Unusual Metabolism and Hypervariation in the Genome of a Gracilibacterium (BD1-5) from an Oil-Degrading Community.

The candidate phyla radiation (CPR) comprises a large monophyletic group of bacterial lineages known almost exclusively based on genomes obtained using cultivation-independent methods. Within the CPR, Gracilibacteria (BD1-5) are particularly poorly understood due to undersampling and the inherent fragmented nature of available genomes. Here, we report the first closed, curated genome of a gracilibacterium from an enrichment experiment inoculated from the Gulf of Mexico and designed to investigate hydrocarbon degradation. The gracilibacterium rose in abundance after the community switched to dominance by Colwellia Notably, we predict that this gracilibacterium completely lacks glycolysis, the pentose phosphate and Entner-Doudoroff pathways. It appears to acquire pyruvate, acetyl coenzyme A (acetyl-CoA), and oxaloacetate via degradation of externally derived citrate, malate, and amino acids and may use compound interconversion and oxidoreductases to generate and recycle reductive power. The initial genome assembly was fragmented in an unusual gene that is hypervariable within a repeat region. Such extreme local variation is rare but characteristic of genes that confer traits under pressure to diversify within a population. Notably, the four major repeated 9-mer nucleotide sequences all generate a proline-threonine-aspartic acid (PTD) repeat. The genome of an abundant Colwellia psychrerythraea population has a large extracellular protein that also contains the repeated PTD motif. Although we do not know the host for the BD1-5 cell, the high relative abundance of the C. psychrerythraea population and the shared surface protein repeat may indicate an association between these bacteria.IMPORTANCE CPR bacteria are generally predicted to be symbionts due to their extensive biosynthetic deficits. Although monophyletic, they are not monolithic in terms of their lifestyles. The organism described here appears to have evolved an unusual metabolic platform not reliant on glucose or pentose sugars. Its biology appears to be centered around bacterial host-derived compounds and/or cell detritus. Amino acids likely provide building blocks for nucleic acids, peptidoglycan, and protein synthesis. We resolved an unusual repeat region that would be invisible without genome curation. The nucleotide sequence is apparently under strong diversifying selection, but the amino acid sequence is under stabilizing selection. The amino acid repeat also occurs in a surface protein of a coexisting bacterium, suggesting colocation and possibly interdependence

Resistance training and testosterone levels in male patients with chronic kidney disease undergoing dialysis

Background. We investigated serum testosterone and insulin-like growth factor 1 (IGF-1) levels’ associations with muscle fibre size and resistance training in male dialysis patients. Methods. Male patients were included in a 16-week control period followed by 16 weeks of resistance training thrice weekly. Blood samples were obtained to analyse testosterone, luteinizing hormone (LH), IGF-1, and IGF-binding protein 3. Muscle fibres’ size was analysed in biopsies from m. vastus lateralis. Results. The patients’ testosterone levels were within the normal range at baseline (n=20) (19.5 (8.2–52.1) nmol/L versus 17.6 (16.1–18.0), resp.) whereas LH levels were higher (13.0 (5.5–82.8) U/L versus 4.3 (3.3–4.6), P<0.001, resp.). IGF-1 and IGF-binding protein 3 levels were higher in the patients compared with reference values (203 (59–590) ng/mL versus 151 (128–276), P=0.014, and 5045 (3370–9370) ng/mL versus 3244 (3020–3983), P<0.001, resp.). All hormone levels and muscle fibre size (n=12) remained stable throughout the study. Age-adjusted IGF-1 was associated with type 1 and 2 fibre sizes (P<0.05). Conclusion. Patients’ total testosterone values were normal due to markedly increased LH values, which suggest a compensated primary insufficiency of the testosterone producing Leydig cell. Even though testosterone values were normal, resistance training was not associated with muscle hypertrophy. This trial is registered with ISRCTN72099857

Association between congenital toxoplasmosis and preterm birth, low birthweight and small for gestational age birth.

OBJECTIVE: To determine the association between congenital toxoplasmosis and preterm birth, low birthweight and small for gestational age birth. DESIGN: Multicentre prospective cohort study. SETTING: Ten European centres offering prenatal screening for toxoplasmosis. POPULATION: Deliveries after 23 weeks of gestation in 386 women with singleton pregnancies who seroconverted to toxoplasma infection before 20 weeks of gestation. Deliveries after 36 weeks in 234 women who seroconverted at 20 weeks or later, and tested positive before 37 weeks. METHODS: Comparison of infected and uninfected births, adjusted for parity and country of birth. MAIN OUTCOME MEASURES: Differences in gestational age at birth, birthweight and birthweight centile. RESULTS: Infected babies were born or delivered earlier than uninfected babies: the mean difference for seroconverters before 20 weeks was -5.4 days (95% CI: -1.4, -9.4), and at 20 weeks or more, -2.6 days (95% CI: -0.5, -4.7). Congenital infection was associated with an increased risk of preterm delivery when seroconversion occurred before 20 weeks (OR 4.71; 95% CI: 2.03, 10.9). No significant differences were detected for birthweight or birthweight centile. CONCLUSION: Babies with congenital toxoplasmosis were born earlier than uninfected babies but the mechanism leading to shorter length of gestation is unknown. Congenital infection could precipitate early delivery or prompt caesarean section or induction of delivery. We found no evidence for a significant association between congenital toxoplasmosis and reduced birthweight or small for gestational age birth

