CpG promoter methylation of the ALKBH3 alkylation repair gene in breast cancer.

To access publisher's full text version of this article, please click on the hyperlink in Additional Links field or click on the hyperlink at the top of the page marked FilesDNA repair of alkylation damage is defective in various cancers. This occurs through somatically acquired inactivation of the MGMT gene in various cancer types, including breast cancers. In addition to MGMT, the two E. coli AlkB homologs ALKBH2 and ALKBH3 have also been linked to direct reversal of alkylation damage. However, it is currently unknown whether ALKBH2 or ALKBH3 are found inactivated in cancer.Methylome datasets (GSE52865, GSE20713, GSE69914), available through Omnibus, were used to determine whether ALKBH2 or ALKBH3 are found inactivated by CpG promoter methylation. TCGA dataset enabled us to then assess the impact of CpG promoter methylation on mRNA expression for both ALKBH2 and ALKBH3. DNA methylation analysis for the ALKBH3 promoter region was carried out by pyrosequencing (PyroMark Q24) in 265 primary breast tumours and 30 proximal normal breast tissue samples along with 8 breast-derived cell lines. ALKBH3 mRNA and protein expression were analysed in cell lines using RT-PCR and Western blotting, respectively. DNA alkylation damage assay was carried out in cell lines based on immunofluorescence and confocal imaging. Data on clinical parameters and survival outcomes in patients were obtained and assessed in relation to ALKBH3 promoter methylation.The ALKBH3 gene, but not ALKBH2, undergoes CpG promoter methylation and transcriptional silencing in breast cancer. We developed a quantitative alkylation DNA damage assay based on immunofluorescence and confocal imaging revealing higher levels of alkylation damage in association with epigenetic inactivation of the ALKBH3 gene (P = 0.029). In our cohort of 265 primary breast cancer, we found 72 cases showing aberrantly high CpG promoter methylation over the ALKBH3 promoter (27%; 72 out of 265). We further show that increasingly higher degree of ALKBH3 promoter methylation is associated with reduced breast-cancer specific survival times in patients. In this analysis, ALKBH3 promoter methylation at >20% CpG methylation was found to be statistically significantly associated with reduced survival (HR = 2.3; P = 0.012). By thresholding at the clinically relevant CpG methylation level (>20%), we find the incidence of ALKBH3 promoter methylation to be 5% (13 out of 265).ALKBH3 is a novel addition to the catalogue of DNA repair genes found inactivated in breast cancer. Our results underscore a link between defective alkylation repair and breast cancer which, additionally, is found in association with poor disease outcome.Icelandic Centre for Researc

Effects of hand orientation on motor imagery - event related potentials suggest kinesthetic motor imagery to solve the hand laterality judgment task

Motor imagery (MI) refers to the process of imagining the execution of a specific motor action without actually producing an overt movement. Two forms of MI have been distinguished: visual MI and kinesthetic MI. To distinguish between these forms of MI we employed an event related potential (ERP) study to measure interference effects induced by hand orientation manipulations in a hand laterality judgement task. We hypothesized that this manipulation should only affect kinesthetic MI but not visual MI. The ERPs elicited by rotated hand stimuli contained the classic rotation related negativity (RRN) with respect to palm view stimuli. We observed that laterally rotated stimuli led to a more marked RRN than medially rotated stimuli. This RRN effect was observed when participants had their hands positioned in either a straight (control) or an inward rotated posture, but not when their hands were positioned in an outward rotated posture. Posture effects on the ERP-RRN have not previously been studied. Apparently, a congruent hand posture (hands positioned in an outward rotated fashion) facilitates the judgement of the otherwise more demanding laterally rotated hand stimuli. These ERP findings support a kinesthetic interpretation of MI involved in solving the hand laterality judgement task. The RRN may be used as a non-invasive marker for kinesthetic MI and seems useful in revealing the covert behavior of MI in e.g. rehabilitation programs

Production of He-4 and (4) in Pb-Pb collisions at root(NN)-N-S=2.76 TeV at the LHC

