Swarming Characteristics of Proteus mirabilis Under Anaerobic and Aerobic Conditions

Nutrients have a pronounced effect on the growth and swarming behaviour of Proteus mirabilis 7002. Iron, zinc, amino acids, and dioxygen are important for rapid growth and normal swarming. Anaerobically grown cultures of P. mirabilis 7002 were unable to swarm on anaerobically maintained rich nutrient agar. Upon exposure to aerobic conditions, P. mirabilis 7002 resumed swarming behaviour. Scanning electron microscopy was used to demonstrate the presence of community organization and mature rafts during normal swarming. These results support the importance of dioxygen and redox status in cell differentiation.     

An approach for the separation of mononuclear inflammatory cells from central nervous system tissue

It is not known whether currently available methods separate lymphoid cells from nervous system sites of immunologic disorders without the selective enrichment or depletion of particular cell subpopulations. To test the validity of a cell separation technique we developed, we applied this technique to a mixture of guinea pig blood mononuclear cells already characterized for surface membrane characteristics with autologous spinal cord tissue. Using this method, 10–20% of the original blood cell population was recovered. The percentages of E-rosetting and surface immunoglobulin cells in the separated cells was quite similar to that in the added blood cells. EAC-rosetting cell percentages were somewhat lower. This method shows promise for the in vitro study of cells obtained from lesions of autoimmune diseases in the central nervous system.     

Bluejay 1.0: genome browsing and comparison with rich customization provision and dynamic resource linking

Background  

The Bluejay genome browser has been developed over several years to address the challenges posed by the ever increasing number of data types as well as the increasing volume of data in genome research. Beginning with a browser capable of rendering views of XML-based genomic information and providing scalable vector graphics output, we have now completed version 1.0 of the system with many additional features. Our development efforts were guided by our observation that biologists who use both gene expression profiling and comparative genomics gain functional insights above and beyond those provided by traditional per-gene analyses.     

Acute blood biochemical alterations in response to marathon running.

Adrenal-sympathico function, blood carbohydrates and lipids, and water and electrolyte balance were studied in six highly trained male marathon runners prior to and after running a marathon (26.2 miles; 42.2 km) and on control days corresponding to the above times. Fluid intake was not sufficient to maintain body weight, the runners losing approximately 2.8 kg. Estimated plasma volume losses (161 ml, 4.4%) indicated that most of the fluid loss was extravascular. Tre rose an average 2.4 degrees C and a significant negative correlation between running time and rise in Tre was observed. Glucose, fatty acids, glycerol, hemoglobin, and plasma proteins were significantly elevated after the race. Small but statistically significant increments in lactate and pyruvate were also observed. Alterations in adrenal-sympathico function were indicated by increased levels of cortisol, epinephrine, and norepinephrine.     

Disaster and Contingency Planning for Scientific Shared Resource Cores

Progress in biomedical research is largely driven by improvements, innovations, and breakthroughs in technology, accelerating the research process, and an increasingly complex collaboration of both clinical and basic science. This increasing sophistication has driven the need for centralized shared resource cores (“cores”) to serve the scientific community. From a biomedical research enterprise perspective, centralized resource cores are essential to increased scientific, operational, and cost effectiveness; however, the concentration of instrumentation and resources in the cores may render them highly vulnerable to damage from severe weather and other disasters. As such, protection of these assets and the ability to recover from a disaster is increasingly critical to the mission and success of the institution. Therefore, cores should develop and implement both disaster and business continuity plans and be an integral part of the institution’s overall plans. Here we provide an overview of key elements required for core disaster and business continuity plans, guidance, and tools for developing these plans, and real-life lessons learned at a large research institution in the aftermath of Superstorm Sandy.     

Influence of L-NAME on pulmonary O2 uptake kinetics during heavy-intensity cycle exercise.

