Modal Codon Usage: Assessing the Typical Codon Usage of a Genome

Most genomes are heterogeneous in codon usage, so a codon usage study should start by defining the codon usage that is typical to the genome. Although this is commonly taken to be the genomewide average, we propose that the mode—the codon usage that matches the most genes—provides a more useful approximation of the typical codon usage of a genome. We provide a method for estimating the modal codon usage, which utilizes a continuous approximation to the number of matching genes and a simplex optimization. In a survey of bacterial and archaeal genomes, as many as 20% more of the genes in a given genome match the modal codon usage than the average codon usage. We use the mode to examine the evolution of the multireplicon genomes of Agrobacterium tumefaciens C58 and Borrelia burgdorferi B31. In A. tumefaciens, the circular and linear chromosomes are characterized by a common “chromosome-like” codon usage, whereas both plasmids share a distinct “plasmid-like” codon usage. In B. burgdorferi, in addition to different codon-usage biases on the leading and lagging strands of DNA replication found by McInerney (McInerney JO. 1998. Replicational and transcriptional selection on codon usage in Borrelia burgdorferi. Proc Natl Acad Sci USA. 95:10698–10703), we also detect a codon-usage similarity between linear plasmid lp38 and the leading strand of the chromosome and a high similarity among the cp32 family of plasmids

A New Bioassay for Auxins and Cytokinins

The authors have developed a sensitive bioassay that can be used to detect auxins as well as cytokinins. The bioassay is based on the expression in transformed tobacco (Nicotiana tabacum) mesophyll protoplasts of a chimeric gene, consisting of the upstream sequences of the Agrobacterium tumefaciens gene 5, coupled to the coding sequence of the β-glucuronidase. The expression of this gene is induced by the presence of both auxin and cytokinin in the culture medium. Using this assay, indole-3-acetic acid was detected at 5 × 10(−8) molar, whereas trans-zeatin could be detected at 5 × 10(−11) molar. The assay can be performed in microtiter plates, allowing numerous samples to be analyzed simultaneously. Only 2.5 × 10(5) protoplasts are required for one individual assay in 250 microliters of culture medium and for qualitative results, the reaction is readily visualized by ultraviolet light

Sequence context of the T-DNA border repeat element determines its relative activity during T-DNA transfer to plant cells

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The long‐term effect and adherence of a low fermentable oligosaccharides disaccharides monosaccharides and polyols (FODMAP) diet in patients with irritable bowel syndrome

Background Short-term trials with a low-FODMAP (fermentable oligosaccharides disaccharides monosaccharides and polyols) diet (LFD) show promising results in the symptomatic management of irritable bowel syndrome (IBS). The present study investigated the long-term adherence to an LFD diet, factors associated with adherence, and associations between LFD and quality of life (QOL), IBS symptoms and disease course on a long-term basis. Methods A retrospective cross-sectional study was conducted. Two hundred and thirty-four patients were enrolled from Ghent University hospital. Health-related QOL, long-term adherence to the LFD, disease course and IBS symptoms were assessed using a validated and self-developed questionnaire. Results Ninety (38.5%) patients completed the questionnaires. The median time span between the first dietary consultation and completion of the questionnaires was 99.5 weeks (approaching 2 years). The predominant disease course was mild IBS with an indolent course (43.0%). Eighty percent reported still following a diet in which certain FODMAP-rich food types are avoided. Eighty patients (88.9%) were satisfied that they follow or had followed the diet. The IBS-QOL did not differ between patients following the diet strictly and patients deviating from the diet (P = 0.669). Patients still following the LFD experienced less severe abdominal pain than patients who stopped following the diet (P = 0.044). Conclusions The long-term adherence and satisfaction with the LFD is high in patients with IBS. Nevertheless, patients indicated that it was difficult to follow the LFD in daily life. Practical issues, social factors and the absence of symptoms were indicated as the main reasons for a drop in adherence