Annotation of the modular polyketide synthase and nonribosomal peptide synthetase gene clusters in the genome of Streptomyces tsukubaensis NRRL18488

et al.The high G+C content and large genome size make the sequencing and assembly of Streptomyces genomes more difficult than for other bacteria. Many pharmaceutically important natural products are synthesized by modular polyketide synthases (PKSs) and nonribosomal peptide synthetases (NRPSs). The analysis of such gene clusters is difficult if the genome sequence is not of the highest quality, because clusters can be distributed over several contigs, and sequencing errors can introduce apparent frameshifts into the large PKS and NRPS proteins. An additional problem is that the modular nature of the clusters results in the presence of imperfect repeats, which may cause assembly errors. The genome sequence of Streptomyces tsukubaensis NRRL18488 was scanned for potential PKS and NRPS modular clusters. A phylogenetic approach was used to identify multiple contigs belonging to the same cluster. Four PKS clusters and six NRPS clusters were identified. Contigs containing cluster sequences were analyzed in detail by using the ClustScan program, which suggested the order and orientation of the contigs. The sequencing of the appropriate PCR products confirmed the ordering and allowed the correction of apparent frameshifts resulting from sequencing errors. The product chemistry of such correctly assembled clusters could also be predicted. The analysis of one PKS cluster showed that it should produce a bafilomycin-like compound, and reverse transcription (RT)-PCR was used to show that the cluster was transcribed. © 2012, American Society for Microbiology.We thank the Government of Slovenia, Ministry of Higher Education, Science and Technology (Slovenian Research Agency [ARRS]), for the award of grant no. J4-9331 and L4-2188 to H.P. We also thank the Ministry of the Economy, the JAPTI Agency, and the European Social Fund (contract no. 102/2008) for the funds awarded for the employment of G.K. This work was also funded by a cooperation grant of the German Academic Exchange Service (DAAD) and the Ministry of Science, Education, and Sports, Republic of Croatia (to J.C. and D.H.), and by grant 09/5 (to D.H.) from the Croatian Science Foundation.Peer Reviewe

Efficient computation of the outer hull of a discrete path

We present here a linear time and space algorithm for computing the outer hull of any discrete path encoded by its Freeman chain code. The basic data structure uses an enriched version of the data structure introduced by Brlek, Koskas and Provençal: using quadtrees for representing points in the discrete plane ℤ×ℤ with neighborhood links, deciding path intersection is achievable in linear time and space. By combining the well-known wall follower algorithm for traversing mazes, we obtain the desired result with two passes resulting in a global linear time and space algorithm. As a byproduct, the convex hull is obtained as well

Nonspecific motility disorders, irritable esophagus, and chest pain

This paper presents commentaries on whether Starling's law applies to the esophagus; whether erythromycin affects esophageal motility; the relationship between hypertensive lower esophageal sphincter and vigorous achalasia; whether ethnic- and gender-based norms affect diagnosis and treatment of esophageal motor disorders; health care and epidemiology of chest pain; whether normal pH excludes esophageal pain; the role of high-resolution manometry in noncardiac chest pain; whether pH-impedance should be included in the evaluation of noncardiac chest pain; whether there are there alternative therapeutic options to PPI for treating noncardiac chest pain; and the usefulness of psychological treatment and alternative medicine in noncardiac chest pain. \ua9 2013 New York Academy of Sciences

Optically active defects at the Si C/Si O2 interface

The SiC/SiO2 interface is a central component of many SiC electronic devices. Defects intrinsic to this interface can have a profound effect on their operation and reliability. It is therefore crucial to both understand the nature of these defects and develop characterization methods to enable optimized SiC-based devices. Here we make use of confocal microscopy to address single SiC/SiO2-related defects and show the technique to be a noncontact, nondestructive, spatially resolved and rapid means of assessing thequality of the SiC/SiO2 interface. This is achieved by a systematic investigation of the defect density of the SiC/SiO2 interface by varying the parameters of a nitric oxide passivation anneal after oxidation. Standard capacitance-based characterization techniques are used to benchmark optical emission rates and densities of the optically active SiC/SiO2-related defects. Further insight into the nature of these defects is provided by low-temperature optical measurements on single defects.ISSN:2331-701