Recognition of pyrrolysine tRNA by the Desulfitobacterium hafniense pyrrolysyl-tRNA synthetase

Pyrrolysine (Pyl), the 22nd co-translationally inserted amino acid, is incorporated in response to a UAG amber stop codon. Pyrrolysyl-tRNA synthetase (PylRS) attaches Pyl to its cognate tRNA, the special amber suppressor tRNA(Pyl). The genes for tRNA(Pyl) (pylT) and PylRS (pylS) are found in all members of the archaeal family Methanosarcinaceae, and in Desulfitobacterium hafniense. The activation and aminoacylation properties of D. hafniense PylRS and the nature of the tRNA(Pyl) identity elements were determined by measuring the ability of 24 mutant tRNA(Pyl) species to be aminoacylated with the pyrrolysine analog N-ε-cyclopentyloxycarbonyl-l-lysine. The discriminator base G73 and the first base pair (G1·C72) in the acceptor stem were found to be major identity elements. Footprinting analysis showed that PylRS binds tRNA(Pyl) predominantly along the phosphate backbone of the T-loop, the D-stem and the acceptor stem. Significant contacts with the anticodon arm were not observed. The tRNA(Pyl) structure contains the highly conserved T-loop contact U54·A58 and position 57 is conserved as a purine, but the canonical T- to D-loop contact between positions 18 and 56 was not present. Unlike most tRNAs, the tRNA(Pyl) anticodon was shown not to be important for recognition by bacterial PylRS

mpower: An R Package for Power Analysis via Simulation for Correlated Data

Estimating sample size and statistical power is an essential part of a good study design. This R package allows users to conduct power analysis based on Monte Carlo simulations in settings in which consideration of the correlations between predictors is important. It runs power analyses given a data generative model and an inference model. It can set up a data generative model that preserves dependence structures among variables given existing data (continuous, binary, or ordinal) or high-level descriptions of the associations. Users can generate power curves to assess the trade-offs between sample size, effect size, and power of a design. This paper presents tutorials and examples focusing on applications for environmental mixture studies when predictors tend to be moderately to highly correlated. It easily interfaces with several existing and newly developed analysis strategies for assessing associations between exposures and health outcomes. However, the package is sufficiently general to facilitate power simulations in a wide variety of settings

The amino-terminal domain of pyrrolysyl-tRNA synthetase is dispensable in vitro but required for in vivo activity

AbstractPyrrolysine (Pyl) is co-translationally inserted into a subset of proteins in the Methanosarcinaceae and in Desulfitobacterium hafniense programmed by an in-frame UAG stop codon. Suppression of this UAG codon is mediated by the Pyl amber suppressor tRNA, tRNAPyl, which is aminoacylated with Pyl by pyrrolysyl-tRNA synthetase (PylRS). We compared the behavior of several archaeal and bacterial PylRS enzymes towards tRNAPyl. Equilibrium binding analysis revealed that archaeal PylRS proteins bind tRNAPyl with higher affinity (KD=0.1–1.0μM) than D. hafniense PylRS (KD=5.3–6.9μM). In aminoacylation the archaeal PylRS enzymes did not distinguish between archaeal and bacterial tRNAPyl species, while the bacterial PylRS displays a clear preference for the homologous cognate tRNA. We also show that the amino-terminal extension present in archaeal PylRSs is dispensable for in vitro activity, but required for PylRS function in vivo

Prenatal exposure to environmental phenols and childhood fat mass in the Mount Sinai Children's Environmental Health Study

Early life exposure to endocrine disrupting chemicals may alter adipogenesis and energy balance leading to changes in obesity risk. Several studies have evaluated the association of prenatal bisphenol A exposure with childhood body size but only one study of male infants has examined other environmental phenols. Therefore, we assessed associations between prenatal exposure to environmental phenols and fat mass in a prospective birth cohort. We quantified four phenol biomarkers in third trimester maternal spot urine samples in a cohort of women enrolled in New York City between 1998 and 2002 and evaluated fat mass in their children using a Tanita scale between ages 4 and 9 years (173 children with 351 total observations). We estimated associations of standard deviation differences in natural log creatinine-standardized phenol biomarker concentrations with percent fat mass using linear mixed effects regression models. We did not observe associations of bisphenol A or triclosan with childhood percent fat mass. In unadjusted models, maternal urinary concentrations of 2,5-dichlorophenol were associated with greater percent fat mass and benzophenone-3 was associated with lower percent fat mass among children. After adjustment, phenol biomarkers were not associated with percent fat mass. However, the association between benzophenone-3 and percent fat mass was modified by child’s sex: benzophenone-3 concentrations were inversely associated with percent fat mass in girls (beta = −1.51, 95% CI = −3.06, 0.01) but not boys (beta = −0.20, 95% CI = −1.69, 1.26). Although we did not observe strong evidence that prenatal environmental phenols exposures influence the development of childhood adiposity, the potential antiadipogenic effect of benzophenone-3 in girls may warrant further investigation

