RegulomePA: a database of transcriptional regulatory interactions in Pseudomonas aeruginosa PAO1.

We present RegulomePA, a database that contains biological information on regulatory interactions between transcription factors (TFs), sigma factor (SFs) and target genes in Pseudomonas aeruginosa PAO1. RegulomePA consists of 4827 regulatory interactions between 2831 nodes, which represent the interactions of TFs and SFs with their target genes, from the total of predicted RegulomePA including 27.27% of the TFs, 54.16% of SFs and 50.8% of the total genes. Each entry in the database corresponds to one node in the network and provides comprehensive details about the gene and its regulatory interactions such as gene description, nucleotide sequence, genome-strand position and links to other databases as well as the type of regulation it exerts or to which it is being subject (repression or activation), the associated experimental evidence and references, and topological information. Additionally, RegulomePA provides a way to recover information on the regulatory circuits of the network to which a gene pertains and also makes available the source codes to analyze the topology of any other regulatory network. The database will be updated yearly, by our team, with the contributions from ourselves and users, since the users are provided with an interactive platform where they can add interactions to the regulatory network feeding it with their respective references. Database URL: www.regulome.pcyt.unam.mx.

Persistent BK viremia does not increase intermediate-term graft loss but is associated with de novo donor-specific antibodies.

There are limited data regarding intermediate-term outcomes in patients with persistent BK viremia. Other viral infections have been implicated in the development of allosensitization through heterologous immunity, but the relationship between BK viremia and donor-specific antibodies (DSAs) is unexplored. In 2008, we initiated routine post-transplant BK viremia and DSA screening at our center; 785 kidney or kidney-pancreas transplant recipients were included in our study. Of these recipients, 132 (17%) recipients developed BK viremia during the study period. The median duration of BK viremia was 140 days (interquartile range=40-393 days), and persistent BK viremia was defined as lasting ≥140 days. Kaplan-Meier curves were generated to assess differences in patient and allograft survival on the basis of BK viremia status; survival was modeled using Cox proportional hazard regression. After a median follow-up of 3 years, there was no significant difference in terms of patient (hazard ratio [HR], 0.83; 95% confidence interval [95% CI], 0.28 to 2.49) or allograft survival (HR, 0.80; 95% CI, 0.37 to 1.73) between patients with and without BK viremia, which was confirmed in a time-varying analysis. In our logistic regression model, persistent BK viremia was strongly associated with the development of class II (HR, 2.55; 95% CI, 1.30 to 4.98) but not class I (HR, 1.13; 95% CI, 0.46 to 2.77) DSAs. These data suggest that persistent BK viremia does not negatively affect intermediate-term patient or allograft survival but is associated with increased risk for de novo DSA, although the exact mechanism is unclear.

Antagonism influences assembly of a Bacillus guild in a local community and is depicted as a food-chain network.

Understanding the principles that govern community assemblages is a central goal of ecology. There is limited experimental evidence in natural settings showing that microbial assembly in communities are influenced by antagonistic interactions. We, therefore, analyzed antagonism among bacterial isolates from a taxonomically related bacterial guild obtained from five sites in sediments from a fresh water system. We hypothesized that if antagonistic interactions acted as a shaping force of the community assembly, then the frequency of resistance to antagonism among bacterial isolates originating from a given site would be higher than the resistance to conspecifics originating from a different assemblage. Antagonism assays were conducted between 78 thermoresistant isolates, of which 72 were Bacillus spp. Sensitive, resistant and antagonistic isolates co-occurred at each site, but the within-site frequency of resistance observed was higher than that observed when assessed across-sites. We found that antagonism results from bacteriocin-like substances aimed at the exclusion of conspecifics. More than 6000 interactions were scored and described by a directed network with hierarchical structure that exhibited properties that resembled a food chain, where the different Bacillus taxonomic groups occupied specific positions. For some tested interacting pairs, the unidirectional interaction could be explained by competition that inhibited growth or completely excluded one of the pair members. This is the first report on the prevalence and specificity of Bacillus interactions in a natural setting and provides evidence for the influence of bacterial antagonist interactions in the assemblage of a taxonomically related guild in local communities.

Regulatory dynamics of standard two-component systems in bacteria.

Complex cellular networks regulate metabolism, environmental adaptation, and phenotypic changes in biological systems. Among the elements forming regulatory networks in bacteria are regulatory proteins such as transcription factors, which respond to exogenous and endogenous conditions. To perceive their surroundings, bacteria have evolved sensory regulatory systems of two-components. The archetype of these systems is made up of two proteins--a signal sensor and a response regulator-whose genes are usually located together in a single transcription unit. These units switch transcriptional programs in response to environmental conditions. Here, we study 14 two-component systems in Escherichia coli, which have been experimentally characterized with respect to their transcriptional regulation and their perceived signal. Given that the activity of these sensory units is connected to the rest of the transcriptional network, we first classify them as autonomous, semiautonomous or dependent, according to whether or not they use additional regulators to be transcribed. Next, we use discrete-time models to simulate their qualitative regulatory dynamics in response to their transcriptional regulation and to the activation of these systems by their cognate signals. Compared to more traditional ordinary differential equations method, ours has the advantage of being computationally simple and mathematically tractable, while keeping the ability to reproduce the phenomenology described by non-linear models. The aim of the present work is not the study of all possible behaviors of these two-component systems, but to exemplify those behaviors reported in the literature. On the other hand, most of these systems are auto-activating switches, a property that distinguishes them from the other transcription factors in the regulatory network, which are mostly auto-repressing. Based on the data, our models show dynamic behaviors that explain how most of these sensory systems convey abilities for multistationarity, and these dynamic properties could explain the phenotypic heterogeneity observed in bacterial populations. Our results are likely to have an impact in the design of synthetic signaling modules.

Protección contra inundaciones en un cruce vial bajo nivel con un retardo pluvial enterrado

Trabajo enmarcado dentro del proyecto Remodelación Acceso Bv. Oroño (Rosario, Pcia. de Santa Fe), que incluye la sistematización vial y la readecuación de la red de desagües pluviales existente. Se contempla un paso inferior bajo las vías de ferrocarril, que facilite la circulación vehicular, y cuyo desagüe evacúe el aporte pluvial que se genera en sus rampas de acceso. El sistema utilizado es el de retardo de agua pluvial, con la misión de reducir los riesgos de inundación