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Birth weight variation is influenced by fetal and maternal genetic and non-genetic factors, and has been reproducibly associated with future cardio-metabolic health outcomes. In expanded genome-wide association analyses of own birth weight (n = 321,223) and offspring birth weight (n = 230,069 mothers), we identified 190 independent association signals (129 of which are novel). We used structural equation modeling to decompose the contributions of direct fetal and indirect maternal genetic effects, then applied Mendelian randomization to illuminate causal pathways. For example, both indirect maternal and direct fetal genetic effects drive the observational relationship between lower birth weight and higher later blood pressure: maternal blood pressure-raising alleles reduce offspring birth weight, but only direct fetal effects of these alleles, once inherited, increase later offspring blood pressure. Using maternal birth weight-lowering genotypes to proxy for an adverse intrauterine environment provided no evidence that it causally raises offspring blood pressure, indicating that the inverse birth weight-blood pressure association is attributable to genetic effects, and not to intrauterine programming.
The cell interior is a highly packed environment in which biological macromolecules evolve and function. This crowded media has effects in many biological processes such as protein-protein binding, gene regulation, and protein folding. Thus, biochemical reactions that take place in such crowded conditions differ from diluted test tube conditions, and a considerable effort has been invested in order to understand such differences.
In this work, we combine different computationally tools to disentangle the effects of molecular crowding on biochemical processes. First, we propose a lattice model to study the implications of molecular crowding on enzymatic reactions. We provide a detailed picture of how crowding affects binding and unbinding events and how the separate effects of crowding on binding equilibrium act together. Then, we implement a lattice model to study the effects of molecular crowding on facilitated diffusion. We find that obstacles on the DNA impair facilitated diffusion. However, the extent of this effect depends on how dynamic obstacles are on the DNA. For the scenario in which crowders are only present in the bulk solution, we find that at some conditions presence of crowding agents can enhance specific-DNA binding. Finally, we make use of structure-based techniques to look at the impact of the presence of crowders on the folding a protein. We find that polymeric crowders have stronger effects on protein stability than spherical crowders. The strength of this effect increases as the polymeric crowders become longer. The methods we propose here are general and can also be applied to more complicated systems.
A novel common variant in DCST2 is associated with length in early life and height in adulthood
(2015)
Common genetic variants have been identified for adult height, but not much is known about the genetics of skeletal growth in early life. To identify common genetic variants that influence fetal skeletal growth, we meta-analyzed 22 genome-wide association studies (Stage 1; N = 28 459). We identified seven independent top single nucleotide polymorphisms (SNPs) (P < 1 x 10(-6)) for birth length, of which three were novel and four were in or near loci known to be associated with adult height (LCORL, PTCH1, GPR126 and HMGA2). The three novel SNPs were followed-up in nine replication studies (Stage 2; N = 11 995), with rs905938 in DC-STAMP domain containing 2 (DCST2) genome-wide significantly associated with birth length in a joint analysis (Stages 1 + 2; beta = 0.046, SE = 0.008, P = 2.46 x 10(-8), explained variance = 0.05%). Rs905938 was also associated with infant length (N = 28 228; P = 5.54 x 10(-4)) and adult height (N = 127 513; P = 1.45 x 10(-5)). DCST2 is a DC-STAMP-like protein family member and DC-STAMP is an osteoclast cell-fusion regulator. Polygenic scores based on 180 SNPs previously associated with human adult stature explained 0.13% of variance in birth length. The same SNPs explained 2.95% of the variance of infant length. Of the 180 known adult height loci, 11 were genome-wide significantly associated with infant length (SF3B4, LCORL, SPAG17, C6orf173, PTCH1, GDF5, ZNFX1, HHIP, ACAN, HLA locus and HMGA2). This study highlights that common variation in DCST2 influences variation in early growth and adult height.
Stars are uniform spheres, but only to first order. The way in which stellar rotation and magnetism break this symmetry places important observational constraints on stellar magnetic fields, and factors in the assessment of the impact of stellar activity on exoplanet atmospheres. The spatial distribution of flares on the solar surface is well known to be nonuniform, but elusive on other stars. We briefly review the techniques available to recover the loci of stellar flares, and highlight a new method that enables systematic flare localization directly from optical light curves. We provide an estimate of the number of flares we may be able to localize with the Transiting Exoplanet Survey Satellite, and show that it is consistent with the results obtained from the first full sky scan of the mission. We suggest that nonuniform flare latitude distributions need to be taken into account in accurate assessments of exoplanet habitability.
The low-mass star GJ 1151 has been reported to display variable low-frequency radio emission, which has been interpreted as a signpost of coronal star-planet interactions with an unseen exoplanet. Here we report the first X-ray detection of GJ 1151's corona based on the XMM-Newton data. We find that the star displays a small flare during the X-ray observation. Averaged over the observation, we detect the star with a low coronal temperature of 1.6 MK and an X-ray luminosity of L-X = 5.5 x 10(26) erg s(-1). During the quiescent time periods excluding the flare, the star remains undetected with an upper limit of L-X,L- qui <= 3.7 x 10(26) erg s(-1). This is compatible with the coronal assumptions used in a recently published model for a star-planet interaction origin of the observed radio signals from this star.
