Nuclear Architecture Organized by Rif1 Underpins the Replication-Timing Program.

DNA replication is temporally and spatially organized in all eukaryotes, yet the molecular control and biological function of the replication-timing program are unclear. Rif1 is required for normal genome-wide regulation of replication timing, but its molecular function is poorly understood. Here we show that in mouse embryonic stem cells, Rif1 coats late-replicating domains and, with Lamin B1, identifies most of the late-replicating genome. Rif1 is an essential determinant of replication timing of non-Lamin B1-bound late domains. We further demonstrate that Rif1 defines and restricts the interactions between replication-timing domains during the G1 phase, thereby revealing a function of Rif1 as organizer of nuclear architecture. Rif1 loss affects both number and replication-timing specificity of the interactions between replication-timing domains. In addition, during the S phase, Rif1 ensures that replication of interacting domains is temporally coordinated. In summary, our study identifies Rif1 as the molecular link between nuclear architecture and replication-timing establishment in mammals.

Brown Carbon in Primary and Aged Coal Combustion Emission.

Smog chamber experiments were conducted to characterize the light absorption of brown carbon (BrC) from primary and photochemically aged coal combustion emissions. Light absorption was measured by the UV-visible spectrophotometric analysis of water and methanol extracts of filter samples. The single-scattering albedo at 450 nm was 0.73 ± 0.10 for primary emissions and 0.75 ± 0.13 for aged emissions. The light absorption coefficient at 365 nm of methanol extracts was higher than that of water extracts by a factor of 10 for primary emissions and a factor of 7 for aged emissions. This suggests that the majority of BrC is water-insoluble even after aging. The mass absorption efficiency of this BrC (MAE365) for primary OA (POA) was dependent on combustion conditions, with an average of 0.84 ± 0.54 m2 g-1, which was significantly higher than that for aged OA (0.24 ± 0.18 m2 g-1). Secondary OA (SOA) dominated aged OA and the decreased MAE365 after aging indicates that SOA is less light absorbing than POA and/or that BrC is bleached (oxidized) with aging. The estimated MAE365 of SOA (0.14 ± 0.08 m2 g-1) was much lower than that of POA. A comparison of MAE365 of residential coal combustion with other anthropogenic sources suggests that residential coal combustion emissions are among the strongest absorbing BrC organics.

Enhancer loops appear stable during development and are associated with paused polymerase.

Developmental enhancers initiate transcription and are fundamental to our understanding of developmental networks, evolution and disease. Despite their importance, the properties governing enhancer-promoter interactions and their dynamics during embryogenesis remain unclear. At the ß-globin locus, enhancer-promoter interactions appear dynamic and cell-type specific, whereas at the HoxD locus they are stable and ubiquitous, being present in tissues where the target genes are not expressed. The extent to which preformed enhancer-promoter conformations exist at other, more typical, loci and how transcription is eventually triggered is unclear. Here we generated a high-resolution map of enhancer three-dimensional contacts during Drosophila embryogenesis, covering two developmental stages and tissue contexts, at unprecedented resolution. Although local regulatory interactions are common, long-range interactions are highly prevalent within the compact Drosophila genome. Each enhancer contacts multiple enhancers, and promoters with similar expression, suggesting a role in their co-regulation. Notably, most interactions appear unchanged between tissue context and across development, arising before gene activation, and are frequently associated with paused RNA polymerase. Our results indicate that the general topology governing enhancer contacts is conserved from flies to humans and suggest that transcription initiates from preformed enhancer-promoter loops through release of paused polymerase.

Effect of Stove Technology and Combustion Conditions on Gas and Particulate Emissions from Residential Biomass Combustion.

We have systematically examined the gas and particle phase emissions from seven wood combustion devices. Among total carbon mass emitted (excluding CO2), CO emissions were dominant, together with nonmethane volatile organic compounds (NMVOCs) (10-40%). Automated devices emitted 1-3 orders of magnitude lower CH4 (0.002-0.60 g kg-1 of wood) and NMVOCs (0.01-1 g kg-1 of wood) compared to batch-operated devices (CH4: 0.25-2.80 g kg-1 of wood; NMVOCs: 2.5-19 g kg-1 of wood). 60-90% of the total NMVOCs were emitted in the starting phase of batch-operated devices, except for the first load cycles. Partial-load conditions or deviations from the normal recommended operating conditions, such as use of wet wood/wheat pellets, oxygen rich or deficit conditions, significantly enhanced the emissions. NMVOCs were largely dominated by small carboxylic acids and alcohols, and furans. Despite the large variability in NMVOCs emission strengths, the relative contribution of different classes showed large similarities among different devices and combustion phases. We show that specific improper operating conditions may even for advanced technology not result in the emission reduction of secondary organic aerosol (SOA) forming compounds and thus not reduce the impact of wood combustion on climate and health.

