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.     

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.     

Phylogeny and species delimitation of North European Lumbricillus (Clitellata,Enchytraeidae)

The enchytraeid genus Lumbricillus comprises about 80 described species of clitellate worms, which are up to a few centimetres long, and they mostly inhabit the littoral zone of non‐tropical marine and brackish waters world‐wide. The phylogeny of this genus is poorly studied, but previous work has suggested that Lumbricillus is a non‐monophyletic group. In this study, species boundaries and the phylogeny of this genus is re‐assessed using more than 300 DNA‐barcoded specimens (using COI mtDNA), part of which was also sequenced for two additional mitochondrial and four nuclear molecular markers. Statistical and coalescent based applications were used for the delimitation of a total of 24 species, of which 20 were identified as belonging to 17 described morphospecies; one morphospecies was found to be a complex of four delimited species, and another four delimited species could not be matched with any described species. Furthermore, gene trees, concatenation and multispecies coalescent based species trees were estimated using Bayesian inference. The estimated phylogenies confirm a non‐monophyletic Lumbricillus as L. semifuscus is clearly excluded from the genus. Furthermore, the placement of a monophyletic clade consisting of L. arenarius, L. dubius, and an unidentified species varies between analyses; they are either found as the sister‐group to the genus Grania or as sister‐group to the remaining Lumbricillus, where the latter relationship is supported by the multispecies coalescent, which we consider as the most reliable method.