Heterogeneous ribonucleoprotein m is a splicing regulatory protein that can enhance or silence splicing of alternatively spliced exons

Splicing of fibroblast growth factor receptor 2 (FGFR2) alternative exons IIIb and IIIc is regulated by the auxiliary RNA cis-element ISE/ISS-3 that promotes splicing of exon IIIb and silencing of exon IIIc. Using RNA affinity chromatography, we have identified heterogeneous nuclear ribonucleoprotein M (hnRNP M) as a splicing regulatory factor that binds to ISE/ISS-3 in a sequence-specific manner. Overexpression of hnRNP M promoted exon IIIc skipping in a cell line that normally includes it, and association of hnRNP M with ISE/ISS-3 was shown to contribute to this splicing regulatory function. Thus hnRNP M, along with other members of the hnRNP family of RNA-binding proteins, plays a combinatorial role in regulation of FGFR2 alternative splicing. We also determined that hnRNP M can affect the splicing of several other alternatively spliced exons. This activity of hnRNP M included the ability not only to induce exon skipping but also to promote exon inclusion. This is the first report demonstrating a role for this abundant hnRNP family member in alternative splicing in mammals and suggests that this protein may broadly contribute to the fidelity of splice site recognition and alternative splicing regulation.     

The role of Stn1p in Saccharomyces cerevisiae telomere capping can be separated from its interaction with Cdc13p

The function of telomeres is twofold: to facilitate complete chromosome replication and to protect chromosome ends against fusions and illegitimate recombination. In the budding yeast Saccharomyces cerevisiae, interactions among Cdc13p, Stn1p, and Ten1p are thought to be critical for promoting these processes. We have identified distinct Stn1p domains that mediate interaction with either Ten1p or Cdc13p, allowing analysis of whether the interaction between Cdc13p and Stn1p is indeed essential for telomere capping or length regulation. Consistent with the model that the Stn1p essential function is to promote telomere end protection through Cdc13p, stn1 alleles that truncate the C-terminal 123 residues fail to interact with Cdc13p and do not support viability when expressed at endogenous levels. Remarkably, more extensive deletions that remove an additional 185 C-terminal residues from Stn1p now allow cell growth at endogenous expression levels. The viability of these stn1-t alleles improves with increasing expression level, indicating that increased stn1-t dosage can compensate for the loss of Cdc13p-Stn1p interaction. However, telomere length is misregulated at all expression levels. Thus, an amino-terminal region of Stn1p is sufficient for its essential function, while a central region of Stn1p either negatively regulates the STN1 essential function or destabilizes the mutant Stn1 protein.     

Autumn migration of Montagu’s harriers Circus pygargus tracked by satellite telemetry

Although there is a general understanding of Montagu’s harriers migration routes and wintering areas, detailed information on the species’ migration is still lacking. However, improvements in satellite tracking technology in recent years, have enabled the study of medium-sized species by means of satellite telemetry. In 2006, ten adult Montagu’s harriers were fitted with satellite transmitters in northeastern Spain and tracked during their autumn migration to their wintering grounds in sub-Saharan Africa. The migration took between 10 and 30 days, and the end point was determined using breakpoint regressions. Whereas some birds had stopovers of more than a week, others stayed at the same site for only 1 or 2 days at the most. The tagged birds ultimately established at wintering grounds located along the border of Mauritania with Mali and Senegal, a distance of nearly 3000 km from the breeding sites. These sites are situated within a small range of latitudes (14° and 17°N), although distributed over a wider range of longitudes (−15°E and −4°E), with some birds occupying sites more than 1000 km apart. The distance covered in 1 day during the migration ranged between 93 and 219 km, with peaks of traveling speed of up to 65 km/h. Harriers were recorded traveling only during daytime, covering the longest distances in the late afternoon, suggesting that they are daytime migrants. Most of the distance was covered between 1500 and 2000 hours, and no traveling was recorded between 2000 and 0500 hours. During migration, harriers flew close to the ground (40–100 m on average). Improved knowledge of the harriers’ exact wintering sites may provide insights on the problems Montagu’s harriers face during the winter, highlighting the need to take into account what happens in both the breeding and wintering grounds to implement successful conservation measures.     

Understanding the structural requirements of 4-anilidopiperidine analogues for biological activities at mu and delta opioid receptors

New 4-anilidopiperidine analogues in which the phenethyl group of fentanyl was replaced by several aromatic ring-contained amino acids (or acids) were synthesized to study the biological effect of the substituents on mu and delta opioid receptor interactions. These analogues showed broad (47 nM-76 microM) but selective (up to 17-fold) binding affinities at the mu opioid receptor over the delta opioid receptor, as predicted from the message-address concept.     

