Targeted Mutagenesis of Tsix Leads to Nonrandom X Inactivation

AbstractDuring X inactivation, mammalian female cells make the selection of one active and one inactive X chromosome. X chromosome choice occurs randomly and results in Xist upregulation on the inactive X. We have hypothesized that the antisense gene, Tsix, controls Xist expression. Here, we create a targeted deletion of Tsix in female and male mouse cells. Despite a deficiency of Tsix RNA, X chromosome counting remains intact: female cells still inactivate one X, while male cells block X inactivation. However, heterozygous female cells show skewed Xist expression and primary nonrandom inactivation of the mutant X. The ability of the mutant X to block Xist accumulation is compromised. We conclude that Tsix regulates Xist in cis and determines X chromosome choice without affecting silencing. Therefore, counting, choice, and silencing are genetically separable. Contrasting effects in XX and XY cells argue that negative and positive factors are involved in choosing active and inactive Xs

Aerosol effects on the photochemistry in Mexico City during MCMA-2006/MILAGRO campaign

In the present study, the impact of aerosols on the photochemistry in Mexico City is evaluated using the WRF-CHEM model for the period from 24 to 29 March during the MCMA-2006/MILAGRO campaign. An aerosol radiative module has been developed with detailed consideration of aerosol size, composition, and mixing. The module has been coupled into the WRF-CHEM model to calculate the aerosol optical properties, including optical depth, single scattering albedo, and asymmetry factor. Calculated aerosol optical properties are in good agreement with the surface observations and aircraft and satellite measurements during daytime. In general, the photolysis rates are reduced due to the absorption by carbonaceous aerosols, particularly in the early morning and late afternoon hours with a long aerosol optical path. However, with the growth of aerosol particles and the decrease of the solar zenith angle around noontime, aerosols can slightly enhance photolysis rates when ultraviolet (UV) radiation scattering dominates UV absorption by aerosols at the lower-most model layer. The changes in photolysis rates due to aerosols lead to about 2–17 % surface ozone reduction during daytime in the urban area in Mexico City with generally larger reductions during early morning hours near the city center, resulting in a decrease of OH level by about 9 %, as well as a decrease in the daytime concentrations of nitrate and secondary organic aerosols by 5–6 % on average. In addition, the rapid aging of black carbon aerosols and the enhanced absorption of UV radiation by organic aerosols contribute substantially to the reduction of photolysis rates.National Science Foundation (U.S.). Atmospheric Chemistry Program (ATM-0528227)National Science Foundation (U.S.). Atmospheric Chemistry Program (ATM-0810931)Molina Center for Energy and the Environmen

Combinatorial regulation of transcription factors and microRNAs

<p>Abstract</p> <p>Background</p> <p>Gene regulation is a key factor in gaining a full understanding of molecular biology. <it>Cis</it>-regulatory modules (CRMs), consisting of multiple transcription factor binding sites, have been confirmed as the main regulators in gene expression. In recent years, a novel regulator known as microRNA (miRNA) has been found to play an important role in gene regulation. Meanwhile, transcription factor and microRNA co-regulation has been widely identified. Thus, the relationships between CRMs and microRNAs have generated interest among biologists.</p> <p>Results</p> <p>We constructed new combinatorial regulatory modules based on CRMs and miRNAs. By analyzing their effect on gene expression profiles, we found that genes targeted by both CRMs and miRNAs express in a significantly similar way. Furthermore, we constructed a regulatory network composed of CRMs, miRNAs, and their target genes. Investigating its structure, we found that the feed forward loop is a significant network motif, which plays an important role in gene regulation. In addition, we further analyzed the effect of miRNAs in embryonic cells, and we found that mir-154, as well as some other miRNAs, have significant co-regulation effect with CRMs in embryonic development.</p> <p>Conclusions</p> <p>Based on the co-regulation of CRMs and miRNAs, we constructed a novel combinatorial regulatory network which was found to play an important role in gene regulation, particularly during embryonic development.</p

Impacts of sea-land and mountain-valley circulations on the air pollution in Beijing-Tianjin-Hebei (BTH): A case study

