Promotor-gestützte in vivo-Markierung stabil transfizierter embryonaler Stammzellen zur Aufreinigung kardial differenzierter Subpopulationen: Ansatz zur Zelltherapie ischämischer Herzerkrankungen

Embryonale Stammzellen stellen aufgrund ihrer Fähigkeit, in vitro in verschiedene Subtypen von Kardiomyozyten zu differenzieren, eine vielversprechende Quelle für eine spezifische Zellersatztherapie ischämischer Herzerkrankungen dar. Ein wesentliches Hindernis, das große therapeutische Potenzial embryonaler Stammzellen für klinische Zelltransplantationen zu nutzen, besteht darin, dass es bisher kein geeignetes Verfahren gibt, den gewünschten Zelltyp zu isolieren. Die Applikation hochaufgereinigter definierter Subpopulationen ist jedoch Voraussetzung, um optimale funktionelle Effekte zu erzielen und andererseits eine potenzielle intramyokardiale Teratomformation aus mittransplantierten undifferenzierten ES-Zellen zu vermeiden. Die Verwendung Zelltyp-spezifischer Promotoren zur Expression eines transgenen Oberflächenmarkers könnte die zellschonende und nicht immunogene Aufreinigung eines gewünschten aus ES-Zellen gewonnenen Zelltyps mit hoher Ausbeute ermöglichen und damit eine wichtige Basis für künftige Zelltransplantationen liefern. In der vorliegenden Arbeit wurde ein Protokoll etabliert, um mittels der magnetischen Zellsortierung (MACS), dem gegenwärtigen Goldstandard einer zellschonenden und effizienten Zellseparation, stabil transfizierte murine embryonale Stammzellen aufzureinigen. Für MACS wurden ES-Zellen markiert, die ein intrazellulär trunkiertes CD4-Oberflächenprotein (∆CD4) unter der Kontrolle des konstitutiv aktiven PGK-Promotors stabil exprimierten. Um die markierten Zellen in vivo fluoreszenzmikroskopisch detektieren zu können, erfolgte in einem Parallelansatz eine Fusion des ∆CD4 mit einem intrazellulären EGFP-Teil (∆CD4EGFP). Die Funktionalität dieses Fusionsproteins wurde ebenso gezeigt wie dessen Eignung für die MACS-Aufreinigung, mit welcher Reinheiten von über 97% erzielt wurden. Die Expression des ∆CD4-Moleküls ohne EGFP-Anteil führte nach MACS zu über 98% positiven vitalen Zellen. Dabei waren die jeweils erzielten Reinheiten unabhängig von dem Differenzierungszustand der Zellen und der initialen Frequenz positiver Zellen (0,6% bis 16%). Die Vitalität der aufgereinigten Zellen nach dem MACS-Prozess wurde dadurch belegt, dass diese in der Lage waren, zu reaggregieren und normale „Embryoid Bodies“ auszubilden, die Marker aller drei embryonaler Keimblätter exprimierten. Parallel zur Etablierung der MACS-Methode wurde der kardial spezifische humane 2,75kb Nkx2.5-Promotor über die Expression des in vivo-Markers EGFP in murinen embryonalen Stammzellen untersucht. Die fluoreszenzmikroskopischen und durchflusszytometrischen Ergebnisse korrelierten mit dem erwarteten embryonalen Aktivitätsprofil des Nkx2.5-Promotors. RT-PCR-Analysen früher kardialer Marker zeigten, dass der hNkx2.5-Promotor Zellen markiert, deren Expressionsmuster dem früher kardial determinierter Zellen entspricht. Der 2,75 kb lange hNkx2.5-Promotor bietet damit einen vielversprechenden Ansatz, kardiale Vorläuferzellen innerhalb des heterogenen Zellspektrums sich differenzierender ES-Zellen zu identifizieren. Ein Transfer auf das in dieser Arbeit etablierte MACS-System könnte die effiziente, zellschonende und nicht immunogene Aufreinigung kardialer Vorläuferzellen aus humanen ES-Zellen ermöglichen. Dieser Ansatz könnte die Therapie ischämischer Herzmuskelerkrankungen mit embryonalen Stammzellen der klinischen Anwendung einen entscheidenden Schritt näher bringen

