Continuous cerebral function monitoring in neonatal intensive care

Peer Reviewe

Geophysical analysis of an area affected by subsurface dissolution - case study of an inland salt marsh in northern Thuringia, Germany

The subsurface dissolution of soluble rocks can affect areas over a long period of time and pose a severe hazard. We show the benefits of a combined approach using P-wave and SH-wave reflection seismics, electrical resistivity tomography, transient electromagnetics, and gravimetry for a better understanding of the dissolution process. The study area, "Esperstedter Ried"in northern Thuringia, Germany, located south of the Kyffhäuser hills, is a large inland salt marsh that developed due to dissolution of soluble rocks at approximately 300 m depth. We were able to locate buried dissolution structures and zones, faults and fractures, and potential fluid pathways, aquifers, and aquitards based on seismic and electromagnetic surveys. Further improvement of the model was accomplished by analyzing gravimetry data that indicates dissolution-induced mass movement, as shown by local minima of the Bouguer anomaly for the Esperstedter Ried. Forward modeling of the gravimetry data, in combination with the seismic results, delivered a cross section through the inland salt marsh from north to south. We conclude that tectonic movements during the Tertiary, which led to the uplift of the Kyffhäuser hills and the formation of faults parallel and perpendicular to the low mountain range, were the initial trigger for subsurface dissolution. The faults and the fractured Triassic and lower Tertiary deposits serve as fluid pathways for groundwater to leach the deep Permian Zechstein deposits, since dissolution and erosional processes are more intense near faults. The artesian-confined saltwater rises towards the surface along the faults and fracture networks, and it formed the inland salt marsh over time. In the past, dissolution of the Zechstein formations formed several, now buried, sagging and collapse structures, and, since the entire region is affected by recent sinkhole development, dissolution is still ongoing. From the results of this study, we suggest that the combined geophysical investigation of areas prone to subsurface dissolution can improve the knowledge of control factors, hazardous areas, and thus local dissolution processes

Advanced seismic characterization of a geothermal carbonate reservoir – insight into the structure and diagenesis of a reservoir in the German Molasse Basin

The quality of geothermal carbonate reservoirs is controlled by, for instance, depositional environment, lithology, diagenesis, karstification, fracture networks, and tectonic deformation. Carbonatic rock formations are thus often extremely heterogeneous, and reservoir parameters and their spatial distribution difficult to predict. Using a 3D seismic dataset combined with well data from Munich, Germany, we demonstrate how a comprehensive seismic attribute analysis can significantly improve the understanding of a complex carbonate reservoir. We deliver an improved reservoir model concept and identify possible exploitation targets within the Upper Jurassic carbonates. We use seismic attributes and different carbonate lithologies from well logs to identify parameter correlations. From this, we obtain a supervised neural-network-based 3D lithology model of the geothermal reservoir. Furthermore, we compare fracture orientations measured in seismic (ant-tracking analysis) and well scale (image log analysis) to address scalability. Our results show that, for example, acoustic impedance is suitable to identify reefs and karst-related dolines, and sweetness proves useful to analyse the internal reef architecture, whereas frequency- and phase-related attributes allow the detection of karst. In addition, reef edges, dolines, and fractures, associated with high permeabilities, are characterized by strong phase changes. Fractures are also identified using variance and ant tracking. Morphological characteristics, like dolines, are captured using the shape index. Regarding the diagenetic evolution of the reservoir and the corresponding lithology distribution, we show that the Upper Jurassic carbonate reservoir experienced a complex evolution, consisting of at least three dolomitization phases, two karstification phases, and a phase of tectonic deformation. We observe spatial trends in the degree of dolomitization and show that it is mainly facies-controlled and that karstification is facies- and fault-controlled. Karstification improves porosity and permeability, whereas dolomitization can either increase or decrease porosity. Therefore, reservoir zones should be exploited that experienced only weak diagenetic alteration, i.e. the dolomitic limestone in the upper part of the Upper Jurassic carbonates. Regarding the fracture scalability across seismic and well scales, we note that a general scalability is, due to a combination of methodological limitations and geological reasons, not possible. Nevertheless, both methods provide an improved understanding of the fracture system and possible fluid pathways. By integrating all the results, we are able to improve and adapt recent reservoir concepts, to outline the different phases of the reservoir's structural and diagenetic evolution, and to identify high-quality reservoir zones in the Munich area. These are located southeast at the Ottobrunn Fault and north of the Munich Fault close to the Nymphenburg Fault.</p