Results on the production of He-4 and (4) nuclei in Pb-Pb collisions at root(NN)-N-S = 2.76 TeV in the rapidity range vertical bar y vertical bar <1, using the ALICE detector, are presented in this paper. The rapidity densities corresponding to 0-10% central events are found to be dN/dy4(He) = (0.8 +/- 0.4 (stat) +/- 0.3 (syst)) x 10(-6) and dN/dy4 = (1.1 +/- 0.4 (stat) +/- 0.2 (syst)) x 10(-6), respectively. This is in agreement with the statistical thermal model expectation assuming the same chemical freeze-out temperature (T-chem = 156 MeV) as for light hadrons. The measured ratio of (4)/He-4 is 1.4 +/- 0.8 (stat) +/- 0.5 (syst). (C) 2018 Published by Elsevier B.V.Peer reviewe

Epigenetic modifications of DNA repair genes in breast cancer

Every day the cell is exposed to internal and external stress which can lead to genome instability. Over the years of evolution, the cell developed the DNA damage response (DDR). Genetic and epigenetic changes of genes involved in the DDR can increase the risk of developing cancer. By linking together DNA methylation and RNA sequencing data derived from The Cancer Genome Atlas (TCGA), EYA2 and DMC1 were identified as candidates of gene silencing by CpG promoter methylation in breast cancer. Primary breast cancer tissue samples, normal breast tissue samples and cell lines were pyrosequenced to validate aberrant promoter methylation in breast cancer patients. After establishing model cell lines, mRNA expression levels were measured in cell lines and breast tissue samples to confirm gene silencing by promoter methylation. Both EYA2 and DMC1 are found aberrantly promoter methylated in primary breast tumour samples compared to normal breast tissue. EYA2 mRNA expression is reduced in cancer cell lines with aberrant EYA2 promoter methylation. However, aberrant EYA2 promoter methylation does not associate with impact on survival. There is a strong indication of a negative correlation in our sample set, between DMC1 promoter methylation and DMC1 mRNA expression. Survival analyses indicate that aberrant DMC1 promoter methylation could impact breast cancer-specific survival. QPCR results indicate that DMC1 (m)RNA is expressed in normal breast tissue samples and breast tissue cell lines (normal and cancer). To our knowledge, this study shows for the first time that DMC1 is expressed in somatic cells, without being under extreme conditions of stress.The Icelandic Centre for Research: grant IDs #14193-051 and #152077-05

The first integrated speed management program benefitting vulnerable road users in Bangladesh : results and implications for LMICS

Over 20,000 people are killed due to road traffic crashes in Bangladesh annually. The country has over 100 road traffic deaths per 10,000 motor vehicles, one of the highest rates in the world. 70% of crash fatalities occur in rural areas. In 2014, Safe Crossings (Netherlands) and CIPRB (Bangladesh) received permission from the government of Bangladesh to design and implement an integrated speed management program to prevent road traffic injuries at three locations on a national highway that passes through villages. The study goal was to understand and quantify the improvement in road safety as a result of small-scale infrastructural adaptations combined with active community involvement and road user education. We had a specific interest in the effects on VRUs. Prior to installing the interventions, the three intervention locations combined had, on average, per year: 110 serious accidents, 12 deaths, and 240 injured people. Pedestrians accounted for 63% of all fatalities in the Before Period. In an ideal world one would like to use accident statistics as the ultimate measure of road safety. In reality, this was not possible as the accident statistics were neither sufficiently accurate nor complete. Hence we had to design an alternative monitoring &amp; evaluation approach. The basic research design is a Before and After study using three methods: i) speed measurement (also in control locations), ii) an accident recording system using local record keepers that we set up ourselves, and iii) conflict observation using the DOCTOR method with video recording. Implementation of all infrastructural interventions was completed in April 2015. The integrated speed management for three locations in Bangladesh has resulted a reduction in road traffic injuries and fatalities of around 60%. The net speed effect is a reduction on average of 13,3 km/h (or 20% in relative terms), suggesting a reduction in the number of people killed of 59% using Nilsson’s power law. Our accident recording system shows a 66% reduction in the number of serious accidents (significant at p &lt; 0.01), a 73% reduction in the number of injured people (significant at p &lt; 0.01), and a 67% reduction in the number of road traffic deaths (significant at p &lt; 0.10).Analysis of the conflict data revealed a 54% reduction in relative terms (52% reduction when taking the traffic volumes into account) in the number of serious conflicts. In addition, no conflicts of the highest severity category occurred in the after period. An additional advantage of the integrated speed management program is that it can be implemented relatively quickly (in 6 to 12 months) and the cost-effectiveness is very high. Our calculation suggests a ‘cost per DALY saved’ of below USD 100. We would like to suggest three specific areas of future research based on this study: i) traffic calming in city environments in LMICs, ii) interventions to further reduce the speed of fast-moving traffic in general and buses in particular and iii) investigating the potential of an integrated speed management program in a large number of locations in LMICs with the joint aim of significantly improving road safety and generating valuable road safety data on (cost-) effectiveness and implementation challenges and solutions

Transient exposure of hydrophobic surface in the photoactive yellow protein monitored with Nile Red.

