Analysis of a nuclease activity of catalytic domain of Thermus thermophilus MutS2 by high-accuracy mass spectrometry

Electrospray ionization with Fourier-transform ion cyclotron resonance mass spectrometry (ESI–FT ICR MS) is a powerful tool for analyzing the precise structural features of biopolymers, including oligonucleotides. Here, we described the detailed characterization of a newly discovered nuclease activity of the C-terminal domain of Thermus thermophilus MutS2 (ttMutS2). Using this method, the length, nucleotide content and nature of the 5′- and 3′-termini of the product oligonucleotides were accurately identified. It is revealed that the C-terminal domain of ttMutS2 incised the phosphate backbone of oligodeoxynucleotides non-sequence-specifically at the 3′ side of the phosphates. The simultaneous identification of the innumerable fragments was achieved by the extremely high-accuracy of ESI–FT ICR MS

Evaluation of heterogeneity dose distributions for Stereotactic Radiotherapy (SRT): comparison of commercially available Monte Carlo dose calculation with other algorithms

<p>Abstract</p> <p>Background</p> <p>The purpose of this study was to compare dose distributions from three different algorithms with the x-ray Voxel Monte Carlo (XVMC) calculations, in actual computed tomography (CT) scans for use in stereotactic radiotherapy (SRT) of small lung cancers.</p> <p>Methods</p> <p>Slow CT scan of 20 patients was performed and the internal target volume (ITV) was delineated on Pinnacle³. All plans were first calculated with a scatter homogeneous mode (SHM) which is compatible with Clarkson algorithm using Pinnacle³treatment planning system (TPS). The planned dose was 48 Gy in 4 fractions. In a second step, the CT images, structures and beam data were exported to other treatment planning systems (TPSs). Collapsed cone convolution (CCC) from Pinnacle³, superposition (SP) from XiO, and XVMC from Monaco were used for recalculating. The dose distributions and the Dose Volume Histograms (DVHs) were compared with each other.</p> <p>Results</p> <p>The phantom test revealed that all algorithms could reproduce the measured data within 1% except for the SHM with inhomogeneous phantom. For the patient study, the SHM greatly overestimated the isocenter (IC) doses and the minimal dose received by 95% of the PTV (PTV95) compared to XVMC. The differences in mean doses were 2.96 Gy (6.17%) for IC and 5.02 Gy (11.18%) for PTV95. The DVH's and dose distributions with CCC and SP were in agreement with those obtained by XVMC. The average differences in IC doses between CCC and XVMC, and SP and XVMC were -1.14% (p = 0.17), and -2.67% (p = 0.0036), respectively.</p> <p>Conclusions</p> <p>Our work clearly confirms that the actual practice of relying solely on a Clarkson algorithm may be inappropriate for SRT planning. Meanwhile, CCC and SP were close to XVMC simulations and actual dose distributions obtained in lung SRT.</p

The 1988-1989 explosive eruption of Tokachi-dake, central Hokkaido, Its sequence and mode

On December 16, 1988, after 26 years of dormancy since the last eruption in 1962, Tokachi-dake began to erupt from the 62-II crater. The eruption started with phreatic explosions. Then, on December 19, the activity changed into phreatomagmatic explosions of Vulcanian type and continued intermittently until March 5, 1989. Although the composition of the essential ejecta, mafic andesite, is similar to those of 1926 and 1962 eruptions, the mode of the present eruption is considerably diffrent The present eruption consists of a series of 23 discrete cannon-like explosions, being frequently accompanied with small-scale pyrcclastic surges and flows. The total volume of ejecta amounts to approximately 6×105 m3, of which about 20% is essential ejecta. A complete sequence of events was compiled and distribution maps of the ash-fall, ballistic blocks, and pyroclastic surges and flows were drawn for each of the larger eruptions. The pyrrolastic surges and flows of the present eruption were small scale, low temperature pyroclastic flows, rich in accessory clasts and unaccompanied by sector collapse. Therefore, the sudden melting of snow causing disastrous mudflows, as in the case of the 1926 eruption, fortunately did not occur

Functional mutations in spike glycoprotein of Zaire ebolavirus associated with an increase in infection efficiency

Ebola virus (EBOV) is extremely virulent, and its glycoprotein is necessary for viral entry. EBOV may adapt to its new host humans during outbreaks by acquiring mutations especially in glycoprotein, which allows EBOV to spread more efficiently. To identify these evolutionary selected mutations and examine their effects on viral infectivity, we used experimental–phylogenetic–structural interdisciplinary approaches. In evolutionary analysis of all available Zaire ebolavirus glycoprotein sequences, we detected two codon sites under positive selection, which are located near/within the region critical for the host‐viral membrane fusion, namely alanine‐to‐valine and threonine‐to‐isoleucine mutations at 82 (A82V) and 544 (T544I), respectively. The fine‐scale transmission dynamics of EBOV Makona variants that caused the 2014–2015 outbreak showed that A82V mutant was fixed in the population, whereas T544I was not. Furthermore, pseudotype assays for the Makona glycoprotein showed that the A82V mutation caused a small increase in viral infectivity compared with the T544I mutation. These findings suggest that mutation fixation in EBOV glycoprotein may be associated with their increased infectivity levels; the mutant with a moderate increase in infectivity will fix. Our findings showed that a driving force for Ebola virus evolution via glycoprotein may be a balance between costs and benefits of its virulence