YY1 controls Igκ repertoire and B‐cell development,and localizes with condensin on the Igκ locus

Conditional knock‐out (KO) of Polycomb Group (PcG) protein YY1 results in pro‐B cell arrest and reduced immunoglobulin locus contraction needed for distal variable gene rearrangement. The mechanisms that control these crucial functions are unknown. We deleted the 25 amino‐acid YY1 REPO domain necessary for YY1 PcG function, and used this mutant (YY1ΔREPO), to transduce bone marrow from YY1 conditional KO mice. While wild‐type YY1 rescued B‐cell development, YY1ΔREPO failed to rescue the B‐cell lineage yielding reduced numbers of B lineage cells. Although the IgH rearrangement pattern was normal, there was a selective impact at the Igκ locus that showed a dramatic skewing of the expressed Igκ repertoire. We found that the REPO domain interacts with proteins from the condensin and cohesin complexes, and that YY1, EZH2 and condensin proteins co‐localize at numerous sites across the Ig kappa locus. Knock‐down of a condensin subunit protein or YY1 reduced rearrangement of Igκ Vκ genes suggesting a direct role for YY1‐condensin complexes in Igκ locus structure and rearrangement.     

Sero‐taxonomy of skeletal macromolecules in living Terebratulid brachiopods

Antibodies prepared against macromolecules isolated from the shells of three living brachiopod genera have proved to be of considerable taxonomic significance, in that the pattern of cross‐reactivity of all three antisera consistently points to a new interpretation for the evolution of the largest extant brachiopod order, the Terebratulida. This new molecular evidence actually complements rather than contradicts the existing morphology‐based taxonomy, since detailed systematic investigation of the taxa in question has already demonstrated subtle but significant morphological differences in the major taxonomic characters which appear to reflect this new interpretation.

As fragments of skeletal macromolecules, including antigenic determinants, are known to survive for many millions of years within the protected micro‐environments provided by enclosing biominerals, these results suggest that such molecular fossils could well provide important insights on at least the high‐level taxonomic relationships of fossil organisms.     

Diversity of movements by individual anadromous coastal cutthroat trout Oncorhynchus clarkii clarkii

Wild, downstream‐migrating cutthroat trout, Oncorhynchus clarkii clarkii, smolts and adults were captured at a weir in Big Beef Creek, Hood Canal, Washington, surgically implanted with acoustic tags and tracked to identify spring and summer movements using stationary receivers in order to test the assumption that the species moves little while in marine waters. Overall, 93–96% migrated from the stream into the east side of the long narrow fjord, where they dispersed north and south along the shoreline. Most O. c. clarkii were detected nearshore within 10 km of the release site, with declining detection rates to 77 km. Over one‐third (36%) crossed c. 2–4 km of deep water to the other side but only one O. c. clarkii left the Hood Canal basin. Movements and behaviour patterns did not differ between smolts and adults but cluster analysis revealed two modes of distribution, here categorized as residents and migrants. Within these categories of overall distribution, a range of finer‐scale behaviour patterns was observed, including sedentary individuals, daily moving between proximate sites and more continuous long‐distance travel. Diel movement patterns varied markedly among individuals but overall activity increased near dawn, peaked around mid‐day and declined but continued at night. These patterns contrast with sympatric and closely related steelhead trout, Oncorhynchus mykiss, providing new insights into the diversity of salmonid behaviour.     

Matrix Fixed Charge Density Modulates Exudate Concentration during Cartilage Compression

Electrolyte filtration arises due to the presence of fixed charges in cartilage extracellular matrix glycosaminoglycans (GAGs). Commonly assumed negligible, it can be important for design and interpretation of streaming potential measurements and modeling assumptions. To quantify the scale of this phenomenon, chloride ion concentration in exudate of compressed cartilage was measured by Mohr’s titration and explant GAG content was colorimetrically assayed. Pilot studies indicated that an appropriate strain rate for experiments was 8 × 10⁻³ s⁻¹ to eliminate concerns of exudate evaporation and explant damage (at low and high strain rates, respectively). Exudate chloride concentration of explants equilibrated in 1× PBS was significantly (p < 0.05) lower than the bath chloride concentration at strains of 37.5, 50, and 62.5%, with clear dependence on strain magnitude. Exudate chloride concentration was also significantly lower than that of the bath when 50% strain was applied after equilibration in 0.5, 1, and 2× PBS, with a trend for an increase in this relative difference with decreasing bath concentration (p = 0.065 between 0.5 and 2× PBS). Decreasing exudate chloride concentration correlated negatively with increasing postcompression GAG concentration. No difference between exudate chloride concentration and bath chloride concentration was ever observed for compression of uncharged agarose gel controls. Findings show that exudate from compressed cartilage is dilute relative to the bath due to the presence of matrix fixed charges, and this difference can generate diffusion potentials external to the explant, which may affect streaming potential measurements particularly under conditions of low strain rates and high strains.     

