Vergleichende genomische Hybridisierung (CGH) zur Aufklärung genomischer Imbalancen bei hämatologischen Neoplasien mit Chromosomensätzen über 50 Elemente

In der vorliegenden Arbeit wurde untersucht, inwieweit die CGH zur Charakterisierung komplexer Tumorkaryotypen bei hämatologischen Neoplasien mit mehr als 50 Chromosomen beitragen kann. Erstmals wurden in dieser Arbeit CGH-Untersuchungen bei der ALL des Erwachsenen durchgeführt und aus archivierten Zellsuspensionen von Leukämien DNA für die CGH gewonnen. Es wurden 20 Fälle hämatologischer Neoplasien mit Chromosomensätzen aus über 50 Elementen bei Erwachsenen mittels CGH untersucht. Dabei handelte es sich in 16 Fällen um eine ALL und in je zwei Fällen um eine AML oder ein NHL. Bei acht der 20 Patienten wurde die DOP-PCR nach Chelexaufbereitung eingesetzt, um aus archivierten Zellsuspensionen DNA für die CGH zu gewinnen. Durch die vorliegende Untersuchung konnte gezeigt werden, dass es auch bei Leukämien möglich ist, aus archiviertem Zellmaterial CGH-Untersuchungen durchzuführen. Es wurde deutlich, dass sowohl die Referenz- als auch die Test-DNA mittels DOP-PCR aufbereitet werden muss, um falsch positive Ergebnisse zu verhindern, und dass es sich bei diesen falsch positiven Befunden um wiederkehrende Ereignisse handelt, die für eine spezifische, durch die DOP-PCR verursachte Fehlerquelle sprechen. Die ALL>50 des Erwachsenen besitzt im Gegensatz zur ALL>50 des Kindesalters keine ausgezeichnete Prognose. Die vorliegende CGH-Untersuchung ließ nicht erkennen, dass unterschiedliche Verteilungsmuster hinzugewonnener Chromosomen diese Unterschiede bezüglich der Heilungsrate erklären. Bei den vorliegenden Fällen mit hyperdiploider ALL waren die Chromosomen 4, 6, 10, 14, 17, 18, 21 und X mit etwa den gleichen Häufigkeitsmustern wie bei Kindern hinzugewonnen. Die CGH konnte wesentlich zur Klärung der chromosomalen Zusammensetzung beitragen und korrigierte die Zytogenetik bezüglich der Häufigkeitsverteilung hinzugewonnener, prognostisch relevanter Chromosomen. Partielle Imbalancen in der CGH lassen Rückschlüsse auf unbalanciert vorliegende strukturelle Aberrationen zu. Bei der ALL>50 des Erwachsenen fand sich in der kombinierten Auswertung von zytogenetischem Befund und CGH ein im Vergleich zu Kindern erhöhter Anteil an strukturellen Veränderungen, was eine Ursache für die schlechtere Prognose der ALL>50 bei Erwachsenen sein könnte. Die CGH konnte bei der ALL>50 partielle Imbalancen aufdecken, die zytogenetisch nicht gesehen wurden und die von prognostischer Bedeutung sind: Die CGH konnte 9p-Verluste detektieren, von denen bekannt ist, dass sie auf eine schlechtere Prognose hindeuten und dass sie zytogenetisch häufig nicht erkannt werden. In den Regionen 2q21q31, 3q24q26 und 13q21q32 fanden sich partielle Zugewinne, bei denen es sich möglicherweise um spezifische, wiederkehrende Aberrationen der ALL>50 des Erwachsenen handelt. Die CGH konnte zur Aufklärung der Entstehungsmechanismen chromosomaler Zugewinne bei der ALL beitragen: Bei einem Fall mit einem nahezu triploiden Chromosomensatz erhärtete die CGH die Vermutung, dass dieser durch Verdopplung aus einem hypodiploiden Chromosomensatz hervorgegangen ist. Bei einem tetraploiden Fall detektierte die CGH partielle Imbalancen entsprechend einem Isochromosom 17q, das zytogenetisch nicht erkennbar war. Dies deutet auf die Entstehung des tetraploiden Karyotyps durch Verlust des Tumorsuppressorgens TP53 und nachfolgender Verdopplung des Karyotyps hin. Bei den zwei untersuchten Fällen mit leukämischen Non-Hodgkin-Lymphomen konnte die CGH Imbalancen detektieren, die zytogenetisch nicht erkennbar waren und die mit aggressiven Verlaufsformen, leukämischem Verlauf oder der Ausbildung tetraploider Karyotypen assoziiert sind: Verluste im Bereich 17p, Zugewinne im Bereich 1q, 3q, 8q, 13q und 18q. In der Region Xq28 fand sich ein weiterer Hinweis für ein in dieser Region vermutetes Onkogen für Non-Hodgkin-Lymphome. Bei einem tetraploiden Fall von AML konnte die CGH Befunde liefern, die nahe legen, dass es sich bei einem Isochromosom 8q um einen Marker für eine sekundäre myeloische Leukämie handelt, und es im Rahmen einer sekundären Leukämie zu einer Polyploidisierung des Chromosomensatzes kam. Einschränkend fand sich erneut die limitierte Aussagekraft der CGH bei einem geringen Anteil von Leukämiezellen in der Probe und ganzzahligen Vermehrungen des Chromosomensatzes. Im Rahmen der vergleichenden Auswertung von zytogenetischen und CGH-Befunden wurde zusätzlich deutlich, dass eine kritische Auswertung der CGH die zytogenetischen Befunde und den Ratioprofilverlauf der CGH heranziehen sollte, um die Gefahr falsch positiver Befunde so gering wie möglich zu halten

