Molecular prognostic markers for adult acute myeloid leukemia with normal cytogenetics

Acute myeloid leukemia (AML) is a heterogenous disorder that results from a block in the differentiation of hematopoietic progenitor cells along with uncontrolled proliferation. In approximately 60% of cases, specific recurrent chromosomal aberrations can be identified by modern cytogenetic techniques. This cytogenetic information is the single most important tool to classify patients at their initial diagnosis into three prognostic categories: favorable, intermediate, and poor risk. Currently, favorable risk AML patients are usually treated with contemporary chemotherapy while poor risk AML patients receive allogeneic stem cell transplantation if suitable stem cell donors exist. The largest subgroup of AML patients (~40%) have no identifiable cytogenetic abnormalities and are classified as intermediate risk. The optimal therapeutic strategies for these patients are still largely unclear. Recently, it is becoming increasingly evident that it is possible to identify a subgroup of poorer risk patients among those with normal cytogenic AML (NC-AML). Molecular risk stratification for NC-AML patients may be possible due to mutations of NPM1, FLT3, MLL, and CEBPα as well as alterations in expression levels of BAALC, MN1, ERG, and AF1q. Further prospective studies are needed to confirm if poorer risk NC-AML patients have improved clinical outcomes after more aggressive therapy

Low Mutational Burden of Extranodal Marginal Zone Lymphoma of Mucosa-Associated Lymphoid Tissue in Patients with Primary Sjogren's Syndrome

SIMPLE SUMMARY: Patients with primary Sjogren’s syndrome (pSS) are at risk of developing extranodal marginal zone lymphoma (ENMZL) of the mucosa-associated lymphoid tissue (MALT) in the parotid glands. The genetic mechanism underlying development of MALT lymphoma in the context of pSS is unknown. The aim of our study was to define the genomic landscape of pSS-associated MALT lymphoma. For 17 localized pSS-associated MALT lymphomas, we analyzed the presence of nonsynonymous mutations, copy number alterations (CNAs) and MALT1 translocations. pSS-associated MALT lymphomas were characterized by a low mutational load (median number of nonsynonymous somatic variants per case was 7, range 2–78) and a limited number of CNAs. Unlike the recurrent genomic aberrations observed in MALT lymphoma, which were not associated with pSS, pSS-associated MALT lacked a clear lymphoma-related profile. The data suggest that localized pSS-associated MALT lymphomas are a distinct type of ENMZL, which are genomically stable and most likely depend on a stimulatory micro-environment. ABSTRACT: Patients with primary Sjogren’s syndrome (pSS) are at risk of developing extranodal marginal zone lymphoma (ENMZL) of the mucosa-associated lymphoid tissue (MALT) in the parotid glands. Unlike recurrent genomic aberrations observed in MALT lymphoma, which were not associated with pSS (non-pSS), it is unknown which somatic aberrations underlie the development of pSS-associated MALT lymphomas. Whole-exome sequencing was performed on 17 pSS-associated MALT lymphomas. In total, 222 nonsynonymous somatic variants affecting 182 genes were identified across the 17 cases. The median number of variants was seven (range 2–78), including three cases with a relatively high mutational load (≥24/case). Out of 16 recurrently mutated genes, ID3, TBL1XR1, PAX5, IGLL5 and APC are known to be associated with lymphomagenesis. A total of 18 copy number alterations were detected in eight cases. MALT1 translocations were not detected. With respect to outcome, only two cases relapsed outside of the salivary glands. Both had a high mutational load, suggesting a more advanced stage of lymphoma. The low mutational load and lack of a clear lymphoma-related mutation profile suggests that localized pSS-associated MALT lymphomas are genomically more stable than non-pSS MALT lymphomas and most likely depend on a stimulatory micro-environment

Viability of meta-populations of wetland birds in a fragmented landscape: Testing the key-patch approach

The key patch approach assumes that metapopulations in fragmented landscapes are likely to be viable with at least one "key" sub-population that is sufficiently large to ensure re-colonization of surrounding minor habitat patches. It is based on a minimum viable number of breeding pairs and within-breeding season dispersal distance, linked to size of the animal and longevity. It was tested using census data of 15 wetland bird species (bearded tit, bluethroat, great reed warbler, sedge warbler, Savi's warbler, grasshopper warbler, spotted crake, water rail, common snipe, common teal, garganey, little bittern, night heron, great bittern and marsh harrier) in 14 wetland complexes of variable size (3-55 k

