ShuffleAnalyzer: A Comprehensive Tool to Visualize DNA Shuffling.

DNA shuffling is a powerful technique for generating synthetic DNA via recombination of homologous parental sequences. Resulting chimeras are often incorporated into complex libraries for functionality screenings that identify novel variants with improved characteristics. To survey shuffling efficiency, subsequences of chimeras can be computationally assigned to their corresponding parental counterpart, yielding insight into frequency of recombination events, diversity of shuffling libraries and actual composition of final variants. Whereas tools for parental assignment exist, they do not provide direct visualization of the results, making the analysis time-consuming and cumbersome. Here we present ShuffleAnalyzer, a comprehensive, user-friendly, Python-based analysis tool that directly generates graphical outputs of parental assignments and is freely available under a BSD-3 license (https://github.com/joerg-swg/ShuffleAnalyzer/releases). Besides DNA shuffling, peptide insertions can be simultaneously analyzed and visualized, which makes ShuffleAnalyzer a highly valuable tool for integrated approaches often used in synthetic biology, such as AAV capsid engineering in gene therapy applications.

Kinetic and Thermodynamic Study of the Thermally Induced (E/Z)-Isomerization of the retro-Carotenoid Rhodoxanthin.

The hitherto scarcely investigated retro-carotenoid rhodoxanthin possesses high potential for coloration in the food and beverage industry using technofunctional formulations prepared thereof. Hence, we studied (E/Z)-isomerization pathways of rhodoxanthin, including seven (E/Z)-isomers comprising (Z)-configured double bonds at unusual exocyclic and inner polyene chain positions. A mathematical approach was developed to deduce kinetic and thermodynamic parameters of six parallel equilibrium reactions interconnecting (all-E)-rhodoxanthin with mono-, di-, and tri-(Z)-isomers using multiresponse modeling. At 40-70 °C in ethyl acetate, reaction rate constants regarding the rotation from (all-E)- to (6Z)-rhodoxanthin were 11-14 times higher than those of the common (E/Z)-isomerization reaction at C-13,14 of the non-retro-structured carotenoid canthaxanthin. Moreover, the equilibrium reaction between (all-E)- and (6Z)-rhodoxanthin was strongly product favored as indicated by negative Gibbs energies (-1.6 to -2.2 kJ mol-1), which is unusual for carotenoids within the studied temperatures. Overall, this study provides novel insights into structure-related dependencies of (E/Z)-isomerization reaction kinetics and thermodynamics of polyenes.

On the classification of prostate carcinoma with methods from spatial statistics.

Gleason grading is a common method used by pathologists to determine the aggressivity of prostate cancer on the basis of histological slide preparations. The advantage of this grading system is a good correlation with the biological behavior of the tumor, while its drawback is the subjectivity underlying the judgements of pathologists. Therefore, an automation of Gleason grading would be desirable. In this paper, we examined 780 digitized grayscale images of 78 different cases, which were split into a training and a test set. We developed two methods based on combinations of morphological characteristics like area fraction, line length, and Euler number to classify into the categories "Gleason score < 7" and "Gleason score > or = 7." In particular, the distinction between these two classes has great impact on the prognosis of patients. The agreement of each method with visual diagnosis was 87.18% and 92.31% within the training set and 66.67% and 64.10% within the test set, respectively.

A framework for diabetes documentation and quality management in Germany: 10 years of experience with DPV.

The DPV approach for quality management and documentation of diabetes in Germany consists of three basic modules: the diabetes documentation software DPV, semi-annual benchmarking for diabetes units (QC-DPV), and a data pool for diabetes research (DPV-SCIENT). The documentation system is available for general practices as well as for hospitals, and it supports the daily routine work of the diabetes team. The system covers a superset for all important data sets of quality initiatives in Germany. Longitudinal analyses of quality indicators related to diabetes are integrated. Twice a year, nation-wide benchmarking for pediatric diabetic units are performed, evaluating the outcome of their diabetes therapy. An improvement in completeness of control examinations could be observed during the last years in QC-DPV. The DPV-SCIENT data pool contains about 251000 single examinations of 21000 patients with diabetes. At least 53% of all patients with Type 1 diabetes in Germany who are less than 20 years of age are documented in DPV-SCIENT.