Seasonal release from competition explains partial migration in European moose

Partial migration, whereby a proportion of a population migrates between distinct seasonal ranges, is common throughout the animal kingdom. However, studies linking existing theoretical models of migration probability, with empirical data are lacking. The competitive release hypothesis for partial migration predicts that due to density-dependent habitat selection, the proportion of migrants increases as the relative quality and size of the seasonal range increases, but decreases with increasing migration cost and population density. To test this prediction, we developed a quantitative framework to predict the proportion of migrants, using empirical data from 545 individually GPS-marked moose Alces alces from across Fennoscandia, spanning latitudes of 56° to 68°N. Moose contracted their ranges to common and spatially limited winter areas (typically at lower elevation), but expanded them during summer due to an increase in suitable habitat (at highland ranges). As predicted from our model, a better and larger highland range relative to the lowland range corresponded to a higher proportion of migrants in an area. Quantitative predictions coupling the balance of habitat availability of seasonal ranges with the probability of migrating in a large herbivore is a necessary step towards an enhanced understanding of the mechanisms underlying migration at the population level.     

An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies

Background

Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology. Here, we investigated the quality of genome assemblies of Illumina GAIIx 75 bp paired-end reads from Ostreococcus tauri, thereby also improving the existing assembly and showing the genome to be stably maintained in culture.

Results

The 3 assemblers used, ABySS, CLCBio and Velvet, produced 95% complete genomes in 1402 to 2080 scaffolds with a very low rate of misassembly. Reciprocally, these assemblies improved the original genome assembly by filling in 930 gaps. Combined with additional analysis of raw reads and PCR sequencing effort, 1194 gaps have been solved in total adding up to 460 kb of sequence. Mapping of RNAseq Illumina data on this updated genome led to a twofold reduction in the proportion of multi-exon protein coding genes, representing 19% of the total 7699 protein coding genes. The comparison of the DNA extracted in 2001 and 2009 revealed the fixation of 8 single nucleotide substitutions and 2 deletions during the approximately 6000 generations in the lab. The deletions either knocked out or truncated two predicted transmembrane proteins, including a glutamate-receptor like gene.

Conclusion

High coverage (>80 fold) paired-end Illumina sequencing enables a high quality 95% complete genome assembly of a compact ~13 Mb haploid eukaryote. This genome sequence has remained stable for 6000 generations of lab culture.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-1103) contains supplementary material, which is available to authorized users.     

Generalization of Human Fear Acquisition and Extinction within a Novel Arbitrary Stimulus Category

Adaptive anxiety relies on a balance between the generalization of fear acquisition and fear extinction. Research on fear (extinction) generalization has focused mostly on perceptual similarity, thereby ignoring the importance of conceptual stimulus relations in humans. The present study used a laboratory procedure to create de novo conceptual categories of arbitrary stimuli and investigated fear and extinction generalization among these stimuli. A matching-to-sample task produced two four-member categories of abstract figures. Next, a member from one category was coupled with an aversive electrical stimulation, while a member from the other category was presented alone. As expected, conditioned fear responses generalized to the other members of the first category (skin conductance and online shock-expectancy). Subsequent extinction of the conditioned member also generalized to the other members. However, extinguishing a non-conditioned member failed to reduce fear of the conditioned member itself. We conclude that fears generalize readily across conceptually related stimuli, but that the degree of extinction generalization depends on the stimulus subjected to extinction.     

CASP8 SNP D302H (rs1045485) Is Associated with Worse Survival in MYCN-Amplified Neuroblastoma Patients

Background

Neuroblastoma is a pediatric cancer that exhibits a wide clinical spectrum ranging from spontaneous regression in low-risk patients to fatal disease in high-risk patients. The identification of single nucleotide polymorphisms (SNPs) may help explain the heterogeneity of neuroblastoma and assist in identifying patients at higher risk for poor survival. SNPs in the TP53 pathway are of special importance, as several studies have reported associations between TP53 pathway SNPs and cancer. Of note, less than 2% of neuroblastoma tumors have a TP53 mutation at diagnosis.

