A computational approach for genome-wide mapping of splicing factor binding sites

Alternative splicing is regulated by splicing factors that serve as positive or negative effectors, interacting with regulatory elements along exons and introns. Here we present a novel computational method for genome-wide mapping of splicing factor binding sites that considers both the genomic environment and the evolutionary conservation of the regulatory elements. The method was applied to study the regulation of different alternative splicing events, uncovering an interesting network of interactions among splicing factors.     

A sensitive branched DNA HIV-1 signal amplification viral load assay with single day turnaround

Branched DNA (bDNA) is a signal amplification technology used in clinical and research laboratories to quantitatively detect nucleic acids. An overnight incubation is a significant drawback of highly sensitive bDNA assays. The VERSANT® HIV-1 RNA 3.0 Assay (bDNA) (“Versant Assay”) currently used in clinical laboratories was modified to allow shorter target incubation, enabling the viral load assay to be run in a single day. To dramatically reduce the target incubation from 16–18 h to 2.5 h, composition of only the “Lysis Diluent” solution was modified. Nucleic acid probes in the assay were unchanged. Performance of the modified assay (assay in development; not commercially available) was evaluated and compared to the Versant Assay. Dilution series replicates (>950 results) were used to demonstrate that analytical sensitivity, linearity, accuracy, and precision for the shorter modified assay are comparable to the Versant Assay. HIV RNA-positive clinical specimens (n = 135) showed no significant difference in quantification between the modified assay and the Versant Assay. Equivalent relative quantification of samples of eight genotypes was demonstrated for the two assays. Elevated levels of several potentially interfering endogenous substances had no effect on quantification or specificity of the modified assay. The modified assay with drastically improved turnaround time demonstrates the viability of signal-amplifying technology, such as bDNA, as an alternative to the PCR-based assays dominating viral load monitoring in clinical laboratories. Highly sensitive bDNA assays with a single day turnaround may be ideal for laboratories with especially stringent cost, contamination, or reliability requirements.     

Formulation matters! A spectroscopic and molecular dynamics investigation on the peptide CIGB552 as itself and in its therapeutical formulation

Synthetic therapeutic peptides (STP) are intensively studied as new-generation drugs, characterized by high purity, biocompatibility, selectivity and stereochemical control. However, most of the studies are focussed on the bioactivity of STP without considering how the formulation actually used for therapy administration could alter the physico-chemical properties of the active principle. The aggregation properties of a 20-mer STP (Ac-His-Ala-Arg-Ile-Lys-D-Pro-Thr-Phe-Arg-Arg-D-Leu-Lys-Trp-Lys-Tyr-Lys-Gly-Lys-Phe-Trp-NH₂), showing antitumor activity, were investigated by optical spectroscopy and atomic force microscopy imaging, as itself (CIGB552) and in its therapeutic formulation (CIGB552TF). It has found that the therapeutic formulation deeply affects the aggregation properties of the investigated peptide and the morphology of the aggregates formed on mica by deposition of CIGB552 and CIGB552TF millimolar solutions. Molecular dynamics simulations studied the first steps of CIGB552 aggregation under physiological ionic strength conditions (NaCl 150 mM), showing that peptide oligomers, from dimers to tetramers, are preferentially formed in this environment. Interestingly, cell viability assays performed on H-460 cell lines indicate a major antiproliferative activity of the peptide in its therapeutic formulation with respect to the peptide aqueous solution.     

Effect of Food Status on the Gastrointestinal Transit of Amphotericin B-Containing Solid Lipid Nanoparticles in Rats

