Fachbereich Ingenieur- und Naturwissenschaften
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DNA sequencing continues to evolve quickly even after > 30 years. Many new platforms suddenly appeared and former established systems have vanished in almost the same manner. Since establishment of next-generation sequencing devices, this progress gains momentum due to the continually growing demand for higher throughput, lower costs and better quality of data. In consequence of this rapid development, standardized procedures and data formats as well as comprehensive quality management considerations are still scarce. Here, we listed and summarized current standardization efforts and quality management initiatives from companies, organizations and societies in form of published studies and ongoing projects. These comprise on the one hand quality documentation issues like technical notes, accreditation checklists and guidelines for validation of sequencing workflows. On the other hand, general standard proposals and quality metrics are developed and applied to the sequencing workflow steps with the main focus on upstream processes. Finally, certain standard developments for downstream pipeline data handling, processing and storage are discussed in brief. These standardization approaches represent a first basis for continuing work in order to prospectively implement next-generation sequencing in important areas such as clinical diagnostics, where reliable results and fast processing is crucial. Additionally, these efforts will exert a decisive influence on traceability and reproducibility of sequence data.
Why does Planck (1900), referring to Boltzmann’s 1877 probabilistic treatment, obtain his quantum distribution function while Boltzmann did not? To answer this question, both treatments are compared on the basis of Boltzmann’s 1868 three-level scheme (configuration—occupation—occupancy). Some calculations by Planck (1900, 1901, and 1913) and Einstein (1907) are also sketched. For obtaining a quantum distribution, it is crucial to stick with a discrete energy spectrum and to make the limit transitions to infinity at the right place. For correct state counting, the concept of interchangeability of particles is superior to that of indistinguishability.
The redox behavior of proteins plays a crucial part in the design of bioelectronic systems. We have demonstrated several functional systems exploiting the electron exchange properties of the redox protein cytochrome c (cyt c) in combination with enzymes and photoactive proteins. The operation is based on an effective reaction at modified electrodes but also to a large extent on the capability of self-exchange between cyt c molecules in a surface-fixed state. In this context, different variants of human cyt c have been examined here with respect to an altered heterogeneous electron transfer (ET) rate in a monolayer on electrodes as well as an enhanced self-exchange rate while being incorporated in multilayer architectures. For this purpose, mutants of the wild-type (WT) protein have been prepared to change the chemical nature of the surface contact area near the heme edge. The structural integrity of the variants has been verified by NMR and UV–vis measurements. It is shown that the single-point mutations can significantly influence the heterogeneous ET rate at thiol-modified gold electrodes and that electroactive protein/silica nanoparticle multilayers can be constructed with all forms of human cyt c prepared. The kinetic behavior of electron exchange for the mutant proteins in comparison with that of the WT has been found altered in some multilayer arrangements. Higher self-exchange rates have been found for K79A. The results demonstrate that the position of the introduced change in the charge situation of cyt c has a profound influence on the exchange behavior. In addition, the behavior of the cyt c variants in assembled multilayers is found to be rather similar to the situation of cyt c self-exchange in solution verified by NMR.
The Gleason score (GS) of prostate cancer on diagnostic biopsies is an important parameter for therapeutic decision-making. Biopsy GS under-estimates the actual GS at radical prostatectomy in a significant number of patients due to samplingartifact. The aim of this study was to identify markers that are differentially expressed in Gleason grade 3 (GG3) tumor glands embedded in GS 4 + 3 = 7 and GS 3 + 3 = 6 prostate cancer using laser capture microdissection and RNA sequencing.
GG3 tumor glands embedded in nine GS 3 + 3 = 6 and nine GS 4 + 3 = 7 prostate cancers were isolated by laser capture microdissection of frozen radical prostatectomy specimens. After RNA amplification and RNA sequencing, differentially expressed genes in both GG3 components were identified by a 2log fold change > 1.0 and p-value < 0.05. We applied immunohistochemistry on a tissue micro-array representing 481 radical prostatectomy samples for further validation on protein level.
