Population genetic variation in gene expression is associated with phenotypic variation in Saccharomyces cerevisiae

BACKGROUND: The relationship between genetic variation in gene expression and phenotypic variation observable in nature is not well understood. Identifying how many phenotypes are associated with differences in gene expression and how many gene-expression differences are associated with a phenotype is important to understanding the molecular basis and evolution of complex traits. RESULTS: We compared levels of gene expression among nine natural isolates of Saccharomyces cerevisiae grown either in the presence or absence of copper sulfate. Of the nine strains, two show a reduced growth rate and two others are rust colored in the presence of copper sulfate. We identified 633 genes that show significant differences in expression among strains. Of these genes, 20 were correlated with resistance to copper sulfate and 24 were correlated with rust coloration. The function of these genes in combination with their expression pattern suggests the presence of both correlative and causative expression differences. But the majority of differentially expressed genes were not correlated with either phenotype and showed the same expression pattern both in the presence and absence of copper sulfate. To determine whether these expression differences may contribute to phenotypic variation under other environmental conditions, we examined one phenotype, freeze tolerance, predicted by the differential expression of the aquaporin gene AQY2. We found freeze tolerance is associated with the expression of AQY2. CONCLUSIONS: Gene expression differences provide substantial insight into the molecular basis of naturally occurring traits and can be used to predict environment dependent phenotypic variation

Hubble Space Telescope Near-IR Transmission Spectroscopy of the Super-Earth HD 97658b

Recent results from the Kepler mission indicate that super-Earths (planets with masses between 1-10 times that of the Earth) are the most common kind of planet around nearby Sun-like stars. These planets have no direct solar system analogue, and are currently one of the least well-understood classes of extrasolar planets. Many super-Earths have average densities that are consistent with a broad range of bulk compositions, including both water-dominated worlds and rocky planets covered by a thick hydrogen and helium atmosphere. Measurements of the transmission spectra of these planets offer the opportunity to resolve this degeneracy by directly constraining the scale heights and corresponding mean molecular weights of their atmospheres. We present Hubble Space Telescope near-infrared spectroscopy of two transits of the newly discovered transiting super-Earth HD 97658b. We use the Wide Field Camera 3's scanning mode to measure the wavelength-dependent transit depth in thirty individual bandpasses. Our averaged differential transmission spectrum has a median 1 sigma uncertainty of 23 ppm in individual bins, making this the most precise observation of an exoplanetary transmission spectrum obtained with WFC3 to date. Our data are inconsistent with a cloud-free solar metallicity atmosphere at the 10 sigma level. They are consistent at the 0.4 sigma level with a flat line model, as well as effectively flat models corresponding to a metal-rich atmosphere or a solar metallicity atmosphere with a cloud or haze layer located at pressures of 10 mbar or higher.Comment: ApJ in press; revised version includes an updated orbital ephemeris for the plane

Infrared Transmission Spectroscopy of the Exoplanets HD209458b and XO-1b Using the Wide Field Camera-3 on the Hubble Space Telescope

Exoplanetary transmission spectroscopy in the near-infrared using the Hubble Space Telescope (HST) NICMOS is currently ambiguous because different observational groups claim different results from the same data, depending on their analysis methodologies. Spatial scanning with HST/WFC3 provides an opportunity to resolve this ambiguity. We here report WFC3 spectroscopy of the giant planets HD 209458b and XO-1b in transit, using spatial scanning mode for maximum photon-collecting efficiency. We introduce an analysis technique that derives the exoplanetary transmission spectrum without the necessity of explicitly decorrelating instrumental effects, and achieves nearly photon-limited precision even at the high flux levels collected in spatial scan mode. Our errors are within 6% (XO-1) and 26% (HD 209458b) of the photon-limit at a resolving power of λ/δλ ~ 70, and are better than 0.01% per spectral channel. Both planets exhibit water absorption of approximately 200 ppm at the water peak near 1.38 μm. Our result for XO-1b contradicts the much larger absorption derived from NICMOS spectroscopy. The weak water absorption we measure for HD 209458b is reminiscent of the weakness of sodium absorption in the first transmission spectroscopy of an exoplanet atmosphere by Charbonneau et al. Model atmospheres having uniformly distributed extra opacity of 0.012 cm2 g−1 account approximately for both our water measurement and the sodium absorption. Our results for HD 209458b support the picture advocated by Pont et al. in which weak molecular absorptions are superposed on a transmission spectrum that is dominated by continuous opacity due to haze and/or dust. However, the extra opacity needed for HD 209458b is grayer than for HD 189733b, with a weaker Rayleigh component

Alcohol intake and endogenous sex hormones in women: Meta‐analysis of cohort studies and Mendelian randomization

