Direct comparison of nick-joining activity of the nucleic acid ligases from bacteriophage T4

The genome of bacteriophage T4 encodes three polynucleotide ligases, which seal the backbone of nucleic acids during infection of host bacteria. The T4Dnl (T4 DNA ligase) and two RNA ligases [T4Rnl1 (T4 RNA ligase 1) and T4Rnl2] join a diverse array of substrates, including nicks that are present in double-stranded nucleic acids, albeit with different efficiencies. To unravel the biochemical and functional relationship between these proteins, a systematic analysis of their substrate specificity was performed using recombinant proteins. The ability of each protein to ligate 20 bp double-stranded oligonucleotides containing a single-strand break was determined. Between 4 and 37 °C, all proteins ligated substrates containing various combinations of DNA and RNA. The RNA ligases ligated a more diverse set of substrates than T4Dnl and, generally, T4Rnl1 had 50-1000-fold lower activity than T4Rnl2. In assays using identical conditions, optimal ligation of all substrates was at pH 8 for T4Dnl and T4Rnl1 and pH 7 for T4Rnl2, demonstrating that the protein dictates the pH optimum for ligation. All proteins ligated a substrate containing DNA as the unbroken strand, with the nucleotides at the nick of the broken strand being RNA at the 3'-hydroxy group and DNA at the 5'-phosphate. Since this RNA-DNA hybrid was joined at a similar maximal rate by T4Dnl and T4Rnl2 at 37 °C, we consider the possibility that this could be an unexpected physiological substrate used during some pathways of 'DNA repair'

Performance of a C4F8O Gas Radiator Ring Imaging Cherenkov Detector Using Multi-anode Photomultiplier Tubes

We report on test results of a novel ring imaging Cherenkov (RICH) detection system consisting of a 3 meter long gaseous C4F8O radiator, a focusing mirror, and a photon detector array based on Hamamatsu multi-anode photomultiplier tubes. This system was developed to identify charged particles in the momentum range from 3-70 GeV/c for the BTeV experiment.Comment: 28 pages, 23 figures, submitted to Nuclear Instruments and Method

A new educational software tool for robust control design using the QFT method

We present a new educational software tool for robust control design based on the Quantitative Feedback Design (QFT) method. This is a graphical design methodology for systems with large parametric uncertainty, which has been successfully applied to many complex practical problems. The software tool is implemented in Matlab and may be used to introduce students to robust control methods via small and medium-size design applications. The software is a library of programmable M-files with open access to users and is intended as a test-bed for developing new techniques in this area and for automating parts of the design procedure, such as loop-shaping. A simple design problem is used to illustrate the main features of the software

Fish biomass estimation by calibrating the echointegrator deflection against catch data

Acoustic survey for fish resources was conducted using echosounder (EK-400) with echointegrator (QD). The echointegrator coupled with echosounder sums-up the echo signal received. The sum of the echo signal received per nautical mile covered is an index of the quantum of fish recorded and therefore a measure of the relative density of fish in surveyed area. It is converted into absolute biomass using the calibrarion constant obtained by correlating the trawl catch data against the echointegrator reading corresponding to the opening of the net. The calibration constant thus arrived at was 1327 kg/n.mile corresponding to 1 mm integrator deflection per nautical mile covered

Continuous infusion of an agonist of the tumor necrosis factor receptor 2 in the spinal cord improves recovery after traumatic contusive injury.

AimThe activation of the TNFR2 receptor is beneficial in several pathologies of the central nervous system, and this study examines whether it can ameliorate the recovery process following spinal cord injury.MethodsEHD2-sc-mTNFR2 , an agonist specific for TNFR2, was used to treat neurons exposed to high levels of glutamate in vitro. In vivo, it was infused directly to the spinal cord via osmotic pumps immediately after a contusion to the cord at the T9 level. Locomotion behavior was assessed for 6 weeks, and the tissue was analyzed (lesion size, RNA and protein expression, cell death) after injury. Somatosensory evoked potentials were also measured in response to hindlimb stimulation.ResultsThe activation of TNFR2 protected neurons from glutamate-mediated excitotoxicity through the activation of phosphoinositide-3 kinase gamma in vitro and improved the locomotion of animals following spinal cord injury. The extent of the injury was not affected by infusing EHD2-sc-mTNFR2 , but higher levels of neurofilament H and 2', 3'-cyclic-nucleotide 3'-phosphodiesterase were observed 6 weeks after the injury. Finally, the activation of TNFR2 after injury increased the neural response recorded in the cortex following hindlimb stimulation.ConclusionThe activation of TNFR2 in the spinal cord following contusive injury leads to enhanced locomotion and better cortical responses to hindlimb stimulation