In the study, observational data analyses and the WRF-CHEM model simulations are used to investigate the role of sea-land and mountain-valley breeze circulations in a severe air pollution event occurred in Beijing-Tianjin-Hebei (BTH) during August 9-10, 2013. Both the wind observations and the model simulations have clearly indicated the evolution of the sea-land and mountain-valley breeze circulations during the event. The WRF-CHEM model generally reproduces the local meteorological circulations and also performs well in simulating temporal variations and spatial distributions of fine particulate matters (PM2.5) and ozone (O-3) concentrations compared to observations in BTH. The model results have shown that the offshore land breeze transports the pollutants formed in Shandong province to the Bohai Gulf in the morning, causing the formation of high O-3 and PM2.5 concentrations over the gulf. The onshore sea breeze not only causes the formation of a convergence zone to induce upward movement, mitigating the surface pollution to some degree, also recirculates the pollutants over the gulf to deteriorate the air quality in the coastal area. The upward valley breeze brings the pollutants in the urban area of Beijing to the mountain area in the afternoon, and the downward mountain breeze transports the pollutants back during nighttime. The intensity of the mountain-valley breeze circulation is weak compared to the land-sea breeze circulation in BTH. It is worth noting that the local circulations play an important role when the large-scale meteorological conditions are relatively weak. (C) 2017 Elsevier Ltd. All rights reserved

Evaluation of WRF mesoscale simulations and particle trajectory analysis for the MILAGRO field campaign

Accurate numerical simulations of the complex wind flows in the Mexico City Metropolitan Area (MCMA) can be an invaluable tool for interpreting the MILAGRO field campaign results. This paper uses three methods to evaluate numerical simulations of basin meteorology using the MM5 and WRF models: statistical comparisons with observations, "Concentration Field Analysis" (CFA) using measured air pollutant concentrations, and comparison of flow features using cluster analysis. CFA is shown to be a better indication of simulation quality than statistical metrics, and WRF simulations are shown to be an improvement on the MM5 ones. Comparisons with clusters identifies an under-representation of the drainage flows into the basin and an over-representation of wind shear in the boundary layer. Particle trajectories simulated with WRF-FLEXPART are then used to analyse the transport of the urban plume and show rapid venting and limited recirculation during MILAGRO. Lagrangian impacts were identified at the campaign supersites, and age spectra of the pollutants evaluated at those same sites. The evaluation presented in the paper show that mesoscale meteorological simulations are of sufficient accuracy to be useful for MILAGRO data analysis.National Science Foundation (U.S.) (Award ATM-0511803)National Science Foundation (U.S.) (Award ATM-0810950)National Science Foundation (U.S.) (Award ATM-0810931)Molina Center for Energy and the Environmen

Sources and production of organic aerosol in Mexico City: insights from the combination of a chemical transport model (PMCAMx-2008) and measurements

Urban areas are large sources of organic aerosols and their precursors. Nevertheless, the contributions of primary (POA) and secondary organic aerosol (SOA) to the observed particulate matter levels have been difficult to quantify. In this study the three-dimensional chemical transport model PMCAMx-2008 is used to investigate the temporal and geographic variability of organic aerosol in the Mexico City Metropolitan Area (MCMA) during the MILAGRO campaign that took place in the spring of 2006. The organic module of PMCAMx-2008 includes the recently developed volatility basis-set framework in which both primary and secondary organic components are assumed to be semi-volatile and photochemically reactive and are distributed in logarithmically spaced volatility bins. The MCMA emission inventory is modified and the POA emissions are distributed by volatility based on dilution experiments. The model predictions are compared with observations from four different types of sites, an urban (T0), a suburban (T1), a rural (T2), and an elevated site in Pico de Tres Padres (PTP). The performance of the model in reproducing organic mass concentrations in these sites is encouraging. The average predicted PM[subscript 1] organic aerosol (OA) concentration in T0, T1, and T2 is 18 μg m[superscript −3], 11.7 μg m[superscript −3], and 10.5 μg m[superscript −3] respectively, while the corresponding measured values are 17.2 μg m[superscript −3], 11 μg m[superscript −3], and 9 μg m[superscript −3]. The average predicted locally-emitted primary OA concentrations, 4.4 μg m[superscript −3] at T0, 1.2 μg m[superscript −3] at T1 and 1.7 μg m[superscript −3] at PTP, are in reasonably good agreement with the corresponding PMF analysis estimates based on the Aerosol Mass Spectrometer (AMS) observations of 4.5, 1.3, and 2.9 μg m[superscript −3] respectively. The model reproduces reasonably well the average oxygenated OA (OOA) levels in T0 (7.5 μg m[superscript −3] predicted versus 7.5 μg m[superscript −3] measured), in T1 (6.3 μg m[superscript −3] predicted versus 4.6 μg m[superscript −3] measured) and in PTP (6.6 μg m[superscript −3] predicted versus 5.9 μg m[superscript −3] measured). The rest of the OA mass (6.1 μg m[superscript −3] and 4.2 μg m[superscript −3] in T0 and T1 respectively) is assumed to originate from biomass burning activities and is introduced to the model as part of the boundary conditions. Inside Mexico City (at T0), the locally-produced OA is predicted to be on average 60 % locally-emitted primary (POA), 6 % semi-volatile (S-SOA) and intermediate volatile (I-SOA) organic aerosol, and 34 % traditional SOA from the oxidation of VOCs (V-SOA). The average contributions of the OA components to the locally-produced OA for the entire modelling domain are predicted to be 32 % POA, 10 % S-SOA and I-SOA, and 58 % V-SOA. The long range transport from biomass burning activities and other sources in Mexico is predicted to contribute on average almost as much as the local sources during the MILAGRO period.European UnionSeventh Framework Programme (European Commission) (Grant agreement no.: 212520)National Science Foundation (U.S.) (ATM 0732598)Molina Center for Energy and the EnvironmentNational Science Foundation (U.S.) (ATM 0528227)National Science Foundation (U.S.) (ATM 0810931