Whole genome sequencing and the application of a SNP panel reveal primary evolutionary lineages and genomic variation in the lion (Panthera leo)

Background Previous phylogeographic studies of the lion (Panthera leo) have improved our insight into the distribution of genetic variation, as well as a revised taxonomy which now recognizes a northern (Panthera leo leo) and a southern (Panthera leo melanochaita) subspecies. However, existing whole range phylogeographic studies on lions either consist of very limited numbers of samples, or are focused on mitochondrial DNA and/or a limited set of microsatellites. The geographic extent of genetic lineages and their phylogenetic relationships remain uncertain, clouded by massive sampling gaps, sex-biased dispersal and incomplete lineage sorting. Results In this study we present results of low depth whole genome sequencing and subsequent variant calling in ten lions sampled throughout the geographic range, resulting in the discovery of >150,000 Single Nucleotide Polymorphisms (SNPs). Phylogenetic analyses revealed the same basal split between northern and southern populations, as well as four population clusters on a more local scale. Further, we designed a SNP panel, including 125 autosomal and 14 mitochondrial SNPs, which was tested on >200 lions from across their range. Results allow us to assign individuals to one of these four major clades (West & Central Africa, India, East Africa, or Southern Africa) and delineate these clades in more detail. Conclusions The results presented here, particularly the validated SNP panel, have important applications, not only for studying populations on a local geographic scale, but also for tracing samples of unknown origin for forensic purposes, and for guiding conservation management of ex situ populations. Thus, these genomic resources not only contribute to our understanding of the evolutionary history of the lion, but may also play a crucial role in conservation efforts aimed at protecting the species in its full diversity.Environmental Biolog

Modelled atmospheric contribution to nitrogen eutrophication in the English Channel and the Southern North Sea

Eutrophication of the coastal waters results in algal blooms which may be harmful to the marine ecosystem and coastal economy. The main sources of nutrients are the rivers but an unquantified amount of nitrogen is also transported from ground sources via the atmosphere and deposited to the sea directly by rain and turbulent diffusion. A Lagrangian Particle Dispersion (LPD) model based on the open source code FLEXPART (http://flexpart.eu) is described that quantifies the dissolved nitrogen coming from the air in the English Channel and Southern North Sea (the ‘2Seas’ geographical region). The model uses meteorological records, emissions data and LPD computations to simulate the motion and deposition of nitrogen compounds. The emission sources contributing to the deposition are individually identified, and calculated concentrations are compared with ground measurements in selected locations. The highest calculated atmospheric depositions to the sea in the considered region are found to be along the Belgium–Netherlands coast

Social and cultural factors underlying generational differences in overweight: a cross-sectional study among ethnic minorities in the Netherlands

<p>Abstract</p> <p>Background</p> <p>The prevalence of overweight appears to vary in people of first and second generation ethnic minority groups. Insight into the factors that underlie these weight differences might help in understanding the health transition that is taking place across generations following migration. We studied the role of social and cultural factors associated with generational differences in overweight among young Turkish and Moroccan men and women in the Netherlands.</p> <p>Methods</p> <p>Cross-sectional data were derived from the LASER-study in which information on health-related behaviour and socio-demographic factors, level of education, occupational status, acculturation (cultural orientation and social contacts), religious and migration-related factors was gathered among Turkish and Moroccan men (n = 334) and women (n = 339) aged 15-30 years. Participants were interviewed during a home visit. Overweight was defined as a Body Mass Index ≥ 25 kg/m². Using logistic regression analyses, we tested whether the measured social and cultural factors could explain differences in overweight between first and second generation ethnic groups.</p> <p>Results</p> <p>Second generation women were less often overweight than first generation women (21.8% and 45.0% respectively), but this association was no longer significant when adjusting for the socioeconomic position (i.e. higher level of education) of second generation women (Odds Ratio (OR) = 0.77, 95%, Confidence Interval (CI) 0.40-1.46). In men, we observed a reversed pattern: second generation men were more often overweight than first generation men (32.7% and 27.8%). This association (OR = 1.89, 95% CI 1.09-3.24) could not be explained by the social and cultural factors because none of these factors were associated with overweight among men.</p> <p>Conclusions</p> <p>The higher socio-economic position of second generation Turkish and Moroccan women may partly account for the lower prevalence of overweight in this group compared to first generation women. Further research is necessary to elucidate whether any postulated socio-biological or other processes are relevant to the opposite pattern of overweight among men.</p

Spatial extent and historical context of North Sea oxygen depletion in August 2010