Multi-monoubiquitylation controls VASP-mediated actin dynamics Icon for The Forest of Biologists

The actin cytoskeleton performs multiple cellular functions, and as such, actin polymerization must be tightly regulated. We previously demonstrated that reversible, non-degradative ubiquitylation regulates the function of the actin polymerase VASP in developing neurons. However, the underlying mechanism of how ubiquitylation impacts VASP activity was unknown. Here, we show that mimicking multi-monoubiquitylation of VASP at K240 and K286 negatively regulates VASP interactions with actin. Using in vitro biochemical assays, we demonstrate the reduced ability of multi-monoubiquitylated VASP to bind, bundle, and elongate actin filaments. However, multi-monoubiquitylated VASP maintained the ability to bind and protect barbed ends from capping protein. Finally, we demonstrate the electroporation of recombinant multi-monoubiquitylated VASP protein altered cell spreading morphology. Collectively, these results suggest a mechanism in which ubiquitylation controls VASP-mediated actin dynamics

Plasmodium falciparum malaria in 1 st –2 nd century CE southern Italy

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Prenatal Phthalate Exposures and Childhood Fat Mass in a New York City Cohort

Background:Experimental animal studies and limited epidemiologic evidence suggest that prenatal exposure to phthalates may be obesogenic, with potential sex-specific effects of phthalates having anti-androgenic activity.Objectives:We aimed to assess associations between prenatal phthalate exposures and childhood fat mass in a prospective cohort study.Methods:We measured phthalate metabolite concentrations in third-trimester maternal urine in a cohort of women enrolled in New York City between 1998 and 2002 (n = 404). Among 180 children (82 girls and 98 boys), we evaluated body composition using a Tanita scale at multiple follow-up visits between ages 4 and 9 years (363 total visits). We estimated associations of standard deviation differences or tertiles of natural log phthalate metabolite concentrations with percent fat mass using linear mixed-effects regression models with random intercepts for repeated outcome measurements. We assessed associations in multiple metabolite models and adjusted for covariates including prepregnancy body mass index, gestational weight gain, maternal smoking during pregnancy, and breastfeeding.Results:We did not observe associations between maternal urinary phthalate concentrations and percent body fat in models examining continuous exposures. Fat mass was 3.06% (95% CI: –5.99, –0.09%) lower among children in the highest tertile of maternal urinary concentrations of summed di(2-ethylhexyl) phthalate (ΣDEHP) metabolites than in children in the lowest tertile. Though estimates were imprecise, there was little evidence that associations between maternal urinary phthalate concentrations and percent fat mass were modified by child’s sex.Conclusions:Prenatal phthalate exposures were not associated with increased body fat among children 4–9 years of age, though high prenatal DEHP exposure may be associated with lower fat mass in childhood.Citation:Buckley JP, Engel SM, Mendez MA, Richardson DB, Daniels JL, Calafat AM, Wolff MS, Herring AH. 2016. Prenatal phthalate exposures and childhood fat mass in a New York City cohort. Environ Health Perspect 124:507–513; http://dx.doi.org/10.1289/ehp.150978

Bayesian Matrix Completion for Hypothesis Testing

High-throughput screening (HTS) is a well-established technology that rapidly and efficiently screens thousands of chemicals for potential toxicity. Massive testing using HTS primarily aims to differentiate active vs inactive chemicals for different types of biological endpoints. However, even using high-throughput technology, it is not feasible to test all possible combinations of chemicals and assay endpoints, resulting in a majority of missing combinations. Our goal is to derive posterior probabilities of activity for each chemical by assay endpoint combination, addressing the sparsity of HTS data. We propose a Bayesian hierarchical framework, which borrows information across different chemicals and assay endpoints in a low-dimensional latent space. This framework facilitates out-of-sample prediction of bioactivity potential for new chemicals not yet tested. Furthermore, this paper makes a novel attempt in toxicology to simultaneously model heteroscedastic errors as well as a nonparametric mean function. It leads to a broader definition of activity whose need has been suggested by toxicologists. Simulation studies demonstrate that our approach shows superior performance with more realistic inferences on activity than current standard methods. Application to an HTS data set identifies chemicals that are most likely active for two disease outcomes: neurodevelopmental disorders and obesity. Code is available on Github

Prenatal Phthalate Exposures and Body Mass Index Among 4- to 7-Year-old Children: A Pooled Analysis

Phthalates are hypothesized to cause obesity, but few studies have assessed whether prenatal phthalate exposures are related to childhood body mass index (BMI)

Maternal ethnic ancestry and adverse perinatal outcomes in New York City

To examine the association between narrowly defined subsets of maternal ethnicity and birth outcomes