The pUltra plasmid series: a robust and flexible tool for fluorescent labeling of Enterobacteria

Fluorescent labeling has been an invaluable tool for the study of living organisms and bacterial species are no exception to this. Here we present and characterize the pUltra plasmids which express constitutively a fluorescent protein gene (GFP, RFP, YFP or CFP) from a strong synthetic promoter and are suitable for the fluorescent labeling of a broad range of Enterobacteria. The amount of expressed fluorophore from these genetic constructs is such, that the contours of the cells can be delineated on the basis of the fluorescent signal only. In addition, labeling through the pUltra plasmids can be used successfully for fluorescence and confocal microscopy while unambiguous distinction of cells labeled with different colors can be carried out efficiently by microscopy or flow cytometry. We compare the labeling provided by the pUltra plasmids with that of another plasmid series encoding fluorescent proteins and we show that the pUltra constructs are vastly superior in signal intensity and discrimination power without having any detectable growth rate effects for the bacterial population. We also use the pUltra plasmids to produce mixtures of differentially labeled pathogenic Escherichia, Shigella and Salmonella species which we test during infection of mammalian cells. We find that even inside the host cell, different strains can be distinguished effortlessly based on their fluorescence. We, therefore, conclude that the pUltra plasmids are a powerful labeling tool especially useful for complex biological experiments such as the visualization of ecosystems of different bacterial species or of enteric pathogens in contact with their hosts

Costs and benefits of provocation in bacterial warfare.

Competition in animals involves a wide variety of aggressive behaviors. One of the most sophisticated strategies for a focal actor is to provoke a competitor into uncontrolled aggression toward other competitors. Like animals, bacteria rely on a broad spectrum of molecular weapons, some of which provoke potential rivals by triggering retaliation. While bacterial provocation is well documented, its potential adaptive value has received little attention. Here, we examine the costs and benefits of provocation using mathematical modeling and experiments with <i>Escherichia coli</i> strains encoding colicin toxins. We show that provocation is typically costly in one-to-one encounters because a provoking strain receives a strong reciprocal attack compared with nonprovoking strains. By contrast, provocation can be strongly beneficial in communities including more than two toxin-producing strains, especially when the provoker is shielded from, or resistant to, its opponents' toxins. In these scenarios, we demonstrate that the benefit of provocation derives from a "divide-and-conquer" effect by which aggression-provoking toxin producers force their competitors into increased reciprocal aggression, leading to their cross-elimination. Furthermore, we show that this effect can be mimicked by using antibiotics that promote warfare among strains in a bacterial community, highlighting the potential of provocation as an antimicrobial approach

Designing Secure Ethereum Smart Contracts: A Finite State Machine Based Approach

The adoption of blockchain-based distributed computation platforms is growing fast. Some of these platforms, such as Ethereum, provide support for implementing smart contracts, which are envisioned to have novel applications in a broad range of areas, including finance and Internet-of-Things. However, a significant number of smart contracts deployed in practice suffer from security vulnerabilities, which enable malicious users to steal assets from a contract or to cause damage. Vulnerabilities present a serious issue since contracts may handle financial assets of considerable value, and contract bugs are non-fixable by design. To help developers create more secure smart contracts, we introduce FSolidM, a framework rooted in rigorous semantics for designing con- tracts as Finite State Machines (FSM). We present a tool for creating FSM on an easy-to-use graphical interface and for automatically generating Ethereum contracts. Further, we introduce a set of design patterns, which we implement as plugins that developers can easily add to their contracts to enhance security and functionality

Using Facial Gestures to Drive Narrative in VR

We developed an exploratory VR environment, where spatial features and narratives can be manipulated in real time by the facial and head gestures of the user. We are using the Faceteq prototype, exhibited in 2017, as the interactive interface. Faceteq consists of a wearable technology that can be adjusted on commercial HMDs for measuring facial expressions and biometric responses. Faceteq project was founded with the aim to provide a human-centred additional tool for affective human-computer interaction. The proposed demo will exhibit the hardware and the functionality of the demo in real time

