Objective quality evaluation of fluorescence images to optimize automatic image acquisition.

BACKGROUND: Because different spectral sensitivities of human eye and image sensor lead to different perception of fluorescence signals, data generation is an important step in image analysis, because following work steps depend on it. METHODS: We developed a method to determine image parameters allowing an objective appraisal of quality of image data as well as a separation of object and background. RESULTS: Calculated parameters can be used for an automated adjustment of camera parameters in image analysis systems. DISCUSSION: Our approach for objective adjusted data generation achieves an improvement of analysis quality.     

High recurrence of rearrangements involving chromosome 14 in an ataxia telangiectasia lymphoblastoid cell line and in its mutagen-treated derivatives

Summary The cytogenetic characterization of CH cell line obtained by Epstein-Barr-virus transformation of the lymphocytes of a patient affected by ataxia telangiectasia is reported. Control CH cells and 2 subcultures treated with the mutagens R7000 or NQO were developed in parallel and studied. A common chromosome anomaly, a der(14) t(11;14) (q13.2;q32), was found in all the studied karyotypes, indicating that it occurred either in vivo or early in vitro. In non-treated cultures, additional anomalies were present in 6 derived subclones. All R-7000 treated cells had the same karyotype corresponding to one of the subclones observed without prior treatment. All NQO-treated cells acquired 2 common anomalies, and could be differentiated into 2 subclones because of the addition of a t(7;14) or a t(11;14). Chromosome 14 was involved in various rearrangements after breakage in band q11.2 or q12 in 6/8 subclones. This was not correlated with tumorigenicity, which was clearly increased in mutagen-treated cells as tested by in vitro growth in semi-solid medium and in vivo by grafts into nude mice or growth on the chorio-allantoic membrane of chick embryos. The CH cell line and its derivatives appear to be a promising in vitro system, showing various stages progressing towards malignancy, and reproducing a number of chromosome anomalies spontaneously occurring in AT patients.     

Distribution of regional lung aeration and perfusion during conventional and noisy pressure support ventilation in experimental lung injury

In acute lung injury (ALI), pressure support ventilation (PSV) may improve oxygenation compared with pressure-controlled ventilation (PCV), and benefit from random variation of pressure support (noisy PSV). We investigated the effects of PCV, PSV, and noisy PSV on gas exchange as well as the distribution of lung aeration and perfusion in 12 pigs with ALI induced by saline lung lavage in supine position. After injury, animals were mechanically ventilated with PCV, PSV, and noisy PSV for 1 h/mode in random sequence. The driving pressure was set to a mean tidal volume of 6 ml/kg and positive end-expiratory pressure to 8 cmH?O in all modes. Functional variables were measured, and the distribution of lung aeration was determined by static and dynamic computed tomography (CT), whereas the distribution of pulmonary blood flow (PBF) was determined by intravenously administered fluorescent microspheres. PSV and noisy PSV improved oxygenation and reduced venous admixture compared with PCV. Mechanical ventilation with PSV and noisy PSV did not decrease nonaerated areas but led to a redistribution of PBF from dorsal to ventral lung regions and reduced tidal reaeration and hyperinflation compared with PCV. Noisy PSV further improved oxygenation and redistributed PBF from caudal to cranial lung regions compared with conventional PSV. We conclude that assisted ventilation with PSV and noisy PSV improves oxygenation compared with PCV through redistribution of PBF from dependent to nondependent zones without lung recruitment. Random variation of pressure support further redistributes PBF and improves oxygenation compared with conventional PSV.     

Multiplexing clonality: combining RGB marking and genetic barcoding

RGB marking and DNA barcoding are two cutting-edge technologies in the field of clonal cell marking. To combine the virtues of both approaches, we equipped LeGO vectors encoding red, green or blue fluorescent proteins with complex DNA barcodes carrying color-specific signatures. For these vectors, we generated highly complex plasmid libraries that were used for the production of barcoded lentiviral vector particles. In proof-of-principle experiments, we used barcoded vectors for RGB marking of cell lines and primary murine hepatocytes. We applied single-cell polymerase chain reaction to decipher barcode signatures of individual RGB-marked cells expressing defined color hues. This enabled us to prove clonal identity of cells with one and the same RGB color. Also, we made use of barcoded vectors to investigate clonal development of leukemia induced by ectopic oncogene expression in murine hematopoietic cells. In conclusion, by combining RGB marking and DNA barcoding, we have established a novel technique for the unambiguous genetic marking of individual cells in the context of normal regeneration as well as malignant outgrowth. Moreover, the introduction of color-specific signatures in barcodes will facilitate studies on the impact of different variables (e.g. vector type, transgenes, culture conditions) in the context of competitive repopulation studies.     

