RegPrecise web services interface: programmatic access to the transcriptional regulatory interactions in bacteria reconstructed by comparative genomics.

Web services application programming interface (API) was developed to provide a programmatic access to the regulatory interactions accumulated in the RegPrecise database (http://regprecise.lbl.gov), a core resource on transcriptional regulation for the microbial domain of the Department of Energy (DOE) Systems Biology Knowledgebase. RegPrecise captures and visualize regulogs, sets of genes controlled by orthologous regulators in several closely related bacterial genomes, that were reconstructed by comparative genomics. The current release of RegPrecise 2.0 includes >1400 regulogs controlled either by protein transcription factors or by conserved ribonucleic acid regulatory motifs in >250 genomes from 24 taxonomic groups of bacteria. The reference regulons accumulated in RegPrecise can serve as a basis for automatic annotation of regulatory interactions in newly sequenced genomes. The developed API provides an efficient access to the RegPrecise data by a comprehensive set of 14 web service resources. The RegPrecise web services API is freely accessible at http://regprecise.lbl.gov/RegPrecise/services.jsp with no login requirements

Accessibility Characteristics of Community Acupuncture Clinics

This study provides a profile of some of the characteristics of 114 Community Acupuncture Network (CAN) clinics as of June, 2011. Characteristics of clinics that affect their accessibility are examined. Most clinics offered a sliding scale fee structure to patients; the lower end of this scale ranged from 10 to 25 dollars and the higher end ranged from 35 to 45 dollars. On average, CAN clinics were open for 31 hours per week but had limited opening hours during hours at the start and end of weekdays and on Sundays. The typical clinic was operated by 1.48 acupuncturists, 69% of whom were women. Clinics typically had 7.6 chairs/recliners and 0.8 treatment tables (but half of all clinics had no tables). Suggestions are made for increasing clinic accessibility that focus on the number of practitioners, opening hours, and clinic configuration.American Association of Acupuncture and Oriental Medicin

Lateral gene transfer and ancient paralogy of operons containing redundant copies of tryptophan-pathway genes in Xylella species and in heterocystous cyanobacteria

BACKGROUND: Tryptophan-pathway genes that exist within an apparent operon-like organization were evaluated as examples of multi-genic genomic regions that contain phylogenetically incongruous genes and coexist with genes outside the operon that are congruous. A seven-gene cluster in Xylella fastidiosa includes genes encoding the two subunits of anthranilate synthase, an aryl-CoA synthetase, and trpR. A second gene block, present in the Anabaena/Nostoc lineage, but not in other cyanobacteria, contains a near-complete tryptophan operon nested within an apparent supraoperon containing other aromatic-pathway genes. RESULTS: The gene block in X. fastidiosa exhibits a sharply delineated low-GC content. This, as well as bias of codon usage and 3:1 dinucleotide analysis, strongly implicates lateral gene transfer (LGT). In contrast, parametric studies and protein tree phylogenies did not support the origination of the Anabaena/Nostoc gene block by LGT. CONCLUSIONS: Judging from the apparent minimal amelioration, the low-GC gene block in X. fastidiosa probably originated by LGT at a relatively recent time. The surprising inability to pinpoint a donor lineage still leaves room for alternative, albeit less likely, explanations other than LGT. On the other hand, the large Anabaena/Nostoc gene block does not seem to have arisen by LGT. We suggest that the contemporary Anabaena/Nostoc array of divergent paralogs represents an ancient ancestral state of paralog divergence, with extensive streamlining by gene loss occurring in the lineage of descent representing other (unicellular) cyanobacteria

Fundamental limits of super-resolution microscopy by dielectric microspheres and microfibers

In recent years, optical super-resolution by microspheres and microfibers emerged as a new paradigm in nanoscale label-free and fluorescence imaging. However, the mechanisms of such imaging are still not completely understood and the resolution values are debated. In this work, the fundamental limits of super-resolution imaging by high-index barium-titanate microspheres and silica microfibers are studied using nanoplasmonic arrays made from Au and Al. A rigorous resolution analysis is developed based on the object's convolution with the point-spread function that has width well below the conventional (∼λ/2) diffraction limit, where λ is the illumination wavelength. A resolution of ∼λ/6-λ/7 is demonstrated for imaging nanoplasmonic arrays by microspheres. Similar resolution was demonstrated for microfibers in the direction perpendicular to the fiber axis with hundreds of times larger field-of-view in comparison to microspheres. Using numerical solution of Maxwell's equations, it is shown that extraordinary close point objects can be resolved in the far field, if they oscillate out of phase. Possible super-resolution using resonant excitation of whispering gallery modes is also studied. Keywords: Optical super-resolution; near-field microscopy; confocal microscop

Complete genome sequence of Kribbella flavida type strain (IFO 14399).

The genus Kribbella consists of 15 species, with Kribbella flavida (Park et al. 1999) as the type species. The name Kribbella was formed from the acronym of the Korea Research Institute of Bioscience and Biotechnology, KRIBB. Strains of the various Kribbella species were originally isolated from soil, potato, alum slate mine, patinas of catacombs or from horse racecourses. Here we describe the features of K. flavida together with the complete genome sequence and annotation. In addition to the 5.3 Mbp genome of Nocardioides sp. JS614, this is only the second completed genome sequence of the family Nocardioidaceae. The 7,579,488 bp long genome with its 7,086 protein-coding and 60 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project