Ozone response to emission changes: a modeling study during the MCMA-2006/MILAGRO Campaign

The sensitivity of ozone production to precursor emissions was investigated under five different meteorological conditions in the Mexico City Metropolitan Area (MCMA) during the MCMA-2006/MILAGRO field campaign using the gridded photochemical model CAMx driven by observation-nudged WRF meteorology. Precursor emissions were constrained by the comprehensive data from the field campaign and the routine ambient air quality monitoring network. Simulated plume mixing and transport were examined by comparing with measurements from the G-1 aircraft during the campaign. The observed concentrations of ozone precursors and ozone were reasonably well reproduced by the model. The effects of reducing precursor emissions on urban ozone production were performed for three representative emission control scenarios. A 50% reduction in VOC emissions led to 7 to 22 ppb decrease in daily maximum ozone concentrations, while a 50% reduction in NOx [NO subscript x] emissions leads to 4 to 21 ppb increase, and 50% reductions in both NOx [NO subscript x] and VOC emission decrease the daily maximum ozone concentrations up to 10 ppb. These results along with a chemical indicator analysis using the chemical production ratios of H2O2 [H subscript 2 O subscript 2] to HNO3 [HNO subscript 3] demonstrate that the MCMA urban core region is VOC-limited for all meteorological episodes, which is consistent with the results from MCMA-2003 field campaign; however the degree of the VOC-sensitivity is higher during MCMA-2006 due to lower VOCs, lower VOC reactivity and moderately higher NOx [NO subscript x] emissions. Ozone formation in the surrounding mountain/rural area is mostly NOx-limited [NO subscript x - limited], but can be VOC-limited, and the range of the NOx-limited [NO subscript x - limited] or VOC-limited areas depends on meteorology.United States. Dept. of Energy. Office of Biological and Environmental Research. Atmospheric Science Program (DE-FG02-05ER63980)National Science Foundation (U.S.). Atmospheric Chemistry Program (ATM-0528227)National Science Foundation (U.S.). Atmospheric Chemistry Program (ATM-810931)Mexico. Comisión Ambiental MetropolitanaMolina Center for Energy and the Environmen

First in Man Studies of Pharmacokinetic Profiles of a Novel Oral PTH(1-34)

