Application of three-level linear mixed-effects model incorporating gene-age interactions for association analysis of longitudinal family data

Longitudinal studies that collect repeated measurements on the same subjects over time have long been considered as being more powerful and providing much better information on individual changes than cross-sectional data. We propose a three-level linear mixed-effects model for testing genetic main effects and gene-age interactions with longitudinal family data. The simulated Genetic Analysis Workshop 16 Problem 3 data sets were used to evaluate the method. Genome-wide association analyses were conducted based on cross-sectional data, i.e., each of the three single-visit data sets separately, and also on the longitudinal data, i.e., using data from all three visits simultaneously. Results from the analysis of coronary artery calcification phenotype showed that the longitudinal association tests were much more powerful than those based on single-visit data only. Gene-age interactions were evaluated under the same framework for detecting genetic effects that are modulated by age

Aggregate blood pressure responses to serial dietary sodium and potassium intervention: Defining responses using independent component analysis

BACKGROUND: Hypertension is a complex trait that often co-occurs with other conditions such as obesity and is affected by genetic and environmental factors. Aggregate indices such as principal components among these variables and their responses to environmental interventions may represent novel information that is potentially useful for genetic studies. RESULTS: In this study of families participating in the Genetic Epidemiology Network of Salt Sensitivity (GenSalt) Study, blood pressure (BP) responses to dietary sodium interventions are explored. Independent component analysis (ICA) was applied to 20 variables indexing obesity and BP measured at baseline and during low sodium, high sodium and high sodium plus potassium dietary intervention periods. A “heat map” protocol that classifies subjects based on risk for hypertension is used to interpret the extracted components. ICA and heat map suggest four components best describe the data: (1) systolic hypertension, (2) general hypertension, (3) response to sodium intervention and (4) obesity. The largest heritabilities are for the systolic (64 %) and general hypertension (56 %) components. There is a pattern of higher heritability for the component response to intervention (40–42 %) as compared to those for the traditional intervention responses computed as delta scores (24 %–40 %). CONCLUSIONS: In summary, the present study provides intermediate phenotypes that are heritable. Using these derived components may prove useful in gene discovery applications. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12863-015-0226-8) contains supplementary material, which is available to authorized users

Flexible microelectrode arrays to interface epicardial electrical signals with intracardial calcium transients in zebrafish hearts

The zebrafish (Danio rerio) is an emerging genetic model for regenerative medicine. In humans, myocardial infarction results in the irreversible loss of cardiomyocytes. However, zebrafish hearts fully regenerate after a 20% ventricular resection, without either scarring or arrhythmias. To study this cardiac regeneration, we developed implantable flexible multi-microelectrode membrane arrays that measure the epicardial electrocardiogram signals of zebrafish in real-time. The microelectrode electrical signals allowed for a high level of both temporal and spatial resolution (~20 μm), and the signal to noise ratio of the epicardial ECG was comparable to that of surface electrode ECG (7.1 dB vs. 7.4 dB, respectively). Processing and analysis of the signals from the microelectrode array demonstrated distinct ECG signals: namely, atrial conduction (P waves), ventricular contraction (QRS), and ventricular repolarization (QT interval). The electrical signals were in synchrony with optically measured Calcium concentration gradients in terms of d[Ca^(2+)]/dt at both whole heart and tissue levels. These microelectrodes therefore provide a real-time analytical tool for monitoring conduction phenotypes of small vertebral animals with a high temporal and spatial resolution

Neutron-Scattering Evidence for a Periodically Modulated Superconducting Phase in the Underdoped Cuprate La1.905Ba0.095CuO4