Prompted by recent observations of seasonal low dissolved oxygen from two moorings in the North Sea, a hydrographic survey in August 2010 mapped the spatial extent of summer oxygen depletion. Typical near-bed dissolved oxygen saturations in the stratified regions of the North Sea were 75–80 % while the well-mixed regions of the southern North Sea reached 90 %. Two regions of strong thermal stratification, the area between the Dooley and Central North Sea Currents and the area known as the Oyster Grounds, had oxygen saturations as low as 65 and 70 % (200 and 180 µmol dm-3) respectively. Low dissolved oxygen was apparent in regions characterised by low advection, high stratification, elevated organic matter production from the spring bloom and a deep chlorophyll maximum. Historical data over the last century from the International Council for the Exploration of the Sea oceanographic database highlight an increase in seasonal oxygen depletion and a warming over the past 20 years. The 2010 survey is consistent with, and reinforces, the signal of recent depleted oxygen at key locations seen in the (albeit sparse) historical data

Ethnic variation in validity of the estimated obesity prevalence using self-reported weight and height measurements

<p>Abstract</p> <p>Background</p> <p>We examined ethnic differences between levels of body mass index (BMI) based on self-reported and measured body height and weight and the validity of self-reports used to estimate the prevalence of obesity (BMI≥30 kg/m²) in Turkish, Moroccan, and Dutch people in the Netherlands. Furthermore, we investigated whether BMI levels and the prevalence of obesity in Turkish and Moroccan people with incomplete self-reports (missing height or weight) differ from those with complete self-reports.</p> <p>Methods</p> <p>Data on self-reported and measured height and weight were collected in a population-based survey among 441 Dutch, 414 Turks and 344 Moroccans aged 18 to 69 years in Amsterdam, the Netherlands in 2004. BMI and obesity were calculated from self-reported and measured height and weight.</p> <p>Results</p> <p>The difference between measured and estimated BMI was larger in Turkish and Moroccan women than in Dutch women, which was explained by the higher BMI of the Turkish and Moroccan women. In men we found no ethnic differences between measured and estimated BMI. Sensitivity to detect obesity was low and specificity was high. In participants with available self-reported and measured height and weight, self-reports produced a similar underestimation of the obesity prevalence in all ethnic groups. However, many obese Turkish and Moroccan women had incomplete self-reports, missing height or weight, resulting in an additional underestimation of the prevalence of obesity. Among men (all ethnicities) and Dutch women, the availability of height or weight by self-report did not differ between obese and non obese participants.</p> <p>Conclusions</p> <p>BMI based on self-reports is underestimated more by Turkish and Moroccan women than Dutch women, which is explained by the higher BMI of Turkish and Moroccan women. Further, in women, ethnic differences in the estimation of obesity prevalence based on self-reports do exist and are due to incomplete self-reports in obese Turkish and Moroccan women. In men, ethnicity is not associated with discrepancies between levels of BMI and obesity prevalence based on measurements and self-reports. Hence, our results indicate that using measurements to accurately determine levels of BMI and obesity prevalence in public health research seems even more important in Turkish and Moroccan migrant women than in other populations.</p

Clustering of health and risk behaviour in immigrant and indigenous Dutch residents aged 19–40 years

Objectives\ud Studies on the co-occurrence, ‘clustering’ of health and other risk behaviours among immigrants from non-industrialised countries lack until now. The aim of this study was to compare this clustering in immigrant and indigenous adults.\ud \ud Methods\ud A representative sample (N = 2,982; response 71%) of the Dutch population aged 19–40, with 247 respondents from non-industrialized countries (Turkey, Morocco, Surinam, Netherlands Antilles), was asked about health behaviours (alcohol, smoking, drugs, unsafe sex, exercise, nutrition, sleep behaviour, traffic behaviour), and about rule-breaking behaviour and aggression. Data were collected using internet questionnaires, which excluded respondents unable to read Dutch.\ud \ud Results\ud Among indigenous adults, health and risk behaviours co-occur in three clusters (alcohol, health-enhancing behaviour, and rule-breaking behaviour), whereas among immigrant groups two clusters were found (alcohol and rule-breaking behaviour/smoking). Differences mostly concerned health-enhancing behaviours such as nutrition, which was not part of any cluster, and physical activity.\ud \ud Conclusions\ud This supports an integrated promotion of healthier lifestyles to immigrants who are able to read Dutch. Regarding potentially risky behaviours like alcohol use and rule-breaking behaviours, this could be similar to that for indigenous people\u