Radiative and Dynamical Influences on Polar Stratospheric Temperature Trends

Radiative and dynamical heating rates control stratospheric temperatures. In this study, radiative temperature trends due to ozone depletion and increasing well-mixed greenhouse gases from 1980 to 2000 in the polar stratosphere are directly evaluated, and the dynamical contributions to temperature trends are estimated as the residual between the observed and radiative trends. The radiative trends are obtained from a seasonally evolving fixed dynamical heating calculation with the Parallel Offline Radiative Transfer model using four different ozone datasets, which provide estimates of observed ozone changes. In the spring and summer seasons, ozone depletion leads to radiative cooling in the lower stratosphere in the Arctic and Antarctic. In Arctic summer there is weak wave driving, and the radiative cooling due to ozone depletion is the dominant driver of observed trends. In late winter and early spring, dynamics dominate the changes in Arctic temperatures. In austral spring and summer in the Antarctic, strong dynamical warming throughout the mid- to lower stratosphere acts to weaken the strong radiative cooling associated with the Antarctic ozone hole and is indicative of a strengthening of the Brewer–Dobson circulation. This dynamical warming is a significant term in the thermal budget over much of the Antarctic summer stratosphere, including in regions where strong radiative cooling due to ozone depletion can still lead to net cooling despite dynamical terms. Quantifying the contributions of changes in radiation and dynamics to stratospheric temperature trends is important for understanding how anthropogenic forcings have affected the historical trends and necessary for projecting the future.National Science Foundation (U.S.) (NSF Grant 1419667

Projecting policy – relevant metrics for high summertime ozone pollution events over the 1 Eastern United States due to climate and emission changes during the 21st century

Over the eastern United States (EUS), nitrogen oxides (NOx) emission controls have led to improved air quality over the past two decades, but concerns have been raised that climate warming may offset some of these gains. Here we analyze the effect of changing emissions and climate, in isolation and combination, on EUS summertime surface ozone (O3) over the recent past and the 21st century in an ensemble of simulations performed with the Geophysical Fluid Dynamics Laboratory CM3 chemistry-climate model. The simulated summertime EUS O3 is biased high but captures the structure of observed changes in regional O3 distributions following NOx emission reductions. We introduce a statistical bias correction, which allows derivation of policy-relevant statistics by assuming a stationary mean state bias in the model, but accurate simulation of changes at each quantile of the distribution. We contrast two different 21st century scenarios: (i) representative concentration pathway (RCP) 4.5 and (ii) simulations with well-mixed greenhouse gases (WMGG) following RCP4.5 but with emissions of air pollutants and precursors held fixed at 2005 levels (RCP4.5_WMGG). We find under RCP4.5 no exceedance of maximum daily 8 hour average ozone above 75 ppb by mid-21st century, reflecting the U.S. NOx emissions reductions projected in RCP4.5, while more than half of the EUS exceeds this level by the end of the 21st century under RCP4.5_WMGG. Further, we find a simple relationship between the changes in estimated 1 year return levels and regional NOx emission changes, implying that our results can be generalized to estimate changes in the frequency of EUS pollution events under different regional NOx emission scenarios

The paths of extratropical cyclones associated with wintertime high wind events in the Northeast United States