Patients and Methods

We selected 21 of the most frequently studied SNPs in the TP53 pathway and evaluated their association with outcome in 500 neuroblastoma patients using TaqMan allelic discrimination assays.

Results and Conclusion

We investigated the impact of 21 SNPs on overall survival, event-free survival, age at diagnosis, MYCN status, and stage of the disease in 500 neuroblastoma patients. A missense SNP in exon 10 of the CASP8 gene SNP D302H was associated with worse overall and event-free survival in patients with MYCN-amplified neuroblastoma tumors.     

KymographClear and KymographDirect: two tools for the automated quantitative analysis of molecular and cellular dynamics using kymographs

Dynamic processes are ubiquitous and essential in living cells. To properly understand these processes, it is imperative to measure them in a time-dependent way and analyze the resulting data quantitatively, preferably with automated tools. Kymographs are single images that represent the motion of dynamic processes and are widely used in live-cell imaging. Although they contain the full range of dynamics, it is not straightforward to extract this quantitative information in a reliable way. Here we present two complementary, publicly available software tools, KymographClear and KymographDirect, that have the power to reveal detailed insight in dynamic processes. KymographClear is a macro toolset for ImageJ to generate kymographs that provides automatic color coding of the different directions of movement. KymographDirect is a stand-alone tool to extract quantitative information from kymographs obtained from a wide range of dynamic processes in an automated way, with high accuracy and reliability. We discuss the concepts behind these software tools, validate them using simulated data, and test them on experimental data. We show that these tools can be used to extract motility parameters from a diverse set of cell-biological experiments in an automated and user-friendly way.     

Spatiotemporal dynamics of duck harvest distributions in the Central and Mississippi flyways, 1960–2019

Geographical distributions of waterfowl exhibit annual variation in response to spatiotemporal variation in weather conditions, habitat availability, and other factors. Continuing changes in climate and land use could lead to persistent shifts of waterfowl distributions, potentially causing a mismatch with habitat conservation planning, wetland restoration efforts, and harvest management decisions informed by historical distributions. We used band recoveries and harvest records (i.e., hunter-harvested wings) from the United States Fish and Wildlife Service Waterfowl Parts Collection Survey as indices of duck distribution in autumn and winter, and quantified intra-annual, interannual, and interspecific variation in their geographic distributions across 6 decades (1960–2019) for 15 duck species in the Central and Mississippi flyways in North America. Specifically, we tested for annual and decadal shifts in mean latitude and longitude of recoveries for each month (Oct–Jan) by species and taxonomic guild (i.e., dabbling, diving ducks). Overall, species varied in the extent, timing, and sometimes direction, of distributional change in recoveries. From 1960–2019, mean recovery locations for dabbling ducks shifted south 105–296 km in October and 27 km in November (wings only), whereas mean latitudes shifted north 144–234 km in December and 186–301 km in January. Mean recovery locations for diving ducks shifted north 162 km in October (wings only), 84–173 km in December, and 66–120 km in January, but shifted 99–512 km south in November. Shifts in longitude were less consistent between guilds and data types. Finally, distributional change rarely accelerated during recent decades, except for southward shifts of band recoveries of diving ducks in November and northward shifts of band and wing recoveries of dabbling ducks in January. Although anecdotal accounts of large-scale northward shifts in duck distributions are prolific in the land management and hunting communities, our data demonstrate more subtle shifts that vary considerably by species and month. Observed changes in recovery distributions could necessitate changes in timing of habitat management practices throughout the Central and Mississippi flyways and may result in fewer hunting and recreational opportunities for some species in southern states. Quantifying patterns of historical change is a necessary first step to understanding temporal and interspecific variation in waterfowl distributions, which will help with landscape-scale conservation and management efforts in the future and enable effective communication to core constituencies regarding ongoing changes and their implications for recreational engagement.     

Site-specific transamidation and deamidation of the small heat-shock protein Hsp20 by tissue transglutaminase

Crosslinking of small heat-shock proteins (sHsps) by tissue transglutaminase (tTG) is enhanced by stress and under pathological conditions. We here used hexapeptide probes to determine the amine donor (K) and acceptor (Q) sites for tTG in Hsp20. Mass spectrometric peptide mass fingerprinting and peptide fragmentation established that Q31 and the C-terminal K162 are involved in inter- and intramolecular crosslinking (transamidation). Q31 is a conserved glutamine in sHsps where the neighboring residue determines its reactivity. Moreover, we detected highly efficient simultaneous deamidation of Q66, which suggests that tTG-catalyzed transamidation and deamidation is specific for different glutamine residues.     

