Transkingdom Networks: A Systems Biology Approach to Identify Causal Members of Host-Microbiota Interactions

Improvements in sequencing technologies and reduced experimental costs have resulted in a vast number of studies generating high-throughput data. Although the number of methods to analyze these "omics" data has also increased, computational complexity and lack of documentation hinder researchers from analyzing their high-throughput data to its true potential. In this chapter we detail our data-driven, transkingdom network (TransNet) analysis protocol to integrate and interrogate multi-omics data. This systems biology approach has allowed us to successfully identify important causal relationships between different taxonomic kingdoms (e.g. mammals and microbes) using diverse types of data

Children struggle beyond preschool-age in a continuous version of the ambiguous figures task

Children until the age of five are only able to reverse an ambiguous figure when they are informed about the second interpretation. In two experiments, we examined whether children’s difficulties would extend to a continuous version of the ambiguous figures task. Children (Experiment 1: 66 3- to 5-year olds; Experiment 2: 54 4- to 9-year olds) and adult controls saw line drawings of animals gradually morph—through well-known ambiguous figures—into other animals. Results show a relatively late developing ability to recognize the target animal, with difficulties extending beyond preschool-age. This delay can neither be explained with improvements in theory of mind, inhibitory control, nor individual differences in eye movements. Even the best achieving children only started to approach adult level performance at the age of 9, suggesting a fundamentally different processing style in children and adults

Detection of <it>P. aeruginosa </it> harboring <it>bla </it>_CTX-M-2, <it>bla </it>_GES-1 and <it>bla </it>_GES-5,<it>bla </it>_IMP-1 and <it>bla </it>_SPM-1 causing infections in Brazilian tertiary-care hospital

<p>Abstract</p> <p>Background</p> <p>Nosocomial infections caused by <it>Pseudomonas aeruginosa</it> presenting resistance to beta-lactam drugs are one of the most challenging targets for antimicrobial therapy, leading to substantial increase in mortality rates in hospitals worldwide. In this context, <it>P. aeruginosa</it> harboring acquired mechanisms of resistance, such as production of metallo-beta-lactamase (MBLs) and extended-spectrum beta-lactamases (ESBLs) have the highest clinical impact. Hence, this study was designed to investigate the presence of genes codifying for MBLs and ESBLs among carbapenem resistant <it>P. aeruginosa</it> isolated in a Brazilian 720-bed teaching tertiary care hospital.</p> <p>Methods</p> <p>Fifty-six carbapenem-resistant <it>P. aeruginosa</it> strains were evaluated for the presence of MBL and ESBL genes. Strains presenting MBL and/or ESBL genes were submitted to pulsed-field gel electrophoresis for genetic similarity evaluation.</p> <p>Results</p> <p>Despite the carbapenem resistance, genes for MBLs (<it>bla</it>_SPM-1 or <it>bla</it>_IMP-1) were detected in only 26.7% of isolates. Genes encoding ESBLs were detected in 23.2% of isolates. The <it>bla</it>_CTX-M-2 was the most prevalent ESBL gene (19.6%), followed by <it>bla</it>_GES-1 and <it>bla</it>_GES-5 detected in one isolate each. In all isolates presenting MBL phenotype by double-disc synergy test (DDST), the <it>bla</it>_SPM-1 or <it>bla</it>_IMP-1 genes were detected. In addition, <it>bla</it>_IMP-1 was also detected in three isolates which did not display any MBL phenotype. These isolates also presented the <it>bla</it>_CTX-M-2 gene. The co-existence of <it>bla</it>_CTX-M-2 with <it>bla</it>_IMP-1 is presently reported for the first time, as like as co-existence of <it>bla</it>_GES-1 with <it>bla</it>_IMP-1.</p> <p>Conclusions</p> <p>In this study MBLs production was not the major mechanism of resistance to carbapenems, suggesting the occurrence of multidrug efflux pumps, reduction in porin channels and production of other beta-lactamases. The detection of <it>bla</it>_CTX-M-2,<it>bla</it>_GES-1 and <it>bla</it>_GES-5 reflects the recent emergence of ESBLs among antimicrobial resistant <it>P. aeruginosa</it> and the extraordinary ability presented by this pathogen to acquire multiple resistance mechanisms. These findings raise the concern about the future of antimicrobial therapy and the capability of clinical laboratories to detect resistant strains, since simultaneous production of MBLs and ESBLs is known to promote further complexity in phenotypic detection. Occurrence of intra-hospital clonal dissemination enhances the necessity of better observance of infection control practices.</p