Quantification of the impact of cooking processes on indoor concentrations of volatile organic species and primary and secondary organic aerosols.

Cooking is recognized as an important source of particulate pollution in indoor and outdoor environments. We conducted more than 100 individual experiments to characterize the particulate and non-methane organic gas emissions from various cooking processes, their reaction rates, and their secondary organic aerosol yields. We used this emission data to develop a box model, for simulating the cooking emission concentrations in a typical European home and the indoor gas-phase reactions leading to secondary organic aerosol production. Our results suggest that about half of the indoor primary organic aerosol emission rates can be explained by cooking. Emission rates of larger and unsaturated aldehydes likely are dominated by cooking while the emission rates of terpenes are negligible. We found that cooking dominates the particulate and gas-phase air pollution in non-smoking European households exceeding 1000 µg m-3 . While frying processes are the main driver of aldehyde emissions, terpenes are mostly emitted due to the use of condiments. The secondary aerosol production is negligible with around 2 µg m-3 . Our results further show that ambient cooking organic aerosol concentrations can only be explained by super-polluters like restaurants. The model offers a comprehensive framework for identifying the main parameters controlling indoor gas- and particle-phase concentrations.

Characterization of Gas-Phase Organics Using Proton Transfer Reaction Time-of-Flight Mass Spectrometry: Residential Coal Combustion.

Residential coal combustion is a significant contributor to particulate urban air pollution in Chinese mega cities and some regions in Europe. While the particulate emission factors and the chemical characteristics of the organic and inorganic aerosol from coal combustion have been extensively studied, the chemical composition and nonmethane organic gas (NMOG) emission factors from residential coal combustion are mostly unknown. We conducted 23 individual burns in a traditional Chinese stove used for heating and cooking using five different coals with Chinese origins, characterizing the NMOG emissions using a proton transfer reaction time-of-flight mass spectrometer. The measured emission factors range from 1.5 to 14.1 g/kgcoal for bituminous coals and are below 0.1 g/kgcoal for anthracite coals. The emission factors from the bituminous coals are mostly influenced by the time until the coal is fully ignited. The emissions from the bituminous coals are dominated by aromatic and oxygenated aromatic compounds with a significant contribution of hydrocarbons. The results of this study can help to improve urban air pollution modeling in China and Eastern Europe and can be used to constrain a coal burning factor in ambient gas phase positive matrix factorization studies.

A discrete transition zone organizes the topological and regulatory autonomy of the adjacent tfap2c and bmp7 genes.

Despite the well-documented role of remote enhancers in controlling developmental gene expression, the mechanisms that allocate enhancers to genes are poorly characterized. Here, we investigate the cis-regulatory organization of the locus containing the Tfap2c and Bmp7 genes in vivo, using a series of engineered chromosomal rearrangements. While these genes lie adjacent to one another, we demonstrate that they are independently regulated by distinct sets of enhancers, which in turn define non-overlapping regulatory domains. Chromosome conformation capture experiments reveal a corresponding partition of the locus in two distinct structural entities, demarcated by a discrete transition zone. The impact of engineered chromosomal rearrangements on the topology of the locus and the resultant gene expression changes indicate that this transition zone functionally organizes the structural partition of the locus, thereby defining enhancer-target gene allocation. This partition is, however, not absolute: we show that it allows competing interactions across it that may be non-productive for the competing gene, but modulate expression of the competed one. Altogether, these data highlight the prime role of the topological organization of the genome in long-distance regulation of gene expression.

A novel inflammatory pathway mediating rapid hepcidin-independent hypoferremia.

