Effect of attC structure on cassette excision by integron integrases

<p>Abstract</p> <p>Background</p> <p>Integrons are genetic elements able to integrate and disseminate genes as cassettes by a site-specific recombination mechanism. These elements contain a gene coding for an integrase that carries out recombination by interacting with two different target sites; the <it>attI </it>site in <it>cis </it>with the integrase and the palindromic <it>attC </it>site of a gene cassette. Integron integrases (IntIs) bind specifically to the bottom strand of <it>attC </it>sites. The extrahelical bases resulting from folding of <it>attC </it>bottom strands are important for the recognition by integrases. These enzymes are directly involved in the accumulation and formation of new cassette arrangements in the variable region of integrons. Thus, it is important to better understand interactions between IntIs and their substrates.</p> <p>Results</p> <p>We compared the ability of five IntIs to carry out excision of several cassettes flanked by different <it>attC </it>sites. The results showed that for most cassettes, IntI1 was the most active integrase. However, IntI2*179E and SonIntIA could easily excise cassettes containing the <it>attC_dfrA1</it>site located upstream, whereas IntI1 and IntI3 had only a weak excision activity for these cassettes. Analysis of the secondary structure adopted by the bottom strand of <it>attC_dfrA1</it>has shown that the identity of the extrahelical bases and the distance between them (A-N_7-8-C) differ from those of <it>attC</it>s contained in the cassettes most easily excisable by IntI1 (T-N₆-G). We used the <it>attC_dfrA1</it>site upstream of the <it>sat2 </it>gene cassette as a template and varied the identity and spacing between the extrahelical bases in order to determine how these modifications influence the ability of IntI1, IntI2*179E, IntI3 and SonIntIA to excise cassettes. Our results show that IntI1 is more efficient in cassette excision using T-N₆-G or T-N₆-C <it>attC</it>s while IntI3 recognizes only a limited range of <it>attC</it>s. IntI2*179E and SonIntIA are more tolerant of changes to the identity and spacing of extrahelical bases.</p> <p>Conclusions</p> <p>This study provides new insights into the factors that influence the efficiency of cassette excision by integron integrases. It also suggests that IntI2 and SonIntIA have an evolutionary path that is different from IntI1 and IntI3, in their ability to recognize and excise cassettes.</p

Draft Genome Sequence of an International Clonal Lineage 1 Acinetobacter baumannii Strain from Argentina

In the last few years Acinetobacter baumannii has emerged worldwide as an important nosocomial pathogen in medical institutions. Here, we present the draft genome sequence of the international clonal lineage 1 (ICL1) A. baumannii strain A144 that was isolated in a hospital in Buenos Aires City in the year 1997. The strain is susceptible to carbapenems and resistant to trimethoprim and gentamicin.Fil: Vilacoba, Elisabet. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Déraspe, Maxime. Laval University; CanadáFil: Traglia, German Matias. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Roy, Paul H.. Laval University; CanadáFil: Ramirez, Maria Soledad. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentina. California State University; Estados UnidosFil: Centron, Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentin

A blaVIM-2 Plasmid Disseminating in Extensively Drug-Resistant Clinical Pseudomonas aeruginosa and Serratia marcescens Isolates

