magellanicum has been viewed as being a predominantly circumpolar species in the northern hemisphere, but it occurs in the southern hemisphere and was originally described from the southern parts of Chile. It is an ecologically important species in mire ecosystems and has been extensively used as a model to study processes of growth, carbon sequestration and peat decomposition. Molecular and experimental studies have, however, revealed genetic structure within S. magellanicum, and morphological differences associated with these genetic groups. Here we describe Sphagnum divinum in Sphagnum subgenus Sphagnum (Sphagnaceae, Bryophyta) as a new species, based on molecular and morphological evidence. Sphagnum medium is reinstated as a distinct species and is epitypified. Consequently, a new species concept of S. magellanicum is presented including an epitypification. Important morphological characters to separate these three species in the field and under the microscope are presented. Ecology and distribution differ among the species; S. divinium has a wide habitat range including mire margin, forested peatlands and moist heaths, and a circumpolar distribution around the northern hemisphere. Sphagnum medium seems to be more restricted to ombrotrophic mire expanse habitats and shows an amphi-Atlantic distribution in the northern hemisphere. Sphagnum magellanicum has a very broad ecological niche in peatlands and is found in most mire habitats in Tierra del Fuego on the southern tip of South America.     

The impact of host genetic diversity on virus evolution and emergence

Accumulating evidence indicates that biodiversity has an important impact on parasite evolution and emergence. The vast majority of studies in this area have only considered the diversity of species within an environment as an overall measure of biodiversity, overlooking the role of genetic diversity within a particular host species. Although theoretical models propose that host genetic diversity in part shapes that of the infecting parasite population, and hence modulates the risk of parasite emergence, this effect has seldom been tested empirically. Using Rabies virus (RABV) as a model parasite, we provide evidence that greater host genetic diversity increases both parasite genetic diversity and the likelihood of a host being a donor in RABV cross‐species transmission events. We conclude that host genetic diversity may be an important determinant of parasite evolution and emergence.