Imprecision and DNA break repair biased towards incompatible end joining in leukemia

Cancer is a genetic disease caused by mutations and chromosomal abnormalities that contribute to uncontrolled cell growth. In addition, cancer cells can rapidly respond to conventional and targeted therapies by accumulating novel and often specific genetic lesions leading to acquired drug resistance and relapsing disease. In chronic lymphocytic leukemia (CLL), however, diverse chromosomal aberrations often occur. In many cases, improper repair of DNA double-strand breaks (DSB) is a major source for genomic abnormalities. Therefore, this study examined the repair of DNA DSBs by nonhomologous end joining (NHEJ) in CLL by performing plasmid-based repair assays in primary CLL cells and normal B cells, isolated from patients, as well as TALEN/Cas9–induced chromosomal deletions in the CLL cell line Mec1. It is demonstrated that DNA repair is aberrant in CLL cells, featuring perturbed DNA break structure preference with efficient joining of noncohesive ends and more deletions at repair junctions. In addition, increased microhomology-mediated end joining (MMEJ) of DNA substrates was observed in CLL together with increased expression of MMEJ-specific repair factors. In summary, these data identify major differences in DNA repair efficiency between CLL cells and normal B cells isolated from patients

The Choice of the Filtering Method in Microarrays Affects the Inference Regarding Dosage Compensation of the Active X-Chromosome

The hypothesis of dosage compensation of genes of the X chromosome, supported by previous microarray studies, was recently challenged by RNA-sequencing data. It was suggested that microarray studies were biased toward an over-estimation of X-linked expression levels as a consequence of the filtering of genes below the detection threshold of microarrays.To investigate this hypothesis, we used microarray expression data from circulating monocytes in 1,467 individuals. In total, 25,349 and 1,156 probes were unambiguously assigned to autosomes and the X chromosome, respectively. Globally, there was a clear shift of X-linked expressions toward lower levels than autosomes. We compared the ratio of expression levels of X-linked to autosomal transcripts (X∶AA) using two different filtering methods: 1. gene expressions were filtered out using a detection threshold irrespective of gene chromosomal location (the standard method in microarrays); 2. equal proportions of genes were filtered out separately on the X and on autosomes. For a wide range of filtering proportions, the X∶AA ratio estimated with the first method was not significantly different from 1, the value expected if dosage compensation was achieved, whereas it was significantly lower than 1 with the second method, leading to the rejection of the hypothesis of dosage compensation. We further showed in simulated data that the choice of the most appropriate method was dependent on biological assumptions regarding the proportion of actively expressed genes on the X chromosome comparative to the autosomes and the extent of dosage compensation.This study shows that the method used for filtering out lowly expressed genes in microarrays may have a major impact according to the hypothesis investigated. The hypothesis of dosage compensation of X-linked genes cannot be firmly accepted or rejected using microarray-based data

AID induces intraclonal diversity and genomic damage in CD86(+) chronic lymphocytic leukemia cells

The activation-induced cytidine deaminase (AID) mediates somatic hypermutation and class switch recombination of the Ig genes by directly deaminating cytosines to uracils. As AID causes a substantial amount of off-target mutations, its activity has been associated with lymphomagenesis and clonal evolution of B-cell malignancies. Although it has been shown that AID is expressed in B-cell chronic lymphocytic leukemia (CLL), a clear analysis of in vivo AID activity in this B-cell malignancy remained elusive. In this study performed on primary human CLL samples, we report that, despite the presence of a dominant VDJ heavy chain region, a substantial intraclonal diversity was observed at VDJ as well as at IgM switch regions (Sμ), showing ongoing AID activity in vivo during disease progression. This AID-mediated heterogeneity was higher in CLL subclones expressing CD86, which we identified as the proliferative CLL fraction. Finally, CD86 expression correlated with shortened time to first treatment and increased γ-H2AX focus formation. Our data demonstrate that AID is active in CLL in vivo and thus, AID likely contributes to clonal evolution of CLL

Solidified-air energy storage: conceptualization and thermodynamic analysis

Grid-scale electrical energy storage (EES) is a key component in cost-effective transition scenarios to renewable energy sources. The requirement of scalability favors EES approaches such as pumped-storage hydroelectricity (PSH) or compressed-air energy storage (CAES), which utilize the cheap and abundant storage materials water and air, respectively. To overcome the site restriction and low volumetric energy densities attributed to PSH and CAES, liquid-air energy storage (LAES) has been devised; however, it suffers from a rather small round-trip efficiency (RTE) and challenging storage conditions. Aiming to overcome these drawbacks, a novel system for EES is developed using solidified air (i.e., clathrate hydrate of air) as the storable phase of air. A reference plant for solidified-air energy storage (SAES) is conceptualized and modeled thermodynamically using the software CoolProp for water and air as well as empirical data and first-order approximations for the solidified air (SA). The reference plant exhibits a RTE of 52% and a volumetric storage density of 47 kWh per m3 of SA. While this energy density relates to only one half of that in LAES plants, the modeled RTE of SAES is comparable already. Since improved thermal management and the use of thermodynamic promoters can further increase the RTEs in SAES, the technical potential of SAES is in place already. Yet, for a successful implementation of the concept - in addition to economic aspects - questions regarding the stability of SA must be first clarified and challenges related to the processing of SA resolved

COLOMBO Deliverable 5.1: Prototype of overall System Architecture and Definition of Interfaces

This Deliverable 5.1 contains the design and a description of the work undertaken to combine and integrate the engaged software (SUMO, ns3, iCS, PHEM, ...) to suite the investigation tasks of the COLOMBO project. Requirements from the traffic management solutions to be developed in COLOMBO put on the overall simulation system have been collected. They are given in D5.1 together with short explanations about the implementation of the solutions using the COLOMBO suite of simulation applications. Both the components of the simulation system as well as the system’s architecture are described. Additionally, the software development process in COLOMBO is also described in the document

Is auditory evoked potential augmenting/reducing affected by acute tryptophan depletion

Several lines of evidence suggest that the auditory evoked potential (AEP) augmenting/reducing slope may serve as a biological marker of central serotonergic activity. According to Hegerl and Juckel (Biol. Psychiatry, 33, 1993, 173), reduced serotonergic activity is hypothesized to increase the slope of the AEP amplitude stimulus intensity function (ASF-slope). Hints for this hypothesis were investigated by employing the acute tryptophan depletion paradigm in 18 healthy females. A within-subject, placebo controlled double-blind cross over design was used for that purpose. Subjects ingested both a 50 g amino-acid drink with (placebo condition) and without tryptophan (depletion condition). With respect to the N1/P2-slope, test–retest reliability of a 1 week interval ranged between r=0.56 and 0.58 for the pre-ingestion baseline recording sessions. Affect was not altered by tryptophan depletion and not related to the ASF-slope. The comparison between placebo and depletion conditions did not reveal significant alterations of the ASF-slope, neither after 5 nor 6 h post-ingestion. Thus, the results do not support the assumption of the ASF-slope reflecting central serotonergic function