Isolation and characterization of microsatellites in the woody shrub,Calothamnus quadrifidus (Myrtaceae)

Microsatellite loci were developed for genetic analysis of the bird pollinated woody shrub Calothamnus quadrifidus. A genomic library was constructed and screened with dinucleotide and trinucleotide repeat sequences. Ten dinucleotide microsatellite markers were developed, and polymorphism in a population of C. quadrifidus was investigated for six of these markers, which showed an average of 12.7 alleles per locus. Mendelian inheritance of the loci was confirmed through analysis of open pollinated progeny arrays of 10 plants. These loci will be used to study gene flow patterns between isolated populations of this species in southwest Western Australia.     

Trophic level asynchrony in rates of phenological change for marine,freshwater and terrestrial environments

Recent changes in the seasonal timing (phenology) of familiar biological events have been one of the most conspicuous signs of climate change. However, the lack of a standardized approach to analysing change has hampered assessment of consistency in such changes among different taxa and trophic levels and across freshwater, terrestrial and marine environments. We present a standardized assessment of 25 532 rates of phenological change for 726 UK terrestrial, freshwater and marine taxa. The majority of spring and summer events have advanced, and more rapidly than previously documented. Such consistency is indicative of shared large scale drivers. Furthermore, average rates of change have accelerated in a way that is consistent with observed warming trends. Less coherent patterns in some groups of organisms point to the agency of more local scale processes and multiple drivers. For the first time we show a broad scale signal of differential phenological change among trophic levels; across environments advances in timing were slowest for secondary consumers, thus heightening the potential risk of temporal mismatch in key trophic interactions. If current patterns and rates of phenological change are indicative of future trends, future climate warming may exacerbate trophic mismatching, further disrupting the functioning, persistence and resilience of many ecosystems and having a major impact on ecosystem services.     

Deep sequencing reveals clonal evolution patterns and mutation events associated with relapse in B-cell lymphomas

Background

Molecular mechanisms associated with frequent relapse of diffuse large B-cell lymphoma (DLBCL) are poorly defined. It is especially unclear how primary tumor clonal heterogeneity contributes to relapse. Here, we explore unique features of B-cell lymphomas - VDJ recombination and somatic hypermutation - to address this question.

Results

We performed high-throughput sequencing of rearranged VDJ junctions in 14 pairs of matched diagnosis-relapse tumors, among which 7 pairs were further characterized by exome sequencing. We identify two distinctive modes of clonal evolution of DLBCL relapse: an early-divergent mode in which clonally related diagnosis and relapse tumors diverged early and developed in parallel; and a late-divergent mode in which relapse tumors developed directly from diagnosis tumors with minor divergence. By examining mutation patterns in the context of phylogenetic information provided by VDJ junctions, we identified mutations in epigenetic modifiers such as KMT2D as potential early driving events in lymphomagenesis and immune escape alterations as relapse-associated events.

Conclusions

Altogether, our study for the first time provides important evidence that DLBCL relapse may result from multiple, distinct tumor evolutionary mechanisms, providing rationale for therapies for each mechanism. Moreover, this study highlights the urgent need to understand the driving roles of epigenetic modifier mutations in lymphomagenesis, and immune surveillance factor genetic lesions in relapse.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0432-0) contains supplementary material, which is available to authorized users.     

Distribution and behaviour of Common Scoter Melanitta nigra relative to prey resources and environmental parameters

Offshore wind farms are proposed around the coast of the UK and elsewhere in Europe. These sites tend to be located in shallow coastal waters that often coincide with areas used by over-wintering Common Scoter Melanitta nigra . A large-scale study was undertaken to ascertain the relationship of the spatial distribution of Common Scoter in Liverpool Bay with prey abundance and environmental and anthropogenic variables that may affect foraging efficiency. The highest numbers of Common Scoter coincided with sites that had a high abundance and biomass of bivalve prey species. There was strong evidence that the maximum observed biomass of bivalves occurred at a mean depth of c. 14 m off the Lancashire coast and at c. 8 m off the north Wales coast. This coincided well with the distribution of Common Scoter at Shell Flat, but less well with the distribution of birds off North Wales. Common Scoters were observed in lowest numbers or were absent from areas in which anthropogenic disturbance (shipping activity) was relatively intense, even when these areas held a high prey biomass. Commercial fishing activities did not appear to contribute to this disturbance.     

