Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT

<p>Abstract</p> <p>Background</p> <p>Haplotype inference based on unphased SNP markers is an important task in population genetics. Although there are different approaches to the inference of haplotypes in diploid species, the existing software is not suitable for inferring haplotypes from unphased SNP data in polyploid species, such as the cultivated potato (<it>Solanum tuberosum</it>). Potato species are tetraploid and highly heterozygous.</p> <p>Results</p> <p>Here we present the software SATlotyper which is able to handle polyploid and polyallelic data. SATlo-typer uses the Boolean satisfiability problem to formulate Haplotype Inference by Pure Parsimony. The software excludes existing haplotype inferences, thus allowing for calculation of alternative inferences. As it is not known which of the multiple haplotype inferences are best supported by the given unphased data set, we use a bootstrapping procedure that allows for scoring of alternative inferences. Finally, by means of the bootstrapping scores, it is possible to optimise the phased genotypes belonging to a given haplotype inference. The program is evaluated with simulated and experimental SNP data generated for heterozygous tetraploid populations of potato. We show that, instead of taking the first haplotype inference reported by the program, we can significantly improve the quality of the final result by applying additional methods that include scoring of the alternative haplotype inferences and genotype optimisation. For a sub-population of nineteen individuals, the predicted results computed by SATlotyper were directly compared with results obtained by experimental haplotype inference via sequencing of cloned amplicons. Prediction and experiment gave similar results regarding the inferred haplotypes and phased genotypes.</p> <p>Conclusion</p> <p>Our results suggest that Haplotype Inference by Pure Parsimony can be solved efficiently by the SAT approach, even for data sets of unphased SNP from heterozygous polyploids. SATlotyper is freeware and is distributed as a Java JAR file. The software can be downloaded from the webpage of the GABI Primary Database at <url>http://www.gabipd.org/projects/satlotyper/</url>. The application of SATlotyper will provide haplotype information, which can be used in haplotype association mapping studies of polyploid plants.</p

Performance Index

In this Basel-based index of nearly 70 European performance artists, various essays consider the contemporary situation of performance art today, body-performance in the European context, the problem of documenting performances, and the recent interest in the highly-mediated virtual body. Includes artist's statements. Texts are almost entirely in German, only a couple in French. 13 bibl. ref

Gesundheit fördern in vernetzten Strukturen

Kolip P, Gerken U, Schaefer I, Mühlbach A, Gebhardt B. Gesundheit fördern in vernetzten Strukturen. Weinheim: Beltz Juventa; 2013

Enzyme-assisted deacidification of Jatropha crude oil by statistical design of experiments

Jatropha curcas L. crude oil has variable and often high free fatty acid content. As free fatty acids are corrosive, the crude oil has to be refined prior to its utilization in technical applications. Conventional refining processes have several environmental and energetic shortcomings, and there is a clear need for more sustainable pathways. In this study, an enzymatic method was studied for the neutralization of Jatropha oil. Detailed insight into the process was achieved by means of a statistical design of experiments utilizing an immobilized lipase from Rhizomucor miehei. The free fatty acids were esterified with glycerol. The most important impact factors and interactions between factors were identified with regard to acid number reduction and the MAG, DAG, and glycerol content. Validation experiments showed that the models obtained for acid number and, mono- and DAG development were valid and adequate for optimizing the esterification reaction for the desired application. The results generated in this study open the possibility of modifying – within limits – the vegetable oil composition depending on the target application requirements. The acid number of the crude Jatropha oil could be decreased to 0.4 mg KOH per g oil by means of enzymatic esterification. The MAG content can be adjusted between 1.5 and 5.0% (w/w) and DAG content between 15.6 and 27.1% (w/w). The enzyme regeneration procedure that was developed allows multiple use of the enzyme at practically constant activity. Practical applications: Due to the advantages of an enzyme-assisted neutralization procedure, future industrial application of this technology is of great interest. Higher oil yields, no generation of waste water, and the avoidance of aggressive chemicals mean this process has greater sustainability than the conventional approach requiring the addition of strong bases to the oil in order to saponify the free fatty acids. Currently, enzymatic processes tend not to be economically viable due the relatively high cost of the enzymes. However, the costs are likely to decrease in the future as demand for them increases. Additionally, enzyme regeneration, which was carried out successfully in this work, offers the opportunity to further lower the process costs

Risk assessment of manual handling operations at work with the key indicator method (KIM-MHO) — determination of criterion validity regarding the prevalence of musculoskeletal symptoms and clinical conditions within a cross-sectional study

Abstract Background Manual handling operations (MHO) are known to be risk factors for work-related upper limb disorders (WRULDs), e.g. symptoms and conditions such as carpal tunnel syndrome. To estimate the risk of WRULDs, a Key Indicator Method (KIM) for the risk assessment of MHO was developed. The method was validated in regard to different criteria, including face validity, criterion validity, reliability and further aspects concerning utility. This paper describes the KIM-MHO and criterion validity of this method with reference to prevalence of musculoskeletal disorders (MSDs). Methods A cross-sectional sample of 643 employees exposed to MHO was compared to a reference group of 804 unexposed subjects predominantly working at visual display terminals. The Nordic Questionnaire and a standardized clinical examination were used to obtain the 7-day and 12-months prevalence of symptoms and clinical conditions of the musculoskeletal system. Job specific exposure levels to MHO were assessed by ergonomists using the KIM-MHO. The resulting risk scores were categorized into risk categories 1 - low risk (reference group), 2 - increased risk, 3 - highly increased risk, and 4 - high risk. Log-linear Poisson regression models were applied to obtain adjusted prevalence ratios (PR) with 95%-confidence intervals. Results The 7-day prevalence of symptoms for subjects in risk category 3 compared to risk category 1 was significant for the regions shoulder [women (w): PR 1.8 (1.2–2.7), men (m): PR 2.3 (1.2–4.4)], elbow [w: PR 3.3 (1.5–7.2), m: PR 2.4 (0.8–7.3)], and hand/wrist [w: PR 3.0 (1.7–5.3), m: PR 5.5 (2.7–11.3)]. The 7-day prevalence of symptoms for risk category 4 was also significant for the regions shoulder [w: PR 1.9 (1.3–2.8), m: PR 1.9 (1.3–2.7)], elbow [w: PR 4.5 (2.3–8.7), m: PR 3.3 (2.1–5.4)], and hand/wrist [w: PR 4.2 (2.6–6.9), m: PR 5.5 (3.5–8.5)]. The 12-months prevalence in these joint regions show comparable increases in the risk categories 3 and 4. Conclusions The KIM-MHO is valid in regard to criterion validity. The hypothesis could be confirmed, that high risk scores were associated with an increased prevalence of symptoms and clinical conditions especially in the shoulder, elbow and hand/wrist regions among employees exposed to MHO

Evaluation der Förderinitiative "Aktionsbündnisse Gesunde Lebensstile und Lebenswelten" - Instrumentarium und erste Ergebnisse zur Planungsqualität

Gerken U, Schaefer I, Mühlbach A, Morin Elias G, Gebhardt B, Kolip P. Evaluation der Förderinitiative "Aktionsbündnisse Gesunde Lebensstile und Lebenswelten" - Instrumentarium und erste Ergebnisse zur Planungsqualität. Das Gesundheitswesen. 2012;74(2):112-116