Amphotericin B (AmB) is poorly absorbed from the gastrointestinal tract. Recent studies have suggested enhanced drug absorption from solid lipid nanoparticles (SLN). Little is known of the fate of AmB absorption within the gastrointestinal tract, and no gastrointestinal transit study has yet been performed on AmB-containing nano-formulations. We aimed to investigate the effect of food on the gastrointestinal transit properties of an AmB-containing SLN in rats. Three SLNs containing AmB, paracetamol, or sulfasalazine were formulated using cocoa butter and beeswax as lipid matrices and simultaneously administered orally to Sprague-Dawley rats. Paracetamol and sulfapyridine were used as marker drugs for estimating gastric emptying and cecal arrival, respectively. The pharmacokinetic data generated for paracetamol and sulfapyridine were used in estimating the absorption of the AmB SLNs in the small and large intestines, respectively. A delayed rate of AmB absorption was observed in the fed state; however, the extent of absorption was not affected by food. Specifically, the percentages of AmB absorption during the fasted state in the stomach, small intestine, and colon were not significantly different from absorption within the respective regions in the fed state. In both states, however, absorption was highest in the colon and appeared to be a combination of absorption from the small intestine plus absorption proper within the colon. The study suggests that AmB SLN, irrespective of food status, is slowly but predominantly taken up by the lymph, making the small intestine the most favorable site for the delivery of the AmB SLNs.     

Mobile Unit for Screening for Cervical and Breast Cancer

In 12 months'' use of a mobile unit for cervical and breast cancer screening in Gloucestershire 3,211 women attended at an average of five sessions a week. Clinic sessions were organized and the running costs of the service met by a voluntary organization. The keeping of records, provision of laboratory facilities, and the follow-up of patients were carried out in close cooperation with the county health department.     

The role played by invasive species in interactions with endangered and threatened species in the United States: a systematic review

Invasive species are considered to be a leading cause of the decline of threatened species. However, this view has been disputed because much of the evidence base is anecdotal. This systematic review, through an extensive, repeatable search using agreed selection criteria, examined the available scientific evidence on invasive species’ interactions with the 1363 endangered and threatened species protected under the United States Endangered Species Act (ESA). The review found scientific evidence available for 116 endangered or threatened species (8.5% of the ESA list). Of these, 85 species (6.2%) were reported as being negatively impacted by invasive species: 39 located on the continental US and 39 on islands, with seven marine species. The relative percentages of species impacted differed according to location: 4.3% (n?=?906) on the continental US, 9.3% (n?=?420) on islands. It was found that predation by invasive vertebrates on birds on islands and competition between invasive plants and endangered or threatened plants on the mainland were the main mechanisms of impact. The results of this study contrast markedly with a previous study which found that 49% of imperilled species in the United States were threatened by invasive species. Further research is essential in order to evaluate the impact of invasive species on imperilled species on the ESA list; this would help to reduce the high degree of uncertainty regarding the threat of invasive species due to the lack of empirical information.     

Contribution to the linkage theory of autopolyploids: I

A theory of linkage of autopolyploids is developed under consideration ofm loci andr alleles. The simplifying assumption of chromosome segregation, which may be considered as an approximation to the more adequate theory of chromatid segregation, is made throughout. Random mating and distinct, non-overlapping generations are assumed. Under these assumptions the problem is determined by three basic probability distributions—the distributions of genotypes and of gametes, and the segregation distribution. The segregation distribution is assumed to be the same for males and for females. The aim of the paper is to establish recurrence formulas (which allow to find the distributions of gametes and of genotypes from generation to generation, if the distribution of genotypes for an initial generation is known) and to investigate the limit behavior of these distributions as the number of generations increases indefinitely. In the present paper (hereafter referred to as I) the problem is explained, and the three characteristic distributions are introduced for the general case of a 2s-ploid,m loci, andr alleles. Recurrence relations are established for tetraploids,s=2 andm=2 loci, while the recurrence relations for the general case as well as the limit theorems will be given in the second part of this paper (hereafter referred to as II).     

Contribution to the linkage theory of autopolyploids: II

In the first part of this paper, hereinafter referred to as I, a general segregation, distribution was introduced for autopolyploids (2s-ploids) withm, loci, andr alleles. Random mating, chromosome segragation, distinct generations, and equal segregation distributions for males and females were assumed. In this second part, using this segregation distribution as a basis, a recurrence formula is established which enables us to compute the distribution of gametes for any generation, if this distribution is known for an initial generation. This initial distribution of gametes is derived from the initial distribution of genotypes. The limit behavior of these distributions is completely described in a general limit theorem which contains as particular cases the limit theorems for diploids withm loci, and for 2s-ploids with one locus (Geiringer, 1944, 1945, 1948).