TY - JOUR A1 - Tannenberg, Robert A1 - Tscheuschner, Georg A1 - Raab, Christopher A1 - Flemig, Sabine A1 - Döring, Sarah A1 - Ponader, Marco A1 - Thurmann, Melinda A1 - Paul, Martin A1 - Weller, Michael G. T1 - Simplified Sample Preparation and Lateral Flow Immunoassay for the Detection of Plant Viruses JF - Biosensors N2 - Lateral flow immunoassays (LFAs) are widely used for on-site testing; however, their use for the rapid detection of plant viruses in the field is often limited by inconvenient sample preparation. Here, we present a new sampling method and a simplified dipstick LFA format for the detection and monitoring of cowpea chlorotic mottle virus (CCMV) as a model plant pathogen. The assay employs a monoclonal mouse antibody for capture and a poly-clonal rabbit antibody conjugated to 80 nm gold nanoparticles for detection. Conventional sample and conjugate pads are omitted, allowing the test strips to be dipped directly into wells containing plant extract and antibody–gold conjugate. No plastic casing was required, which could lead to a reduction in waste. It was shown that CCMV concentrations as low as 3.5 μg/L or 350 pg per sample could be reliably detected in 15 min. Specificity tests confirmed that other plant viruses, cowpea mosaic virus (CPMV) and tobacco mosaic virus (TMV), did not produce false-positive results. In addition, we describe a new method for on-site sampling using a manual punch and a syringe equipped with a frit. This step combines grinding the sample, extraction, filtration, and reconstitution and mixing of the antibody-gold conjugate, enabling the analysis of punched leaf disks without laboratory equipment. When applied to CCMV-infected cowpea plants, the assay revealed systemic infection before visual symptoms became apparent. This work demonstrates that simplified LFAs combined with innovative sampling techniques can provide sensitive, specific, and rapid diagnostics for crop monitoring and support early intervention strategies in agriculture. KW - LFA format KW - Vigna unguiculata KW - cowpea chlorotic mottle virus KW - crop monitoring KW - lateral flow immunoassay KW - plant virus KW - sample preparation KW - waste reduction Y1 - 2026 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-21294 VL - 16 IS - 2 PB - MDPI ER - TY - JOUR A1 - Zesch, Christoph A1 - Finkelstein, Daniel A1 - Regehly, Martin A1 - Reif, Jürgen A1 - Schrader, Sigurd T1 - Efficient nanosecond barium nitrate Raman laser for the visible spectral range JF - Optics Express N2 - We report on the design and performance of two solid-state Raman lasers, pumped by a frequency-doubled Nd:YAG laser at 532 nm (8 ns FWHM, 10 Hz, up to 10 mJ), that generate either the first or second Stokes radiation with wavelengths of 563 nm and 598 nm. Barium nitrate crystals with a 1 cm² face area and lengths of 3 cm and 5 cm were used as the Raman-active medium in stable semi-spherical resonators. The Raman lasers produced first Stokes and second Stokes pulses, achieving pulse energies up to 2.3 mJ and conversion efficiencies up to 35% (first Stokes, 5 cm crystal) and 21% (second Stokes, 5 cm crystal). The output beams exhibit nearly Gaussian profiles with beam quality factors of M² = 1.67 and M² = 1.83, respectively. The proposed design and characterization demonstrated a Raman laser with high efficiency and superior beam quality. After subsequent frequency doubling, the output appears well dedicated for future differential absorption LiDAR (DIAL) applications. KW - Gaussian beam KW - laser source KW - Nd:YAG laser KW - Raman laser KW - solid state laser KW - ultraviolet laser Y1 - 2026 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-21320 VL - 34 IS - 4 SP - 6355 EP - 6363 PB - Optica ER - TY - JOUR A1 - Steglich, Patrick A1 - Mai, Christian A1 - Villringer, Claus A1 - Dietzel, Birgit A1 - Bondarenko, Siegfried A1 - Ksianzou, Viachaslau A1 - Villasmunta, Francesco A1 - Zesch, Christoph A1 - Pulwer, Silvio A1 - Burger, Martin A1 - Bauer, Joachim A1 - Heinrich, Friedhelm A1 - Schrader, Sigurd A1 - Vitale, Francesco A1 - De Matteis, Fabio A1 - Prosposito, Paolo A1 - Casalboni, Mauro A1 - Mai, Andreas T1 - Silicon-organic hybrid photonics: