Diesel exhaust and house dust mite allergen lead to common changes in the airway methylome and hydroxymethylome.

Exposures to diesel exhaust particles (DEP) from traffic and house dust mite (HDM) allergens significantly increase risks of airway diseases, including asthma. This negative impact of DEP and HDM may in part be mediated by epigenetic mechanisms. Beyond functioning as a mechanical barrier, airway epithelial cells provide the first line of immune defense towards DEP and HDM exposures. To understand the epigenetic responses of airway epithelial cells to these exposures, we exposed human bronchial epithelial cells to DEP and HDM and studied genome-wide 5-methyl-cytosine (5mC) and 5-hydroxy-methylcytosine (5hmC) at base resolution. We found that exposures to DEP and HDM result in elevated TET1 and DNMT1 expression, associated with 5mC and 5hmC changes. Interestingly, over 20% of CpG sites are responsive to both exposures and changes in 5mC at these sites negatively correlated with gene expression differences. These 5mC and 5hmC changes are located in genes and pathways related to oxidative stress responses, epithelial function and immune cell responses and are enriched for binding sites of transcription factors (TFs) involved in these pathways. Histone marks associated with promoters, enhancers and actively transcribed gene bodies were associated with exposure-induced DNA methylation changes. Collectively, our data suggest that exposures to DEP and HDM alter 5mC and 5hmC levels at regulatory regions bound by TFs, which coordinate with histone marks to regulate gene networks of oxidative stress responses, epithelial function and immune cell responses. These observations provide novel insights into the epigenetic mechanisms that mediate the epithelial responses to DEP and HDM in airways

The androgen receptor and signal-transduction pathways in hormone-refractory prostate cancer. Part 2: androgen-receptor cofactors and bypass pathways

Prostate cancer is the second leading cause of cancer related deaths in men from the western world. Treatment of prostate cancer has relied on androgen deprivation therapy for the past 50 years. Response rates are initially high (70-80%), however almost all patients develop androgen escape and subsequently die within 1-2 years. Unlike breast cancer, alternative approaches (chemotherapy and radiotherapy) do not increase survival time. The high rate of prostate cancer mortality is therefore strongly linked to both development of androgen escape and the lack of alternate therapies. AR mutations and amplifications can not explain all cases of androgen escape and post-translational modification of the AR has become an alternative theory. However recently it has been suggested that AR co-activators e.g. SRC-1 or pathways the bypass the AR (Ras/MAP kinase or PI3K/Akt) may stimulated prostate cancer progression independent of the AR. This review will focus on how AR coactivators may act to increase AR transactivation during sub-optimal DHT concentrations and also how signal transduction pathways may promote androgen escape via activation of transcription factors, e.g. AP-1, c-Myc and Myb, that induce cell proliferation or inhibit apoptosis

Trace chemical measurements from the northern midlatitude lowermost stratosphere in early spring: Distributions, correlations, and fate

In situ measurements of a large number of trace chemicals from the midlatitude (37-57°N) lower stratosphere were performed with the NASA DC-8 aircraft during March 1994. Deepest penetrations into the stratosphere (550 ppb O3, 279 ppb N2O, and 350 K potential temperature) corresponded to a region that has been defined as the "lowermost stratosphere" (LS) by Holton et al [1995]. Analysis of data shows that the mixing ratios of long-lived tracer species (e. g. CH4, HNO3, NOy, CFCs) are linearly correlated with those of O3 and N2O. A ΔNOy/ΔO3 of 0.0054 ppb/ppb and ΔNOy/ΔN2O of -0.081 ppb/ppb is in good agreement with other reported measurements from the DC-8. These slopes are however, somewhat steeper than those reported from the ER-2 airborne studies. We find that the reactive nitrogen budget in the LS is largely balanced with HNO3 accounting for 80% of NOy, and PAN and NOx together accounting for 5%. A number of oxygenated species (e. g. acetone, H2O2) were present and may provide an important in situ source of HOx in the LS. SO2 mixing ratios were found to increase in the stratosphere at a rate that was comparable to the decline in OCS levels. No evidence of particle formation could be observed. Ethane, propane, and acetylene mixing ratios declined rapidly in the LS with Cl atoms likely playing a key role in this process. A number of reactive hydrocarbons/halocarbons (e. g. C6H6, CH3I) were present at low but measurable concentrations

Latitudinal distribution of reactive nitrogen in the free troposphere over the Pacific Ocean in late winter/early spring

The late winter/early spring (February/March, 1994) measurements of Pacific Exploratory Mission-West (PEM-W) B have been analyzed to show latitudinal distributions (45°N to 10°S) of the mixing ratios of reactive nitrogen species (NO, peroxyacetylnitrate (PAN), HNO3, and NOy), ozone, and chemical tracers (CO, NMHCs, acetone, and C2Cl4) with a focus on the upper troposphere. Mixing ratios of all species are relatively low in the warm tropical and subtropical air south of the polar jetstream (≈28°N) but increase sharply with latitude in the cold polar air north of the jetstream. Noteworthy is the continuous increase in reservoir species (PAN and HNO3) and the simultaneous decrease in NOx toward the northern midlatitudes. The Harvard global three-dimensional model of tropospheric chemistry has been used to compare these observations with predictions. In the upper troposphere the magnitude and distribution of measured NOy and PAN as a function of latitude is well represented by this model, while NOx (measured NO + model calculated NO2) is underpredicted, especially in the tropics. Unlike several previous studies, where model-predicted HNO3 exceeded observations by as much as a factor of 10, the present data/model comparison is improved to within a factor of 2. The predicted upper tropospheric HNO3 is generally below or near measured values, and there is little need to invoke particle reactions as a means of removing or recycling HNO3. Comparison between measured NOy and the sum of its three main constituents (PAN + NOx + HNO3) on average show a small mean shortfall (<15%). This shortfall could be attributed to the presence of known but unmeasured species (e.g., peroxynitric acid and alkyl nitrates) as well as to instrument errors. Copyright 1998 by the American Geophysical Union

Genetic steps to organ laterality in zebrafish.