A novel statistical approach for the evaluation of comet assay data

The present study forms part of a weight-of-evidence framework including genotoxicological studies in the upper Danube River basin, which aim at elucidating the reasons for the decline in fish catch. The major focus of this paper is the assessment of genotoxicity of sediments from the Danube River basin by use of the comet assay with RTL-W1 cells and with embryos of zebrafish (Danio rerio). A frequently discussed question in this type of approach is how to aggregate and compare the data obtained from genotoxicity testing. There is a need to develop mathematical method combining the information from dose-response curves and level of effectiveness (maximum genotoxic effect). For comparison and ranking of the genotoxic potential of samples from different locations along the Danube River, several methods based on EC50, Lowest Observed Effect Concentration (LOEC), and maximum induction factor were compared with respect to their validity. An evaluation system termed the "3-step analysis" was developed to facilitate consideration of a maximum number of aspects of the raw data. The so-called "concentration-dependent induction factor" (CDI) introduces an index for a straightforward, precise and realistic assessment of the genotoxic potential of any kind of field sample or genotoxic agent.     

Molecular recognition of the protein phosphatase 1 glycogen targeting subunit by glycogen phosphorylase

Disrupting the interaction between glycogen phosphorylase and the glycogen targeting subunit (G(L)) of protein phosphatase 1 is emerging as a novel target for the treatment of type 2 diabetes. To elucidate the molecular basis of binding, we have determined the crystal structure of liver phosphorylase bound to a G(L)-derived peptide. The structure reveals the C terminus of G(L) binding in a hydrophobically collapsed conformation to the allosteric regulator-binding site at the phosphorylase dimer interface. G(L) mimics interactions that are otherwise employed by the activator AMP. Functional studies show that G(L) binds tighter than AMP and confirm that the C-terminal Tyr-Tyr motif is the major determinant for G(L) binding potency. Our study validates the G(L)-phosphorylase interface as a novel target for small molecule interaction.     

Solution and solid state conformational preferences of a family of cyclic disulphide bridged tetrapeptides

A set of cyclic tetrapeptides of the general form cyclo (Boc‐Cys‐Pro‐ X ‐Cys‐OMe) with X being L‐ / D‐Ala , L‐ / D‐Val , and L‐ / D‐Trp was synthesized. These peptides serve as model systems for structure elucidation in solution and feature a variety of structural motifs — namely a β‐turn with intramolecular hydrogen bonding interactions, cis/trans isomerism, and a disulphide bond. In this work, we performed a comprehensive structural analysis focussing on their β‐turn conformational preferences using NMR, VCD, and Raman spectroscopy. Our results provide evidence for a strong influence of a single stereocenter on the structures of the peptides whereas solvent polarity does not significantly affect them. Additionally, the solid state conformational preferences were studied by crystal structure analysis. Overall, a general trend for the conformational preferences of this set of peptides can be concluded from the results of the complementary investigations.     

Pectoral girdle movements and the role of the glenohumeral joint during landing in the toad, Rhinella marina (Linnaeus, 1758)

Compared to anurans from other families, landings of toads (Bufonidae) during saltation appear well coordinated and the initial landing impact is absorbed exclusively by the forelimbs. Although the forelimbs and particularly the pectoral girdle have been suggested to be important for shock absorption, the functional roles of its various elements have not been evaluated in detail. This study addresses open questions regarding the kinematics of the forelimbs during landing in Rhinella marina using X-ray reconstruction of moving morphology and scientific rotoscoping. The kinematic analysis clearly showed that in addition to motions in the shoulder and elbow joints, substantial movements of the pectoral girdle in toto as well as of its elements relative to each other do occur during landing. The pectoral girdle showed first and foremost rotations about its latero-lateral axis as well as dorso-ventral translations relative to the spine. Our results quantify the extent of flexion and extension in the suprascapula-scapular synchondrosis during landing. Forelimb kinematics in R. marina differed from that of other anurans in starting elbow extension relatively early during the landing process, which likely prevents the chest from contacting the ground. Furthermore, the animal regains an upright and ready-to-hop-again position quickly and the recovery phase is short compared to other anurans. Humeral kinematics and anatomy confirm that the glenohumeral interlocking mechanism guides the humerus during the initial landing phase. Cranio-ventral ridges on the humeral head and the paraglenoid cartilage interlock in anteverted and slightly retroverted humeral positions. This occurs at the beginning of the landing. When interlocked, adduction/abduction as well as long-axis rotation of the humerus are restricted. During the course of landing, the humerus retroverts and is gradually freed from interlocking restrictions due to a smoother relief at the caudal aspect of the humeral head.