ACLAME: A CLAssification of Mobile genetic Elements, update 2010

The ACLAME database is dedicated to the collection, analysis and classification of sequenced mobile genetic elements (MGEs, in particular phages and plasmids). In addition to providing information on the MGEs content, classifications are available at various levels of organization. At the gene/protein level, families group similar sequences that are expected to share the same function. Families of four or more proteins are manually assigned with a functional annotation using the GeneOntology and the locally developed ontology MeGO dedicated to MGEs. At the genome level, evolutionary cohesive modules group sets of protein families shared among MGEs. At the population level, networks display the reticulate evolutionary relationships among MGEs. To increase the coverage of the phage sequence space, ACLAME version 0.4 incorporates 760 high-quality predicted prophages selected from the Prophinder database. Most of the data can be downloaded from the freely accessible ACLAME web site (http://aclame.ulb.ac.be). The BLAST interface for querying the database has been extended and numerous tools for in-depth analysis of the results have been added

PHACTS, a computational approach to classifying the lifestyle of phages

Motivation: Bacteriophages have two distinct lifestyles: virulent and temperate. The virulent lifestyle has many implications for phage therapy, genomics and microbiology. Determining which lifestyle a newly sequenced phage falls into is currently determined using standard culturing techniques. Such laboratory work is not only costly and time consuming, but also cannot be used on phage genomes constructed from environmental sequencing. Therefore, a computational method that utilizes the sequence data of phage genomes is needed

Disentangling environmental effects in microbial association networks

Background Ecological interactions among microorganisms are fundamental for ecosystem function, yet they are mostly unknown or poorly understood. High-throughput-omics can indicate microbial interactions through associations across time and space, which can be represented as association networks. Associations could result from either ecological interactions between microorganisms, or from environmental selection, where the association is environmentally driven. Therefore, before downstream analysis and interpretation, we need to distinguish the nature of the association, particularly if it is due to environmental selection or not. Results We present EnDED (environmentally driven edge detection), an implementation of four approaches as well as their combination to predict which links between microorganisms in an association network are environmentally driven. The four approaches are sign pattern, overlap, interaction information, and data processing inequality. We tested EnDED on networks from simulated data of 50 microorganisms. The networks contained on average 50 nodes and 1087 edges, of which 60 were true interactions but 1026 false associations (i.e., environmentally driven or due to chance). Applying each method individually, we detected a moderate to high number of environmentally driven edges—87% sign pattern and overlap, 67% interaction information, and 44% data processing inequality. Combining these methods in an intersection approach resulted in retaining more interactions, both true and false (32% of environmentally driven associations). After validation with the simulated datasets, we applied EnDED on a marine microbial network inferred from 10 years of monthly observations of microbial-plankton abundance. The intersection combination predicted that 8.3% of the associations were environmentally driven, while individual methods predicted 24.8% (data processing inequality), 25.7% (interaction information), and up to 84.6% (sign pattern as well as overlap). The fraction of environmentally driven edges among negative microbial associations in the real network increased rapidly with the number of environmental factors. Conclusions To reach accurate hypotheses about ecological interactions, it is important to determine, quantify, and remove environmentally driven associations in marine microbial association networks. For that, EnDED offers up to four individual methods as well as their combination. However, especially for the intersection combination, we suggest using EnDED with other strategies to reduce the number of false associations and consequently the number of potential interaction hypotheses. Video abstrac

Assessment of conflicts between mangroves and human occupation in Subaé river outfall between the years 1988 to 2017

Coastal zones fulfill important ecological, social and economic functions. Because soil flooded by tidal variations and due to great variation in salinity. Mangroves cover these regions. They are also a tropical coastal ecological system, always in the lowlands, at the mouths of rivers and estuaries. Despite their important environmental role, mangrove areas have been continuously decreasing worldwide, with an average reduction of 30% in the last 30 years. Thus, this research sought to determine land use and land cover change in low Subaé. With emphasis on Mangrove areas and urban occupation. We used supervised classifications of satellite images to evaluate the changes. We chose images from 1988, 2003, and 2017. And used images from the Landsat series (30m) and an image from the PlanetScope satellite (3m). We validated classifications through the Tau and Geographical Simultaneity concordance measures. We observed that performing the spatio-temporal analysis observing only the variation of areas may not represent the phenomena that occurred. The overall Tau index calculation for the ratings was 0.89. During the period 1988-2017 there was a significant reduction in Agricultural areas, corresponding to around 15% of the study area. Meanwhile, growth of pasture from 24km² to 48Km² and the Urban Zone, occurred over all classes, including mangroves

