Highly Conserved Non-Coding Sequences Are Associated with Vertebrate Development

In addition to protein coding sequence, the human genome contains a significant amount of regulatory DNA, the identification of which is proving somewhat recalcitrant to both in silico and functional methods. An approach that has been used with some success is comparative sequence analysis, whereby equivalent genomic regions from different organisms are compared in order to identify both similarities and differences. In general, similarities in sequence between highly divergent organisms imply functional constraint. We have used a whole-genome comparison between humans and the pufferfish, Fugu rubripes, to identify nearly 1,400 highly conserved non-coding sequences. Given the evolutionary divergence between these species, it is likely that these sequences are found in, and furthermore are essential to, all vertebrates. Most, and possibly all, of these sequences are located in and around genes that act as developmental regulators. Some of these sequences are over 90% identical across more than 500 bases, being more highly conserved than coding sequence between these two species. Despite this, we cannot find any similar sequences in invertebrate genomes. In order to begin to functionally test this set of sequences, we have used a rapid in vivo assay system using zebrafish embryos that allows tissue-specific enhancer activity to be identified. Functional data is presented for highly conserved non-coding sequences associated with four unrelated developmental regulators (SOX21, PAX6, HLXB9, and SHH), in order to demonstrate the suitability of this screen to a wide range of genes and expression patterns. Of 25 sequence elements tested around these four genes, 23 show significant enhancer activity in one or more tissues. We have identified a set of non-coding sequences that are highly conserved throughout vertebrates. They are found in clusters across the human genome, principally around genes that are implicated in the regulation of development, including many transcription factors. These highly conserved non-coding sequences are likely to form part of the genomic circuitry that uniquely defines vertebrate development

Narrow-band imaging does not improve detection of colorectal polyps when compared to conventional colonoscopy: a randomized controlled trial and meta-analysis of published studies

<p>Abstract</p> <p>Background</p> <p>A colonoscopy may frequently miss polyps and cancers. A number of techniques have emerged to improve visualization and to reduce the rate of adenoma miss.</p> <p>Methods</p> <p>We conducted a randomized controlled trial (RCT) in two clinics of the Gastrointestinal Department of the Sanitas University Foundation in Bogota, Colombia. Eligible adult patients presenting for screening or diagnostic elective colonoscopy were randomlsy allocated to undergo conventional colonoscopy or narrow-band imaging (NBI) during instrument withdrawal by three experienced endoscopists. For the systematic review, studies were identified from the Cochrane Library, PUBMED and LILACS and assessed using the Cochrane risk of bias tool.</p> <p>Results</p> <p>We enrolled a total of 482 patients (62.5% female), with a mean age of 58.33 years (SD 12.91); 241 into the intervention (NBI) colonoscopy and 241 into the conventional colonoscopy group. Most patients presented for diagnostic colonoscopy (75.3%). The overall rate of polyp detection was significantly higher in the conventional group compared to the NBI group (RR 0.75, 95%CI 0.60 to 0.96). However, no significant differences were found in the mean number of polyps (MD -0.1; 95%CI -0.25 to 0.05), and the mean number of adenomas (MD 0.04 95%CI -0.09 to 0.17). Meta-analysis of studies (regardless of indication) did not find any significant differences in the mean number of polyps (5 RCT, 2479 participants; WMD -0.07 95% CI -0.21 to 0.07; I2 68%), the mean number of adenomas (8 RCT, 3517 participants; WMD -0.08 95% CI -0.17; 0.01 to I2 62%) and the rate of patients with at least one adenoma (8 RCT, 3512 participants, RR 0.96 95% CI 0.88 to 1,04;I2 0%).</p> <p>Conclusion</p> <p>NBI does not improve detection of colorectal polyps when compared to conventional colonoscopy (Australian New Zealand Clinical Trials Registry <a href="http://www.anzctr.org.au/ACTRN12610000456055.aspx">ACTRN12610000456055</a>).</p