Combined with measurements made by very-long-baseline interferometry, the observations of fast TeV gamma-ray flares probe the structure and emission mechanism of blazar jets. However, only a handful of such flares have been detected to date, and only within the last few years have these flares been observed from lower-frequency-peaked BL. Lac objects and flat-spectrum radio quasars. We report on a fast TeV gamma-ray flare from the blazar BL. Lacertae observed by the Very Energetic Radiation Imaging Telescope Array System (VERITAS). with a rise time of similar to 2.3 hr and a decay time of similar to 36 min. The peak flux above 200 GeV is (4.2 +/- 0.6) x 10(-6) photon m(-2) s(-1) measured with a 4-minute-binned light curve, corresponding to similar to 180% of the flux that is observed from the Crab Nebula above the same energy threshold. Variability contemporaneous with the TeV gamma-ray flare was observed in GeV gamma-ray, X-ray, and optical flux, as well as in optical and radio polarization. Additionally, a possible moving emission feature with superluminal apparent velocity was identified in Very Long Baseline Array observations at 43 GHz, potentially passing the radio core of the jet around the time of the gamma-ray flare. We discuss the constraints on the size, Lorentz factor, and location of the emitting region of the flare, and the interpretations with several theoretical models that invoke relativistic plasma passing stationary shocks.
The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas.
Spring Issue
(2024)
Solar H alpha excess during Solar Cycle 24 from full-disk filtergrams of the Chromospheric Telescope
(2022)
Context
The chromospheric H alpha spectral line is a strong line in the spectrum of the Sun and other stars. In the stellar regime, this spectral line is already used as a powerful tracer of stellar activity. For the Sun, other tracers, such as Ca II K, are typically used to monitor solar activity. Nonetheless, the Sun is observed constantly in H alpha with globally distributed ground-based full-disk imagers.
Aims
The aim of this study is to introduce the imaging H alpha excess and deficit as tracers of solar activity and compare them to other established indicators. Furthermore, we investigate whether the active region coverage fraction or the changing H alpha excess in the active regions dominates temporal variability in solar H alpha observations.
Methods
We used observations of full-disk H alpha filtergrams of the Chromospheric Telescope and morphological image processing techniques to extract the imaging H alpha excess and deficit, which were derived from the intensities above or below 10% of the median intensity in the filtergrams, respectively. These thresholds allowed us to filter for bright features (plage regions) and dark absorption features (filaments and sunspots). In addition, the thresholds were used to calculate the mean intensity I-mean(E/D) for H alpha excess and deficit regions. We describe the evolution of the H alpha excess and deficit during Solar Cycle 24 and compare it to the mean intensity and other well established tracers: the relative sunspot number, the F10.7 cm radio flux, and the Mg II index. In particular, we tried to determine how constant the H alpha excess and number density of H alpha excess regions are between solar maximum and minimum. The number of pixels above or below the intensity thresholds were used to calculate the area coverage fraction of H alpha excess and deficit regions on the Sun, which was compared to the imaging H alpha excess and deficit and the respective mean intensities averaged for the length of one Carrington rotation. In addition, we present the H alpha excess and mean intensity variation of selected active regions during their disk passage in comparison to the number of pixels of H alpha excess regions.
Results.
The H alpha excess and deficit follow the behavior of the solar activity over the course of the cycle. They both peak around solar maximum, whereby the peak of the H alpha deficit is shortly after the solar maximum. Nonetheless, the correlation of the monthly averages of the H alpha excess and deficit is high with a Spearman correlation of rho = 0.91. The H alpha excess is closely correlated to the chromospheric Mg II index with a correlation of 0.95. The highest correlation of the H alpha deficit is found with the F10.7 cm radio flux, with a correlation of 0.89, due to their peaks after the solar activity maximum. Furthermore, the H alpha deficit reflects the cyclic behavior of polar crown filaments and their disappearance shortly before the solar maximum. We investigated the mean intensity distribution for H alpha excess regions for solar minimum and maximum. The shape of the distributions for solar minimum and maximum is very similar, but with different amplitudes. Furthermore, we found that the area coverage fraction of H alpha excess regions and the H alpha excess are strongly correlated with an overall Spearman correlation of 0.92. The correlation between the H alpha excess and the mean intensity of H alpha excess regions is 0.75. The correlation of the area coverage fraction and the mean intensity of H alpha excess regions is in general relatively low (rho = 0.45) and only for few active regions is this correlation above 0.7. The weak correlation between the area coverage fraction and mean intensity leaves us pessimistic that the degeneracy between these two quantities can be broken for the modeling of unresolved stellar surfaces.
Massive stars that become stripped of their hydrogen envelope through binary interaction or winds can be observed either as Wolf-Rayet stars, if they have optically thick winds, or as transparent-wind stripped-envelope stars. We approximate their evolution through evolutionary models of single helium stars, and compute detailed model grids in the initial mass range 1.5-70 M. for metallicities between 0.01 and 0.04, from core helium ignition until core collapse. Throughout their lifetimes some stellar models expose the ash of helium burning. We propose that models that have nitrogen-rich envelopes are candidate WN stars, while models with a carbon-rich surface are candidate WC stars during core helium burning, and WO stars afterwards. We measure the metallicity dependence of the total lifetimes of our models and the duration of their evolutionary phases. We propose an analytic estimate of the wind's optical depth to distinguish models of Wolf-Rayet stars from transparent-wind stripped-envelope stars, and find that the luminosity ranges at which WN-, WC-, and WO-type stars can exist is a strong function of metallicity. We find that all carbon-rich models produced in our grids have optically thick winds and match the luminosity distribution of observed populations. We construct population models and predict the numbers of transparent-wind stripped-envelope stars and Wolf-Rayet stars, and derive their number ratios at different metallicities. We find that as metallicity increases, the number of transparent-wind stripped-envelope stars decreases and the number of Wolf-Rayet stars increases. At high metallicities WC- and WO-type stars become more common. We apply our population models to nearby galaxies, and find that populations are more sensitive to the transition luminosity between Wolf-Rayet stars and transparent-wind helium stars than to the metallicity-dependent mass loss rates.