Ética pública frente a corrupción. Instrumentos éticos de aplicación práctica

La corrupción en los albores del siglo XXI es una característica generalizada en distintos gobiernos y administraciones públicas. México no está exento de esta lacra. Casos escandalosos protagonizados por servidores públicos sin escrúpulos salen a la luz cotidianamente. Dichas conductas desgastan la confianza ciudadana, aumentando el desprestigio de las instituciones públicas

A Random Growth Model with any Real or Theoretical Degree Distribution

The degree distributions of complex networks are usually considered to be power law. However, it is not the case for a large number of them. We thus propose a new model able to build random growing networks with (almost) any wanted degree distribution. The degree distribution can either be theoretical or extracted from a real-world network. The main idea is to invert the recurrence equation commonly used to compute the degree distribution in order to find a convenient attachment function for node connections - commonly chosen as linear. We compute this attachment function for some classical distributions, as the power-law, broken power-law, geometric and Poisson distributions. We also use the model on an undirected version of the Twitter network, for which the degree distribution has an unusual shape. We finally show that the divergence of chosen attachment functions is heavily links to the heavy-tailed property of the obtained degree distributions.Comment: 23 pages, 3 figure

Architecture, constraints, and behavior

This paper aims to bridge progress in neuroscience involving sophisticated quantitative analysis of behavior, including the use of robust control, with other relevant conceptual and theoretical frameworks from systems engineering, systems biology, and mathematics. Familiar and accessible case studies are used to illustrate concepts of robustness, organization, and architecture (modularity and protocols) that are central to understanding complex networks. These essential organizational features are hidden during normal function of a system but are fundamental for understanding the nature, design, and function of complex biologic and technologic systems

System-on-chip design of the cortical-diencephalic centre of the lower urinary tract

This article presents the design of a field programmable gate array (FPGA)-based prototype of a system on chip (SoC) capable of behaving as one of the nerve centres comprising the neuroregulatory system in humans: the cortical-diencephalic nerve centre. The neuroregulatory system is a complex nerve system consisting of a heterogeneous group of nerve centres. These centres are distributed throughout the length of the spinal cord, are autonomous, communicate via interneurons, and govern and regulate the behaviour of multiple organs and systems in the human body. As a result of years of study of the functioning and composition of the neuroregulatory system of the lower urinary tract (LUT), the centres that regulate this system have been isolated. The objective of this study is to understand the individual functioning of each centre in order to create a general model of the neuroregulatory system that is capable of operating at the level of the actual nerve centre. This model represents an advancement of the current black box models that do not allow for isolated or independent treatment of system dysfunction. In this study, we re-visit our research into the viability of the hardware design of one of these centres—the cortical-diencephalic centre. We describe this hardware because functioning of the centre is completely configurable and programmable, which validates the design for other centres that comprise the neuroregulatory system. In this document, we succinctly present the formal model of the centre, propose a hardware design and an FPGA-based prototype, construct a testing and simulation environment to evaluate it and, lastly, analyse and contrast the results using data obtained from real patients, verifying that the functional behaviour fits that observed in humans.This work has been supported by grant University of Alicante projects GRE14-02 and Smart University