Infections caused by carbapenem-resistant Enterobacteriaceae isolates are an issue of major global concern (1). Genes coding for metallo-β-lactamases (MβLs) identified in clinical isolates are associated with mobile elements and subject to horizontal genetic transfer (HGT) events (2–6). VIM-2 is present on numerous plasmids, but only pNOR-2000 from Pseudomonas aeruginosa COL-1 from France (7, 8) and pLD209 from Pseudomonas putida LD209 from Argentina (9) have been completely sequenced. Here, we report the complete sequence and characterization of plasmid pDCPR1 harboring a blaVIM-2 gene cassette in a Tn402-type class 1 integron, which was isolated from two extensively drug-resistant strains: P. aeruginosa 802 (from a burn patient at the Hospital Municipal de Quemados, Argentina, 2005) and S. marcescens 68313 (Sanatorio Sagrado Corazón, Argentina, 2012).Fil: Vilacoba, Elisabet. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Quiroga, Cecilia. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Pistorio, Mariano. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Biotecnología y Biología Molecular. Universidad Nacional de La Plata. Facultad de Ciencias Exactas. Instituto de Biotecnología y Biología Molecular; ArgentinaFil: Famiglietti, Angela María Rosa. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Rodriguez, Hernan Bernardo. Universidad de Buenos Aires. Facultad de Medicina. Hospital de Clínicas General San Martín; ArgentinaFil: Kovensky, Jaime. Ciudad Autónoma de Buenos Aires. Hospital Municipal de Quemados; ArgentinaFil: Deraspe, Maxime. Université du Québec a Montreal; Canadá. Laval University; CanadáFil: Raymond, Frédéric. Université du Québec a Montreal; Canadá. Laval University; CanadáFil: Roy, Paul H.. Université du Québec a Montreal; Canadá. Laval University; CanadáFil: Centron, Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentin

Piezoelectric aluminum nitride thin films for microelectromechanical systems

This article reports on the state-of-the-art of the development of aluminum nitride (AlN) thin-film microelectromechanical systems (MEMS) with particular emphasis on acoustic devices for radio frequency (RF) signal processing. Examples of resonant devices are reviewed to highlight the capabilities of AlN as an integrated circuit compatible material for the implementation of RF filters and oscillators. The commercial success of thin-film bulk acoustic resonators is presented to show how AlN has de facto become an industrial standard for the synthesis of high performance duplexers. The article also reports on the development of a new class of AlN acoustic resonators that are directly integrated with circuits and enable a new generation of reconfigurable narrowband filters and oscillators. Research efforts related to the deposition of doped AlN films and the scaling of sputtered AlN films into the nano realm are also provided as examples of possible future material developments that could expand the range of applicability of AlN MEM

SAGA: A project to automate the management of software production systems

The SAGA system is a software environment that is designed to support most of the software development activities that occur in a software lifecycle. The system can be configured to support specific software development applications using given programming languages, tools, and methodologies. Meta-tools are provided to ease configuration. The SAGA system consists of a small number of software components that are adapted by the meta-tools into specific tools for use in the software development application. The modules are design so that the meta-tools can construct an environment which is both integrated and flexible. The SAGA project is documented in several papers which are presented

Longitudinal evaluation of cognitive functioning in young children with type 1 diabetes over 18 months

OBJECTIVE: Decrements in cognitive function may already be evident in young children with type 1 diabetes (T1D). Here we report prospectively acquired cognitive results over 18 months in a large cohort of young children with and without T1D. METHODS: 144 children with T1D (mean HbA1c: 7.9%) and 70 age-matched healthy controls (mean age both groups 8.5 years; median diabetes duration 3.9 yrs; mean age of onset 4.1 yrs) underwent neuropsychological testing at baseline and after 18-months of follow-up. We hypothesized that group differences observed at baseline would be more pronounced after 18 months, particularly in those T1D patients with greatest exposure to glycemic extremes. RESULTS: Cognitive domain scores did not differ between groups at the 18 month testing session and did not change differently between groups over the follow-up period. However, within the T1D group, a history of diabetic ketoacidosis (DKA) was correlated with lower Verbal IQ and greater hyperglycemia exposure (HbA1c area under the curve) was inversely correlated to executive functions test performance. In addition, those with a history of both types of exposure performed most poorly on measures of executive function. CONCLUSIONS: The subtle cognitive differences between T1D children and nondiabetic controls observed at baseline were not observed 18 months later. Within the T1D group, as at baseline, relationships between cognition (VIQ and executive functions) and glycemic variables (chronic hyperglycemia and DKA history) were evident. Continued longitudinal study of this T1D cohort and their carefully matched healthy comparison group is planned