In this study we have investigated binding of the fluorescent hydrophobicity probe Nile Red to the photoactive yellow protein (PYP), to characterize the exposure and accessibility of hydrophobic surface upon formation of the signaling state of this photoreceptor protein. Binding of Nile Red, reflected by a large blue shift and increase in fluorescence quantum yield of the Nile Red emission, is observed exclusively when PYP resides in its signaling state. N-terminal truncation of the protein allows assignment of the region surrounding the chromophore as the site where Nile Red binds to PYP. We also observed a pH dependence of the affinity of Nile Red for pB, which we propose is caused by pH dependent differences of the structure of the signaling state. From a comparative analysis of the kinetics of Nile Red binding and transient absorption changes in the visible region we can conclude that protonation of the chromophore precedes the exposure of a hydrophobic surface near the chromophore binding site, upon formation of the signaling state. Furthermore, the data presented here favor the view that the signaling state is structurally heterogeneous

Tree Reconstruction from a Point Cloud using an L-system

Storing accurate models of complex geometries in a compact way has become an increasingly challenging issue, especially when dealing with large datasets. One of such datasets is Cobra-Groeninzicht's database of all trees in the Netherlands. In the gaming industry, a new technique is being used to generate tree models: the L-system. An L-system stores a string representation of the structural model of a tree, with the added possibility for recursive modelling using growing rules. This format proves a promising alternative to more traditional methods of storing complex geometries. However, it remains unclear whether it can be an accurate enough representation for modelling and analysing real-life trees.In this research project, the AdTree algorithm is used to reconstruct a skeleton from a point cloud of a single tree. This skeleton is then transformed to an L-System string format, as well as a CityJSON format (both in JSON structure). The L-system format comes with the advantage that it allows for several methods of increasing its compactness further (growing, generalisation). The overall size of these files also indicates fewer storage space is needed to store the tree geometry. The quality of the L-System skeleton is nearly equal to the input, the skeleton generated by. Assuming it can be read and drawn using a Turtle program, the L-system thus allows for storing the same geometric information more compactly than traditional storage formats, with sufficient accuracy, and the added possibilities of growing or generalising the model.Synthesis Project 2021Geomatic

Tissue advanced glycation end products are associated with diastolic function and aerobic exercise capacity in diabetic heart failure patients

Aims Advanced glycation end products (AGEs) are increased in patients with diabetes and are associated with diastolic dysfunction through the formation of collagen crosslinks in the heart. The association among AGEs, diastolic function, and aerobic capacity in heart failure (HF) patients with and without diabetes is, however, unknown. We therefore studied the association among tissue AGEs, diastolic function, and aerobic capacity in patients with HF with or without diabetes. Methods and results In chronic HF patients (with and without left ventricular systolic dysfunction), tissue AGEs [skin autofluorescence (AF)], diastolic function (echocardiographic mean E' and E/E'), and aerobic capacity [peak oxygen uptake (VO(2)) on cardiopulmonary exercise testing] were obtained. A total of 49 diabetics and 156 non-diabetics were included. Diabetics were older and had more cardiovascular risk factors, but left ventricular ejection fractions (LVEF) were similar. Tissue AGEs were higher in diabetics compared with non-diabetics (2.8 +/- 0.8 vs. 2.3 +/- 0.7 a.u.; P <0.001). Furthermore, there was a correlation between tissue AGEs and mean E' (r = -0.30; P <0.001, after adjustment for age, r = -0.21; P = 0.004). Aerobic capacity was significantly lower in diabetic patients with HF (peak VO(2): 17.4 +/- 5.1 vs. 21.7 +/- 6.1 mL/min/kg; P = 0.001), even after adjustment for age and LVEF. Peak VO(2) was related to skin AF (P = 0.03), independent of age, diabetes, LVEF, and New York Heart Association functional class. Conclusion Patients with diabetes and HF have similar LVEF but poorer exercise capacity compared with non-diabetic HF patients. Our data suggest that these findings might be explained by the observed association among tissue AGE levels, diastolic function, and exercise capacity