System on chip design of the nerve centres of the human neuroregulatory system

Introducción: El sistema neurorregulador humano es un sistema nervioso complejo compuesto por un grupo heterogéneo de centros nerviosos distribuidos a lo largo de la médula espinal. Estos centros actúan de forma autónoma, se comunican mediante interconexiones nerviosas y gobiernan y regulan el comportamiento de órganos en los seres humanos. Por más de 20 años se viene estudiando el sistema neurorregulador del tracto urinario inferior, responsable de los órganos y sistemas que intervienen en el proceso de micción. El objetivo de la investigación ha sido comprender el papel individual de cada centro para crear un modelo general del sistema neurorregulador capaz de operar a nivel de centro nervioso. Métodos: El modelo creado se ha formalizado mediante la teoría de sistemas multiagente de forma que cada agente modele el comportamiento de un centro nervioso. Su granularidad ha abierto la posibilidad de actuar a nivel de centro, lo cual ha sido especialmente interesante en el tratamiento de disfunciones. Resultados y discusión: En este trabajo se enriqueció este modelo teórico con un modelo arquitectural que lo hiciera adecuado para su implementación en hardware. A partir del nuevo modelo, se propuso el diseño system on chip de un procesador específico capaz de desempeñar las funciones de un centro nervioso. En conclusión, la investigación supuso un enfoque original con el objetivo final de crear un chip parametrizable, capaz de desarrollar cualquier función neurorreguladora, que pudiera ser implantable en el cuerpo y con capacidad para trabajar de forma coordinada con el sistema neurorregulador biológico.Introduction: The human neuroregulatory system is a complex nervous system composed of a heterogeneous group of nerve centres distributed along the spinal cord. These centres act autonomously, communicate through neural interconnections, and govern and regulate the behavior of organs in humans. For more than twenty years, the neuroregulatory system of the lower urinary tract has been studied, which controls the organs and systems involved in the urination process. Based on the study of the behavior and composition of the lower urinary tract, we have succeeded in isolating the centres involved in its functioning. The goal has been to understand the individual role played by each centre to create a general model of the neuroregulatory system capable of operating at the level of the nerve centre. Methods: The model has been created and formalized based on Multi-Agent Systems theory: each agent thus models the behaviour of a nerve centre. Its granularity opens up the possibility of acting at the level of the centre, of particular interest to treat dysfunctions. Results and discussion: The present study enriches this theoretical model with an architectural model that makes it suitable to implement in hardware. Based on this new model, we propose a System on Chip (SoC) design of a specific processor capable of performing a nerve centre’s functions. Although this processor can be entirely configured and programmed to adjust to the functioning of the different centres, the present work aimed at facilitating the understanding and validation of the proposal. We thus focused on the cortical-diencephalic centre, responsible for voluntary micturition. As conclusions, the research adopted an original approach with the aim of creating a configurable chip, capable of developing any neuroregulatory function, implantable in the body and being able to function in a coordinated way with the biological neuroregulatory system

Mainstreams of horizontal gene exchange in enterobacteria : consideration of the outbreak of enterohemorrhagic E. coli O104:H4 in Germany in 2011

BACKGROUND: Escherichia coli O104:H4 caused a severe outbreak in Europe in 2011. The strain TY-2482 sequenced from this outbreak allowed the discovery of its closest relatives but failed to resolve ways in which it originated and evolved. On account of the previous statement, may we expect similar upcoming outbreaks to occur recurrently or spontaneously in the future? The inability to answer these questions shows limitations of the current comparative and evolutionary genomics methods. PRINCIPAL FINDINGS: The study revealed oscillations of gene exchange in enterobacteria, which originated from marine c- Proteobacteria. These mobile genetic elements have become recombination hotspots and effective ‘vehicles’ ensuring a wide distribution of successful combinations of fitness and virulence genes among enterobacteria. Two remarkable peculiarities of the strain TY-2482 and its relatives were observed: i) retaining the genetic primitiveness by these strains as they somehow avoided the main fluxes of horizontal gene transfer which effectively penetrated other enetrobacteria; ii) acquisition of antibiotic resistance genes in a plasmid genomic island of b-Proteobacteria origin which ontologically is unrelated to the predominant genomic islands of enterobacteria. CONCLUSIONS: Oscillations of horizontal gene exchange activity were reported which result from a counterbalance between the acquired resistance of bacteria towards existing mobile vectors and the generation of new vectors in the environmental microflora. We hypothesized that TY-2482 may originate from a genetically primitive lineage of E. coli that has evolved in confined geographical areas and brought by human migration or cattle trade onto an intersection of several independent streams of horizontal gene exchange. Development of a system for monitoring the new and most active gene exchange events was proposed.This work was funded by the National Research Foundation (South Africa) grant #71261 for National Bioinformatics and Functional Genomics Programme.http://www.plosone.or