Quantitative Assessment of Mycoplasma Hemadsorption Activity by Flow Cytometry

A number of adherent mycoplasmas have developed highly complex polar structures that are involved in diverse aspects of the biology of these microorganisms and play a key role as virulence factors by promoting adhesion to host cells in the first stages of infection. Attachment activity of mycoplasma cells has been traditionally investigated by determining their hemadsorption ability to red blood cells and it is a distinctive trait widely examined when characterizing the different mycoplasma species. Despite the fact that protocols to qualitatively determine the hemadsorption or hemagglutination of mycoplasmas are straightforward, current methods when investigating hemadsorption at the quantitative level are expensive and poorly reproducible. By using flow cytometry, we have developed a procedure to quantify rapidly and accurately the hemadsorption activity of mycoplasmas in the presence of SYBR Green I, a vital fluorochrome that stains nucleic acids, allowing to resolve erythrocyte and mycoplasma cells by their different size and fluorescence. This method is very reproducible and permits the kinetic analysis of the obtained data and a precise hemadsorption quantification based on standard binding parameters such as the dissociation constant Kd. The procedure we developed could be easily implemented in a standardized assay to test the hemadsorption activity of the growing number of clinical isolates and mutant strains of different mycoplasma species, providing valuable data about the virulence of these microorganisms

Gene Ontology Function prediction in Mollicutes using Protein-Protein Association Networks

<p>Abstract</p> <p>Background</p> <p>Many complex systems can be represented and analysed as networks. The recent availability of large-scale datasets, has made it possible to elucidate some of the organisational principles and rules that govern their function, robustness and evolution. However, one of the main limitations in using protein-protein interactions for function prediction is the availability of interaction data, especially for Mollicutes. If we could harness predicted interactions, such as those from a Protein-Protein Association Networks (PPAN), combining several protein-protein network function-inference methods with semantic similarity calculations, the use of protein-protein interactions for functional inference in this species would become more potentially useful.</p> <p>Results</p> <p>In this work we show that using PPAN data combined with other approximations, such as functional module detection, orthology exploitation methods and Gene Ontology (GO)-based information measures helps to predict protein function in <it>Mycoplasma genitalium</it>.</p> <p>Conclusions</p> <p>To our knowledge, the proposed method is the first that combines functional module detection among species, exploiting an orthology procedure and using information theory-based GO semantic similarity in PPAN of the <it>Mycoplasma </it>species. The results of an evaluation show a higher recall than previously reported methods that focused on only one organism network.</p

A novel sigma factor reveals a unique regulon controlling cell-specific recombination in Mycoplasma genitalium

The Mycoplasma genitalium MG428 protein shows homology to members of the sigma-70 family of sigma factors. Herein, we found that MG428 activates transcription of recA, ruvA and ruvB as well as several genes with unknown function. Deletion of MG_428 or some of the up-regulated unknown genes led to severe recombination defects. Single cell analyses revealed that activation of the MG428-regulon is a rare event under laboratory growth conditions. A conserved sequence with sigma-70 promoter architecture (TTGTCA-N-ATTWAT) was identified in the upstream region of all of the MG428-regulated genes or operons. Primer extension analyses demonstrated that transcription initiates immediately downstream of this sigma70-type promoter in a MG428-dependent manner. Furthermore, mutagenesis of the conserved −10 and −35 elements corroborated the requirement of these regions for promoter function. Therefore, a new mycoplasma promoter directs transcription of a unique recombination regulon. Additionally, MG428 was found to interact with the RNAP core enzyme, reinforcing the predicted role of this protein as an alternative sigma factor. Finally, our results indicate that MG428 contributes to the generation of genetic diversity in this model organism. Since recombination is an important mechanism to generate antigenic variation, MG428 emerges as a novel factor contributing to M. genitalium virulence

Application Acceleration on FPGAs with OmpSs@FPGA

© 2019 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes,creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.OmpSs@FPGA is the flavor of OmpSs that allows offloading application functionality to FPGAs. Similarly to OpenMP, it is based on compiler directives. While the OpenMP specification also includes support for heterogeneous execution, we use OmpSs and OmpSs@FPGA as prototype implementation to develop new ideas for OpenMP. OmpSs@FPGA implements the tasking model with runtime support to automatically exploit all SMP and FPGA resources available in the execution platform. In this paper, we present the OmpSs@FPGA ecosystem, based on the Mercurium compiler and the Nanos++ runtime system. We show how the applications are transformed to run on the SMP cores and the FPGA. The application kernels defined as tasks to be accelerated, using the OmpSs directives are: 1) transformed by the compiler into kernels connected with the proper synchronization and communication ports, 2) extracted to intermediate files, 3) compiled through the FPGA vendor HLS tool, and 4) used to configure the FPGA. Our Nanos++ runtime system schedules the application tasks on the platform, being able to use the SMP cores and the FPGA accelerators at the same time. We present the evaluation of the OmpSs@FPGA environment with the Matrix Multiplication, Cholesky and N-Body benchmarks, showing the internal details of the execution, and the performance obtained on a Zynq Ultrascale+ MPSoC (up to 128x). The source code uses OmpSs@FPGA annotations and different Vivado HLS optimization directives are applied for acceleration.This work is partially supported by the European Union H2020 program through the EuroEXA project (grant 754337), and HiPEAC (GA 687698), by the Spanish Government through Programa Severo Ochoa (SEV-2015- 0493), by the Spanish Ministry of Science and Technology (TIN2015-65316-P) and the Departament d’Innovació Universitats i Empresa de la Generalitat de Catalunya, under project MPEXPAR: Models de Programació i Entorns d’Execució Paral·lels (2014-SGR-1051).Peer ReviewedPostprint (author's final draft