Regulation of iron metabolism and innate immunity are tightly interlinked. The acute phase response to infection and inflammation induces alterations in iron homeostasis that reduce iron supplies to pathogens. The iron hormone hepcidin is activated by such stimuli causing degradation of the iron exporter ferroportin and reduced iron release from macrophages, suggesting that hepcidin is the crucial effector of inflammatory hypoferremia. Here, we report the discovery of an acute inflammatory condition that is mediated by Toll-like receptors 2 and 6 (TLR2 and TLR6) and which induces hypoferremia in mice injected with TLR ligands. Stimulation of TLR2/TLR6 triggers profound decreases in ferroportin messenger RNA and protein expression in bone marrow-derived macrophages, liver, and spleen of mice without changing hepcidin expression. Furthermore, C326S ferroportin mutant mice with a disrupted hepcidin/ferroportin regulatory circuitry respond to injection of the TLR2/6 ligands FSL1 or PAM3CSK4 by ferroportin downregulation and a reduction of serum iron levels. Our findings challenge the prevailing role of hepcidin in hypoferremia and suggest that rapid hepcidin-independent ferroportin downregulation in the major sites of iron recycling may represent a first-line response to restrict iron access for numerous pathogens.

Characterization of Gas-Phase Organics Using Proton Transfer Reaction Time-of-Flight Mass Spectrometry: Aircraft Turbine Engines.

Nonmethane organic gas emissions (NMOGs) from in-service aircraft turbine engines were investigated using a proton transfer reaction time-of-flight mass spectrometer (PTR-ToF-MS) at an engine test facility at Zurich Airport, Switzerland. Experiments consisted of 60 exhaust samples for seven engine types (used in commercial aviation) from two manufacturers at thrust levels ranging from idle to takeoff. Emission indices (EIs) for more than 200 NMOGs were quantified, and the functional group fractions (including acids, carbonyls, aromatics, and aliphatics) were calculated to characterize the exhaust chemical composition at different engine operation modes. Total NMOG emissions were highest at idling with an average EI of 7.8 g/kg fuel and were a factor of ∼40 lower at takeoff thrust. The relative contribution of pure hydrocarbons (particularly aromatics and aliphatics) of the engine exhaust decreased with increasing thrust while the fraction of oxidized compounds, for example, acids and carbonyls increased. Exhaust chemical composition at idle was also affected by engine technology. Older engines emitted a higher fraction of nonoxidized NMOGs compared to newer ones. Idling conditions dominated ground level organic gas emissions. Based on the EI determined here, we estimate that reducing idle emissions could substantially improve air quality near airports.

FourCSeq: analysis of 4C sequencing data.

MOTIVATION: Circularized Chromosome Conformation Capture (4C) is a powerful technique for studying the spatial interactions of a specific genomic region called the 'viewpoint' with the rest of the genome, both in a single condition or comparing different experimental conditions or cell types. Observed ligation frequencies typically show a strong, regular dependence on genomic distance from the viewpoint, on top of which specific interaction peaks are superimposed. Here, we address the computational task to find these specific peaks and to detect changes between different biological conditions. RESULTS: We model the overall trend of decreasing interaction frequency with genomic distance by fitting a smooth monotonically decreasing function to suitably transformed count data. Based on the fit, z-scores are calculated from the residuals, and high z-scores are interpreted as peaks providing evidence for specific interactions. To compare different conditions, we normalize fragment counts between samples, and call for differential contact frequencies using the statistical method DESEQ2: adapted from RNA-Seq analysis. AVAILABILITY AND IMPLEMENTATION: A full end-to-end analysis pipeline is implemented in the R package FourCSeq available at www.bioconductor.org. CONTACT: felix.klein@embl.de or whuber@embl.de SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A chemical-genetic interaction map of small molecules using high-throughput imaging in cancer cells.

Small molecules often affect multiple targets, elicit off-target effects, and induce genotype-specific responses. Chemical genetics, the mapping of the genotype dependence of a small molecule's effects across a broad spectrum of phenotypes can identify novel mechanisms of action. It can also reveal unanticipated effects and could thereby reduce high attrition rates of small molecule development pipelines. Here, we used high-content screening and image analysis to measure effects of 1,280 pharmacologically active compounds on complex phenotypes in isogenic cancer cell lines which harbor activating or inactivating mutations in key oncogenic signaling pathways. Using multiparametric chemical-genetic interaction analysis, we observed phenotypic gene-drug interactions for more than 193 compounds, with many affecting phenotypes other than cell growth. We created a resource termed the Pharmacogenetic Phenome Compendium (PGPC), which enables exploration of drug mode of action, detection of potential off-target effects, and the generation of hypotheses on drug combinations and synergism. For example, we demonstrate that MEK inhibitors amplify the viability effect of the clinically used anti-alcoholism drug disulfiram and show that the EGFR inhibitor tyrphostin AG555 has off-target activity on the proteasome. Taken together, this study demonstrates how combining multiparametric phenotyping in different genetic backgrounds can be used to predict additional mechanisms of action and to reposition clinically used drugs.