Background: The mechanisms underlying alcohol‐induced breast carcinogenesis are not fully understood but may involve hormonal changes. Methods: Cross‐sectional associations were investigated between self‐reported alcohol intake and serum or plasma concentrations of estradiol, estrone, progesterone (in premenopausal women only), testosterone, androstenedione, dehydroepiandrosterone sulfate, and sex hormone binding globulin (SHBG) in 45 431 premenopausal and 173 476 postmenopausal women. Multivariable linear regression was performed separately for UK Biobank, European Prospective Investigation into Cancer and Nutrition, and Endogenous Hormones and Breast Cancer Collaborative Group, and meta‐analyzed the results. For testosterone and SHBG, we also conducted Mendelian randomization and colocalization using the ADH1B (alcohol dehydrogenase 1B) variant (rs1229984). Results: Alcohol intake was positively, though weakly, associated with all hormones (except progesterone in premenopausal women), with increments in concentrations per 10 g/day increment in alcohol intake ranging from 1.7% for luteal estradiol to 6.6% for postmenopausal dehydroepiandrosterone sulfate. There was an inverse association of alcohol with SHBG in postmenopausal women but a small positive association in premenopausal women. Two‐sample randomization identified positive associations of alcohol intake with total testosterone (difference per 10 g/day increment: 4.1%; 95% CI, 0.6–7.6) and free testosterone (7.8%; 4.1–11.5), and an inverse association with SHBG (–8.1%; –11.3% to –4.9%). Colocalization suggested a shared causal locus at ADH1B between alcohol intake and higher free testosterone and lower SHBG (posterior probability for H4, 0.81 and 0.97, respectively). Conclusions: Alcohol intake was associated with small increases in sex hormone concentrations, including bioavailable fractions, which may contribute to its effect on breast cancer risk

Vitamin D pathway gene polymorphisms, diet, and risk of postmenopausal breast cancer: a nested case-control study

INTRODUCTION: Vitamin D receptor (VDR) polymorphisms have been inconsistently associated with breast cancer risk. Whether risk is influenced by polymorphisms in other vitamin D metabolism genes and whether calcium or vitamin D intake modifies risk by genotype have not been evaluated. METHODS: We conducted a nested case-control study within the Cancer Prevention Study II Nutrition Cohort of associations between breast cancer and four VDR single-nucleotide polymorphisms (SNPs), Bsm1,Apa1,Taq1, and Fok1, a poly(A) microsatellite, and associated haplotypes (baTL and BAtS). We also examined one SNP in the 24-hydroxylase gene (CYP24A1) and two in the vitamin D-binding protein (group-specific component [GC]) gene. Participants completed a questionnaire on diet and medical history at baseline in 1992. This study includes 500 postmenopausal breast cancer cases and 500 controls matched by age, race/ethnicity, and date of blood collection. RESULTS: Incident breast cancer was not associated with any genotype examined. However, women with the Bsm1 bb SNP who consumed greater than the median intake of total calcium (≥902 mg/day) had lower odds of breast cancer compared to women with the Bb or BB genotype and less than the median calcium intake (odds ratio 0.61, 95% confidence interval 0.38 to 0.96; p(interaction )= 0.01). Similar interactions were observed for Taq1 (T allele) and the poly(A) (LL) repeat. CONCLUSION: We found no overall association between selected vitamin D pathway genes and postmenopausal breast cancer risk. However, certain VDR gene polymorphisms were associated with lower risk in women consuming high levels of calcium, suggesting that dietary factors may modify associations by VDR genotype

Vitamin D Receptor Polymorphisms and Breast Cancer Risk: Results from the National Cancer Institute Breast and Prostate Cancer Cohort Consortium

Background: Vitamin D is hypothesized to lower the risk of breast cancer by inhibiting cell proliferation via the nuclear vitamin D receptor (VDR). Two common single nucleotide polymorphisms (SNP) in the VDR gene ( VDR ), rs1544410 ( Bsm I), and rs2228570 ( Fok I), have been inconsistently associated with breast cancer risk. Increased risk has been reported for the Fok I ff genotype, which encodes a less transcriptionally active isoform of VDR , and reduced risk has been reported for the Bsm I BB genotype, a SNP in strong linkage disequilibrium with a 3′-untranslated region, which may influence VDR mRNA stability. Methods: We pooled data from 6 prospective studies in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium to examine associations between these SNPs and breast cancer among >6,300 cases and 8,100 controls for each SNP using conditional logistic regression. Results: The odds ratio (OR) for the rs2228570 ( Fok I) ff versus FF genotype in the overall population was statistically significantly elevated [OR, 1.16; 95% confidence interval (95% CI), 1.04-1.28] but was weaker once data from the cohort with previously published positive findings were removed (OR, 1.10; 95% CI, 0.98-1.24). No association was noted between rs1544410 ( Bsm I) BB and breast cancer risk overall (OR, 0.98; 95% CI, 0.89-1.09), but the BB genotype was associated with a significantly lower risk of advanced breast cancer (OR, 0.74; 95% CI, 0.60-0.92). Conclusions: Although the evidence for independent contributions of these variants to breast cancer susceptibility remains equivocal, future large studies should integrate genetic variation in VDR with biomarkers of vitamin D status. (Cancer Epidemiol Biomarkers Prev 2009;18(1):297–305