Observation of many-body long-range tunneling after a quantum quench

Quantum tunneling constitutes one of the most fundamental processes in nature. We observe resonantly-enhanced long-range quantum tunneling in one-dimensional Mott-insulating Hubbard chains that are suddenly quenched into a tilted configuration. Higher-order many-body tunneling processes occur over up to five lattice sites when the tilt per site is tuned to integer fractions of the Mott gap. Starting from a one-atom-per-site Mott state the response of the many-body quantum system is observed as resonances in the number of doubly occupied sites and in the emerging coherence in momentum space. Second- and third-order tunneling shows up in the transient response after the tilt, from which we extract the characteristic scaling in accordance with perturbation theory and numerical simulations.Comment: 22 pages, 7 figure

The site-specific primary calibration conditions for the Brewer spectrophotometer

The Brewer ozone spectrophotometer (the Brewer) is one of the World Meteorological Organization (WMO) Global Atmosphere Watch (GAW)’s standard ozone-monitoring instruments since the 1980s. The entire global Brewer ozone-monitoring network is operated and maintained via a hierarchical calibration chain, which started from world reference instruments that are independently calibrated via the primary calibration method (PCM) at a premium site (National Oceanic and Atmospheric Administration’s (NOAA) Mauna Loa Observatory, Hawaii). These world reference instruments have been maintained by Environment and Climate Change Canada (ECCC) in Toronto for the last 4 decades. Their calibration is transferred to the travelling standard instrument and then to network (field) Brewer instruments at their monitoring sites (all via the calibration transfer method; CTM)

Validation of OMI erythemal doses with multi-sensor ground-based measurements in Thessaloniki, Greece

The aim of this study is to validate the Ozone Monitoring Instrument (OMI) erythemal dose rates using ground-based measurements in Thessaloniki, Greece. In the Laboratory of Atmospheric Physics of the Aristotle University of Thessaloniki, a Yankee Environmental System UVB-1 radiometer measures the erythemal dose rates every minute, and a Norsk Institutt for Luftforskning (NILU) multi-filter radiometer provides multi-filter based irradiances that were used to derive erythemal dose rates for the period 2005–2014. Both these datasets were independently validated against collocated UV irradiance spectra from a Brewer MkIII spectrophotometer. Cloud detection was performed based on measurements of the global horizontal radiation from a Kipp & Zonen pyranometer and from NILU measurements in the visible range. The satellite versus ground observation validation was performed taking into account the effect of temporal averaging, limitations related to OMI quality control criteria, cloud conditions, the solar zenith angle and atmospheric aerosol loading. Aerosol optical depth was also retrieved using a collocated CIMEL sunphotometer in order to assess its impact on the comparisons. The effect of total ozone columns satellite versus ground-based differences on the erythemal dose comparisons was also investigated. Since most of the public awareness alerts are based on UV Index (UVI) classifications, an analysis and assessment of OMI capability for retrieving UVIs was also performed. An overestimation of the OMI erythemal product by 3–6% and 4–8% with respect to ground measurements is observed when examining overpass and noontime estimates respectively. The comparisons revealed a relatively small solar zenith angle dependence, with the OMI data showing a slight dependence on aerosol load, especially at high aerosol optical depth values. A mean underestimation of 2% in OMI total ozone columns under cloud-free conditions was found to lead to an overestimation in OMI erythemal doses of 1–5%.While OMI overestimated the erythemal dose rates over the range of cloudiness conditions examined, its UVIs were found to be reliable for the purpose of characterising the ambient UV radiation impact

A comprehensive assessment of somatic mutation detection in cancer using whole-genome sequencing.