The role of antiferromagnetic spin correlations in high-temperature superconductors remains a matter of debate. We present inelastic neutron scattering evidence that gapless spin fluctuations coexist with superconductivity in La$_{1.905}$Ba$_{0.095}$CuO$_4$. Furthermore, we observe that both the low-energy magnetic spectral weight and the spin incommensurability are enhanced by the onset of superconducting correlations. We propose that the coexistence occurs through intertwining of spatial modulations of the pair wave function and the antiferromagnetic correlations. This proposal is also directly relevant to sufficiently underdoped La$_{2-x}$Sr$_x$CuO$_4$ and YBa$_2$Cu$_3$O$_{6+x}$.Comment: 5 pages, 3 figures, plus 2 pages of supplemental material; version accepted for publication in PR

High energy pseudogap and its evolution with doping in Fe-based superconductors as revealed by optical spectroscopy

We report optical spectroscopic measurements on electron- and hole-doped BaFe2As2. We show that the compounds in the normal state are not simple metals. The optical conductivity spectra contain, in addition to the free carrier response at low frequency, a temperature-dependent gap-like suppression at rather high energy scale near 0.6 eV. This suppression evolves with the As-Fe-As bond angle induced by electron- or hole-doping. Furthermore, the feature becomes much weaker in the Fe-chalcogenide compounds. We elaborate that the feature is caused by the strong Hund's rule coupling effect between the itinerant electrons and localized electron moment arising from the multiple Fe 3d orbitals. Our experiments demonstrate the coexistence of itinerant and localized electrons in iron-based compounds, which would then lead to a more comprehensive picture about the metallic magnetism in the materials.Comment: 6 pages, 7 figure

Search for D to phi l nu and measurement of the branching fraction for D to phi pi

Using a data sample of integrated luminosity of about 33 pb$^{-1}$ collected around 3.773 GeV with the BESII detector at the BEPC collider, the semileptonic decays $D^+ \to \phi e ^+\nu_e$, $D^+ \to \phi \mu^+\nu_\mu$ and the hadronic decay $D^+ \to \phi \pi^+$ are studied. The upper limits of the branching fractions are set to be $BF(D^+ \to \phi e ^+\nu_e) <$ 2.01% and $BF(D^+ \to \phi \mu^+ \nu_\mu) <$ 2.04% at the 90% confidence level. The ratio of the branching fractions for $D^+ \to \phi \pi^+$ relative to $D^+ \to K^-\pi^+\pi^+$ is measured to be $0.057 \pm 0.011 \pm 0.003$. In addition, the branching fraction for $D^+ \to \phi \pi^+$ is obtained to be $(5.2 \pm 1.0 \pm 0.4) \times 10^{-3}$.Comment: 6 pages, 5 figures, to be published in Eur.Phys.J.

Measurements of branching fractions for inclusive K0~/K0 and K*(892)+- decays of neutral and charged D mesons

Using the data sample of about 33 pb-1 collected at and around 3.773 GeV with the BES-II detector at the BEPC collider, we have studied inclusive K0~/K0 and K*(892)+- decays of D0 and D+ mesons. The branching fractions for the inclusive K0~/K0 and K*(892)- decays are measured to be BF(D0 to K0~/K0 X)=(47.6+-4.8+-3.0)%, BF(D+ to K0~/K0 X)=(60.5+-5.5+-3.3)%, BF(D0 to K*- X)=(15.3+- 8.3+- 1.9)% and BF(D+ to K*- X)=(5.7+- 5.2+- 0.7)%. The upper limits of the branching fractions for the inclusive K*(892)+ decays are set to be BF(D0 to K*+ X)<3.6% and BF(D+ to K*+ X) <20.3% at 90% confidence level

High-Quality Draft Genome Sequences of Four Lignocellulose-Degrading Bacteria Isolated from Puerto Rican Forest Soil: Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.

Here, we report the high-quality draft genome sequences of four phylogenetically diverse lignocellulose-degrading bacteria isolated from tropical soil (Gordonia sp., Paenibacillus sp., Variovorax sp., and Vogesella sp.) to elucidate the genetic basis of their ability to degrade lignocellulose. These isolates may provide novel enzymes for biofuel production