Self-organising comprehensive handover strategy for multi-tier LTE-advanced heterogeneous networks

Long term evolution (LTE)-advanced was introduced as real fourth generation (4G) with its new features and additional functions, satisfying the growing demands of quality and network coverage for the network operators' subscribers. The term muti-tier has also been recently used with respect to the heterogeneity of the network by applying the various subnetwork cooperative systems and functionalities with self-organising capabilities. Using indoor short-range low-power cellular base stations, for example, femtocells, in cooperation with existing long-range macrocells are considered as the key technical challenge of this multi-tier configuration. Furthermore, shortage of network spectrum is a major concern for network operators which forces them to spend additional attentions to overcome the degradation in performance and quality of services in 4G HetNets. This study investigates handover between the different layers of a heterogeneous LTE-advanced system, as a critical attribute to plan the best way of interactive coordination within the network for the proposed HetNet. The proposed comprehensive handover algorithm takes multiple factors in both handover sensing and decision stages, based on signal power reception, resource availability and handover optimisation, as well as prioritisation among macro and femto stations, to obtain maximum signal quality while avoiding unnecessary handovers

Advanced Query and Data Mining Capabilities for MaROS

The Mars Relay Operational Service (MaROS) comprises a number of tools to coordinate, plan, and visualize various aspects of the Mars Relay network. These levels include a Web-based user interface, a back-end "ReSTlet" built in Java, and databases that store the data as it is received from the network. As part of MaROS, the innovators have developed and implemented a feature set that operates on several levels of the software architecture. This new feature is an advanced querying capability through either the Web-based user interface, or through a back-end REST interface to access all of the data gathered from the network. This software is not meant to replace the REST interface, but to augment and expand the range of available data. The current REST interface provides specific data that is used by the MaROS Web application to display and visualize the information; however, the returned information from the REST interface has typically been pre-processed to return only a subset of the entire information within the repository, particularly only the information that is of interest to the GUI (graphical user interface). The new, advanced query and data mining capabilities allow users to retrieve the raw data and/or to perform their own data processing. The query language used to access the repository is a restricted subset of the structured query language (SQL) that can be built safely from the Web user interface, or entered as freeform SQL by a user. The results are returned in a CSV (Comma Separated Values) format for easy exporting to third party tools and applications that can be used for data mining or user-defined visualization and interpretation. This is the first time that a service is capable of providing access to all cross-project relay data from a single Web resource. Because MaROS contains the data for a variety of missions from the Mars network, which span both NASA and ESA, the software also establishes an access control list (ACL) on each data record in the database repository to enforce user access permissions through a multilayered approach

Real-Time Multimission Event Notification System for Mars Relay

As the Mars Relay Network is in constant flux (missions and teams going through their daily workflow), it is imperative that users are aware of such state changes. For example, a change by an orbiter team can affect operations on a lander team. This software provides an ambient view of the real-time status of the Mars network. The Mars Relay Operations Service (MaROS) comprises a number of tools to coordinate, plan, and visualize various aspects of the Mars Relay Network. As part of MaROS, a feature set was developed that operates on several levels of the software architecture. These levels include a Web-based user interface, a back-end "ReSTlet" built in Java, and databases that store the data as it is received from the network. The result is a real-time event notification and management system, so mission teams can track and act upon events on a moment-by-moment basis. This software retrieves events from MaROS and displays them to the end user. Updates happen in real time, i.e., messages are pushed to the user while logged into the system, and queued when the user is not online for later viewing. The software does not do away with the email notifications, but augments them with in-line notifications. Further, this software expands the events that can generate a notification, and allows user-generated notifications. Existing software sends a smaller subset of mission-generated notifications via email. A common complaint of users was that the system-generated e-mails often "get lost" with other e-mail that comes in. This software allows for an expanded set (including user-generated) of notifications displayed in-line of the program. By separating notifications, this can improve a user's workflow