As whole-genome sequencing for cancer genome analysis becomes a clinical tool, a full understanding of the variables affecting sequencing analysis output is required. Here using tumour-normal sample pairs from two different types of cancer, chronic lymphocytic leukaemia and medulloblastoma, we conduct a benchmarking exercise within the context of the International Cancer Genome Consortium. We compare sequencing methods, analysis pipelines and validation methods. We show that using PCR-free methods and increasing sequencing depth to ∼ 100 × shows benefits, as long as the tumour:control coverage ratio remains balanced. We observe widely varying mutation call rates and low concordance among analysis pipelines, reflecting the artefact-prone nature of the raw data and lack of standards for dealing with the artefacts. However, we show that, using the benchmark mutation set we have created, many issues are in fact easy to remedy and have an immediate positive impact on mutation detection accuracy.We thank the DKFZ Genomics and Proteomics Core Facility and the OICR Genome Technologies Platform for provision of sequencing services. Financial support was provided by the consortium projects READNA under grant agreement FP7 Health-F4-2008-201418, ESGI under grant agreement 262055, GEUVADIS under grant agreement 261123 of the European Commission Framework Programme 7, ICGC-CLL through the Spanish Ministry of Science and Innovation (MICINN), the Instituto de Salud Carlos III (ISCIII) and the Generalitat de Catalunya. Additional financial support was provided by the PedBrain Tumor Project contributing to the International Cancer Genome Consortium, funded by German Cancer Aid (109252) and by the German Federal Ministry of Education and Research (BMBF, grants #01KU1201A, MedSys #0315416C and NGFNplus #01GS0883; the Ontario Institute for Cancer Research to PCB and JDM through funding provided by the Government of Ontario, Ministry of Research and Innovation; Genome Canada; the Canada Foundation for Innovation and Prostate Cancer Canada with funding from the Movember Foundation (PCB). PCB was also supported by a Terry Fox Research Institute New Investigator Award, a CIHR New Investigator Award and a Genome Canada Large-Scale Applied Project Contract. The Synergie Lyon Cancer platform has received support from the French National Institute of Cancer (INCa) and from the ABS4NGS ANR project (ANR-11-BINF-0001-06). The ICGC RIKEN study was supported partially by RIKEN President’s Fund 2011, and the supercomputing resource for the RIKEN study was provided by the Human Genome Center, University of Tokyo. MDE, LB, AGL and CLA were supported by Cancer Research UK, the University of Cambridge and Hutchison-Whampoa Limited. SD is supported by the Torres Quevedo subprogram (MI CINN) under grant agreement PTQ-12-05391. EH is supported by the Research Council of Norway under grant agreements 221580 and 218241 and by the Norwegian Cancer Society under grant agreement 71220-PR-2006-0433. Very special thanks go to Jennifer Jennings for administrating the activity of the ICGC Verification Working Group and Anna Borrell for administrative support.This is the final version of the article. It first appeared from Nature Publishing Group via http://dx.doi.org/10.1038/ncomms1000

Therapeutic targeting of ependymoma as informed by oncogenic enhancer profiling

Genomic sequencing has driven precision-based oncology therapy; however, the genetic drivers of many malignancies remain unknown or non-targetable, so alternative approaches to the identification of therapeutic leads are necessary. Ependymomas are chemotherapy-resistant brain tumours, which, despite genomic sequencing, lack effective molecular targets. Intracranial ependymomas are segregated on the basis of anatomical location (supratentorial region or posterior fossa) and further divided into distinct molecular subgroups that reflect differences in the age of onset, gender predominance and response to therapy1,2,3. The most common and aggressive subgroup, posterior fossa ependymoma group A (PF-EPN-A), occurs in young children and appears to lack recurrent somatic mutations2. Conversely, posterior fossa ependymoma group B (PF-EPN-B) tumours display frequent large-scale copy number gains and losses but have favourable clinical outcomes1,3. More than 70% of supratentorial ependymomas are defined by highly recurrent gene fusions in the NF-κB subunit gene RELA (ST-EPN-RELA), and a smaller number involve fusion of the gene encoding the transcriptional activator YAP1 (ST-EPN-YAP1)1,3,4. Subependymomas, a distinct histologic variant, can also be found within the supratetorial and posterior fossa compartments, and account for the majority of tumours in the molecular subgroups ST-EPN-SE and PF-EPN-SE. Here we describe mapping of active chromatin landscapes in 42 primary ependymomas in two non-overlapping primary ependymoma cohorts, with the goal of identifying essential super-enhancer-associated genes on which tumour cells depend. Enhancer regions revealed putative oncogenes, molecular targets and pathways; inhibition of these targets with small molecule inhibitors or short hairpin RNA diminished the proliferation of patient-derived neurospheres and increased survival in mouse models of ependymomas. Through profiling of transcriptional enhancers, our study provides a framework for target and drug discovery in other cancers that lack known genetic drivers and are therefore difficult to treat.This work was supported by an Alex's Lemonade Stand Young Investigator Award (S.C.M.), The CIHR Banting Fellowship (S.C.M.), The Cancer Prevention Research Institute of Texas (S.C.M., RR170023), Sibylle Assmus Award for Neurooncology (K.W.P.), the DKFZ-MOST (Ministry of Science, Technology & Space, Israel) program in cancer research (H.W.), James S. McDonnell Foundation (J.N.R.) and NIH grants: CA154130 (J.N.R.), R01 CA169117 (J.N.R.), R01 CA171652 (J.N.R.), R01 NS087913 (J.N.R.) and R01 NS089272 (J.N.R.). R.C.G. is supported by NIH grants T32GM00725 and F30CA217065. M.D.T. is supported by The Garron Family Chair in Childhood Cancer Research, and grants from the Pediatric Brain Tumour Foundation, Grand Challenge Award from CureSearch for Children’s Cancer, the National Institutes of Health (R01CA148699, R01CA159859), The Terry Fox Research Institute and Brainchild. M.D.T. is also supported by a Stand Up To Cancer St. Baldrick’s Pediatric Dream Team Translational Research Grant (SU2C-AACR-DT1113)

