Breaking News on Fragile Sites in Cancer

Chromosome rearrangements in B lymphocytes can be initiated by AID-associated double strand breaks (DSBs), with others arising by unclear mechanisms. A recent study by Barlow and colleagues in Cell reports on genomic regions, termed early replicating fragile sites, that may explain many AID-independent DSBs and creates a compelling link between replication stress, transcription, and chromosome rearrangements

An Improved Method for Assessing the Biocidal Activity of Silver-Bearing Wound Dressings Against Staphylococcus Aureus

This investigation evaluated the biocidal efficacy of silver-bearing wound dressings against Staphylococcus aureus, a pervasive wound pathogen. Using the FDA-recognized AATCC-100 cell-viability assay, we found that the silver-bearing wound dressings may no longer be biocidal after 1 day of use, exhibiting only 1 log reduction after 7 days (p < 0.05). * As an alternative to this cell-viability assay, we discuss the advantages of qRT-PCR, including better precision, accuracy, reproducibility, and time-efficiency. We show that the standard deviation in log reduction is on average 13x higher for the plate-based than it is for the qRT-PCR method. While both qRT-PCR and the plate-based method show bacterial persistence after 1 day, the plate-based method may overestimate log reductions when compared to qRT-PCR. We present a standard curve for real time quantification of cell concentration in wound dressing extracts. We test rhodopsin (rho), gyrase (gyr), and universal bacteria 16s rRNA primers and find that 16s rRNA results in 100% reaction efficiency and an optimal quantification limit (~1 x 103 CFU/mL). We also discuss qRT-PCR’s potential for monitoring Staphylococcus aureus persistence and virulence, using assays targeting the associated biomarkers (Staphylococcus protein A, mecA, gamma-hemolysin, beta-toxin, leukotoxin-F). Our preliminary qRT-PCR assay results show that the day 1 wound dressing extracts are negative for the methicillin-resistance gene (mecA), in accordance with the genome sequence for Staphylococcus aureus ATTCC-3556. Using the delta-delta Ct method for these day 1 samples, the relative abundance of the housekeeping gene rhodopsin (rho) is 0.15. The relative abundance of the virulence factor gene Staphylococcus protein A (spA) is 0.0042 and 0.087 for day 1 and day 3 samples, respectively

Antenna subtraction for jet production observables in full colour at NNLO

We describe the details of the calculation of the full colour NNLO QCD corrections to jet production observables at the LHC with antenna subtraction. All relevant matrix elements for the process pp → jj at NNLO in full colour are colour-decomposed and given in a N$_{c}$ and n$_{f}$ expansion, making identification of leading and subleading colour contributions transparent. The colour-ordered antenna subtraction method has previously successfully been used to construct the NNLO subtraction terms for processes with up to five partons or in the leading colour approximation. However, it is challenged by the more involved subleading colour structure of the squared matrix elements in processes with six or more partons. Here, we describe the methods needed to successfully construct the NNLO subtraction terms for the subleading colour contributions to dijet production within the antenna subtraction formalism

Copy number variants are produced in response to low‐dose ionizing radiation in cultured cells

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/106089/1/em21840.pd

Polymerase chain reactions with alphoid-repeat primers in combination with Alu or LINEs primers, generate chromosome-specific DNA fragments

Y alphoid primers in combination with Alu and LINEs primers generated new DNA fragments in polymerase chain reactions (PCR) on DNA from a Y-only somatic cell hybrid but not from X-only, 3-only, or 21-only hybrids. X alphoid primers used in a similar manner generated new DNA fragments from the X-only hybrid, and 1 of the primers (X 2 ) also generated new DNA fragments on 3-only and 21-only hybrids when used in conjunction with Alu or LINEs primers. In all but one case, consensus alphoid primers generated new chromosome-specific fragments in PCR reactions with the Alu or LINEs primers. A search for cryptic Alu- or alphoid-alone PCR products as the source for one Alu -alphoid band (chosen at random) was negative. Partial sequencing of products demonstrated that alphoid and Alu sequences were indeed contiguous in some newly synthesized DNA fragments. While Alu or LINEs primers generate smears of DNA fragments on total human DNA, the alphoid-nonalphoid repeat combinations generated electrophoretically distinguishable bands of DNA when the template was total DNA. While these were distinguishable with different chromosome-specific alphoid primers, the DNA fragments were not of the same sizes as those generated with the chromosome-only hybrids.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/66359/1/j.1469-1809.1991.tb00414.x.pd

NNLO QCD corrections in full colour for jet production observables at the LHC

Abstract: Calculations for processes involving a high multiplicity of coloured particles often employ a leading colour approximation, where only the leading terms in the expansion of the number of colours N$_{c}$ and the number of flavours n$_{f}$ are retained. This approximation of the full colour result is motivated by the 1/${N}_c^2$ suppression of the first subleading terms and by the increasing complexity of including subleading colour contributions to the calculation. In this work, we present the calculations using the antenna subtraction method in the NNLOjet framework for the NNLO QCD corrections at full colour for several jet observables at the LHC. The single jet inclusive cross section is calculated doubly differential in transverse momentum and absolute rapidity and compared with the CMS measurement at 13 TeV. A calculation for dijet production doubly differential in dijet mass and rapidity difference is also performed and compared with the ATLAS 7 TeV data. Lastly, a triply differential dijet cross section in average transverse momentum, rapidity separation and dijet system boost is calculated and compared with the CMS 8 TeV data. The impact of the subleading colour contributions to the leading colour approximation is assessed in detail for all three types of observables and as a function of the jet cone size. The subleading colour contributions play a potentially sizable role in the description of the triply differential distributions, which probe kinematical configurations that are not easily accessed by any of the other observables

Subpicosecond Thomson Scattering Measurements of Optically Ionized Helium Plasmas

We present the first subpicosecond time-resolved temperature measurements of plasmas produced by high-intensity optical ionization. Thomson scattering is used to measure electron and ion temperatures of helium plasmas created by 125 fs, 800 nm laser pulses focused to an intensity of 2 × 1017 W/cm2. We find that the electron temperature is accurately predicted by a tunneling ionization model. The measured ion temperature is consistent with direct heating by the laser pulse