This study analyzes the association between wintertime high wind events (HWEs) in the northeast United States and extratropical cyclones. Sustained wind maxima in the Daily Summary Data from the National Climatic Data Center's Integrated Surface Database are analyzed for 1979-2012. For each station, a Generalized Pareto Distribution (GPD) is fit to the upper tail of the daily maximum wind speed data, and probabilistic return levels at 1, 3 and 5-years are derived. Wind events meeting the return level criteria are termed HWEs. The HWEs occurring on the same day are grouped into simultaneous wind exceedance dates, termed multi-station events. In a separate analysis, extratropical cyclones are tracked using the ECMWF ERA-Interim reanalysis. The multi-station events are associated with the extratropical cyclone tracks based on cyclone proximity on the day of the event. The multi-station wind events are found to be most often associated with cyclones travelling from southwest to northeast, originating west of the Appalachian Mountains. To quantify the relative frequency of the strong wind associated cyclones, the full set of northeastern cyclone tracks are separated based on their path, using a crosshairs algorithm designed for this region. The tracks separate into an evenly distributed set of four pathways approaching the northeast US: from the due west, from the southwest, nor'easters, and storms starting off coast, north of the Carolinas. Using the frequency of the tracks in each of the pathways, it is shown that the storms associated with multi-station wind events are most likely to approach the northeast US from the southwest

Computer aided analysis of additional chromosome aberrations in Philadelphia chromosome positive acute lymphoblastic leukaemia using a simplified computer readable cytogenetic notation

BACKGROUND: The analysis of complex cytogenetic databases of distinct leukaemia entities may help to detect rare recurring chromosome aberrations, minimal common regions of gains and losses, and also hot spots of genomic rearrangements. The patterns of the karyotype alterations may provide insights into the genetic pathways of disease progression. RESULTS: We developed a simplified computer readable cytogenetic notation (SCCN) by which chromosome findings are normalised at a resolution of 400 bands. Lost or gained chromosomes or chromosome segments are specified in detail, and ranges of chromosome breakpoint assignments are recorded. Software modules were written to summarise the recorded chromosome changes with regard to the respective chromosome involvement. To assess the degree of karyotype alterations the ploidy levels and numbers of numerical and structural changes were recorded separately, and summarised in a complex karyotype aberration score (CKAS). The SCCN and CKAS were used to analyse the extend and the spectrum of additional chromosome aberrations in 94 patients with Philadelphia chromosome positive (Ph-positive) acute lymphoblastic leukemia (ALL) and secondary chromosome anomalies. Dosage changes of chromosomal material represented 92.1% of all additional events. Recurring regions of chromosome losses were identified. Structural rearrangements affecting (peri)centromeric chromosome regions were recorded in 24.6% of the cases. CONCLUSIONS: SCCN and CKAS provide unifying elements between karyotypes and computer processable data formats. They proved to be useful in the investigation of additional chromosome aberrations in Ph-positive ALL, and may represent a step towards full automation of the analysis of large and complex karyotype databases

Changes in the frequency and return level of high ozone pollution events over the eastern United States following emission controls

In order to quantify the impact of recent efforts to abate surface ozone (O3) pollution, we analyze changes in the frequency and return level of summertime (JJA) high surface O₃ events over the eastern United States (US) from 1988–1998 to 1999–2009. We apply methods from extreme value theory (EVT) to maximum daily 8-hour average ozone (MDA8 O₃) observed by the Clean Air Status and Trends Network (CASTNet) and define O₃ extremes as days on which MDA8 O₃ exceeds a threshold of 75 ppb (MDA8 O₃>75). Over the eastern US, we find that the number of summer days with MDA8 O₃>75 declined on average by about a factor of two from 1988–1998 to 1999–2009. The applied generalized Pareto distribution (GPD) fits the high tail of MDA8 O₃ much better than a Gaussian distribution and enables the derivation of probabilistic return levels (describing the probability of exceeding a value x within a time window T) for high O₃ pollution events. This new approach confirms the significant decline in both frequency and magnitude of high O₃ pollution events over the eastern US during recent years reported in prior studies. Our analysis of 1-yr and 5-yr return levels at each station demonstrates the strong impact of changes in air quality regulations and subsequent control measures (e.g., the 'NOₓ SIP Call'), as the 5-yr return levels of the period 1999–2009 correspond roughly to the 1-yr return levels of the earlier time period (1988–1998). Regionally, the return levels dropped between 1988–1998 and 1999–2009 by about 8 ppb in the Mid-Atlantic (MA) and Great Lakes (GL) regions, while the strongest decline, about 13 ppb, is observed in the Northeast (NE) region. Nearly all stations (21 out of 23) have 1-yr return levels well below 100 ppb and 5-yr return levels well below 110 ppb in 1999–2009. Decreases in eastern US O₃ pollution are largest after full implementation of the nitrogen oxide (NOₓ) reductions under the 'NOₓ SIP Call'. We conclude that the application of EVT methods provides a useful approach for quantifying return levels of high O₃ pollution in probabilistic terms, which may help to guide long-term air quality planning

