52,665 research outputs found

    Time series genome-centric analysis unveils bacterial response to operational disturbance in activated sludge

    Get PDF
    Understanding ecosystem response to disturbances and identifying the most critical traits for the maintenance of ecosystem functioning are important goals for microbial community ecology. In this study, we used 16S rRNA amplicon sequencing and metagenomics to investigate the assembly of bacterial populations in a full-scale municipal activated sludge wastewater treatment plant over a period of 3 years, including a 9-month period of disturbance characterized by short-term plant shutdowns. Following the reconstruction of 173 metagenome-assembled genomes, we assessed the functional potential, the number of rRNA gene operons, and the in situ growth rate of microorganisms present throughout the time series. Operational disturbances caused a significant decrease in bacteria with a single copy of the rRNA (rrn) operon. Despite moderate differences in resource availability, replication rates were distributed uniformly throughout time, with no differences between disturbed and stable periods. We suggest that the length of the growth lag phase, rather than the growth rate, is the primary driver of selection under disturbed conditions. Thus, the system could maintain its function in the face of disturbance by recruiting bacteria with the capacity to rapidly resume growth under unsteady operating conditions.Fil: Pérez, María Victoria. Agua y Saneamientos Argentinos S.a.; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Guerrero, Leandro Demián. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Orellana, Esteban. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; ArgentinaFil: Figuerola, Eva Lucia Margarita. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; ArgentinaFil: Erijman, Leonardo. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Investigaciones en Ingeniería Genética y Biología Molecular "Dr. Héctor N. Torres"; Argentina. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales. Departamento de Fisiología, Biología Molecular y Celular; Argentin

    Opportunistic linked data querying through approximate membership metadata

    Get PDF
    Between URI dereferencing and the SPARQL protocol lies a largely unexplored axis of possible interfaces to Linked Data, each with its own combination of trade-offs. One of these interfaces is Triple Pattern Fragments, which allows clients to execute SPARQL queries against low-cost servers, at the cost of higher bandwidth. Increasing a client's efficiency means lowering the number of requests, which can among others be achieved through additional metadata in responses. We noted that typical SPARQL query evaluations against Triple Pattern Fragments require a significant portion of membership subqueries, which check the presence of a specific triple, rather than a variable pattern. This paper studies the impact of providing approximate membership functions, i.e., Bloom filters and Golomb-coded sets, as extra metadata. In addition to reducing HTTP requests, such functions allow to achieve full result recall earlier when temporarily allowing lower precision. Half of the tested queries from a WatDiv benchmark test set could be executed with up to a third fewer HTTP requests with only marginally higher server cost. Query times, however, did not improve, likely due to slower metadata generation and transfer. This indicates that approximate membership functions can partly improve the client-side query process with minimal impact on the server and its interface

    Analysis of Trade-offs in Fault-Tolerant Distributed Computing and Replicated Databases

    Get PDF
    This paper examines fundamental trade-offs in fault-tolerant distributed systems and replicated databases built over the Internet. We discuss interplays between consistency, availability, and latency which are in the very nature of globally distributed computer systems and also analyse their interconnection with durability and energy efficiency. In this paper we put forward an idea that consistency, availability, latency, durability and other properties need to be viewed as more continuous than binary in contrast to the well-known CAP/PACELC theorems. We compare different consistency models and highlight the role of the application timeout, replication factor and other settings that essentially determine the interplay between above properties. Our findings may be of interest to software engineers and system architects who develop Internet-scale distributed computer systems and cloud solutions

    Program Transformations for Asynchronous and Batched Query Submission

    Full text link
    The performance of database/Web-service backed applications can be significantly improved by asynchronous submission of queries/requests well ahead of the point where the results are needed, so that results are likely to have been fetched already when they are actually needed. However, manually writing applications to exploit asynchronous query submission is tedious and error-prone. In this paper we address the issue of automatically transforming a program written assuming synchronous query submission, to one that exploits asynchronous query submission. Our program transformation method is based on data flow analysis and is framed as a set of transformation rules. Our rules can handle query executions within loops, unlike some of the earlier work in this area. We also present a novel approach that, at runtime, can combine multiple asynchronous requests into batches, thereby achieving the benefits of batching in addition to that of asynchronous submission. We have built a tool that implements our transformation techniques on Java programs that use JDBC calls; our tool can be extended to handle Web service calls. We have carried out a detailed experimental study on several real-life applications, which shows the effectiveness of the proposed rewrite techniques, both in terms of their applicability and the performance gains achieved.Comment: 14 page

    Skeletal trade-offs in coralline algae in response to ocean acidification

    Get PDF
    Ocean acidification is changing the marine environment, with potentially serious consequences for many organisms. Much of our understanding of ocean acidification effects comes from laboratory experiments, which demonstrate physiological responses over relatively short timescales. Observational studies and, more recently, experimental studies in natural systems suggest that ocean acidification will alter the structure of seaweed communities. Here, we provide a mechanistic understanding of altered competitive dynamics among a group of seaweeds, the crustose coralline algae (CCA). We compare CCA from historical experiments (1981-1997) with specimens from recent, identical experiments (2012) to describe morphological changes over this time period, which coincides with acidification of seawater in the Northeastern Pacific. Traditionally thick species decreased in thickness by a factor of 2.0-2.3, but did not experience a change in internal skeletal metrics. In contrast, traditionally thin species remained approximately the same thickness but reduced their total carbonate tissue by making thinner inter-filament cell walls. These changes represent alternative mechanisms for the reduction of calcium carbonate production in CCA and suggest energetic trade-offs related to the cost of building and maintaining a calcium carbonate skeleton as pH declines. Our classification of stress response by morphological type may be generalizable to CCA at other sites, as well as to other calcifying organisms with species-specific differences in morphological types
    corecore