A total of 501 genes were up-regulated and 421 down-regulated in GG3 glands embedded in GS 4 + 3 = 7 as compared to GS 3 + 3 = 6 prostate cancer. We selected HELLS, ZIC2 and ZIC5 genes for further validation. ZIC5 mRNA was up-regulated 17 fold (p = 8.4E–07), ZIC2 8 fold (p = 1.3E–05) and HELLS 2 fold (p = 0.006) in GG3 glands derived from GS 4 + 3 = 7. HELLS expression of ≥ 1% occurred in 10% GS < 7, 17% GS 7 and 43% GS >7 prostate cancer (p < 0.001). Using a cut-off of ≥ 1%, protein expression of ZIC5 was present in 28% GS < 7, 43% GS 7 and 57% GS > 7 cancer (p < 0.001). ZIC2 was neither associated with GS nor outcome in our validation set. HELLS was independently predictive for biochemical-recurrence after radical prostatectomy (HR 2.3; CI 1.5–3.6; p < 0.01).
In conclusion, HELLS and ZIC5 might be promising candidate markers for selection of biopsy GS 6 prostate cancer being at risk for up-grading at prostatectomy.
Carcinogenesis is a complex multifactorial, multistage process, but the precise mechanisms are not well understood. In this study, we performed a genome-wide analysis of the copy number variation (CNV), breakpoint region (BPR) and fragile sites in 2,737 tumor samples from eight tumor entities and in 432 normal samples. CNV detection and BPR identification revealed that BPRs tended to accumulate in specific genomic regions in tumor samples whereas being dispersed genome-wide in the normal samples. Hotspots were observed, at which segments with similar alteration in copy number were overlapped along with BPRs adjacently clustered. Evaluation of BPR occurrence frequency showed that at least one was detected in about and more than 15% of samples for each tumor entity while BPRs were maximal in 12% of the normal samples. 127 of 2,716 tumor-relevant BPRs (termed ‘common BPRs’) exhibited also a noticeable occurrence frequency in the normal samples. Colocalization assessment identified 20,077 CNV-affecting genes and 169 of these being known tumor-related genes. The most noteworthy genes are KIAA0513 important for immunologic, synaptic and apoptotic signal pathways, intergenic non-coding RNA RP11-115C21.2 possibly acting as oncogene or tumor suppressor by changing the structure of chromatin, and ADAM32 likely importance in cancer cell proliferation and progression by ectodomain-shedding of diverse growth factors, and the well-known tumor suppressor gene p53. The BPR distributions indicate that CNV mutations are likely non-random in tumor genomes. The marked recurrence of BPRs at specific regions supports common progression mechanisms in tumors. The presence of hotspots together with common BPRs, despite its small group size, imply a relation between fragile sites and cancer-gene alteration. Our data further suggest that both protein-coding and non-coding genes possessing a range of biological functions might play a causative or functional role in tumor biology. This research enhances our understanding of the mechanisms for tumorigenesis and progression.
Mit diesem Beitrag soll der Einsatz von iBeacons als Basis eines Indoor-Ortungssystems in der Hochschulbibliothek der Technischen Hochschule Wildau vorgestellt werden. Für die Ortung innerhalb von Gebäuden sind bisher unterschiedliche Strategien zum Einsatz gekommen. Die von Apple Inc. entwickelte iBeacon-Technologie kommuniziert über Bluetooth Low Energy (BLE) und setzt somit eine Technologie ein, die einen großen Kreis von Nutzern erreicht. Als wesentlicher Teil der Campus-App Unidos Wildau operiert das Ortungssystem auf der Basis des Kartendienstes iCampus Wildau Maps. Gemachte Erfahrungen mit der iBeacon-Technologie werden ebenso im Fokus dieses Beitrags stehen wie Ergebnisse der Implementierung unseres Ortungssystems sowie Pläne für die Weiterentwicklung.