an overview of recent advances, electro-optical effects and CMOS integration concepts JF - Journal of Physics: Photonics N2 - In recent decades, much research effort has been invested in the development of photonic integrated circuits, and silicon-on-insulator technology has been established as a reliable platform for highly scalable silicon-based electro-optical modulators. However, the performance of such devices is restricted by the inherent material properties of silicon. An approach to overcoming these deficiencies is to integrate organic materials with exceptionally high optical nonlinearities into a silicon-on-insulator photonic platform. Silicon–organic hybrid photonics has been shown to overcome the drawbacks of silicon-based modulators in terms of operating speed, bandwidth, and energy consumption. This work reviews recent advances in silicon–organic hybrid photonics and covers the latest improvements to single components and device concepts. Special emphasis is given to the in-device performance of novel electro-optical polymers and the use of different electro-optical effects, such as the linear and quadratic electro-optical effect, as well as the electric-field-induced linear electro-optical effect. Finally, the inherent challenges of implementing non-linear optical polymers on a silicon photonic platform are discussed and a perspective for future directions is given. Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-13882 SN - 2515-7647 VL - 3 IS - 2 ER - TY - JOUR A1 - Regehly, Martin A1 - Hecht, Stefan T1 - Split-Aperture Xolography – Linear Volumetric Photoactivation with Short Axial Dimension and Low out of Focus Excitation JF - Advanced Science N2 - Spatially confined photo-excitation with the lowest possible activation of the remaining volume is of central importance for high-resolution high-density optical data storage, fluorescence microscopy, 3D-lithography, and 3D-printing. Two-photon absorption (2PA) enables such applications yet leads to slow processing speed due to the underlying non-linear absorption process. Here, Split-Aperture Xolography (SAX), is introduced which uses stepwise excitation of dual-color responsive molecules to initiate a linear volumetric photo-reaction process that is up to several orders of magnitude more efficient than 2PA. The capabilities of SAX are investigated in a scenario study for focusing systems with high numerical aperture (NA) using a Python implementation of vectorial diffraction theory. The intersecting half-cones generated by the split illuminated entrance aperture of the objective reduce the axial focal spot size of the activation distribution by up to a factor of two compared to 2PA targeting the same electronic transition. A steep average decline of the activation probability with the fifth power away from focus is found for a wide range of directions. This is significantly better in comparison to 2PA and prevents that undesired out-of-focus excitation events sum-up with subsequent irradiations. This approach is expected to be advantageous for volumetric methods at the nanoscale. KW - photoswitch KW - split-aperture xolography KW - two-photon absorption KW - vectorial diffraction KW - volumetric 3D printing Y1 - 2025 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-20749 VL - 12 IS - 31 PB - Wiley ER - TY - JOUR A1 - Bauer, Joachim A1 - Heinrich, Friedhelm A1 - Villasmunta, Francesco A1 - Villringer, Claus A1 - Reck, Johanna A1 - Peters, Sven A1 - Treffer, Alexander A1 - Kuhnt, Christian A1 - Marschmeyer, Steffen A1 - Fursenko, Oksana A1 - Stolarek, David A1 - Mai, Andreas A1 - Regehly, Martin T1 - Reflectometric method for measuring residual oxides in through-silicon vias for 3D chip integration JF - Optics Express N2 - A significant aspect of fabricating 3D chip architectures is ensuring proper contact between the different layers of the chip, which often requires removing the underside of isolation layers before filling vias with conductive material. Currently, scanning electron microscopy is the established method for investigating such structures. In this paper, we propose a rapid, non-destructive optical analysis technique for the simultaneous