Inorganic Salt Interference on CO2+ in Aerodyne AMS and ACSM Organic Aerosol Composition Studies.

Aerodyne aerosol mass spectrometer (AMS) and Aerodyne aerosol chemical speciation monitor (ACSM) mass spectra are widely used to quantify organic aerosol (OA) elemental composition, oxidation state, and major environmental sources. The OA CO2+ fragment is among the most important measurements for such analyses. Here, we show that a non-OA CO2+ signal can arise from reactions on the particle vaporizer, ion chamber, or both, induced by thermal decomposition products of inorganic salts. In our tests (eight instruments, n = 29), ammonium nitrate (NH4NO3) causes a median CO2+ interference signal of +3.4% relative to nitrate. This interference is highly variable between instruments and with measurement history (percentiles P10-90 = +0.4 to +10.2%). Other semi-refractory nitrate salts showed 2-10 times enhanced interference compared to that of NH4NO3, while the ammonium sulfate ((NH4)2SO4) induced interference was 3-10 times lower. Propagation of the CO2+ interference to other ions during standard AMS and ACSM data analysis affects the calculated OA mass, mass spectra, molecular oxygen-to-carbon ratio (O/C), and f44. The resulting bias may be trivial for most ambient data sets but can be significant for aerosol with higher inorganic fractions (>50%), e.g., for low ambient temperatures, or laboratory experiments. The large variation between instruments makes it imperative to regularly quantify this effect on individual AMS and ACSM systems.

Characterization of Gas-Phase Organics Using Proton Transfer Reaction Time-of-Flight Mass Spectrometry: Cooking Emissions.

Cooking processes produce gaseous and particle emissions that are potentially deleterious to human health. Using a highly controlled experimental setup involving a proton-transfer-reaction time-of-flight mass spectrometer (PTR-ToF-MS), we investigate the emission factors and the detailed chemical composition of gas phase emissions from a broad variety of cooking styles and techniques. A total of 95 experiments were conducted to characterize nonmethane organic gas (NMOG) emissions from boiling, charbroiling, shallow frying, and deep frying of various vegetables and meats, as well as emissions from vegetable oils heated to different temperatures. Emissions from boiling vegetables are dominated by methanol. Significant amounts of dimethyl sulfide are emitted from cruciferous vegetables. Emissions from shallow frying, deep frying and charbroiling are dominated by aldehydes of differing relative composition depending on the oil used. We show that the emission factors of some aldehydes are particularly large which may result in considerable negative impacts on human health in indoor environments. The suitability of some of the aldehydes as tracers for the identification of cooking emissions in ambient air is discussed.

Live synthesis.

Synthesis automatically constructs an implementation that satisfies a given logical specification. In this paper, we study the live synthesis problem, where the synthesized implementation replaces an already running system. In addition to satisfying its own specification, the synthesized implementation must guarantee a sound transition from the previous implementation. This version of the synthesis problem is highly relevant in "always-on" applications, where updates happen while the system is running. To specify the correct handover between the old and new implementation, we introduce an extension of linear-time temporal logic (LTL) called LiveLTL. A LiveLTL specification defines separate requirements on the two implementations and ensures that the new implementation satisfies, in addition to its own requirements, any obligations left unfinished by the old implementation. For specifications in LiveLTL, we show that the live synthesis problem can be solved within the same complexity bound as standard reactive synthesis, i.e., in 2EXPTIME. Our experiments show the necessity of live synthesis for LiveLTL specifications created from benchmarks of SYNTCOMP and robot control.

Gain of CTCF-Anchored Chromatin Loops Marks the Exit from Naive Pluripotency.