CrossHybDetector: detection of cross-hybridization events in DNA microarray experiments

Background\ud DNA microarrays contain thousands of different probe sequences represented on their surface. These are designed in such a way that potential cross-hybridization reactions with non-target sequences are minimized. However, given the large number of probes, the occurrence of cross hybridization events cannot be excluded. This problem can dramatically affect the data quality and cause false positive/false negative results.\ud \ud Results\ud CrossHybDetector is a software package aimed at the identification of cross-hybridization events occurred during individual array hybridization, by using the probe sequences and the array intensity values. As output, the software provides the user with a list of array spots potentially &apos;corrupted&apos; and their associated p-values calculated by Monte Carlo simulations. Graphical plots are also generated, which provide a visual and global overview of the quality of the microarray experiment with respect to cross-hybridization issues.\ud \ud Conclusion\ud CrossHybDetector is implemented as a package for the statistical computing environment R and is freely available under the LGPL license within the CRAN project

HumMeth27QCReport: an R package for quality control and primary analysis of Illumina Infinium methylation data

<p>Abstract</p> <p>Background</p> <p>The study of the human DNA methylome has gained particular interest in the last few years. Researchers can nowadays investigate the potential role of DNA methylation in common disorders by taking advantage of new high-throughput technologies. Among these, Illumina Infinium assays can interrogate the methylation levels of hundreds of thousands of CpG sites, offering an ideal solution for genome-wide methylation profiling. However, like for other high-throughput technologies, the main bottleneck remains at the stage of data analysis rather than data production.</p> <p>Findings</p> <p>We have developed <it>HumMeth27QCReport</it>, an R package devoted to researchers wanting to quickly analyse their Illumina Infinium methylation arrays. This package automates quality control steps by generating a report including sample-independent and sample-dependent quality plots, and performs primary analysis of raw methylation calls by computing data normalization, statistics, and sample similarities. This package is available at CRAN repository, and can be integrated in any Galaxy instance through the implementation of ad-hoc scripts accessible at Galaxy Tool Shed.</p> <p>Conclusions</p> <p>Our package provides users of the Illumina Infinium Methylation assays with a simplified, automated, open-source quality control and primary analysis of their methylation data. Moreover, to enhance its use by experimental researchers, the tool is being distributed along with the scripts necessary for its implementation in the Galaxy workbench. Finally, although it was originally developed for HumanMethylation27, we proved its compatibility with data generated with the HumanMethylation450 Bead Chip.</p

Loss of aquaporin-4 expression and putative function in non-small cell lung cancer

<p>Abstract</p> <p>Background</p> <p>Aquaporins (AQPs) have been recognized to promote tumor progression, invasion, and metastasis and are therefore recognized as promising targets for novel anti-cancer therapies. Potentially relevant AQPs in distinct cancer entities can be determined by a comprehensive expression analysis of the 13 human AQPs.</p> <p>Methods</p> <p>We analyzed the presence of all AQP transcripts in 576 different normal lung and non-small cell lung cancer (NSCLC) samples using microarray data and validated our findings by qRT-PCR and immunohistochemistry.</p> <p>Results</p> <p>Variable expression of several AQPs (AQP1, -3, -4, and -5) was found in NSCLC and normal lung tissues. Furthermore, we identified remarkable differences between NSCLC subtypes in regard to AQP1, -3 and -4 expression. Higher transcript and protein levels of AQP4 in well-differentiated lung adenocarcinomas suggested an association with a more favourable prognosis. Beyond water transport, data mining of co-expressed genes indicated an involvement of AQP4 in cell-cell signalling, cellular movement and lipid metabolism, and underlined the association of AQP4 to important physiological functions in benign lung tissue.</p> <p>Conclusions</p> <p>Our findings accentuate the need to identify functional differences and redundancies of active AQPs in normal and tumor cells in order to assess their value as promising drug targets.</p

