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

A novel two-step recombinogenic engineering method for bacterial artificial chromosome manipulation

published_or_final_versio

Effective temperature for black holes

The physical interpretation of black hole's quasinormal modes is fundamental for realizing unitary quantum gravity theory as black holes are considered theoretical laboratories for testing models of such an ultimate theory and their quasinormal modes are natural candidates for an interpretation in terms of quantum levels. The spectrum of black hole's quasinormal modes can be re-analysed by introducing a black hole's effective temperature which takes into account the fact that, as shown by Parikh and Wilczek, the radiation spectrum cannot be strictly thermal. This issue changes in a fundamental way the physical understanding of such a spectrum and enables a re-examination of various results in the literature which realizes important modifies on quantum physics of black holes. In particular, the formula of the horizon's area quantization and the number of quanta of area result modified becoming functions of the quantum "overtone" number n. Consequently, the famous formula of Bekenstein-Hawking entropy, its sub-leading corrections and the number of microstates are also modified. Black hole's entropy results a function of the quantum overtone number too. We emphasize that this is the first time that black hole's entropy is directly connected with a quantum number. Previous results in the literature are re-obtained in the limit n \to \infty.Comment: 10 pages,accepted for publication in Journal of High Energy Physics. Comments are welcom

Proteins across scales through graph partitioning: application to the major peanut allergen Ara h 1

The analysis of community structure in complex networks has been given much attention recently, as it is hoped that the communities at various scales can affect or explain the global behaviour of the system. A plethora of community detection algorithms have been proposed, insightful yet often restricted by certain inherent resolutions. Proteins are multi-scale biomolecular machines with coupled structural organization across scales, which is linked to their function. To reveal this organization, we applied a recently developed multi-resolution method, Markov Stability, which is based on atomistic graph partitioning, along with theoretical mutagenesis that further allows for hot spot identification using Gaussian process regression. The methodology finds partitions of a graph without imposing a particular scale a priori and analyses the network in a computationally efficient way. Here, we show an application on peanut allergenicity, which despite extensive experimental studies that focus on epitopes, groups of atoms associated with allergenic reactions, remains poorly understood. We compare our results against available experiment data, and we further predict distal regulatory sites that may significantly alter protein dynamics

The HATNet and HATSouth Exoplanet Surveys

The Hungarian-made Automated Telescope Network (HATNet) has been in operation since 2003, with the key science goal being the discovery and accurate characterization of transiting extrasolar planets (TEPs) around bright stars. Using six small, 11\,cm\ aperture, fully automated telescopes in Arizona and Hawaii, as of 2017 March, it has discovered and accurately characterized 67 such objects. The HATSouth network of telescopes has been in operation since 2009, using slightly larger, 18\,cm diameter optical tubes. It was the first global network of telescopes using identical instrumentation. With three premier sites spread out in longitude (Chile, Namibia, Australia), the HATSouth network permits round-the-clock observations of a 128 square arcdegree swath of the sky at any given time, weather permitting. As of this writing, HATSouth has discovered 36 transiting exoplanets. Many of the altogether ~100 HAT and HATSouth exoplanets were the first of their kind. They have been important contributors to the rapidly developing field of exoplanets, motivating and influencing observational techniques, theoretical studies, and also actively shaping future instrumentation for the detection and characterization of such objects.Comment: Invited review chapter, accepted for publication in "Handbook of Exoplanets", edited by H.J. Deeg and J.A. Belmonte, Springer Reference Work

High incidence of plasmids in marine Vibrio species isolated from Mai Po Nature Reserve of Hong Kong

Mai Po Nature Reserve is the largest mangrove ecosystem and the most polluted coastal water body in Hong Kong. Plasmids screening of 100 Vibrio isolates randomly showed 45 % of them contained 1-3 plasmids. These plasmid(s)-bearing isolates could be divided into 12 groups based on their plasmid profiles. Phylogenetic analysis of the partial 16S rRNA gene sequences confirmed that all plasmid(s)-bearing isolates belonged to Vibrio cholerae. Full DNA sequences of the plasmids in Groups I (pVCG1.1 and pVCG1.2), II (pVCG2.1), III (pVCG3.2) and IV (pVCG4.1) have been determined and the results showed that pVCG1.1, pVCG2.1 and pVCG3.2 were almost identical. Plasmids pVCG1.1, pVCG1.2 and pVCG4.1 are comprised of 4,439, 2,357 and 2,163 bp with the overall G+C content of 45.57, 53.54 and 43.09 %, respectively. pVCG1.1 is a novel plasmid, and plasmids pVCG1.2 and pVCG4.1 showed homology of replication initiation proteins to that of the theta type replicons. Attempts to cure the plasmids from their hosts were unsuccessful. These data suggest that plasmids of Vibrio spp. are a significant gene reservoir in the marine ecosystem.published_or_final_versio

Holonomic quantum computation using rf superconducting quantum interference devices coupled through a microwave cavity

We propose a different scheme to realize holonomic quantum computation with rf superconducting quantum interference device (SQUID) qubits in a microwave cavity. In this scheme associated with the non-Abelian holonomies, the single-qubit gates and a two-qubit controlled-PHASE gate as well as a controlled-NOT gate can be easily constructed by tuning adiabatically the Rabi frequencies of classical microwave pulses coupled to the SQUIDs. The fidelity of these gates is estimated to be possibly higher than 90% with the current technology. © 2005 The American Physical Society.published_or_final_versio