Nutrient ratios, differential retention, and the effect on nutrient limitation in a deep oligotrophic lake

Nutrient ratios have been related to nutrient limitation of algal growth in lakes. Retention of nutrients in lakes, by sedimentation and by denitrification, reduces the nutrient concentrations in the water column, thereby enhancing nutrient limitation. Differential retention of nitrogen and phosphorus alters their ratios in lakes and thereby contributes to determine whether nitrogen or phosphorus limits algal growth. We examined the relationships between differential nutrient retention, nutrient ratios, and nutrient limitation in Lake Brunner, a deep oligotrophic lake. The observed retention of nitrogen (20%) and phosphorus (47%) agreed with predictions by empirical equations from literature. As a result of differential retention with a much larger proportion of phosphorus retained than that of nitrogen, the nitrogen:phosphorus ratio was higher in the lake (69) than in the inflows (46). While the mean ratio in the inflows suggested no or only moderate phosphorus limitation, the lake appeared to be severely phosphorus limited. Combining empirical equations from literature that predict nitrogen and phosphorus retention suggests that the nitrogen:phosphorus ratio is enhanced by greater retention of phosphorus compared to nitrogen only in deep lakes with relatively short residence times, such as Lake Brunner. In contrast, in most lakes differential retention is expected to result in lower nitrogen:phosphorus ratios.     

Evidence for Geomagnetic Imprinting as a Homing Mechanism in Pacific Salmon

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Highlights? Sockeye salmon use geomagnetic imprinting as a homing mechanism ? The homing route of salmon is predicted by magnetic field drift (secular variation)     

Morphological variation in the deep ocean-dwelling coccolithophore Florisphaera profunda (Haptophyta)

Detailed analysis of the morphology of Florisphaera profunda from plankton samples collected at three sites in the Atlantic and Pacific Oceans reveals wide variation in this deep ocean-dwelling coccolithophore. In addition to the two varieties described previously, we found a third distinctive form, Florisphaera profunda var. rhinocera var. nov. All three varieties occur at each of the sampling sites. The analysis of monthly samples from different levels in the lower photic zone (LPZ) (100–200?m) at the Hawaii Ocean Time series station suggests that the varieties have similar distributions, which are correlated to primary productivity and the availability of light. The analysis of coccolith and coccosphere size in F. profunda reveals the existence of several size modes in Florisphaera profunda var. profunda and F. profunda var. elongata. The biological significance of these modes, or morphotypes is not known. However, their co-occurrence in single samples from different oceanic areas suggests that they are not ecophenotypes. In the light of recent molecular genetic analyses of intraspecific groups within commonly occurring coccolithophores, the varieties and size morphotypes of F. profunda are of significant interest for the study of marine phytoplankton biodiversity. Coccolithophores inhabiting the LPZ may be adapted to the low light, high nutrient conditions of this layer and hold great potential as a means to reconstruct past oceanographic conditions such as the position of the nutricline. However, coccolithophore biodiversity in the LPZ is poorly documented and the number of species may be much higher than previously thought.     

Exploring the implications of recreational disturbance on an endangered butterfly using a novel modelling approach

Site and wildlife managers globally are under increasing pressure to implement management strategies that address the negative implications of outdoor recreational activities on wildlife. For many rare and isolated species any anthropogenic activities that cause disturbance could potentially be detrimental to existing populations. Understanding how non-consumptive recreation can influence a species may therefore be critical to its preservation. We developed a novel approach to specifically address this need. Using a combination of field surveys and simulation modelling exercises, we (1) explored the responses of endangered Karner blue butterflies (Lycaeides melissa samuelis) to recreation, (2) assessed whether such responses influenced oviposition rate and/or host plant choice and (3) tested alternative management strategies that could alleviate the negative impacts of recreation. Our field surveys confirmed that Karner blues were sensitive to recreational disturbance. Butterflies flushed at similar speeds and distances from recreationists (2.2 m at 0.17 m/s), as they would from natural threats, such as predators (2.2 m at 0.19 m/s). Incorporating female response parameters into a simulation model revealed that regular disturbance could reduce egg laying potential and significantly restrict host plant choice, which in turn, could impact the butterfly’s population dynamics. However, we established that it was possible to effectively offset the implications of recreational disturbance using our simulation modelling approach. For example, extending Karner blue breeding habitat from trails and other public rights of way has the potential to alleviate such disturbance. Our study demonstrates that the potential impact of recreation on species of conservation concern should not be overlooked.