Homopolymer tract length dependent enrichments in functional regions of 27 eukaryotes and their novel dependence on the organism DNA (G+C)% composition

BACKGROUND: DNA homopolymer tracts, poly(dA).poly(dT) and poly(dG).poly(dC), are the simplest of simple sequence repeats. Homopolymer tracts have been systematically examined in the coding, intron and flanking regions of a limited number of eukaryotes. As the number of DNA sequences publicly available increases, the representation (over and under) of homopolymer tracts of different lengths in these regions of different genomes can be compared. RESULTS: We carried out a survey of the extent of homopolymer tract over-representation (enrichment) and over-proportional length distribution (above expected length) primarily in the single gene documents, but including some whole chromosomes of 27 eukaryotics across the (G+C)% composition range from 20 – 60%. A total of 5.2 × 10(7 )bases from 15,560 cleaned (redundancy removed) sequence documents were analyzed. Calculated frequencies of non-overlapping long homopolymer tracts were found over-represented in non-coding sequences of eukaryotes. Long poly(dA).poly(dT) tracts demonstrated an exponential increase with tract length compared to predicted frequencies. A novel negative slope was observed for all eukaryotes between their (G+C)% composition and the threshold length N where poly(dA).poly(dT) tracts exhibited over-representation and a corresponding positive slope was observed for poly(dG).poly(dC) tracts. Tract size thresholds where over-representation of tracts in different eukaryotes began to occur was between 4 – 11 bp depending upon the organism (G+C)% composition. The higher the GC%, the lower the threshold N value was for poly(dA).poly(dT) tracts, meaning that the over-representation happens at relatively lower tract length in more GC-rich surrounding sequence. We also observed a novel relationship between the highest over-representations, as well as lengths of homopolymer tracts in excess of their random occurrence expected maximum lengths. CONCLUSIONS: We discuss how our novel tract over-representation observations can be accounted for by a few models. A likely model for poly(dA).poly(dT) tract over-representation involves the known insertion into genomes of DNA synthesized from retroviral mRNAs containing 3' polyA tails. A proposed model that can account for a number of our observed results, concerns the origin of the isochore nature of eukaryotic genomes via a non-equilibrium GC% dependent mutation rate mechanism. Our data also suggest that tract lengthening via slip strand replication is not governed by a simple thermodynamic loop energy model

Spectral tissue sensing to identify intra- and extravascular needle placement - A randomized single-blind controlled trial

Contains fulltext : 175657.pdf (publisher's version ) (Open Access)Safe vascular access is a prerequisite for intravenous drug admission. Discrimination between intra- and extravascular needle position is essential for procedure safety. Spectral tissue sensing (STS), based on optical spectroscopy, can provide tissue information directly from the needle tip. The primary objective of the trial was to investigate if STS can reliably discriminate intra-vascular (venous) from non-vascular punctures. In 20 healthy volunteers, a needle with an STS stylet was inserted, and measurements were performed for two intended locations: the first was subcutaneous, while the second location was randomly selected as either subcutaneous or intravenous. The needle position was assessed using ultrasound (US) and aspiration. The operators who collected the data from the spectral device were blinded to the insertion and ultrasonographic visualization procedure and the physician was blinded to the spectral data. Following offline spectral analysis, a prediction of intravascular or subcutaneous needle placement was made and compared with the "true" needle tip position as indicated by US and aspiration. Data for 19 volunteers were included in the analysis. Six out of 8 intended vascular needle placements were defined as intravascular according to US and aspiration. The remaining two intended vascular needle placements were negative for aspiration. For the other 11 final needle locations, the needle was clearly subcutaneous according to US examination and no blood was aspirated. The Mann-Whitney U test yielded a p-value of 0.012 for the between-group comparison. The differences between extra- and intravascular were in the within-group comparison computed with the Wilcoxon signed-rank test was a p-value of 0.022. In conclusion, STS is a promising method for discriminating between intravascular and extravascular needle placement. The information provided by this method may complement current methods for detecting an intravascular needle position

Barcoding Antarctic biodiversity: current status and the CAML initiative, a case study of marine invertebrates.

The Census of Antarctic Marine Life (CAML) aims to collate DNA barcode data for Antarctic marine species. DNA barcoding is a technique that uses a short gene sequence from a standardised region of the genome as a diagnostic 'biomarker' for species. This study aimed to quantify genetic data currently available in GenBank in order to establish whether a representative cross-section of Antarctic marine taxa and bio-geographic areas has been sequenced and to propose priorities for barcoding, with a particular emphasis on marine invertebrate species. It was found that, amongst marine invertebrate fauna, sequence information covers a limited range of taxa and areas-mainly Crustacea, Annelida and Mollusca from the Weddell Sea and the Antarctic Peninsula. Only 15% of genes sequenced in Antarctic marine invertebrates were the standard barcode gene cytochrome c oxidase subunit 1 (CO1), the majority were other nuclear and mitochondrial genes. There is an urgent need for more in-depth genetic barcoding and species identification studies in Antarctic science, from a range of taxa and areas, given the rate of climate-driven habitat changes that might lead to extinctions in the region. CAML hopes to redress the balance, by collecting and sequencing over the circum-Antarctic area, using material from voyages that occurred during 2008 and 2009, within the framework of the International Polar Year (IPY)