ADP_EM: fast exhaustive multi-resolution docking for high-throughput coverage

MOTIVATION: Efficient fitting tools are needed to take advantage of a fast growth of atomic models of protein domains from crystallography or comparative modeling, and low-resolution density maps of larger molecular assemblies. Here, we report a novel fitting algorithm for the exhaustive and fast overlay of partial high-resolution models into a low-resolution density map. The method incorporates a fast rotational search based on spherical harmonics (SH) combined with a simple translational scanning. RESULTS: This novel combination makes it possible to accurately dock atomic structures into low-resolution electron-density maps in times ranging from seconds to a few minutes. The high-efficiency achieved with simulated and experimental test cases preserves the exhaustiveness needed in these heterogeneous-resolution merging tools. The results demonstrate its efficiency, robustness and high-throughput coverage. AVAILABILITY: http://sbg.cib.csic.es/Software/ADP_EM. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.     

An experimental test of the symbiosis specificity between the ciliate Paramecium bursaria and strains of the unicellular green alga Chlorella

The ciliate Paramecium bursaria living in mutualistic relationship with the unicellular green alga Chlorella is known to be easily infected by various potential symbionts/parasites such as bacteria, yeasts and other algae. Permanent symbiosis, however, seems to be restricted to Chlorella taxa. To test the specificity of this association, we designed infection experiments with two aposymbiotic P. bursaria strains and Chlorella symbionts isolated from four Paramecium strains, seven other ciliate hosts and two Hydra strains, as well as three free-living Chlorella species. Paramecium bursaria established stable symbioses with all tested Chlorella symbionts of ciliates, but never with symbiotic Chlorella of Hydra viridissima or with free-living Chlorella. Furthermore, we tested the infection specificity of P. bursaria with a 1:1:1 mixture of three compatible Chlorella strains, including the native symbiont, and then identified the strain of the newly established symbiosis by sequencing the internal transcribed spacer region 1 of the 18S rRNA gene. The results indicated that P. bursaria established symbiosis with its native symbiont. We conclude that despite clear preferences for their native Chlorella, the host-symbiont relationship in P. bursaria is flexible.     

Seasonal habitat use of three predatory fishes in a freshwater ecosystem

Hydrobiologia - To understand the spatiotemporal overlap in the habitat use of sympatric predators, we studied longitudinal activity and reservoir section and depth use of pike (Esox lucius),...     

Bird movements at rotor heights measured continuously with vertical radar at a Dutch offshore wind farm

Assessing the impacts of avian collisions with wind turbines requires reliable estimates of avian flight intensities and altitudes, to enable accurate estimation of collision rates, avoidance rates and related effects on populations. At sea, obtaining such estimates visually is limited not only by weather conditions but, more importantly, because a high proportion of birds fly at night and at heights above the range of visual observation. We used vertical radar with automated bird‐tracking software to overcome these limitations and obtain data on the magnitude, timing and altitude of local bird movements and seasonal migration measured continuously at a Dutch offshore wind farm. An estimated 1.6 million radar echoes representing individual birds or flocks were recorded crossing the wind farm annually at altitudes between 25 and 115 m (the rotor‐swept zone). The majority of these fluxes consisted of gull species during the day and migrating passerines at night. We demonstrate daily, monthly and seasonal patterns in fluxes at rotor heights and the influence of wind direction on flight intensity. These data are among the first to show the magnitude and variation of low‐altitude flight activity across the North Sea, and are valuable for assessing the consequences of developments such as offshore wind farms for birds.     

Genomic landscape of rat strain and substrain variation

Background

Since the completion of the rat reference genome in 2003, whole-genome sequencing data from more than 40 rat strains have become available. These data represent the broad range of strains that are used in rat research including commonly used substrains. Currently, this wealth of information cannot be used to its full extent, because the variety of different variant calling algorithms employed by different groups impairs comparison between strains. In addition, all rat whole genome sequencing studies to date used an outdated reference genome for analysis (RGSC3.4 released in 2004).

Results

Here we present a comprehensive, multi-sample and uniformly called set of genetic variants in 40 rat strains, including 19 substrains. We reanalyzed all primary data using a recent version of the rat reference assembly (RGSC5.0 released in 2012) and identified over 12 million genomic variants (SNVs, indels and structural variants) among the 40 strains. 28,318 SNVs are specific to individual substrains, which may be explained by introgression from other unsequenced strains and ongoing evolution by genetic drift. Substrain SNVs may have a larger predicted functional impact compared to older shared SNVs.

Conclusions

In summary we present a comprehensive catalog of uniformly analyzed genetic variants among 40 widely used rat inbred strains based on the RGSC5.0 assembly. This represents a valuable resource, which will facilitate rat functional genomic research. In line with previous observations, our genome-wide analyses do not show evidence for contribution of multiple ancestral founder rat subspecies to the currently used rat inbred strains, as is the case for mouse. In addition, we find that the degree of substrain variation is highly variable between strains, which is of importance for the correct interpretation of experimental data from different labs.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1594-1) contains supplementary material, which is available to authorized users.     

CCR2 receptor antagonists: optimization of biaryl sulfonamides to increase activity in whole blood

A series of biarylsulfonamides was identified as hCCR2 receptor antagonist but suffered from high plasma protein binding resulting in a >100 fold shift in activity in a functional GTPγS assay run in tandem in the presence and absence of human serum albumin. Introduction of an aryl amide with ethylenediamine linker led to compounds with reduced shifts and improved activity in whole blood.