Differential transcriptional profiling of damaged and intact adjacent dorsal root ganglia neurons in neuropathic pain

Neuropathic pain, caused by a lesion in the somatosensory system, is a severely impairing mostly chronic disease. While its underlying molecular mechanisms are not thoroughly understood, neuroimmune interactions as well as changes in the pain pathway such as sensitization of nociceptors have been implicated. It has been shown that not only are different cell types involved in generation and maintenance of neuropathic pain, like neurons, immune and glial cells, but, also, intact adjacent neurons are relevant to the process. Here, we describe an experimental approach to discriminate damaged from intact adjacent neurons in the same dorsal root ganglion (DRG) using differential fluorescent neuronal labelling and fluorescence-activated cell sorting (FACS). Two fluorescent tracers, Fluoroemerald (FE) and 1-dioctadecyl-3,3,3,3-tetramethylindocarbocyanine perchlorate (DiI), were used, whose properties allow us to distinguish between damaged and intact neurons. Subsequent sorting permitted transcriptional analysis of both groups. Results and qPCR validation show a strong regulation in damaged neurons versus contralateral controls as well as a moderate regulation in adjacent neurons. Data for damaged neurons reveal an mRNA expression pattern consistent with established upregulated genes like galanin, which supports our approach. Moreover, novel genes were found strongly regulated such as corticotropinreleasing hormone (CRH), providing novel targets for further research. Differential fluorescent neuronal labelling and sorting allows for a clear distinction between primarily damaged neuropathic neurons and "bystanders," thereby facilitating a more detailed understanding of their respective roles in neuropathic processes in the DRG

Tissue Type-Specific Expression of the dsRNA-Binding Protein 76 and Genome-Wide Elucidation of Its Target mRNAs

Background: RNA-binding proteins accompany all steps in the life of mRNAs and provide dynamic gene regulatory functions for rapid adjustment to changing extra-or intracellular conditions. The association of RNA-binding proteins with their targets is regulated through changing subcellular distribution, post-translational modification or association with other proteins. Methodology: We demonstrate that the dsRNA binding protein 76 (DRBP76), synonymous with nuclear factor 90, displays inherently distinct tissue type-specific subcellular distribution in the normal human central nervous system and in malignant brain tumors of glial origin. Altered subcellular localization and isoform distribution in malignant glioma indicate that tumor-specific changes in DRBP76-related gene products and their regulatory functions may contribute to the formation and/or maintenance of these tumors. To identify endogenous mRNA targets of DRBP76, we performed RNA-immunoprecipitation and genome-wide microarray analyses in HEK293 cells, and identified specific classes of transcripts encoding critical functions in cellular metabolism. Significance: Our data suggest that physiologic DRBP76 expression, isoform distribution and subcellular localization are profoundly altered upon malignant transformation. Thus, the functional role of DRBP76 in co- or post-transcriptional gene regulation may contribute to the neoplastic phenotype

Endogenous mouse Dicer is an exclusively cytoplasmic protein

Dicer is a large multi-domain protein responsible for the ultimate step of microRNA and short-interfering RNA biogenesis. In human and mouse cell lines, Dicer has been shown to be important in the nuclear clearance of dsRNA as well as the establishment of chromatin modifications. Here we set out to unambiguously define the cellular localization of Dicer in mice to understand if this is a conserved feature of mammalian Dicer in vivo. To this end, we utilized an endogenously epitope tagged Dicer knock-in mouse allele. From primary mouse cell lines and adult tissues, we determined with certainty by biochemical fractionation and confocal immunofluorescence microscopy that endogenous Dicer is exclusively cytoplasmic. We ruled out the possibility that a fraction of Dicer shuttles to and from the nucleus as well as that FGF or DNA damage signaling induce Dicer nuclear translocation. We also explored Dicer localization during the dynamic and developmental context of embryogenesis, where Dicer is ubiquitously expressed and strictly cytoplasmic in all three germ layers as well as extraembryonic tissues. Our data exclude a direct role for Dicer in the nuclear RNA processing in the mouse