The time delay of the quadruple quasar RX J0911.4+0551

We present optical lightcurves of the gravitationally lensed components A (=A1+A2+A3) and B of the quadruple quasar RX J0911.4+0551 (z = 2.80). The observations were primarily obtained at the Nordic Optical Telescope between 1997 March and 2001 April and consist of 74 I-band data points for each component. The data allow the measurement of a time delay of 146 +- 8 days (2 sigma) between A and B, with B as the leading component. This value is significantly shorter than that predicted from simple models and indicates a very large external shear. Mass models including the main lens galaxy and the surrounding massive cluster of galaxies at z = 0.77, responsible for the external shear, yield H_0 = 71 +- 4 (random, 2 sigma) +- 8 (systematic) km/s/Mpc. The systematic model uncertainty is governed by the surface-mass density (convergence) at the location of the multiple images.Comment: 12 pages, 3 figures, ApJL, in press (June 20, 2002

Scattering theory of interface resistance in magnetic multilayers

The scattering theory of transport has to be applied with care in a diffuse environment. Here we discuss how the scattering matrices of heterointerfaces can be used to compute interface resistances of dirty magnetic multilayers. First principles calculations of these interface resistances agree well with experiments in the CPP (current perpendicular to the interface plane) configuration.Comment: submitted to J. Phys. D (special issue at the occasion of Prof. T. Shinjo's 60th birthday

Variable Curvature Slab Molecular Dynamics as a Method to Determine Surface Stress

A thin plate or slab, prepared so that opposite faces have different surface stresses, will bend as a result of the stress difference. We have developed a classical molecular dynamics (MD) formulation where (similar in spirit to constant-pressure MD) the curvature of the slab enters as an additional dynamical degree of freedom. The equations of motion of the atoms have been modified according to a variable metric, and an additional equation of motion for the curvature is introduced. We demonstrate the method to Au surfaces, both clean and covered with Pb adsorbates, using many-body glue potentials. Applications to stepped surfaces, deconstruction and other surface phenomena are under study.Comment: 16 pages, 8 figures, REVTeX, submitted to Physical Review

Model Channel Ion Currents in NaCl - SPC/E Solution with Applied-Field Molecular Dynamics

Using periodic boundary conditions and a constant applied field, we have simulated current flow through an 8.125 Angstrom internal diameter, rigid, atomistic channel with polar walls in a rigid membrane using explicit ions and SPC/E water. Channel and bath currents were computed from ten 10-ns trajectories for each of 10 different conditions of concentration and applied voltage. An electric field was applied uniformly throughout the system to all mobile atoms. On average, the resultant net electric field falls primarily across the membrane channel, as expected for two conductive baths separated by a membrane capacitance. The channel is rarely occupied by more than one ion. Current-voltage relations are concentration-dependent and superlinear at high concentrations.Comment: Accepted for publication in Biophysical Journa

NFIRAOS: TMT facility adaptive optics with conventional DMs

Although many of the instruments planned for the TMT (Thirty Meter Telescope) have their own closely-coupled adaptive optics systems, TMT will also have a facility Adaptive Optics (AO) system feeding three instruments on the Nasmyth platform. For this Narrow-Field Infrared Adaptive Optics System, NFIRAOS (pronounced nefarious), the TMT project considered two architectures. One, described in this paper, employs conventional deformable mirrors with large diameters of about 300 mm and this is the reference design adopted by the TMT project. An alternative design based on MEMS was also studied, and is being presented separately in this conference. The requirements for NFIRAOS include 0.8-5 microns wavelength range, 30 arcsecond diameter output field of view (FOV), excellent sky coverage, and diffraction- limited atmospheric turbulence compensation (specified at 133 nm RMS including residual telescope and science instrument errors.) The reference design for NFIRAOS includes multiple sodium laser guide stars over a 70 arcsecond FOV, and an infrared tip/tilt/focus/astigmatism natural guide star sensor within instruments. Larger telescopes require greater deformable mirror (DM) stroke. Although initially NFIRAOS will correct a 10 arcsecond science field, it uses two deformable mirrors in series, partly to provide sufficient stroke for atmospheric correction over the 30 m telescope aperture, but mainly to partially correct a 2 arcminute diameter "technical" field to sharpen near-IR natural guide stars and improve sky coverage. The planned upgrade to full performance includes replacing the groundconjugated DM with a higher actuator density, and using a deformable telescope secondary mirror as a "woofer." NFIRAOS incorporates an instrument rotator and selection of three live instruments: a near-Infrared integral field Imaging spectrograph, a near-infrared echelle spectrograph, and after upgrading NFIRAOS to full multi-conjugation, a wide field (30 arcsecond) infrared camera

The Justice Challenge: Honors Endeavors Innovative Pedagogies through the Grand Challenge Scholars Program

Honors practitioners from fourteen colleges and programs across the country at land-grant, public, and minority-serving institutions partner with agricultural experts to secure a United States Department of Agriculture (USDA) Higher Education Challenge grant focused on the themes of food justice, climate justice, and sustainable agriculture. Authors describe the program’s origin, objectives, and curricular outgrowths, highlighting its efficacy for empowering students in areas of systems thinking, career readiness, leadership in the service of addressing social needs, and learning through civic engagement

Complete genome sequence of the epidemic and highly virulent CTX-M-15-producing H30-Rx subclone of Escherichia coli ST131

We report the complete genome sequence, including five complete plasmid sequences, of Escherichia coli ST131 isolate JJ1886. The isolate was obtained in 2007 in the United States from a patient with fatal urosepsis and belongs to the virulent, CTX-M-15-producing H30-Rx sublineage