measurement of through-silicon vias (TSV) depths, silicon wafer thickness, and residual oxide thickness. The proposed method utilizes Fourier peak shift analysis (FPSA) of reflectance measurements in the near-infrared (1200 nm—2200 nm) spectral regions. The application of FPSA to representative samples taken from a commercial TSV integration process for MEMS and CMOS fabrication demonstrated good agreement with reference scanning electron microscopy measurements, confirming the feasibility of the method for in-line and in-situ metrology. The results indicate that FPSA has great potential for real-time process monitoring and control during 3D chip manufacturing. KW - effective refractive index KW - Fourier transforms KW - near infrared KW - ray tracing KW - scanning electron microscopy KW - thin film Y1 - 2025 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-20633 VL - 33 IS - 15 SP - 32175 EP - 32189 PB - Optica ER - TY - JOUR A1 - Holland-Moritz, Ralph A1 - Vandenhouten, Ralf T1 - Detection of Movement Profiles in Facility Management Using Complex Event Processing JF - International Journal of Information Science N2 - This paper presents a solution for detecting movement and spreading profiles by analyzing sensor data in the facility management. First of all, a scenario is defined and described. On the basis of this scenario an approach is made using integration of events over time and location. For making the integration possible the required information, which the data objects have to provide, is identified. At the end a solution is presented using Complex Event Processing to implement the integration of events. KW - facility management KW - complex event processing KW - sensor KW - detector KW - movement profile KW - spatial dimension KW - integration KW - alarm reliability KW - event driven architecture KW - evaluation KW - security KW - intrusion KW - fire Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-9495 UR - http://article.sapub.org/10.5923.j.ijis.20130301.02.html SN - 2163-193X VL - 3 IS - 1 SP - 7 EP - 12 ER - TY - JOUR A1 - Balabanov, Stefan A1 - Wilhelm, Thomas A1 - Venz, Simone A1 - Keller, Gunhild A1 - Scharf, Christian A1 - Pospisil, Heike A1 - Braig, Melanie A1 - Barett, Christine A1 - Bokemeyer, Carsten A1 - Walther, Reinhard A1 - Brümmendorf, Tim H. A1 - Schuppert, Andreas T1 - Combination of a Proteomics Approach and Reengineering of Meso Scale Network Models for Prediction of Mode-of-Action for Tyrosine Kinase Inhibitors JF - PLoS ONE N2 - In drug discovery, the characterisation of the precise modes of action (MoA) and of unwanted off-target effects of novel molecularly targeted compounds is of highest relevance. Recent approaches for identification of MoA have employed various techniques for modeling of well defined signaling pathways including structural information, changes in phenotypic behavior of cells and gene expression patterns after drug treatment. However, efficient approaches focusing on proteome wide data for the identification of MoA including interference with mutations are underrepresented. As mutations are key drivers of drug resistance in molecularly targeted tumor therapies, efficient analysis and modeling of downstream effects of mutations on drug MoA is a key to efficient development of improved targeted anti-cancer drugs. Here we present a combination of a global proteome analysis, reengineering of network models and integration of apoptosis data used to infer the mode-of-action of various tyrosine kinase inhibitors (TKIs) in chronic myeloid leukemia (CML) cell lines expressing wild type as well as TKI resistance conferring mutants of BCR-ABL. The inferred network models provide a tool to predict the main MoA of drugs as well as to grouping of drugs with known similar kinase inhibitory activity patterns in comparison to drugs with an additional MoA. We believe that our direct network reconstruction approach, demonstrated on proteomics data, can provide a complementary method to the established network reconstruction approaches for the preclinical modeling of the MoA of various types of targeted drugs in cancer treatment. Hence it may contribute to the more precise prediction of clinically relevant on- and off-target effects of TKIs. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6370 SN - 1932-6203 VL - 8 IS - 1 ER - TY - JOUR A1 - Thiemann, Alexander A1 - Fu, Junjie A1 - Seifert, Felix A1 - Grant-Downton, Robert T A1 - Schrag, Tobias A A1 - Pospisil, Heike A1 - Frisch, Matthias A1 - Melchinger, Albrecht E A1 - Scholten, Stefan T1 - Genome-wide meta-analysis of maize heterosis reveals the potential role of additive gene expression at pericentromeric loci JF - BMC Plant Biology N2 - The identification of QTL involved in heterosis formation is one approach to unravel the not yet fully understood genetic basis of heterosis - the improved agronomic performance of hybrid F1 plants compared to their inbred parents. The identification of candidate genes underlying a QTL is important both for developing markers and determining the molecular genetic basis of a trait, but remains difficult owing to the large number of genes often contained within individual QTL. To address this problem in heterosis analysis, we applied a meta-analysis strategy for grain yield (GY) of Zea mays L. as example, incorporating QTL-, hybrid field-, and parental gene expression data. KW - heterosis KW - maize KW - QTL KW - grain yield KW - additive gene expression Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-5999 SN - 1471-2229 VL - 14 IS - 88 ER - TY - JOUR A1 - Ummanni, Ramesh A1 - Mundt, Frederike A1 - Pospisil, Heike A1 - Venz, Simone A1 - Scharf, Christian A1 - Barett, Christine A1 - Fälth, Maria A1 - Köllermann, Jens A1 - Walther, Reinhard A1 - Schlomm, Thorsten A1 - Sauter, Guido A1 - Bokemeyer, Carsten A1 - Sültmann, Holger A1 - Schuppert, Andreas A1 - Brümmendorf, Tim H. A1 - Balabanov, Stefan T1 - Identification of Clinically Relevant Protein Targets in Prostate Cancer with 2D-DIGE Coupled Mass Spectrometry and Systems Biology Network Platform JF - PLoS ONE N2 - Prostate cancer (PCa) is the most common type of cancer found in men and among the leading causes of cancer death in the western world. In the present study, we compared the individual protein expression patterns from histologically characterized PCa and the surrounding benign tissue obtained by manual micro dissection using highly sensitive two-dimensional differential gel electrophoresis (2D-DIGE) coupled with mass spectrometry. Proteomic data revealed 118 protein spots to be differentially expressed in cancer (n = 24) compared to benign (n = 21) prostate tissue. These spots were analysed by MALDI-TOF-MS/MS and 79 different proteins were identified. Using principal component analysis we could clearly separate tumor and normal tissue and two distinct tumor groups based on the protein expression pattern. By using a systems biology approach, we could map many of these proteins both into major pathways involved in PCa progression as well as into a group of potential diagnostic and/or prognostic markers. Due to complexity of the highly interconnected shortest pathway network, the functional sub networks revealed some of the potential candidate biomarker proteins for further validation. By using a systems biology approach, our study revealed novel proteins and molecular networks with altered expression in PCa. Further functional validation of individual proteins is ongoing and might provide new insights in PCa progression potentially leading to the design of novel diagnostic and therapeutic strategies. Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6432 SN - 1932-6203 VL - 6 IS - 2 ER - TY - JOUR A1 - Standfuß, Christoph A1 - Pospisil, Heike A1 - Klein, Andreas T1 - SNP microarray analyses reveal copy number alterations and progressive genome reorganization during tumor development in SVT/t driven mice breast cancer JF - BMC Cancer N2 - Tumor development is known to be a stepwise process involving dynamic changes that affect cellular integrity and cellular behavior. This complex interaction between genomic organization and gene, as well as protein expression is not yet fully understood. Tumor characterization by gene expression analyses is not sufficient, since expression levels are only available as a snapshot of the cell status. So far, research