A quantum gas apparatus for ultracold mixtures of K and Cs

-Since the first observation of Bose-Einstein condensation, the field of matter wave optics has progressed enormously and quantum degenerate mixtures of atoms have received special theoretical and experimental attention due to a variety of experiments not possible with single-species experiments. This thesis presents the setup of a new quantum gas apparatus for ultracold mixtures of K and Cs atoms with the capability of producing ultracold samples of KCs ground-state molecules. We describe the experimental apparatus and demonstrate its capabilities by producing Bose-Einstein condensates of 39K and 133Cs. The condensates are created independently without relying on sympathetic cooling. We introduce a sequential scheme that allows to mix degenerate samples of both species in an optical lattice. Our approach is universal and applicable to other species combinations when the two species show dramatically different behavior in terms of loss mechanisms and post laser cooling temperatures, i.e. species combinations that make parallel generation of quantum degenerate samples challenging. The preparation of heteronuclear molecules relies on precise knowledge of the interspecies scattering properties. We perform Feshbach spectroscopy for three different 39K-133Cs spin mixtures. We observe Feshbach resonances as joint atom loss and heating and improve the K-Cs interaction potentials to reproduce the resonance positions. The results open up the possibility to precisely tune the interspecies interaction and to associate free atoms to KCs molecules. We report on a first realization of sub-Doppler laser cooling of 39K atoms by employing degenerate three-dimensional Raman sideband cooling. The scheme takes advantage of the well-resolved excited hyperfine states on the D1 optical transition and results in a spin polarized sample with 1.4 x 10 8 atoms at temperatures of 1.8 K and with phase-space densities 10 (-4). The laser cooling scheme presented can be extended to far off-resonant lattice configurations and allows us to simplify existing high-resolution imaging techniques. Sets of different measurements present the latest results that have been obtained in the very end of this thesis work. We characterize the behavior of degenerate K and Cs samples loaded into a tunable lattice and a superlattice. We perform Kapitza-Dirac scattering to characterize the lattice depths and measure the period of a Bloch oscillation of K atoms confined in a 1D lattice. We show first results towards the production of a self-bound liquidlike droplet consisting of a K spin mixture. We also report on the ongoing work to create ground-state molecules and discuss home-built high-resolution objectives with single-site resolution.by Michael Gröbner, MSc. BSc.Kumulative Dissertation aus zwei ArtikelnIn den Artikeln ist 39 und 133 jeweils hochgestelltUniversity of Innsbruck, Dissertation, 2017OeBB(VLID)220271

Sub-Doppler laser cooling of 39^{39}K via the 4S→\to5P transition

We demonstrate sub-Doppler laser cooling of $^{39}$K using degenerate Raman sideband cooling via the 4S$_{1/2} \rightarrow$5P$_{1/2}$ transition at 404.8 nm. By using an optical lattice in combination with a magnetic field and optical pumping beams, we obtain a spin-polarized sample of up to $5.6 \times 10^{7}$ atoms cooled down to a sub-Doppler temperature of 4 $\mu$K, reaching a peak density of $3.9 \times 10^{9}$ atoms/cm$^{3}$, a phase-space density greater than $10^{-5}$, and an average vibrational level of $\langle \nu \rangle=0.6$ in the lattice. This work opens up the possibility of implementing a single-site imaging scheme in a far-detuned optical lattice utilizing shorter wavelength transitions in alkali atoms, thus allowing improved spatial resolution