Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

DataSheet1_Estimating provisional margins of exposure for data-poor chemicals using high-throughput computational methods.ZIP

Current computational technologies hold promise for prioritizing the testing of the thousands of chemicals in commerce. Here, a case study is presented demonstrating comparative risk-prioritization approaches based on the ratio of surrogate hazard and exposure data, called margins of exposure (MoEs). Exposures were estimated using a U.S. EPA’s ExpoCast predictive model (SEEM3) results and estimates of bioactivity were predicted using: 1) Oral equivalent doses (OEDs) derived from U.S. EPA’s ToxCast high-throughput screening program, together with in vitro to in vivo extrapolation and 2) thresholds of toxicological concern (TTCs) determined using a structure-based decision-tree using the Toxtree open source software. To ground-truth these computational approaches, we compared the MoEs based on predicted noncancer TTC and OED values to those derived using the traditional method of deriving points of departure from no-observed adverse effect levels (NOAELs) from in vivo oral exposures in rodents. TTC-based MoEs were lower than NOAEL-based MoEs for 520 out of 522 (99.6%) compounds in this smaller overlapping dataset, but were relatively well correlated with the same (r2 = 0.59). TTC-based MoEs were also lower than OED-based MoEs for 590 (83.2%) of the 709 evaluated chemicals, indicating that TTCs may serve as a conservative surrogate in the absence of chemical-specific experimental data. The TTC-based MoE prioritization process was then applied to over 45,000 curated environmental chemical structures as a proof-of-concept for high-throughput prioritization using TTC-based MoEs. This study demonstrates the utility of exploiting existing computational methods at the pre-assessment phase of a tiered risk-based approach to quickly, and conservatively, prioritize thousands of untested chemicals for further study.</p

MHz free electron laser x-ray diffraction and modeling of pulsed laser heated diamond anvil cell

International audienceA new diamond anvil cell experimental approach has been implemented at the European x-ray Free Electron Laser, combining pulsed laser heating with MHz x-ray diffraction. Here, we use this setup to determine liquidus temperatures under extreme conditions, based on the determination of time-resolved crystallization. The focus is on a Fe-Si-O ternary system, relevant for planetary cores. This time-resolved diagnostic is complemented by a finite-element model, reproducing temporal temperature profiles measured experimentally using streaked optical pyrometry. This model calculates the temperature and strain fields by including (i) pressure and temperature dependencies of material properties, and (ii) the heat-induced thermal stress, including feedback effect on material parameter variations. Making our model more realistic, these improvements are critical as they give 7000 K temperature differences compared to previous models. Laser intensities are determined by seeking minimal deviation between measured and modeled temperatures. Combining models and streak optical pyrometry data extends temperature determination below detection limit. The presented approach can be used to infer the liquidus temperature by the appearance of SiO2 diffraction spots. In addition, temperatures obtained by the model agree with crystallization temperatures reported for Fe–Si alloys. Our model reproduces the planetary relevant experimental conditions, providing temperature, pressure, and volume conditions. Those predictions are then used to determine liquidus temperatures at experimental timescales where chemical migration is limited. This synergy of novel time-resolved experiments and finite-element modeling pushes further the interpretation capabilities in diamond anvil cell experiments

Dynamic optical spectroscopy and pyrometry of static targets under optical and x-ray laser heating at the European XFEL

Experiments accessing extreme conditions at x-ray free electron lasers (XFELs) involve rapidly evolving conditions of temperature. Here, we report time-resolved, direct measurements of temperature using spectral streaked optical pyrometry of x-ray and optical laser-heated states at the High Energy Density instrument of the European XFEL. This collection of typical experiments, coupled with numerical models, outlines the reliability, precision, and meaning of time dependent temperature measurements using optical emission at XFEL sources. Dynamic temperatures above 1500 K are measured continuously from spectrally- and temporally-resolved thermal emission at 450–850 nm, with time resolution down to 10–100 ns for 1–200 μs streak camera windows, using single shot and integrated modes. Targets include zero-pressure foils free-standing in air and in vacuo, and high-pressure samples compressed in diamond anvil cell multi-layer targets. Radiation sources used are 20-fs hard x-ray laser pulses at 17.8 keV, in single pulses or 2.26 MHz pulse trains of up to 30 pulses, and 250-ns infrared laser single pulses. A range of further possibilities for optical measurements of visible light in x-ray laser experiments using streak optical spectroscopy are also explored, including for the study of x-ray induced optical fluorescence, which often appears as background in thermal radiation measurements. We establish several scenarios where combined emissions from multiple sources are observed and discuss their interpretation. Challenges posed by using x-ray lasers as non-invasive probes of the sample state are addressed.ISSN:0021-8979ISSN:1089-755