TY - JOUR A1 - Arinkin, Vladimir A1 - Digel, Ilya A1 - Porst, Dariusz A1 - Temiz Artmann, Aysegül A1 - Artmann, Gerhard T1 - Phenotyping date palm varieties via leaflet cross-sectional imaging and artificial neural network application JF - BMC bioinformatics N2 - Background True date palms (Phoenix dactylifera L.) are impressive trees and have served as an indispensable source of food for mankind in tropical and subtropical countries for centuries. The aim of this study is to differentiate date palm tree varieties by analysing leaflet cross sections with technical/optical methods and artificial neural networks (ANN). Results Fluorescence microscopy images of leaflet cross sections have been taken from a set of five date palm tree cultivars (Hewlat al Jouf, Khlas, Nabot Soltan, Shishi, Um Raheem). After features extraction from images, the obtained data have been fed in a multilayer perceptron ANN with backpropagation learning algorithm. Conclusions Overall, an accurate result in prediction and differentiation of date palm tree cultivars was achieved with average prediction in tenfold cross-validation is 89.1% and reached 100% in one of the best ANN. Y1 - 2014 U6 - https://doi.org/10.1186/1471-2105-15-55 SN - 1471-2105 VL - 15 IS - 55 SP - 1 EP - 8 ER - TY - JOUR A1 - Sawada, Kazuaki A1 - Nakazawa, Hirokazu A1 - Takenaga, Shoko A1 - Hizawa, Takeshi A1 - Futagawa, Masato A1 - Dasai, Fumihiro A1 - Sakurai, Takashi A1 - Okumura, Koichi A1 - Hattori, Toshiaki A1 - Ishida, Makoto T1 - Multimodal bioimage sensor JF - IEICE transactions on fundamentals of electronics, communidations and computer sciences N2 - To visualize the biochemical distribution two-dimensionally, we invented a solid-state-type ion image sensor that indicates the chemical activity of solutions and cells. The device, which consists of a CCD array covered with a functionalized membrane to detect charge accumulation, is highly sensitive to changes in the concentration and two-dimensional distribution of ions and biomaterials. Y1 - 2014 U6 - https://doi.org/10.1587/transfun.E97.A.726 SN - 0916-8508 (Print) ; 1745-1337 (Online) VL - E97-A (2014) IS - 3 SP - 726 EP - 733 PB - IEICE CY - Tokyo ER - TY - JOUR A1 - Leinhos, Marcel A1 - Schusser, Sebastian A1 - Bäcker, Matthias A1 - Poghossian, Arshak A1 - Schöning, Michael Josef T1 - Micromachined multi-parameter sensor chip for the control of polymer-degradation medium JF - Physica Status Solidi (A) : special issue on engineering and functional interfaces N2 - It is well known that the degradation environment can strongly influence the biodegradability and kinetics of biodegradation processes of polymers. Therefore, besides the monitoring of the degradation process, it is also necessary to control the medium in which the degradation takes place. In this work, a micromachined multi-parameter sensor chip for the control of the polymer-degradation medium has been developed. The chip combines a capacitive field-effect pH sensor, a four-electrode electrolyte-conductivity sensor and a thin-film Pt-temperature sensor. The results of characterization of individual sensors are presented. In addition, the multi-parameter sensor chip together with an impedimetric polymer-degradation sensor was simultaneously characterized in degradation solutions with different pH and electrolyte conductivity. The obtained results demonstrate the feasibility of the multi-parameter sensor chip for the control of the polymer-degradation medium. Y1 - 2014 U6 - https://doi.org/10.1002/pssa.201330364 SN - 1521-396X (E-Journal); 1862-6319 (E-Journal); 0031-8965 (Print); 1862-6300 (Print) VL - 211 IS - 6 SP - 1346 EP - 1351 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Heine, A. A1 - Herrmann, G. A1 - Selmer, Thorsten A1 - Terwesten, F. A1 - Buckel, W. A1 - Reuter, K. T1 - High resolution crystal structure of clostridium propionicum β-Alanyl-CoA:Ammonia Lyase, a new member of the "Hot Dog Fold" protein superfamily JF - Proteins N2 - Clostridium propionicum is the only organism known to ferment β-alanine, a constituent of coenzyme A (CoA) and the phosphopantetheinyl prosthetic group of holo-acyl carrier protein. The first step in the fermentation is a CoA-transfer to β-alanine. Subsequently, the resulting β-alanyl-CoA is deaminated by the enzyme β-alanyl-CoA:ammonia lyase (Acl) to reversibly form ammonia and acrylyl-CoA. We have determined the crystal structure of Acl in its apo-form at a resolution of 0.97 Å as well as in complex with CoA at a resolution of 1.59 Å. The structures reveal that the enyzme belongs to a superfamily of proteins exhibiting a so called “hot dog fold” which is characterized by a five-stranded antiparallel β-sheet with a long α-helix packed against it. The functional