Campylobacter jejuni transcriptome changes during loss of culturability in water

Background: Water serves as a potential reservoir for Campylobacter, the leading cause of bacterial gastroenteritis in humans. However, little is understood about the mechanisms underlying variations in survival characteristics between different strains of C. jejuni in natural environments, including water. Results: We identified three Campylobacter jejuni strains that exhibited variability in their ability to retain culturability after suspension in tap water at two different temperatures (4°C and 25°C). Of the three strains C. jejuni M1 exhibited the most rapid loss of culturability whilst retaining viability. Using RNAseq transcriptomics, we characterised C. jejuni M1 gene expression in response to suspension in water by analyzing bacterial suspensions recovered immediately after introduction into water (Time 0), and from two sampling time/temperature combinations where considerable loss of culturability was evident, namely (i) after 24 h at 25°C, and (ii) after 72 h at 4°C. Transcript data were compared with a culture-grown control. Some gene expression characteristics were shared amongst the three populations recovered from water, with more genes being up-regulated than down. Many of the up-regulated genes were identified in the Time 0 sample, whereas the majority of down-regulated genes occurred in the 25°C (24 h) sample. Conclusions: Variations in expression were found amongst genes associated with oxygen tolerance, starvation and osmotic stress. However, we also found upregulation of flagellar assembly genes, accompanied by down-regulation of genes involved in chemotaxis. Our data also suggested a switch from secretion via the sec system to via the tat system, and that the quorum sensing gene luxS may be implicated in the survival of strain M1 in water. Variations in gene expression also occurred in accessory genome regions. Our data suggest that despite the loss of culturability, C. jejuni M1 remains viable and adapts via specific changes in gene expression

Implementing a Task Specific Grammar for Recognition and Parsing using the CPK NLP Suite for Spoken Language Understanding

This paper describes how a task specific grammar can be implemented using a dedicated "NLP" Augmented Phrase Structure (APS) grammar formalism. The APS is used for generation of appropriate semantic frames to be passed on to the dialogue manager of a spoken dialogue system. In a derived form, conforming to the HTK Standard Lattice format, the same APS may be used for constraining the approved speech recogniser grapHvite by Entropics. APS and HTK (standard lattice) are just two of several NLP and recognition grammar formats supported by the CPK NLP Suite for Spoken Language Understanding. The suite can be downloaded (in C++ source code) for research and other non-commercial use at the web address http://www.cpk.auc.dk/~tb/nlpsuite. 1. INTRODUCTION This paper is a tutorial-like introduction to the CPK NLP suite for Spoken Language Understanding. The suite has been developed and used within a number of national and international projects and supports a number of grammar formalisms. The ..

The linguistic Components of the REWARD Dialogue Creation Environment and Run Time System

The present paper describes the linguistic components of a platform for building spoken language dialogue systems. The platform is being designed and implemented within the EU-language engineering project REWARD. The linguistic components mainly consist of a suite of general unification based natural language processing utilities and a window based Sub Grammar Design Tool which provides non-experts access to the utilities. The Sub Grammar Design Tool enables nonexpert users to implement sub grammars for speech understanding within a minimum of effort. I. INTRODUCTION The three years EU-Language Engineering project REWARD ("Real World Applications of Robust Dialogue" LE1-2632) addresses the needs of organisations which do business over the telephone (i) to automate certain telephone services using spoken language dialogue technology and (ii) to automate the process of creating such services. The project brings together two technology suppliers, Vocalis Ltd. and CPK (Center for PersonK..

Adapting a prosody classification module from German to Danish - A Contrastive Analysis

. This paper describes some problems arising when adapting a German prosody classification module to Danish. The module in question has been developed at the University of Erlangen and Munich and is a component of the German train time table inquiry system EVAR [1][2]. The module which is based on Gaussian classifiers has been trained on real life German inquiry dialogs to distinguish three types of user interruptions, mainly in the form of repetitions of a time of day (RTDs) just given by the officer: 1) Questions (rising intonation, e.g. O:" ...leaves at Ulm at 17 23" U:"17 23?"), 2) confirmation (falling intonation), and 3) feedback (continuation rise). In EVAR, each RTD type leads to a different response (eventually no response) from the system depending on whether the user RTD is wrong or correct, complete or incomplete [1] (p. 7). The prosodic module has been examined at Center for PersonKommunikation, Aalborg University, where a flight ticket reservation system, comparable to E..

The CPK NLP Suite for Spoken Language Understanding

This paper describes a number of freely available tools for implementing and running spoken language understanding systems. Unlike other free tools (e.g. the CSLU toolkit), the main emphasis is on spoken language understanding (syntactic/semantic parsing, generation of language models for recognition etc.). The suite supports (reads and/or writes) a number of grammar formats defined for speech recognisers like Entropic’s GrapHvite (HTK standard lattice) as well as common unification grammar formats used in NLP: The American PATRII and the European EUROTRA (Augmented Phrase Structure Grammar) format. The open architecture is completed by a general API allowing simple interfacing to dialogue management and speech recognition. The suite, implemented in C++ (partly C, Lex, Yacc), can compile and run on any machine under any OS having a 32 bit C++ compiler, Flex/Bison or Lex/Yacc. The suite can be downloaded a