All internal organs are asymmetric along the left-right axis. Here we report a genetic screen to discover mutations which perturb organ laterality. Our particular focus is upon whether, and how, organs are linked to each other as they achieve their laterally asymmetric positions. We generated mutations by ENU mutagenesis and examined F3 progeny using a cocktail of probes that reveal early primordia of heart, gut, liver and pancreas. From the 750 genomes examined, we isolated seven recessive mutations which affect the earliest left-right positioning of one or all of the organs. None of these mutations caused discernable defects elsewhere in the embryo at the stages examined. This is in contrast to those mutations we reported previously (Chen et al., 1997) which, along with left-right abnormalities, cause marked perturbation in gastrulation, body form or midline structures. We find that the mutations can be classified on the basis of whether they perturb relationships among organ laterality. In Class 1 mutations, none of the organs manifest any left-right asymmetry. The heart does not jog to the left and normally leftpredominant BMP4 in the early heart tube remains symmetric. The gut tends to remain midline. There frequently is a remarkable bilateral duplication of liver and pancreas. Embryos with Class 2 mutations have organotypic asymmetry but, in any given embryo, organ positions can be normal, reversed or randomized. Class 3 reveals a hitherto unsuspected gene that selectively affects laterality of heart. We find that visceral organ positions are predicted by the direction of the preceding cardiac jog. We interpret this as suggesting that normally there is linkage between cardiac and visceral organ laterality. Class 1 mutations, we suggest, effectively remove the global laterality signals, with the consequence that organ positions are effectively symmetrical. Embryos with Class 2 mutations do manifest linkage among organs, but it may be reversed, suggesting that the global signals may be present but incorrectly orientated in some of the embryos. That laterality decisions of organs may be independently perturbed, as in the Class 3 mutation, indicates that there are distinctive pathways for reception and organotypic interpretation of the global signals

Complete amino acid sequences of variable regions of two human IgM rheumatoid factors, BOR and KAS of the Wa idiotypic family, reveal restricted use of heavy and light chain variable and joining region gene segments.

Evidence derived from the complete amino acid sequences of the variable regions of both the heavy and light chains of two members (BOR and KAS) of the Wa idiotypic family of human rheumatoid factors suggests that not only are the light chains of these molecules derived from possibly one variable region gene segment, but the heavy chain variable regions are all derived from the VHI subgroup of human V region genes. These molecules exhibit a surprising conservation in the size of D region, and all use the JH4 gene element. This restriction in use of VL, VH, D, and JH suggests all of these elements may play a crucial role in either antigen binding and/or expression of the crossreactive idiotype

Holographic Dual of Linear Dilaton Black Hole in Einstein-Maxwell-Dilaton-Axion Gravity

Motivated by the recently proposed Kerr/CFT correspondence, we investigate the holographic dual of the extremal and non-extremal rotating linear dilaton black hole in Einstein-Maxwell-Dilaton-Axion Gravity. For the case of extremal black hole, by imposing the appropriate boundary condition at spatial infinity of the near horizon extremal geometry, the Virasoro algebra of conserved charges associated with the asymptotic symmetry group is obtained. It is shown that the microscopic entropy of the dual conformal field given by Cardy formula exactly agrees with Bekenstein-Hawking entropy of extremal black hole. Then, by rewriting the wave equation of massless scalar field with sufficient low energy as the SL(2, R)$_L$$\times$SL(2, R)$_R$ Casimir operator, we find the hidden conformal symmetry of the non-extremal linear dilaton black hole, which implies that the non-extremal rotating linear dilaton black hole is holographically dual to a two dimensional conformal field theory with the non-zero left and right temperatures. Furthermore, it is shown that the entropy of non-extremal black hole can be reproduced by using Cardy formula.Comment: 15 pages, no figure, published versio

A simple and robust method for connecting small-molecule drugs using gene-expression signatures

Interaction of a drug or chemical with a biological system can result in a gene-expression profile or signature characteristic of the event. Using a suitably robust algorithm these signatures can potentially be used to connect molecules with similar pharmacological or toxicological properties. The Connectivity Map was a novel concept and innovative tool first introduced by Lamb et al to connect small molecules, genes, and diseases using genomic signatures [Lamb et al (2006), Science 313, 1929-1935]. However, the Connectivity Map had some limitations, particularly there was no effective safeguard against false connections if the observed connections were considered on an individual-by-individual basis. Further when several connections to the same small-molecule compound were viewed as a set, the implicit null hypothesis tested was not the most relevant one for the discovery of real connections. Here we propose a simple and robust method for constructing the reference gene-expression profiles and a new connection scoring scheme, which importantly allows the valuation of statistical significance of all the connections observed. We tested the new method with the two example gene-signatures (HDAC inhibitors and Estrogens) used by Lamb et al and also a new gene signature of immunosuppressive drugs. Our testing with this new method shows that it achieves a higher level of specificity and sensitivity than the original method. For example, our method successfully identified raloxifene and tamoxifen as having significant anti-estrogen effects, while Lamb et al's Connectivity Map failed to identify these. With these properties our new method has potential use in drug development for the recognition of pharmacological and toxicological properties in new drug candidates.Comment: 8 pages, 2 figures, and 2 tables; supplementary data supplied as a ZIP fil