Supramolecular organization and heterochiral recognition in Langmuir monolayers of chiral azobenzene surfactants

We study the self-assembly of novel azobenzene-based chiral surfactants at the air/water interface, and find that while the pure enantiomers lack the ability to organize in ordered mesophases, the racemic mixture spontaneously forms a hexatic phase at low lateral pressures, which we detect by means of Brewster angle microscopy. This work provides a unique example of heterochiral recognition in which the racemic monolayer is not only condensed with respect to the pure enantiomers, but causes an ordered mesophase to form. Although hexatic order vanishes at high surface pressures, long-range orientational order is regained for all compositions upon monolayer collapse, which proceeds through the formation of birefringent trilayers with a well-defined lateral microstructure, as revealed by atomic force microscopy

Comparación de dos técnicas Proteómicas aplicadas al análisis de las proteínas de membrana de Mycoplasma genitalium

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Picos, a hardware task-dependence manager for task-based dataflow programming models

Task-based programming Task-based programming models such as OpenMP, Intel TBB and OmpSs are widely used to extract high level of parallelism of applications executed on multi-core and manycore platforms. These programming models allow applications to be expressed as a set of tasks with dependences to drive their execution at runtime. While managing these dependences for task with coarse granularity proves to be highly beneficial, it introduces noticeable overheads when targeting fine-grained tasks, diminishing the potential speedups or even introducing performance losses. To overcome this drawback, we propose a hardware/software co-design Picos that manages inter-task dependences efficiently. In this paper we describe the main ideas of our proposal and a prototype implementation. This prototype is integrated with a parallel task- based programming model and evaluated with real executions in Linux embedded system with two ARM Cortex-A9 and a FPGA. When compared with a software runtime, our solution results in more than 1.8x speedup and 40% of energy savings with only 2 threads.This work is supported by the projects SEV-2015-0493 and TIN2015-65316-P, by the project 2014-SGR-1051 and 2014-SGR-1272, by the RoMoL GA 321253 and by the project cooperation agreement with LG Electronics, and thank the Xilinx University Program.Postprint (published version

MultitaskProtDB: a database of multitasking proteins

We have compiled MultitaskProtDB, available online at http://wallace.uab.es/multitask, to provide a repository where the many multitasking proteins found in the literature can be stored. Multitasking or moonlighting is the capability of some proteins to execute two or more biological functions. Usually, multitasking proteins are experimentally revealed by serendipity. This ability of proteins to perform multitasking functions helps us to understand one of the ways used by cells to perform many complex functions with a limited number of genes. Even so, the study of this phenomenon is complex because, among other things, there is no database of moonlighting proteins. The existence of such a tool facilitates the collection and dissemination of these important data. This work reports the database, MultitaskProtDB, which is designed as a friendly user web page containing >288 multitasking proteins with their NCBI and UniProt accession numbers, canonical and additional biological functions, monomeric/oligomeric states, PDB codes when available and bibliographic references. This database also serves to gain insight into some characteristics of multitasking proteins such as frequencies of the different pairs of functions, phylogenetic conservation and so forth.Ministerio de Ciencia y Tecnología de Espanya [BIO2007-67904-C02-01, BFU2010-22209-C02-01]; Centre de Referència de R+D de Biotecnologia de la Generalitat de Catalunya; La Marató de TV3 [101930/31/32/33]; Comisión Coordinadora del Interior de Uruguay. The English of this manuscript has been corrected by Ms Lynn Strother. Funding for open access charge: [BIO2007-67904-C02-01 and BFU2010-22209-C02-01]

Activation of r20-dependent recombination and horizontal gene transfer in Mycoplasma genitalium

In the human pathogen Mycoplasma genitalium, homologous recombination is under the control of r, an alternative sigma factor that boosts the generation of genetic and antigenic diversity in the population. Under laboratory growth conditions, r activation is rare and the factors governing its intermittent activity are unknown. Two r-regulated genes, rrlA and rrlB, showed to be important for recombination of homologous DNA sequences in this bacterium. Herein, we demonstrate that rrlA and rrlB code for two small proteins that participate in a feed-forward loop essential for r function. In addition, we identify novel genes regulated by r and show that several non-coding regions, which function as a reservoir for the generation of antigenic diversity, are also activated by this alternative sigma factor. Finally, we reveal that M. genitalium cells can transfer DNA horizontally by a novel mechanism that requires RecA and is facilitated by r overexpression. This DNA transfer system is arguably fundamental for persistence of M. genitalium within the host since it could facilitate a rapid dissemination of successful antigenic variants within the population. Overall, these findings impose a novel conception of genome evolution, genetic variation and survival of M. genitalium within the hos

Extended proteome and membrane subproteome of mycoplasma genitalium

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