Reverse engineering of drug induced DNA damage response signalling pathway reveals dual outcomes of ATM kinase inhibition

The DNA Damage Response (DDR) pathway represents a signalling mechanism that is activated in eukaryotic cells following DNA damage and comprises of proteins involved in DNA damage detection, DNA repair, cell cycle arrest and apoptosis. This pathway consists of an intricate network of signalling interactions driving the cellular ability to recognise DNA damage and recruit specialised proteins to take decisions between DNA repair or apoptosis. ATM and ATR are central components of the DDR pathway. The activities of these kinases are vital in DNA damage induced phosphorylational induction of DDR substrates. Here, firstly we have experimentally determined DDR signalling network surrounding the ATM/ATR pathway induced following double stranded DNA damage by monitoring and quantifying time dependent inductions of their phosphorylated forms and their key substrates. We next involved an automated inference of unsupervised predictive models of time series data to generate in silico (molecular) interaction maps. We characterized the complex signalling network through system analysis and gradual utilisation of small time series measurements of key substrates through a novel network inference algorithm. Furthermore, we demonstrate an application of an assumption-free reverse engineering of the intricate signalling network of the activated ATM/ATR pathway. We next studied the consequences of such drug induced inductions as well as of time dependent ATM kinase inhibition on cell survival through further biological experiments. Intermediate and temporal modelling outcomes revealed the distinct signaling profile associated with ATM kinase activity and inhibition and explained the underlying signalling mechanism for dual ATM functionality in cytotoxic and cytoprotective pathways

Testing strong line metallicity diagnostics at z~2

High-z galaxy gas-phase metallicities are usually determined through observations of strong optical emission lines with calibrations tied to the local universe. Recent debate has questioned if these calibrations are valid in the high-z universe. We investigate this by analysing a sample of 16 galaxies at z~2 available in the literature, and for which the metallicity can be robustly determined using oxygen auroral lines. The sample spans a redshift range of 1.4 < z < 3.6, has metallicities of 7.4-8.4 in 12+log(O/H) and stellar masses 10^7.5-10^11 Msun. We test commonly used strong line diagnostics (R23, O3, O2, O32, N2, O3N2 and Ne3O2 ) as prescribed by four different sets of empirical calibrations, as well as one fully theoretical calibration. We find that none of the strong line diagnostics (or calibration set) tested perform consistently better than the others. Amongst the line ratios tested, R23 and O3 deliver the best results, with accuracies as good as 0.01-0.04 dex and dispersions of ~0.2 dex in two of the calibrations tested. Generally, line ratios involving nitrogen predict higher values of metallicity, while results with O32 and Ne3O2 show large dispersions. The theoretical calibration yields an accuracy of 0.06 dex, comparable to the best strong line methods. We conclude that, within the metallicity range tested in this work, the locally calibrated diagnostics can still be reliably applied at z~2.Comment: 12 pages, 8 Figures, accepted for publication in MNRA

GEMINI: A Natural Language System for Spoken-Language Understanding

Gemini is a natural language understanding system developed for spoken language applications. The paper describes the architecture of Gemini, paying particular attention to resolving the tension between robustness and overgeneration. Gemini features a broad-coverage unification-based grammar of English, fully interleaved syntactic and semantic processing in an all-paths, bottom-up parser, and an utterance-level parser to find interpretations of sentences that might not be analyzable as complete sentences. Gemini also includes novel components for recognizing and correcting grammatical disfluencies, and for doing parse preferences. This paper presents a component-by-component view of Gemini, providing detailed relevant measurements of size, efficiency, and performance.Comment: 8 pages, postscrip

Stable Cytotoxic T Cell Escape Mutation in Hepatitis C Virus Is Linked to Maintenance of Viral Fitness

Mechanisms by which hepatitis C virus (HCV) evades cellular immunity to establish persistence in chronically infected individuals are not clear. Mutations in human leukocyte antigen (HLA) class I-restricted epitopes targeted by CD8+ T cells are associated with persistence, but the extent to which these mutations affect viral fitness is not fully understood. Previous work showed that the HCV quasispecies in a persistently infected chimpanzee accumulated multiple mutations in numerous class I epitopes over a period of 7 years. During the acute phase of infection, one representative epitope in the C-terminal region of the NS3/4A helicase, NS31629-1637, displayed multiple serial amino acid substitutions in major histocompatibility complex (MHC) anchor and T cell receptor (TCR) contact residues. Only one of these amino acid substitutions at position 9 (P9) of the epitope was stable in the quasispecies. We therefore assessed the effect of each mutation observed during in vivo infection on viral fitness and T cell responses using an HCV subgenomic replicon system and a recently developed in vitro infectious virus cell culture model. Mutation of a position 7 (P7) TCR-contact residue, I1635T, expectedly ablated the T cell response without affecting viral RNA replication or virion production. In contrast, two mutations at the P9 MHC-anchor residue abrogated antigen-specific T cell responses, but additionally decreased viral RNA replication and virion production. The first escape mutation, L1637P, detected in vivo only transiently at 3 mo after infection, decreased viral production, and reverted to the parental sequence in vitro. The second P9 variant, L1637S, which was stable in vivo through 7 years of follow-up, evaded the antigen-specific T cell response and did not revert in vitro despite being less optimal in virion production compared to the parental virus. These studies suggest that HCV escape mutants emerging early in infection are not necessarily stable, but are eventually replaced with variants that achieve a balance between immune evasion and fitness for replication