Day–night changes in the spatial distribution and habitat preferences of freshwater shrimps, Gammarus pulex, in a stony stream

1. As many invertebrates are nocturnal, their spatial distribution and habitat preferences may change from day to night. Both aspects are examined for Gammarus pulex by testing the hypotheses: (i) a power function was a suitable model for the spatial distribution of the shrimps in both day and night; (ii) diurnal and nocturnal spatial distributions were significantly different; (iii) diurnal and nocturnal habitat preferences were significantly different. Five different life‐stages were treated separately. To ensure that the conclusions were consistent, large samples were taken near midday and midnight in April, June and November over 4 years at two sites about 3 km apart in a stony stream: downstream (n = 30) and upstream (n = 50). 2. The first and second hypotheses were supported at both sites. A power function, relating spatial variance (s²) to mean (m), was an excellent fit in all analyses (P < 0.001, r² > 0.91), i.e. the spatial variance was density‐dependent. All five life‐stages were aggregated in the day. At night, the degree of aggregation increased for juveniles at higher densities but decreased for juveniles at lower densities, increased for immature females and males, but decreased slightly for mature females and especially mature males, the latter being close to a random distribution. There were no significant differences between sites, in spite of the lower numbers at the downstream site. 3. The third hypothesis was tested at only the upstream site and supported by comparisons between shrimp densities and 13 physical variables (distance from bank, water depth, water velocity, ten particle size‐classes), and three non‐physical variables (dry weights of bryophytes, leaf material, organic detritus). During the day, densities were strongly related to particle sizes with the following preferences: 0.5–8 mm for juveniles, 8–256 mm for the other life‐stages with a weaker relationship for males. There were no significant positive relationships with the other variables, apart from bryophytes for immature shrimps and adults. At night, densities were unrelated to particle size; juveniles and immature shrimps preferred low water velocities near the banks, often where leaf material and organic detritus accumulated, females often preferred medium water velocities slightly away from the banks, and males showed no habitat preferences. 4. Day samples do not provide a complete picture of habitat preferences and probably identify refuge habitats. Day–night changes in spatial distribution and habitat preferences are an essential part of the behavioural dynamics of the shrimps and should be investigated in other species.     

Responses of a C3 and a C4 perennial grass to elevated CO2 and temperature under different water regimes

An experiment was carried out to determine the effects of elevated CO₂, elevated temperatures, and altered water regimes in native shortgrass steppe. Intact soil cores dominated by Bouteloua gracilis, a C₄ perennial grass, or Pascopyrum smithii, a C₃ perennial grass, were placed in growth chambers with 350 or 700 μL L^?1 atmospheric CO₂, and under either normal or elevated temperatures. The normal regime mimicked field patterns of diurnal and seasonal temperatures, and the high-temperature regime was 4 °C warmer. Water was supplied at three different levels in a seasonal pattern similar to that observed in the field. Total biomass after two growing seasons was 19% greater under elevated CO₂, with no significant difference between the C₃ and C₄ grass. The effect of elevated CO₂ on biomass was greatest at the intermediate water level. The positive effect of elevated CO₂ on shoot biomass was greater at normal temperatures in B. gracilis, and greater at elevated temperatures in P. smithii. Neither root-to-shoot ratio nor production of seed heads was affected by elevated CO₂. Plant tissue N and soil inorganic N concentrations were lower under elevated Co₂, but no more so in the C₃ than the C₄ plant. Elevated CO₂ appeared to increase plant N limitation, but there was no strong evidence for an increase in N limitation or a decrease in the size of the CO₂ effect from the first to the second growing season. Autumn samples of large roots plus crowns, the perennial organs, had 11% greater total N under elevated CO₂, in spite of greater N limitation.