Effect of Histamine H₂-Receptor Antagonists on Vitamin B₁₂ Absorption

OBJECTIVE: To discuss the potential of histamine H2-receptor antagonists (H2RAs) to cause malabsorption of vitamin B12 (cyanocobalamin). DATA SOURCES: Pertinent literature was identified via a MEDLINE search. Journals and references cited in published articles also were used as data sources. STUDY SELECTION: Studies evaluating the effect of H2RAs on vitamin B12 absorption were reviewed. DATA SYNTHESIS: H2RAs decrease acid secretion by the gastric parietal cells. Gastric acid and pepsin produced by these cells are required for the cleavage of vitamin B12 from dietary sources. Intrinsic factor (IF), also produced by gastric parietal cells, is required for vitamin B12 absorption from the gastrointestinal tract. Although H2RAs have not conclusively been shown to decrease IF secretion, studies have demonstrated a significant reduction in food-bound vitamin B12 absorption secondary to decreased acid secretion in patients taking these drugs. CONCLUSIONS: H2RAs have the potential to cause vitamin B12 deficiency. This may be important in patients with inadequate stores of vitamin B12 (e.g., poor diet), particularly those receiving H2RA therapy continuously for more than two years. Healthcare providers should be aware of this potential adverse effect. </jats:sec

Salivary Concentrations of Ketoconazole and Fluconazole: Implications for Drug Efficacy in Oropharyngeal and Esophageal Candidiasis

Objective: To determine whether salivary concentrations of ketoconazole and fluconazole may explain the apparent disparity between in vitro activity and clinical efficacy observed with these drugs. Design: Healthy subjects received a single oral dose of ketoconazole 400 mg or fluconazole 100 mg in a randomized, crossover fashion. Saliva was collected at 0, 1, 2, 3, 6, 12, and 24 hours. Blood samples were obtained at 2 and 24 hours. Salivary concentrations and plasma concentrations for each drug were determined by HPLC. Minimum inhibitory concentration (MIC) testing was determined in triplicate on 6 clinical isolates of Candida albicans, and times over the median MIC values were calculated. Participants: Eight subjects completed the study. Results: The mean (± SD) peak salivary concentration for ketoconazole was 0.119 ± 0.050 pg/mL at 3 hours; no subject had a detectable ketoconazole salivary concentration at 24 hours. At 2 and 24 hours, mean ketoconazole plasma concentrations were 7.64 ± 3.87 and 0.11 ± 0.05 μg/mL, respectively. The saliva to plasma concentration ratio at 2 hours was 0.01. The mean peak salivary concentration of fluconazole was 2.56 ± 0.34 pg/mL at 3 hours. At 24 hours, the mean salivary concentration was 1.44 ± 0.33 μg/mL. At 2 and 24 hours, mean fluconazole plasma concentrations were 4.39 ± 3.33 and 3.72 ± 2.83 pg/mL, respectively. The saliva to plasma concentration ratio at 2 hours was 0.55. Median MIC values were 0.0625 μg/mL (range 0.0313-0.125) for ketoconazole and 0.25 μg/mL (range 0.125-0.5) for fluconazole. Calculated times over which ketoconazole and fluconazole exceeded the median MICs in saliva were approximately 13 and greater than 24 hours, respectively. Conclusions: After a single oral dose, fluconazole achieved higher salivary concentrations than did ketoconazole. This may explain the increased clinical efficacy of fluconazole in the treatment of oropharyngeal-esophageal candidiasis when compared with ketoconazole. </jats:sec

Loracarbef: A New Orally Administered Carbacephem Antibiotic

OBJECTIVE: To discuss the in vitro activity, pharmacokinetics, clinical efficacy, adverse effects, and relative merits of loracarbef, a new orally administered carbacephem antibiotic. DATA SOURCES: Pertinent literature was identified by a review of selected journals and a MEDLINE search. Additional information was provided by the manufacturer of loracarbef. STUDY SELECTION: All studies that have evaluated the clinical efficacy of loracarbef were included. In vitro studies were included if they used similar methodologies. Additional information was incorporated regarding the chemistry, pharmacokinetics, and adverse effects of loracarbef. DATA SYNTHESIS: Loracarbef has antibacterial activity against most community-acquired respiratory tract, skin and skin structure, and urinary tract pathogens. The drug is well absorbed after oral administration and plasma concentrations achieved in patients are greater than the in vitro minimum inhibitory concentrations for most of the above bacteria. Although the majority of the clinical studies with loracarbef have methodologic deficiencies, loracarbef therapy has demonstrated similar efficacy in the treatment of upper respiratory tract (except otitis media), lower respiratory tract, skin and skin-structure, and urinary tract infections compared with accepted antibiotics. Potential advantages of the new carbacephem may be improved patient compliance with its less frequent dosing schedule (once or twice a day, depending on the infection), and a low incidence of adverse effects. CONCLUSIONS: Preliminary data indicate that loracarbef may be an alternative agent for the treatment of a variety of community-acquired infections. Additional clinical experience and rigorously controlled comparative clinical trials are necessary to enable practitioners to fully define the therapeutic role of loracarbef. </jats:sec