unit of all “hot dog fold” proteins is a homodimer containing two equivalent substrate binding sites which are established by the dimer interface. In the case of Acl, three functional dimers combine to a homohexamer strongly resembling the homohexamer formed by YciA-like acyl-CoA thioesterases. Here, we propose an enzymatic mechanism based on the crystal structure of the Acl·CoA complex and molecular docking. Proteins 2014; 82:2041–2053. © 2014 Wiley Periodicals, Inc. Y1 - 2014 U6 - https://doi.org/10.1002/prot.24557 SN - 1097-0134 (E-Journal); 0887-3585 (Print) VL - 82 IS - 9 SP - 2041 EP - 2053 PB - Wiley-Liss CY - New York ER - TY - JOUR A1 - Huck, Christina A1 - Poghossian, Arshak A1 - Kerroumi, Iman A1 - Schusser, Sebastian A1 - Bäcker, Matthias A1 - Zander, Willi A1 - Schubert, Jürgen A1 - Buniatyan, Vahe V. A1 - Martirosyan, Norayr W. A1 - Wagner, Patrick A1 - Schöning, Michael Josef T1 - Multiparameter sensor chip with Barium Strontium Titanate as multipurpose material JF - Electroanalysis N2 - It is well known that biochemical and biotechnological processes are strongly dependent and affected by a variety of physico-chemical parameters such as pH value, temperature, pressure and electrolyte conductivity. Therefore, these quantities have to be monitored or controlled in order to guarantee a stable process operation, optimization and high yield. In this work, a sensor chip for the multiparameter detection of three physico-chemical parameters such as electrolyte conductivity, pH and temperature is realized using barium strontium titanate (BST) as multipurpose material. The chip integrates a capacitively coupled four-electrode electrolyte-conductivity sensor, a capacitive field-effect pH sensor and a thin-film Pt-temperature sensor. Due to the multifunctional properties of BST, it is utilized as final outermost coating layer of the processed sensor chip and serves as passivation and protection layer as well as pH-sensitive transducer material at the same time. The results of testing of the individual sensors of the developed multiparameter sensor chip are presented. In addition, a quasi-simultaneous multiparameter characterization of the sensor chip in buffer solutions with different pH value and electrolyte conductivity is performed. To study the sensor behavior and the suitability of BST as multifunctional material under harsh environmental conditions, the sensor chip was exemplarily tested in a biogas digestate. Y1 - 2014 U6 - https://doi.org/10.1002/elan.201400076 SN - 1521-4109 (E-Journal); 1040-0397 (Print) VL - 26 IS - 5 SP - 980 EP - 987 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Bäcker, Matthias A1 - Kramer, F. A1 - Huck, Christina A1 - Poghossian, Arshak A1 - Bratov, A. A1 - Abramova, N. A1 - Schöning, Michael Josef T1 - Planar and 3D interdigitated electrodes for biosensing applications: The impact of a dielectric barrier on the sensor properties JF - Physica Status Solidi (A) - Applications and Materials Science N2 - Planar and three-dimensional (3D) interdigitated electrodes (IDE) with electrode digits separated by an insulating barrier of different heights were electrochemically characterized and compared in terms of their sensing properties. Due to the impact of the surface resistance, both types of IDE structures display a non-linear behavior in low-ionic strength solutions. The experimental data were fitted to an electrical equivalent circuit and interpreted taking into account the surface-charge-governed properties. The effect of a charged polyelectrolyte layer electrostatically assembled onto the sensor surface on the surface resistance in solutions with different KCl concentration is studied. In case of the same electrode footprint, 3D-IDEs show a larger cell constant and a higher sensitivity to molecular adsorption than that of planar IDEs. The obtained results demonstrate the potential of 3D-IDEs as a new transducer structure for a direct label-free sensing of charged molecules. Y1 - 2014 U6 - https://doi.org/10.1002/pssa.201330416 SN - 1521-396X (E-Journal); 1862-6319 (E-Journal); 0031-8965 (Print); 1862-6300 (Print) VL - 211 IS - 6 SP - 1357 EP - 1363 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Takenaga, Shoko A1 - Biselli, Manfred A1 - Schnitzler, Thomas A1 - Öhlschläger, Peter A1 - Wagner, Torsten A1 - Schöning, Michael Josef T1 - Toward multi-analyte bioarray sensors: LAPS-based on-chip determination of a Michaelis–Menten-like kinetics for cell culturing JF - Physica status solidi A : Applications and materials science N2 - The metabolic activity of Chinese hamster ovary (CHO) cells was observed using a light-addressable potentiometric sensor (LAPS). The dependency toward different glucose concentrations (17–200 mM) follows