In this work, a measurement concept based on triangulation was developed for borescopic 3D-surveying of surface defects. The integration of such measurement system into a borescope environment requires excellent space utilization. The triangulation angle, the projected pattern, the numerical apertures of the optical system, and the viewing angle were calculated using partial coherence imaging and geometric optical raytracing methods. Additionally, optical aberrations and defocus were considered by the integration of Zernike polynomial coefficients. The measurement system is able to measure objects with a size of 50 μm in all dimensions with an accuracy of ± 5 μm. To manage the issue of a low depth of field while using an optical high resolution system, a wavelength dependent aperture was integrated. Thereby, we are able to control depth of field and resolution of the optical system and can use the borescope in measurement mode with high resolution and low depth of field or in inspection mode with low resolution and higher depth of field. First measurements of a demonstrator system are in good agreement with our simulations.
Integrated photonic devices have gained increasing research interests. Especially silicon photonics have become very attractive for various optical applications. Using silicon-on-insulator as a material platform provides the ability to fabricate photonic devices with electronic devices on a single chip. Driven by substantial research investments, the integration of photonic devices on silicon-on-insulator substrates has reached a degree of maturity that already permits industrial adoption. However, silicon has the disadvantage of linear electro-optical effects, and, therefore, advanced modulation formats are difficult to realize when using silicon-based high-speed modulators. Hence, a new approach was proposed: the silicon-organic hybrid technology. This technology is a viable extension of the silicon-on-insulator material system for efficient high-speed modulation. We herewith present our theoretical and experimental investigations of the silicon-organic hybrid slot-waveguide ring resonator. The advanced device design is described in detail, which allows using both, the efficient silicon-on-insulator strip-waveguides and the silicon-organic hybrid slot-waveguides in single ring resonator. For the first time, we report the transmission spectra of such a resonator covered with an electro-optical polymer.
In this work, we present for the first time a partially slotted silicon ring resonator (PSRR) covered with an electro-optical polymer (Poly[(methyl methacrylate)-co-(Disperse Red 1 acrylate)]). The PSRR takes advantage of both a highly efficient vertical slot waveguide based phase shifter and a low loss strip waveguide in a single ring. The device is realized on 200 mm silicon-on-insulator wafers using 248 nm DUV lithography and covered with the electro-optic polymer in a post process. This silicon-organic hybrid ring resonator has a small footprint, high optical quality factor, and high DC device tunability. A quality factor of up to 105 and a DC device tunability of about 700 pm/V is experimentally demonstrated in the wavelength range of 1540 nm to 1590 nm. Further, we compare our results with state-of-the-art silicon-organic hybrid devices by determining the poling efficiency. It is demonstrated that the active PSRR is a promising candidate for efficient optical switches and tunable filters.
Fabry-Perot (FP) polymer film sensors offer high acoustic sensitivity, small element sizes, broadband frequency response and optical transmission to enable high resolution, backward mode photoacoustic (PA) imaging. Typical approaches to sensor fabrication involve the deposition of stacks of alternating dielectric materials to form interferometer mirrors, which are separated by a polymer spacer. If hygroscopic soft dielectric materials are used, a protective polymer layer is typically required. In this study, methods for the deposition of water-resistant, hard dielectric materials onto polymers were explored to improve the robustness and performance of the sensors. This involved the optimisation of the fabrication process, the optical and acoustic characterisation of the sensors, and a comparison of the frequency response with the output of an acoustic forward model. The mirrors, which were separated by a 20 μm Parylene spacer, consisted of eight double layers of Ta2O5 and SiO2 deposited onto polymer substrates using temperature-optimised electron vapour deposition. The free spectral range of the interferometer was 32 nm, its finesse FR = 91, and its visibility V = 0.72. The noise-equivalent pressure was 0.3 kPa (20 MHz bandwidth). The measured frequency response was found to be more resonant at 25 MHz compared to sensors with soft dielectric mirrors, which was also in good agreement with the output of a forward model of the sensor. The sensors were used in a PA scanner to acquire 3-D images in tissue phantoms.