We hypothesized that inhibition of nitric oxide synthase (NOS) by N(G)-nitro-L-arginine methyl ester (L-NAME) would alleviate the inhibition of mitochondrial oxygen uptake (Vo(2)) by nitric oxide and result in a speeding of phase II pulmonary Vo(2) kinetics at the onset of heavy-intensity exercise. Seven men performed square-wave transitions from unloaded cycling to a work rate requiring 40% of the difference between the gas exchange threshold and peak Vo(2) with and without prior intravenous infusion of L-NAME (4 mg/kg in 50 ml saline over 60 min). Pulmonary gas exchange was measured breath by breath, and Vo(2) kinetics were determined from the averaged response to two exercise bouts performed in each condition. There were no significant differences between the control (C) and L-NAME conditions (L) for baseline Vo(2), the duration of phase I, or the amplitude of the primary Vo(2) response. However, the time constant of the Vo(2) response in phase II was significantly smaller (mean +/- SE: C: 25.1 +/- 3.0 s; L: 21.8 +/- 3.3 s; P < 0.05), and the amplitude of the Vo(2) slow component was significantly greater (C: 240 +/- 47 ml/min; L: 363 +/- 24 ml/min; P < 0.05) after L-NAME infusion. These data indicate that inhibition of NOS by L-NAME results in a significant (13%) speeding of Vo(2) kinetics and a significant increase in the amplitude of the Vo(2) slow component in the transition to heavy-intensity cycle exercise in men. The speeding of the primary component Vo(2) kinetics after L-NAME infusion indicates that at least part of the intrinsic inertia to oxidative metabolism at the onset of heavy-intensity exercise may result from inhibition of mitochondrial Vo(2) by nitric oxide. The cause of the larger Vo(2) slow-component amplitude with L-NAME requires further investigation but may be related to differences in muscle blood flow early in the rest-to-exercise transition.     

THE CHEMISTRY OF HUMAN SKIN : IV. THE ELECTROKINETIC EFFECT OF VARIOUS IONS UPON SUSPENDED PARTICLES OF STRATUM CORNEUM

1. The electrophoretic activity of particles of human skin in distilled water and different concentrations of salt solutions has been studied. The electrokinetic potential and the charge density were determined and comparisons made with results obtained by electroendosmosis. 2. The electrokinetic potential is ultimately decreased if sufficient salt is added. The order of inhibition is Al > Ca > Ba > K > Na. 3. The lyotrophic series Li > Na > K > Rb and Cl > I > Br express respectively the comparative effect of the monovalent cations and anions upon the electrokinetic potential of the skin. 4. Since both electrophoresis and electroendosmosis are dependent upon the electrokinetic potential, it follows from the results obtained, that the greatest rate of flow through the human skin under the force of an applied electrical current would be given by concentrations of neutral salts between 0.0001 M and 0.0002 M.     

ReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data

ABSTRACT: BACKGROUND: Next-generation sequencing technologies have become important tools for genome-wide studies. However, the quality scores that are assigned to each base have been shown to be inaccurate. If the quality scores are used in downstream analyses, these inaccuracies can have a significant impact on the results. RESULTS: Here we present ReQON, a tool that recalibrates the base quality scores from an input BAM file of aligned sequencing data using logistic regression. ReQON also generates diagnostic plots showing the effectiveness of the recalibration. We show that ReQON produces quality scores that are both more accurate, in the sense that they more closely correspond to the probability of a sequencing error, and do a better job of discriminating between sequencing errors and non-errors than the original quality scores. We also compare ReQON to other available recalibration tools and show that ReQON is less biased and performs favorably in terms of quality score accuracy. CONCLUSION: ReQON is an open source software package, written in R and available through Bioconductor, for recalibrating base quality scores for next-generation sequencing data. ReQON produces a new BAM file with more accurate quality scores, which can improve the results of downstream analysis, and produces several diagnostic plots showing the effectiveness of the recalibration.     

Formation of blooms by the symbiotic ciliate Mesodinium rubrum: the significance of nitrogen uptake

Mesodinium rubrum, a holotrichous ciliate that harbors endosymbioticchloroplasts, was responsible for patches of red water in thecoastal upweUing ecosystem at 15°S, Peru during March—May1977. Stations within red patches showed elevated concentrationsof paniculate nitrogen, chlorophyll a and dissolved organicnitrogen (DON), and lower concentrations of nitrate comparedwith areas where there were no ciliate blooms. These naturallyoccurring populations of M.rubrum took up nitrate, ammoniumand DON. Light was required for nitrate uptake and to a lesserextent for ammonium uptake. Dark uptake of ammonium occurredin all experiments. There was no effect of light on DON uptake.Possession of endosymbiotic chloroplasts enables this protozoanto use upwelled nitrate efficiently for development of largeblooms and concentrate into patches in the face of relativelystrong advective regimes.