Experimental evidence for a causal effect of pair-bond duration on reproductive performance in oystercatchers (Haematopus ostralegus)

Many studies have suggested that reproductive performance improvesduring the pair-bond, which might explain why individuals rematewith the same partner in many species. However, discussion existsabout whether the association between reproductive performanceand pair-bond duration that is reported in these studies reflectsa causal relationship. Usually it is unclear whether a positiveassociation is caused by pairs improving during their pair-bondor by high-quality pairs staying together for longer. Furthermore,reproductive performance often also depends on the age or breedingexperience of parents, which all covary with pair-bond duration.A much needed experimental approach is lacking so far. We investigatedthe effect of pair-bond duration on reproductive performancein a long-lived monogamous bird species based on natural aswell as experimental variation. The duration of oystercatcher(Haematopus ostralegus) pair-bonds, which were followed for21 years, strongly affected reproductive output, even aftercontrolling for effects of age and breeding experience. Pairsimproved during their pair-bond, and there were no indicationsof selective disappearance of low-quality pairs; however, pairsthat stayed together for very long performed badly. Experimentalremoval of one partner showed that the reproductive cost ofdivorce depended on the pair-bond duration with the old partner.In addition, after remating, the newly formed pairs stronglyimproved again, independent of the age and breeding experienceof the remated pair members. As such, this study provides thefirst experimental evidence of a causal effect of pair-bondduration on reproductive performance.     

Efficient mouse transgenesis using Gateway-compatible ROSA26 locus targeting vectors and F1 hybrid ES cells

The ability to rapidly and efficiently generate reliable Cre/loxP conditional transgenic mice would greatly complement global high-throughput gene targeting initiatives aimed at identifying gene function in the mouse. We report here the generation of Cre/loxP conditional ROSA26-targeted ES cells within 3–4 weeks by using Gateway® cloning to build the target vectors. The cDNA of the gene of interest can be expressed either directly by the ROSA26 promoter providing a moderate level of expression or by a CAGG promoter placed in the ROSA26 locus providing higher transgene expression. Utilization of F1 hybrid ES cells with exceptional developmental potential allows the production of germ line transmitting, fully or highly ES cell-derived mice by aggregation of cells with diploid embryos. The presented streamlined procedures accelerate the examination of phenotypical consequences of transgene expression. It also provides a unique tool for comparing the biological activity of polymorphic or splice variants of a gene, or products of different genes functioning in the same or parallel pathways in an overlapping manner.     

Algal defenses,population stability,and the risk of herbivore extinctions: a chemostat model and experiment

The effects of inducible defenses and constitutive defenses on population dynamics were investigated in a freshwater plankton system with rotifers as predators and different algal strains as prey. We made predictions for these systems using a chemostat predator–prey model and focused on population stability and predator persistence as a function of flow-through rate. The model exhibits three major types of behavior at a high nutrient concentration: (1) at high dilution rates, only algae exist; (2) at intermediate dilution rates, algae and rotifers show stable coexistence; (3) at low dilution rates, large population fluctuations occur, with low minimum densities entailing a risk of stochastic rotifer extinctions. The size and location of the corresponding areas in parameter space critically depend on the type of algal defense strategy. In an 83-day high-nutrient chemostat experiment we changed the dilution rate every 3 weeks, from 0.7 to 0.5 to 0.3 to 0.1 per day. Within this range of dilution rates, rotifers and algae coexisted, and population fluctuations of algae clearly increased as dilution rates decreased. The CV of herbivore densities was highest at the end of the experiment, when the dilution rate was low. On day 80, herbivorous rotifers had become undetectable in all three chemostats with permanently defended algae (where rotifer densities had already been low) and in two out of three chemostats where rotifers had been feeding on algae with inducible defenses (that represented more edible food). We interpret our results in relation to the paradox of enrichment.