has mainly focused on gene expression profiling or alterations in oncogenes, even though DNA microarray platforms would allow for high-throughput analyses of copy number alterations (CNAs). KW - breast cancer KW - genome reorganization KW - copy number alteration KW - CNV KW - fragile site Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6414 SN - 1471-2407 VL - 12 IS - 380 ER - TY - JOUR A1 - Klein, Andreas A1 - Pospisil, Heike T1 - Gene Expression Profiling of Pancreatic Cancer Reveals a Significant Deregulation of the TGF-β Pathway and the Discovery of Genes for Prognosis JF - Global Journal of Human Genetics & Gene Therapy N2 - We have re-analyzed previously published gene expression data from ninety-four pancreatic ductal adenocarcinomas (PDAC) samples. We determined the gene expression profile of genes differentially expressed in PDAC compared to non-malignant pancreatic tissue. Using the 100 top-ranked genes, we were able to discriminate between PDAC and non-malignant pancreatic tissue. A hierarchical cluster analysis revealed only a 6 % false discovery rate. The prognostic strength of these discriminative genes was underscored by a SVM classification and 3-fold cross validation with an 89 % correct class assignment. The annotation of the 100 top-ranked genes revealed that most of the genes were involved in the processes of signal transduction, cell adhesion, extracellular matrix organization and cell migration. The most greatly affected signal cascade was the transforming growth factor β receptor signaling pathway, which was significantly enriched in the top-ranked genes. Furthermore, we identified eleven genes that were associated with good prognosis. KW - pancreatic ductal adenocarcinoma KW - gene expression profiling KW - TGF-β Y1 - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6519 SN - 2311-0309 VL - 2 IS - 1 SP - 30 EP - 39 ER - TY - JOUR A1 - Hannemann, Juliane A1 - Meyer-Staeckling, Sönke A1 - Kemming, Dirk A1 - Alpers, Iris A1 - Joosse, Simon A. A1 - Pospisil, Heike A1 - Kurtz, Stefan A1 - Görndt, Jennifer A1 - Püschel, Klaus A1 - Riethdorf, Sabine A1 - Pantel, Klaus A1 - Brandt, Burkhard T1 - Quantitative High-Resolution Genomic Analysis of Single Cancer Cells JF - PLoS ONE N2 - During cancer progression, specific genomic aberrations arise that can determine the scope of the disease and can be used as predictive or prognostic markers. The detection of specific gene amplifications or deletions in single blood-borne or disseminated tumour cells that may give rise to the development of metastases is of great clinical interest but technically challenging. In this study, we present a method for quantitative high-resolution genomic analysis of single cells. Cells were isolated under permanent microscopic control followed by high-fidelity whole genome amplification and subsequent analyses by fine tiling array-CGH and qPCR. The assay was applied to single breast cancer cells to analyze the chromosomal region centred by the therapeutical relevant EGFR gene. This method allows precise quantitative analysis of copy number variations in single cell diagnostics. Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6426 SN - 1932-6203 VL - 6 IS - 11 ER - TY - JOUR A1 - Silbermann, Jascha A1 - Wernicke, Catrin A1 - Pospisil, Heike A1 - Frohme, Marcus T1 - RefPrimeCouch—a reference gene primer CouchApp JF - Database: The Journal of Biological Databases and Curation N2 - To support a quantitative real-time polymerase chain reaction standardization project, a new reference gene database application was required. The new database application was built with the explicit goal of simplifying not only the development process but also making the user interface more responsive and intuitive. To this end, CouchDB was used as the backend with a lightweight dynamic user interface implemented client-side as a one-page web application. Data entry and curation processes were streamlined using an OpenRefine-based workflow. The new RefPrimeCouch database application provides its data online under an Open Database License. Y1 - 2013 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:526-opus4-6330 SN - 1758-0463 VL - 2013 ER -