Who Shares? Who Doesn't? Factors Associated with Openly Archiving Raw Research Data

Many initiatives encourage investigators to share their raw datasets in hopes of increasing research efficiency and quality. Despite these investments of time and money, we do not have a firm grasp of who openly shares raw research data, who doesn't, and which initiatives are correlated with high rates of data sharing. In this analysis I use bibliometric methods to identify patterns in the frequency with which investigators openly archive their raw gene expression microarray datasets after study publication

Atmospheric retrieval of exoplanets

Exoplanetary atmospheric retrieval refers to the inference of atmospheric properties of an exoplanet given an observed spectrum. The atmospheric properties include the chemical compositions, temperature profiles, clouds/hazes, and energy circulation. These properties, in turn, can provide key insights into the atmospheric physicochemical processes of exoplanets as well as their formation mechanisms. Major advancements in atmospheric retrieval have been made in the last decade, thanks to a combination of state-of-the-art spectroscopic observations and advanced atmospheric modeling and statistical inference methods. These developments have already resulted in key constraints on the atmospheric H2O abundances, temperature profiles, and other properties for several exoplanets. Upcoming facilities such as the JWST will further advance this area. The present chapter is a pedagogical review of this exciting frontier of exoplanetary science. The principles of atmospheric retrievals of exoplanets are discussed in detail, including parametric models and statistical inference methods, along with a review of key results in the field. Some of the main challenges in retrievals with current observations are discussed along with new directions and the future landscape

Study protocol: Determinants of participation and quality of life of adolescents with cerebral palsy: a longitudinal study (SPARCLE2)

<p>Abstract</p> <p>Background</p> <p>Children and adults with impairments such as cerebral palsy have lower participation in life situations than able-bodied people. Less is known about their subjective perception of their lives, called their quality of life.</p> <p>During adolescence, rapid physical and psychological changes occur; although these may be more difficult for disabled than for able-bodied adolescents, little research has examined the lives of disabled adolescents.</p> <p>In 2003-4 a European Union funded project, SPARCLE, visited 818 children aged 8-12 years with cerebral palsy, sampled from population-based registers in nine European regions. The quality of life reported by these disabled children was similar to that of the general population but their participation was lower; levels of participation varied between countries even for children with similar severity of cerebral palsy.</p> <p>We are currently following up these children, now aged 13-17 years, to identify (i) to what extent contemporaneous factors (pain, impairment, psychological health and parental stress) predict their participation and quality of life, (ii) what factors modify how participation and quality of life at age 8-12 years are associated with participation and quality of life in adolescence, and (iii) whether differences between European countries in participation and quality of life can be explained by variations in environmental factors.</p> <p>Methods/Design</p> <p>Trained researchers will visit families to administer questionnaires to capture the adolescents' type and severity of impairment, socio-demographic characteristics, participation, quality of life, psychological health, pain, environmental access and parental stress. We will use multivariable models (linear, logistic or ordinal) to assess how adolescent participation, quality of life, psychological health, pain, environmental access and parental stress, vary with impairment and socio-demographic characteristics and, where possible, how these outcomes compare with general population data. For participation and quality of life, longitudinal analyses will assess to what extent these are predicted by corresponding levels in childhood and what factors modify this relationship. Structural equation modelling will be used to identify indirect relationships mediated by other factors.</p

A continuum from clear to cloudy hot-Jupiter exoplanets without primordial water depletion

Thousands of transiting exoplanets have been discovered, but spectral analysis of their atmospheres has so far been dominated by a small number of exoplanets and data spanning relatively narrow wavelength ranges (such as 1.1–1.7 micrometres). Recent studies show that some hot-Jupiter exoplanets have much weaker water absorption features in their near-infrared spectra than predicted. The low amplitude of water signatures could be explained by very low water abundances, which may be a sign that water was depleted in the protoplanetary disk at the planet’s formation location, but it is unclear whether this level of depletion can actually occur. Alternatively, these weak signals could be the result of obscuration by clouds or hazes, as found in some optical spectra. Here we report results from a comparative study of ten hot Jupiters covering the wavelength range 0.3–5 micrometres, which allows us to resolve both the optical scattering and infrared molecular absorption spectroscopically. Our results reveal a diverse group of hot Jupiters that exhibit a continuum from clear to cloudy atmospheres. We find that the difference between the planetary radius measured at optical and infrared wavelengths is an effective metric for distinguishing different atmosphere types. The difference correlates with the spectral strength of water, so that strong water absorption lines are seen in clear-atmosphere planets and the weakest features are associated with clouds and hazes. This result strongly suggests that primordial water depletion during formation is unlikely and that clouds and hazes are the cause of weaker spectral signatures