Background: PTH(1-34) (Teriparatide) is an anabolic agent used in treatment of osteoporosis. It promotes bone formation and reduces the risk of vertebral and some non-vertebral fractures. The route of administration by daily subcutaneous (sc) injection can cause problems in certain patients. A new oral delivery system for human PTH(1-34) has been developed as a possible treatment option. Galitzer et al. presented pre-clinical data (ASBMR 2012, MO0402) and first-in-human results (ASBMR 2013, FR0378) on safety, tolerability and absorption dynamics of oral PTH(1-34) in various dosages. We now describe the pharmacokinetics (PK) of oral PTH(1-34) compared to sc and placebo in healthy subjects. Objective: A single-center, double blinded, triple crossover study was designed to compare the 1.8 mg optimal dose of oral PTH(1-34) against standard dosage of teriparatide injection and oral placebo. Method: The study was conducted following and in accordance with the Hadassah Medical Center ethical approval committee. 12 healthy volunteers (6m/6f), 18-50y, received three treatments: single sc injection of 20µg FORTEO®, 1.8 mg oral PTH(1-34), or placebo. Blood samples were collected at time 0, 10, 15, 20, 30, 45, 60, 75, 90, 120, 180, 240, 300 minute post dose. Plasma concentration of PTH(1-34) (IDS, Tyne and Wear, UK) and cyclic adenosine 3’,5’monophosphate (cAMP) were measured on all samples. Results: All 12 subjects on oral PTH(1-34) showed rapid, post dose increase then decrease of PTH(1-34), from baseline mean (±SD) of 5.9 (1.8) pg/mL to peak mean of 185.3 (±128.8) pg/mL. PK profiles of oral PTH(1-34) showed Cmax (pg/mL), Tmax (mins), AUC0-last of 238.3 (110.8), 17.5 (5.4) and 6161.7 (2726.7), respectively; whereas sc showed mean Cmax (pg/mL), Tmax (mins), AUC0-last of 172.3 (55.7), 20.8 (8.7) and 13965.9 (2984.8), respectively. Plasma cAMP increased in all subjects in response to oral PTH(1-34) and sc treatment. Serum adjusted calcium in all subjects remained within normal limits throughout the studies. Conclusion: PK profiles showed a single oral dose of 1.8 mg PTH(1-34) is rapidly absorbed, and no significant difference in Cmax and Tmax when compared with 20µg of sc teriparatide. A significant difference in the rate of plasma clearance and AUC0-last value was observed (fig.1). These differing profiles and modality of administration of PTH(1-34) could offer unique advantages in the treatment of calcium and metabolic bone disorders

A possible pathway for rapid growth of sulfate during haze days in China

Rapid industrialization and urbanization have caused frequent occurrence of haze in China during wintertime in recent years. The sulfate aerosol is one of the most important components of fine particles (PM[subscript 2. 5]) in the atmosphere, contributing significantly to the haze formation. However, the heterogeneous formation mechanism of sulfate remains poorly characterized. The relationships of the observed sulfate with PM[subscript 2. 5], iron, and relative humidity in Xi'an, China have been employed to evaluate the mechanism and to develop a parameterization of the sulfate heterogeneous formation involving aerosol water for incorporation into atmospheric chemical transport models. Model simulations with the proposed parameterization can successfully reproduce the observed sulfate rapid growth and diurnal variations in Xi'an and Beijing, China. Reasonable representation of sulfate heterogeneous formation in chemical transport models considerably improves the PM2. 5 simulations, providing the underlying basis for better understanding the haze formation and supporting the design and implementation of emission control strategies

Systematic identification of conserved motif modules in the human genome

Background: The identification of motif modules, groups of multiple motifs frequently occurring in DNA sequences, is one of the most important tasks necessary for annotating the human genome. Current approaches to identifying motif modules are often restricted to searches within promoter regions or rely on multiple genome alignments. However, the promoter regions only account for a limited number of locations where transcription factor binding sites can occur, and multiple genome alignments often cannot align binding sites with their true counterparts because of the short and degenerative nature of these transcription factor binding sites. Results: To identify motif modules systematically, we developed a computational method for the entire non-coding regions around human genes that does not rely upon the use of multiple genome alignments. First, we selected orthologous DNA blocks approximately 1-kilobase in length based on discontiguous sequence similarity. Next, we scanned the conserved segments in these blocks using known motifs in the TRANSFAC database. Finally, a frequent pattern mining technique was applied to identify motif modules within these blocks. In total, with a false discovery rate cutoff of 0.05, we predicted 3,161,839 motif modules, 90.8% of which are supported by various forms of functional evidence. Compared with experimental data from 14 ChIP-seq experiments, on average, our methods predicted 69.6% of the ChIP-seq peaks with TFBSs of multiple TFs. Our findings also show that many motif modules have distance preference and order preference among the motifs, which further supports the functionality of these predictions. Conclusions: Our work provides a large-scale prediction of motif modules in mammals, which will facilitate the understanding of gene regulation in a systematic way