Coordination of Dynamic Software Components with JavaBIP

JavaBIP allows the coordination of software components by clearly separating the functional and coordination aspects of the system behavior. JavaBIP implements the principles of the BIP component framework rooted in rigorous operational semantics. Recent work both on BIP and JavaBIP allows the coordination of static components defined prior to system deployment, i.e., the architecture of the coordinated system is fixed in terms of its component instances. Nevertheless, modern systems, often make use of components that can register and deregister dynamically during system execution. In this paper, we present an extension of JavaBIP that can handle this type of dynamicity. We use first-order interaction logic to define synchronization constraints based on component types. Additionally, we use directed graphs with edge coloring to model dependencies among components that determine the validity of an online system. We present the software architecture of our implementation, provide and discuss performance evaluation results.Comment: Technical report that accompanies the paper accepted at the 14th International Conference on Formal Aspects of Component Softwar

FACETEQ interface demo for emotion expression in VR

© 2017 IEEE.Faceteq prototype v.05 is a wearable technology for measuring facial expressions and biometric responses for experimental studies in Virtual Reality. Developed by Emteq Ltd laboratory, Faceteq can enable new avenues for virtual reality research through combination of high performance patented dry sensor technologies, proprietary algorithms and real-time data acquisition and streaming. Emteq founded the Faceteq project with the aim to provide a human-centered additional tool for emotion expression, affective human-computer interaction and social virtual environments. The proposed demonstration will exhibit the hardware and its functionality by allowing attendees to experience three of the showcasing applications we developed this year

Molecular Characterization and Phylogenetic Analysis of Pseudomonas aeruginosa Isolates Recovered from Greek Aquatic Habitats Implementing the Double-Locus Sequence Typing Scheme.

The recently described double-locus sequence typing (DLST) scheme implemented to deeply characterize the genetic profiles of 52 resistant environmental Pseudomonas aeruginosa isolates deriving from aquatic habitats of Greece. DLST scheme was able not only to assign an already known allelic profile to the majority of the isolates but also to recognize two new ones (ms217-190, ms217-191) with high discriminatory power. A third locus (oprD) was also used for the molecular typing, which has been found to be fundamental for the phylogenetic analysis of environmental isolates given the resulted increased discrimination between the isolates. Additionally, the circulation of acquired resistant mechanisms in the aquatic habitats according to their genetic profiles was proved to be more extent. Hereby, we suggest that the combination of the DLST to oprD typing can discriminate phenotypically and genetically related environmental P. aeruginosa isolates providing reliable phylogenetic analysis at a local level

FACETEQ; A novel platform for measuring emotion in VR

FaceTeq prototype v.05 is a wearable technology for measuring facial expressions and biometric responses for experimental studies in Virtual Reality. Developed by Emteq Ltd laboratory, FaceTeq can enable new avenues for virtual reality research through combination of high performance patented dry sensor technologies, proprietary algorithms and real-time data acquisition and streaming. FaceTeq project was founded with the aim to provide a human-centred additional tool for emotion expression, affective human-computer interaction and social virtual environments. The proposed poster will exhibit the hardware and its functionality

Colistin resistance in Escherichia coli confers protection of the cytoplasmic but not outer membrane from the polymyxin antibiotic

Colistin is a polymyxin antibiotic of last resort for the treatment of infections caused by multi-drug-resistant Gram-negative bacteria. By targeting lipopolysaccharide (LPS), the antibiotic disrupts both the outer and cytoplasmic membranes, leading to bacterial death and lysis. Colistin resistance in Escherichia coli occurs via mutations in the chromosome or the acquisition of mobilized colistin-resistance (mcr) genes. Both these colistin-resistance mechanisms result in chemical modifications to the LPS, with positively charged moieties added at the cytoplasmic membrane before the LPS is transported to the outer membrane. We have previously shown that MCR-1-mediated LPS modification protects the cytoplasmic but not the outer membrane from damage caused by colistin, enabling bacterial survival. However, it remains unclear whether this observation extends to colistin resistance conferred by other mcr genes, or resistance due to chromosomal mutations. Using a panel of clinical E. coli that had acquired mcr −1, –1.5, −2, –3, −3.2 or −5, or had acquired polymyxin resistance independently of mcr genes, we found that almost all isolates were susceptible to colistin-mediated permeabilization of the outer, but not cytoplasmic, membrane. Furthermore, we showed that permeabilization of the outer membrane of colistin-resistant isolates by the polymyxin is in turn sufficient to sensitize bacteria to the antibiotic rifampicin, which normally cannot cross the LPS monolayer. These findings demonstrate that colistin resistance in these E. coli isolates is due to protection of the cytoplasmic but not outer membrane from colistin-mediated damage, regardless of the mechanism of resistance