The genome of pluripotent stem cells adopts a unique three-dimensional architecture featuring weakly condensed heterochromatin and large nucleosome-free regions. Yet, it is unknown whether structural loops and contact domains display characteristics that distinguish embryonic stem cells (ESCs) from differentiated cell types. We used genome-wide chromosome conformation capture and super-resolution imaging to determine nuclear organization in mouse ESC and neural stem cell (NSC) derivatives. We found that loss of pluripotency is accompanied by widespread gain of structural loops. This general architectural change correlates with enhanced binding of CTCF and cohesins and more pronounced insulation of contacts across chromatin boundaries in lineage-committed cells. Reprogramming NSCs to pluripotency restores the unique features of ESC domain topology. Domains defined by the anchors of loops established upon differentiation are enriched for developmental genes. Chromatin loop formation is a pervasive structural alteration to the genome that accompanies exit from pluripotency and delineates the spatial segregation of developmentally regulated genes.

The Shh Topological Domain Facilitates the Action of Remote Enhancers by Reducing the Effects of Genomic Distances.

Gene expression often requires interaction between promoters and distant enhancers, which occur within the context of highly organized topologically associating domains (TADs). Using a series of engineered chromosomal rearrangements at the Shh locus, we carried out an extensive fine-scale characterization of the factors that govern the long-range regulatory interactions controlling Shh expression. We show that Shh enhancers act pervasively, yet not uniformly, throughout the TAD. Importantly, changing intra-TAD distances had no impact on Shh expression. In contrast, inversions disrupting the TAD altered global folding of the region and prevented regulatory contacts in a distance-dependent manner. Our data indicate that the Shh TAD promotes distance-independent contacts between distant regions that would otherwise interact only sporadically, enabling functional communication between them. In large genomes where genomic distances per se can limit regulatory interactions, this function of TADs could be as essential for gene expression as the formation of insulated neighborhoods.

Identification of significant precursor gases of secondary organic aerosols from residential wood combustion.

Organic gases undergoing conversion to form secondary organic aerosol (SOA) during atmospheric aging are largely unidentified, particularly in regions influenced by anthropogenic emissions. SOA dominates the atmospheric organic aerosol burden and this knowledge gap contributes to uncertainties in aerosol effects on climate and human health. Here we characterize primary and aged emissions from residential wood combustion using high resolution mass spectrometry to identify SOA precursors. We determine that SOA precursors traditionally included in models account for only ~3-27% of the observed SOA, whereas for the first time we explain ~84-116% of the SOA by inclusion of non-traditional precursors. Although hundreds of organic gases are emitted during wood combustion, SOA is dominated by the aging products of only 22 compounds. In some cases, oxidation products of phenol, naphthalene and benzene alone comprise up to ~80% of the observed SOA. Identifying the main precursors responsible for SOA formation enables improved model parameterizations and SOA mitigation strategies in regions impacted by residential wood combustion, more productive targets for ambient monitoring programs and future laboratories studies, and links between direct emissions and SOA impacts on climate and health in these regions.

Indoor terpene emissions from cooking with herbs and pepper and their secondary organic aerosol production potential.

Cooking is widely recognized as an important source of indoor and outdoor particle and volatile organic compound emissions with potential deleterious effects on human health. Nevertheless, cooking emissions remain poorly characterized. Here the effect of herbs and pepper on cooking emissions was investigated for the first time to the best of our knowledge using state of the art mass spectrometric analysis of particle and gas-phase composition. Further, the secondary organic aerosol production potential of the gas-phase emissions was determined by smog chamber aging experiments. The emissions of frying meat with herbs and pepper include large amounts of mono-, sesqui- and diterpenes as well as various terpenoids and p-cymene. The average total terpene emission rate from the use of herbs and pepper during cooking is estimated to be 46 ± 5 gg-1Herbs min-1. These compounds are highly reactive in the atmosphere and lead to significant amounts of secondary organic aerosol upon aging. In summary we demonstrate that cooking with condiments can constitute an important yet overlooked source of terpenes in indoor air.

XML3D and Xflow: combining declarative 3D for the Web with generic data flows.

Researchers have combined XML3D, which provides declarative, interactive 3D scene descriptions based on HTML5, with Xflow, a language for declarative, high-performance data processing. The result lets Web developers combine a 3D scene graph with data flows for dynamic meshes, animations, image processing, and postprocessing.