Effects of Spring Temperatures on the Strength of Selection on Timing of Reproduction in a Long-Distance Migratory Bird

Climate change has differentially affected the timing of seasonal events for interacting trophic levels, and this has often led to increased selection on seasonal timing. Yet, the environmental variables driving this selection have rarely been identified, limiting our ability to predict future ecological impacts of climate change. Using a dataset spanning 31 years from a natural population of pied flycatchers (Ficedula hypoleuca), we show that directional selection on timing of reproduction intensified in the first two decades (1980-2000) but weakened during the last decade (2001-2010). Against expectation, this pattern could not be explained by the temporal variation in the phenological mismatch with food abundance. We therefore explored an alternative hypothesis that selection on timing was affected by conditions individuals experience when arriving in spring at the breeding grounds: arriving early in cold conditions may reduce survival. First, we show that in female recruits, spring arrival date in the first breeding year correlates positively with hatch date; hence, early-hatched individuals experience colder conditions at arrival than late-hatched individuals. Second, we show that when temperatures at arrival in the recruitment year were high, early-hatched young had a higher recruitment probability than when temperatures were low. We interpret this as a potential cost of arriving early in colder years, and climate warming may have reduced this cost. We thus show that higher temperatures in the arrival year of recruits were associated with stronger selection for early reproduction in the years these birds were born. As arrival temperatures in the beginning of the study increased, but recently declined again, directional selection on timing of reproduction showed a nonlinear change. We demonstrate that environmental conditions with a lag of up to two years can alter selection on phenological traits in natural populations, something that has important implications for our understanding of how climate can alter patterns of selection in natural populations.

Excitation energy dependent raman signatures of ABA- and ABC-stacked few-layer graphene

The dependence of the Raman spectrum on the excitation energy has been investigated for ABA-and ABC- stacked few-layer graphene in order to establish the fingerprint of the stacking order and the number of layers, which affect the transport and optical properties of few-layer graphene. Five different excitation sources with energies of 1.96, 2.33, 2.41, 2.54 and 2.81â €...eV were used. The position and the line shape of the Raman 2D, G*, N, M, and other combination modes show dependence on the excitation energy as well as the stacking order and the thickness. One can unambiguously determine the stacking order and the thickness by comparing the 2D band spectra measured with 2 different excitation energies or by carefully comparing weaker combination Raman modes such as N, M, or LOLA modes. The criteria for unambiguous determination of the stacking order and the number of layers up to 5 layers are established.

Variation in stable isotope signatures of seston and a zooplanktivorous fish in a eutrophic Chinese lake

Temporal and spatial changes in delta(13)C and delta(15)N of seston (mainly phytoplankton) and isotopic relationship between seston and the lake anchovy (Coilia ectenes) were studied in the large eutrophic freshwater Lake Chaohu in China. Much of the spatial and temporal variation in delta(13)C of lake anchovies was explained by variation in seston, indicating a strong link between pelagic primary production and higher order consumers. Because the lake is shallow, there were no significant differences in delta(13)C and delta(15)N of seston between surface and overlying waters. Spatially, the relatively high delta(13)C and delta(15)N of seston in the western part of the lake might be due to high levels of anthropogenically derived N and C introduced from the surrounding cities through sewage drainage systems. The trophic position of the lake anchovy in the food web of Lake Chaohu was estimated to be 2.9-4.1 (3.5 +/- 0.4), which agrees well with the previous stomach content analysis suggesting that the lake anchovy fed both on zooplankton and small planktivorous fishes.

Expression signatures of TP53 mutations in serous ovarian cancers.

BACKGROUND: Mutations in the TP53 gene are extremely common and occur very early in the progression of serous ovarian cancers. Gene expression patterns that relate to mutational status may provide insight into the etiology and biology of the disease. METHODS: The TP53 coding region was sequenced in 89 frozen serous ovarian cancers, 40 early stage (I/II) and 49 advanced stage (III/IV). Affymetrix U133A expression data was used to define gene expression patterns by mutation, type of mutation, and cancer stage. RESULTS: Missense or chain terminating (null) mutations in TP53 were found in 59/89 (66%) ovarian cancers. Early stage cancers had a significantly higher rate of null mutations than late stage disease (38% vs. 8%, p < 0.03). In advanced stage cases, mutations were more prevalent in short term survivors than long term survivors (81% vs. 30%, p = 0.0004). Gene expression patterns had a robust ability to predict TP53 status within training data. By using early versus late stage disease for out of sample predictions, the signature derived from early stage cancers could accurately (86%) predict mutation status of late stage cancers. CONCLUSIONS: This represents the first attempt to define a genomic signature of TP53 mutation in ovarian cancer. Patterns of gene expression characteristic of TP53 mutation could be discerned and included several genes that are known p53 targets or have been described in the context of expression signatures of TP53 mutation in breast cancer.

Gene expression signatures of radiation response are specific, durable and accurate in mice and humans.

