RSAT: regulatory sequence analysis tools

The regulatory sequence analysis tools (RSAT, http://rsat.ulb.ac.be/rsat/) is a software suite that integrates a wide collection of modular tools for the detection of cis-regulatory elements in genome sequences. The suite includes programs for sequence retrieval, pattern discovery, phylogenetic footprint detection, pattern matching, genome scanning and feature map drawing. Random controls can be performed with random gene selections or by generating random sequences according to a variety of background models (Bernoulli, Markov). Beyond the original word-based pattern-discovery tools (oligo-analysis and dyad-analysis), we recently added a battery of tools for matrix-based detection of cis-acting elements, with some original features (adaptive background models, Markov-chain estimation of P-values) that do not exist in other matrix-based scanning tools. The web server offers an intuitive interface, where each program can be accessed either separately or connected to the other tools. In addition, the tools are now available as web services, enabling their integration in programmatic workflows. Genomes are regularly updated from various genome repositories (NCBI and EnsEMBL) and 682 organisms are currently supported. Since 1998, the tools have been used by several hundreds of researchers from all over the world. Several predictions made with RSAT were validated experimentally and published

Incidence of heat-labile enterotoxin-producing Escherichia coli detected by means of polymerase chain reaction amplification

CITATION: Winterbach, R. et al. 1994. Incidence of heat-labile enterotoxin-producing Escherichia coli detected by means of polymerase chain reaction amplification. South African Medical Journal, 84:85-87.The original publication is available at http://www.samj.org.zaDiarrhoea can be caused by many different organisms, some of which are notoriously difficult to identify. One of these is enterotoxin-producing Escherichia coli. Recently a new diagnostic technique that uses polymerase chain reaction DNA amplification was developed for detection of the 'A' subunit of the labile enterotoxin-producing E. coli gene. This technique was used to evaluate the incidence of heat-labile (LT+) enterotoxin-producing E. coli in the causation of diarrhoea. The results from this study showed that LT+ E. coli is a cause of diarrhoea in the western Cape and that 5,3% of non-diagnosed diarrhoea patients in Tygerberg Hospital were infected with this pathogen. This represented less than 1% of the total number of cases of diarrhoea investigated in this hospital. The peak coincides with the wetter months in this locality and the infection rate is lower than that reported in most other countries. Given the low incidence of occurrence of this organism we do not recommend routine implementation of the diagnostic procedure. However, this test may be useful at times, e.g. to ascertain the source of a diarrhoea epidemic.Publisher’s versio

Cavity ring down spectroscopy on solid C₆₀

The light absorption of a solid sample in the 8.5 μm region is measured via cavity ring down (CRD) absorption spectroscopy, using a free electron laser (FEL) as a source of widely tunable infrared (IR) radiation. A 3 mm thick zinc-selenide (ZnSe) window is used as a substrate for a 20–30 nm thick C60 film. On top of the structureless absorption due to ZnSe (60 is measured with monolayer sensitivity

Genome Biol.

With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to unravel how regulatory information is encoded in the genome

A study of the s-process in the carbon-rich post-AGB stars IRAS06530-0213 and IRAS08143-4406 on the basis of VLT-UVES spectra

In an effort to extend the still limited sample of s-process enriched post-AGB stars, high-resolution, high signal-to-noise VLT+UVES spectra of the optical counterparts of the infrared sources IRAS06530-0213 and IRAS08143-4406 were analysed. The objects are moderately metal deficient by [Fe/H]=-0.5 and -0.4 respectively, carbon-rich and, above all, heavily s-process enhanced with a [ls/Fe] of 1.8 and 1.5 respectively. Especially the spectrum of IRAS06530-0213 is dominated by transitions of s-process species, and therefore resembling the spectrum of IRAS05341+0852, the most s-process enriched object known so far. The two objects are chemically very similar to the 21micron objects discussed in Van Winckel & Reyniers (2000). A homogeneous comparison with the results of these objects reveals that the relation between the third dredge-up efficiency and the neutron nucleosynthesis efficiency found for the 21micron objects, is further strengthened. On the other hand, a detailed comparison with the predictions of the latest AGB models indicates that the observed spread in nucleosynthesis efficiency is certainly intrinsic, and proves that different C-13 pockets are needed for stars with comparable mass and metallicity to explain their abundances.Comment: 14 pages, 10 figures, accepted for publication in A&A; Table 4 is available at ftp://ftp.ster.kuleuven.ac.be/dist/maarten/filescds/ pending upload to CD

Revision of Laparoscopic Adjustable Gastric Banding: Success or Failure?

BACKGROUND: Laparoscopic adjustable gastric banding (LAGB) is a safe and frequently performed bariatric procedure. Unfortunately, re-operations are often necessary. Reports on the success of revisional procedures are scarce and show variable results, either supporting or declining the idea of revising LAGB. This study describes a large cohort of re-operations after failed LAGB to determine the success of revision. METHODS: By use of a prospective cohort, all LAGB revisions performed between 1996 and 2008 were identified. From 301 primary LAGB procedures in our centre, 43 patients (14.3%) required a band revision. In addition, 51 patients were referred from other centres. Our analysis included in total 94 patients with a mean follow-up period of 38 months after revision. RESULTS: Revision was mainly necessary due to anterior slippage (46%) and symmetrical pouch dilatation (36%), which could be resolved by replacing (70%) or refixating the band (27%). Weight loss significantly increased after revision (excess BMI loss (EBMIL), 37.2 +/- 36.3% versus 47.5 +/- 30.4%, P < 0.05). After revision, 23 patients (24%) needed a second re-operation. Patients converted to other procedures (16%) during the second re-operation showed larger weight loss than the revised group (EBMIL, 64.3 +/- 28.1% versus 44.3 +/- 28.7%, P < 0.05). CONCLUSIONS: We report on a large cohort of LAGB revisions with 38 months of follow-up. Revision of failed LAGB by either refixation or replacement of the band is successful and further increases weight loss