Chemical and physical influences on aerosol activation in liquid clouds: a study based on observations from the Jungfraujoch, Switzerland

A simple statistical model to predict the number of aerosols which activate to form cloud droplets in warm clouds has been established, based on regression analysis of data from four summertime Cloud and Aerosol Characterisation Experiments (CLACE) at the high-altitude site Jungfraujoch (JFJ). It is shown that 79 % of the observed variance in droplet numbers can be represented by a model accounting only for the number of potential cloud condensation nuclei (defined as number of particles larger than 80 nm in diameter), while the mean errors in the model representation may be reduced by the addition of further explanatory variables, such as the mixing ratios of O3, CO, and the height of the measurements above cloud base. The statistical model has a similar ability to represent the observed droplet numbers in each of the individual years, as well as for the two predominant local wind directions at the JFJ (northwest and southeast). Given the central European location of the JFJ, with air masses in summer being representative of the free troposphere with regular boundary layer in-mixing via convection, we expect that this statistical model is generally applicable to warm clouds under conditions where droplet formation is aerosol limited (i.e. at relatively high updraught velocities and/or relatively low aerosol number concentrations). A comparison between the statistical model and an established microphysical parametrization shows good agreement between the two and supports the conclusion that cloud droplet formation at the JFJ is predominantly controlled by the number concentration of aerosol particles

Are reprogrammed cells a useful tool for studying dopamine dysfunction in psychotic disorders? A review of the current evidence

Since 2006, reprogrammed cells have increasingly been used as a biomedical research technique in addition to neuro-psychiatric methods. These rapidly evolving techniques allow for the generation of neuronal sub-populations, and have sparked interest not only in monogenetic neuro-psychiatric diseases, but also in poly-genetic and poly-aetiological disorders such as schizophrenia (SCZ) and bipolar disorder (BPD). This review provides a summary of 19 publications on reprogrammed adult somatic cells derived from patients with SCZ, and five publications using this technique in patients with BPD. As both disorders are complex and heterogeneous, there is a plurality of hypotheses to be tested in vitro. In SCZ, data on alterations of dopaminergic transmission in vitro are sparse, despite the great explanatory power of the so-called DA hypothesis of SCZ. Some findings correspond to perturbations of cell energy metabolism, and observations in reprogrammed cells suggest neuro-developmental alterations. Some studies also report on the efficacy of medicinal compounds to revert alterations observed in cellular models. However, due to the paucity of replication studies, no comprehensive conclusions can be drawn from studies using reprogrammed cells at the present time. In the future, findings from cell culture methods need to be integrated with clinical, epidemiological, pharmacological and imaging data in order to generate a more comprehensive picture of SCZ and BPD

A new and reliable culture system for superficial low-grade urothelial carcinoma of the bladder

Several bladder cancer culture systems have been developed in recent years. However, reports about successful primary cultures of superficial urothelial carcinomas (UC) are sparse. Based on the specific growth requirements of UC described previously, we developed a new and reliable culture system for superficial low-grade UC. Between November 2002 and April 2006, 64 primary cultures of bladder cancer specimens were performed. After incubating the specimens overnight in 0.1% ethylenediaminetetraacetic acid solution, tumour cells could easily be separated from the submucosal tissue. Subsequently, cells were seeded in a low-calcium culture medium supplemented with 1% serum, growth factors, non-essential amino acids and glycine. The malignant origin of the cultured cells was demonstrated by spectral karyotyping. Overall culture success rate leading to a homogenous tumour cell population without fibroblast contamination was 63%. Culture success could be remarkably enhanced by the addition of glycine to the culture medium. Interestingly, 86.4% of pTa tumours were cultured successfully compared to only 50% of the pT1 and 38% of advanced stage tumours, respectively. G1 and G2 tumours grew significantly better than G3 tumours (86, 73 and 41%, respectively). Up to three passages of low-grade UC primary cultures were possible. We describe a new and reliable culture system, which is highly successful for primary culture and passage of low-grade UC of the bladder. Therefore, this culture system can widely be used for functional experiments on early stage bladder cance