BACKGROUND: Previous work has demonstrated the potential for peripheral blood (PB) gene expression profiling for the detection of disease or environmental exposures. METHODS AND FINDINGS: We have sought to determine the impact of several variables on the PB gene expression profile of an environmental exposure, ionizing radiation, and to determine the specificity of the PB signature of radiation versus other genotoxic stresses. Neither genotype differences nor the time of PB sampling caused any lessening of the accuracy of PB signatures to predict radiation exposure, but sex difference did influence the accuracy of the prediction of radiation exposure at the lowest level (50 cGy). A PB signature of sepsis was also generated and both the PB signature of radiation and the PB signature of sepsis were found to be 100% specific at distinguishing irradiated from septic animals. We also identified human PB signatures of radiation exposure and chemotherapy treatment which distinguished irradiated patients and chemotherapy-treated individuals within a heterogeneous population with accuracies of 90% and 81%, respectively. CONCLUSIONS: We conclude that PB gene expression profiles can be identified in mice and humans that are accurate in predicting medical conditions, are specific to each condition and remain highly accurate over time.

Functional annotation signatures of disease susceptibility loci improve SNP association analysis.

BACKGROUND: Genetic association studies are conducted to discover genetic loci that contribute to an inherited trait, identify the variants behind these associations and ascertain their functional role in determining the phenotype. To date, functional annotations of the genetic variants have rarely played more than an indirect role in assessing evidence for association. Here, we demonstrate how these data can be systematically integrated into an association study's analysis plan. RESULTS: We developed a Bayesian statistical model for the prior probability of phenotype-genotype association that incorporates data from past association studies and publicly available functional annotation data regarding the susceptibility variants under study. The model takes the form of a binary regression of association status on a set of annotation variables whose coefficients were estimated through an analysis of associated SNPs in the GWAS Catalog (GC). The functional predictors examined included measures that have been demonstrated to correlate with the association status of SNPs in the GC and some whose utility in this regard is speculative: summaries of the UCSC Human Genome Browser ENCODE super-track data, dbSNP function class, sequence conservation summaries, proximity to genomic variants in the Database of Genomic Variants and known regulatory elements in the Open Regulatory Annotation database, PolyPhen-2 probabilities and RegulomeDB categories. Because we expected that only a fraction of the annotations would contribute to predicting association, we employed a penalized likelihood method to reduce the impact of non-informative predictors and evaluated the model's ability to predict GC SNPs not used to construct the model. We show that the functional data alone are predictive of a SNP's presence in the GC. Further, using data from a genome-wide study of ovarian cancer, we demonstrate that their use as prior data when testing for association is practical at the genome-wide scale and improves power to detect associations. CONCLUSIONS: We show how diverse functional annotations can be efficiently combined to create 'functional signatures' that predict the a priori odds of a variant's association to a trait and how these signatures can be integrated into a standard genome-wide-scale association analysis, resulting in improved power to detect truly associated variants.

Time signatures of impulsively generated coronal fast wave trains

Impulsively generated short-period fast magneto-acoustic wave trains, guided by solar and stellar coronal loops, are numerically modelled. In the developed stage of the evolution, the wave trains have a characteristic quasi-periodic signature. The quasi-periodicity results from the geometrical dispersion of the guided fast modes, determined by the transverse profile of the loop. A typical feature of the signature is a tadpole wavelet Spectrum: a narrow-spectrum tail precedes a broad-band head. The instantaneous period of the oscillations in the wave train decreases gradually with time. The period and the spectral amplitude evolution are shown to be determined by the steepness of the transverse density profile and the density contrast ratio in the loop. The propagating wave trains recently discovered with the Solar Eclipse Coronal Imaging System (SECIS) instrument are noted to have similar wavelet spectral features, which strengthens the interpretation of SECIS results as guided fast wave trains.

The first polarimetric signatures of infrared jets in X-ray binaries

We present near-infrared linear spectropolarimetry of a sample of persistent X-ray binaries, Sco X-1, Cyg X-2, and GRS 1915+105. The slopes of the spectra are shallower than what is expected from a standard steady state accretion disk, and can be explained if the near-infrared flux contains a contribution from an optically thin jet. For the neutron star systems, Sco X-1 and Cyg X-2, the polarization levels at 2.4 mu m are 1.3% +/- 0.10% and 5.4% +/- 0.7%, respectively, which is greater than the polarization level at 1.65 mu m. This cannot be explained by interstellar polarization or electron scattering in the anisotropic environment of the accretion flow. We propose that the most likely explanation is that this is the polarimetric signature of synchrotron emission arising from close to the base of the jets in these systems. In the black hole system GRS 1915+105 the observed polarization, although high (5.0% +/- 1.2% at 2.4 mu m), may be consistent with interstellar polarization. For Sco X-1 the position angle of the radio jet on the sky is approximately perpendicular to the near-infrared position angle (electric vector), suggesting that the magnetic field is aligned with the jet. These observations may be a first step toward probing the ordering, alignment, and variability of the outflow magnetic field in a region closer to the central accreting object than is observed in the radio band.