Identification and analysis of integrons and cassette arrays in bacterial genomes

Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program – IntegronFinder – to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as α-Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome.     

Determinants of participation restriction among community dwelling stroke survivors: A path analysis

Background  

Apart from promoting physical recovery and assisting in activities of daily living, a major challenge in stroke rehabilitation is to minimize psychosocial morbidity and to promote the reintegration of stroke survivors into their family and community. The identification of key factors influencing long-term outcome are essential in developing more effective rehabilitation measures for reducing stroke-related morbidity. The aim of this study was to test a theoretical model of predictors of participation restriction which included the direct and indirect effects between psychosocial outcomes, physical outcome, and socio-demographic variables at 12 months after stroke.     

Unexpected photobleaching of Alexa 488 in a fixed bacterial sample during 2-photon excitation

A sample of fixed bacterial cells was examined by immunofluorescence microscopy using an Alexa 488 conjugated secondary antibody for visualization. Excitation using visible light confirmed the expected photostability of this fluorophore; however, when using 2-photon excitation, Alexa 488 was rapidly and substantially photobleached. The unexpected instability of Alexa 488 under certain conditions may have deleterious consequences if not anticipated and accommodated in experimental protocols.     

Inducible nitric oxide synthase mediates cytokine release: the time course in conscious and septic rats

Nitric oxide (NO), tumor necrosis factor-alpha (TNF-alpha), and interleukin 1-beta (IL-1beta) are postulated to play a key pathophysiologic role during sepsis. In this study, we examined the time course of inducible NO synthase (iNOS) mRNA expression and the plasma TNF-alpha and IL-1beta in lipopolysaccharide (LPS)-treated conscious rats. The hemodynamic pattern in septic shock is more similar to clinical conditions without anesthesia. The data showed that a significant increase in iNOS mRNA levels was found in the spleen, lung, liver, with slight elevation in the heart and kidney at 3 h after LPS administration. However, iNOS mRNA levels were not elevated significantly in all tissues examined at 24 h. In the plasma, TNF-alpha and IL-1beta culminated within 1 h, and reduced gradually to baseline levels in a relatively short period (within 9 h). The results suggest that local NO production by activation of iNOS mRNA expression and cytokine release may contribute to LPS-induced organ dysfunction at various time points.     

Implication of life history strategies for prenatal investment in cetaceans

Prenatal investment directly determines the size at birth and fetus growth rate, which affects neonatal survival and growth and potentially affects maternal fitness. This study explored the associated prenatal life history traits of cetaceans. Using multivariate analysis and ANCOVA, baleen whales and toothed cetaceans had distinct energy patterns, with two exceptions including beaked whales and eusocial cetaceans. Baleen whales are characterized by fast prenatal growth, which suggests high prenatal energetics, and utilize the capital breeder tactic. Toothed cetaceans, except for beaked whales, utilize income breeder energetics, which yields relatively slow prenatal growth. However, eusocial cetaceans have especially slow prenatal growth, suggesting very low prenatal energetic effort with social compensation. Although beaked whales are behaviorally income breeders, both discriminant analysis and ANCOVA showed that they are energetically similar to baleen whales, utilizing capital energetics. ANCOVA further revealed that beaked whales have comparatively large calf size, suggesting high prenatal investment. Because all cetaceans wean their calves at comparable size, high prenatal investment may further suggest reduced cost of lactation, which may be behaviorally and energetically adaptive to their specific deep‐dive‐feeding niche.     

Power overshoot in two-chambered microbial fuel cell (MFC)

A two-chamber microbial fuel cell was started using iron-reducing strains as inoculum and acetate as carbon sources. The tested microbial fuel cell had an open-circuit voltage of 0.67 V, and reached 1045 mA m⁻² and a power density of 486 mW m⁻² at 0.46 V before power overshoot occurred. Anodic reactions were identified as the rate-determining steps. Stirring the anolyte insignificantly increased cell performance, suggesting a minimal external mass transfer resistance from the anolyte to the anodic biofilm. Data regression analysis indicates that charge transfer resistance at the biofilm-anode junction was negligible. The order of magnitude estimation of electrical conductance indicates that electron transfer resistance had an insignificant effect on microbial fuel cell performance. Resistance in electrogens for substrate utilization is proposed to induce microbial fuel cell power overshoot.