a Michaelis–Menten kinetics trajectory with Kₘ = 32.8 mM, and the obtained Kₘ value in this experiment was compared with that found in literature. In addition, the pH shift induced by glucose metabolism of tumor cells transfected with the HPV-16 genome (C3 cells) was successfully observed. These results indicate the possibility to determine the tumor cells metabolism with a LAPS-based measurement device. Y1 - 2014 U6 - https://doi.org/10.1002/pssa.201330464 SN - 1521-396X (E); 1862-6319 (E-Journal); 0031-8965 (Print); 1862-6300 (Print) VL - 211 IS - 6 SP - 1410 EP - 1415 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Wu, Chunsheng A1 - Bronder, Thomas A1 - Poghossian, Arshak A1 - Werner, Frederik A1 - Bäcker, Matthias A1 - Schöning, Michael Josef T1 - Label-free electrical detection of DNA with a multi-spot LAPS: First step towards light-addressable DNA chips JF - Physica status solidi A : Applications and materials science N2 - A multi-spot (4 × 4 spots) light-addressable potentiometric sensor (MLAPS) consisting of an Al–p-Si–SiO2 structure has been applied for the label-free electrical detection of DNA (deoxyribonucleic acid) immobilization and hybridization by the intrinsic molecular charge for the first time. Single-stranded probe ssDNA molecules (20 bases) were covalently immobilized onto the silanized SiO2 gate surface. The unspecific adsorption of mismatch ssDNA on the MLAPS gate surface was blocked by bovine serum albumin molecules. To reduce the screening effect and to achieve a high sensor signal, the measurements were performed in a low ionic-strength solution. The photocurrent–voltage (I–V) curves were simultaneously recorded on all 16 spots after each surface functionalization step. Large shifts of I–V curves of 25 mV were registered after the DNA immobilization and hybridization event. In contrast, a small potential shift (∼5 mV) was observed in case of mismatch ssDNA, revealing good specificity of the sensor. The obtained results demonstrate the potential of the MLAPS as promising transducer platform for the multi-spot label-free electrical detection of DNA molecules by their intrinsic molecular charge. Y1 - 2014 U6 - https://doi.org/10.1002/pssa.201330442 SN - 1521-396X (E-Journal); 1862-6319 (E-Journal); 0031-8965 (Print); 1862-6300 (Print) VL - 211 IS - 6 SP - 1423 EP - 1428 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Poghossian, Arshak A1 - Schöning, Michael Josef T1 - Label-free sensing of biomolecules with field-effect devices for clinical applications JF - Electroanalysis N2 - Among the variety of transducer concepts proposed for label-free detection of biomolecules, the semiconductor field-effect device (FED) is one of the most attractive platforms. As medical techniques continue to progress towards diagnostic and therapies based on biomarkers, the ability of FEDs for a label-free, fast and real-time detection of multiple pathogenic and physiologically relevant molecules with high specificity and sensitivity offers very promising prospects for their application in point-of-care and personalized medicine for an early diagnosis and treatment of diseases. The presented paper reviews recent advances and current trends in research and development of different FEDs for label-free, direct electrical detection of charged biomolecules by their intrinsic molecular charge. The authors are mainly focusing on the detection of the DNA hybridization event, antibody-antigen affinity reaction as well as clinically relevant biomolecules such as cardiac and cancer biomarkers. Y1 - 2014 U6 - https://doi.org/10.1002/elan.201400073 SN - 1521-4109 (E-Journal); 1040-0397 (Print) VL - 26 IS - 6 SP - 1197 EP - 1213 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Pham, Phu Tinh A1 - Staat, Manfred T1 - FEM-based shakedown analysis of hardening structures JF - Asia Pacific journal on computational engineering N2 - This paper develops a new finite element method (FEM)-based upper bound algorithm for limit and shakedown analysis of hardening structures by a direct plasticity method. The hardening model is a simple two-surface model of plasticity with a fixed bounding surface. The initial yield surface can translate inside the bounding surface, and it is bounded by one of the two equivalent conditions: (1) it always stays inside the bounding surface or (2) its centre cannot move outside the back-stress surface. The algorithm gives an effective tool to analyze the problems with a very high number of degree of freedom. Our numerical results are very close to the analytical solutions and numerical solutions in literature. Y1 - 2014 U6 - https://doi.org/10.1186/2196-1166-1-4 SN - 2196-1166 (E-Journal) IS - 1 SP - Article No. 4 PB - SpringerOpen CY - Berlin ER -