Recombination dynamics of a human Y-chromosomal palindrome:rapid GC-biased gene conversion, multi-kilobase conversion tracts, and rare inversions

The male-specific region of the human Y chromosome (MSY) includes eight large inverted repeats (palindromes) in which arm-to-arm similarity exceeds 99.9%, due to gene conversion activity. Here, we studied one of these palindromes, P6, in order to illuminate the dynamics of the gene conversion process. We genotyped ten paralogous sequence variants (PSVs) within the arms of P6 in 378 Y chromosomes whose evolutionary relationships within the SNP-defined Y phylogeny are known. This allowed the identification of 146 historical gene conversion events involving individual PSVs, occurring at a rate of 2.9-8.4×10(-4) events per generation. A consideration of the nature of nucleotide change and the ancestral state of each PSV showed that the conversion process was significantly biased towards the fixation of G or C nucleotides (GC-biased), and also towards the ancestral state. Determination of haplotypes by long-PCR allowed likely co-conversion of PSVs to be identified, and suggested that conversion tract lengths are large, with a mean of 2068 bp, and a maximum in excess of 9 kb. Despite the frequent formation of recombination intermediates implied by the rapid observed gene conversion activity, resolution via crossover is rare: only three inversions within P6 were detected in the sample. An analysis of chimpanzee and gorilla P6 orthologs showed that the ancestral state bias has existed in all three species, and comparison of human and chimpanzee sequences with the gorilla outgroup confirmed that GC bias of the conversion process has apparently been active in both the human and chimpanzee lineages

Randomised evaluation of the Italian medicines use review provided by community pharmacists using asthma as a model (RE I-MUR)

Background The Italian Ministry of Health decided to introduce community professional services in 2010. This trial provides an opportunity to evaluate the outcomes of a new professional pharmacy service: Italian Medicines Use Review (I-MUR) aimed at reducing the severity of asthma and its associated costs. Methods/Design This is a cluster randomised controlled trial of the I-MUR service. Data will be collected over time before, during and after pharmacists’ intervention. Fifteen Italian regions will be involved and it is aimed to recruit 360 community pharmacists and 1800 patients. Each pharmacist will receive training in medicines use review, recruit five patients, administer the Asthma Control Test and provide the I-MUR service. Pharmacists will be allocated to different groups, one group will be trained in and provide the I-MUR service immediately after completion of the baseline ACT score, the other group will receive training in the I-MUR and provide this service three months later. Group allocation will be random, after stratification by region of Italy. The I-MUR service will involve gathering data following each patient consultation including demographic details, patients regular medications, including those used for asthma, their attitude towards their medications and self-reported adherence to treatments. In addition, pharmacists will identify and record pharmaceutical care issues and any advice given to patients during the I-MUR, or recommendations given to doctors. Pharmacists will upload trial data onto a web platform for analysis. The primary outcome measure is the severity of asthma before, during and after the I-MUR assessed using the Asthma Control Test score. Secondary measures: number of all active ingredients used by patients during and after the I-MUR, number of pharmaceutical care issues identified during the I-MUR, patients’ self-reported adherence to asthma medication during and after the I-MUR, healthcare costs based on the severity of asthma, before, during and after the I-MUR service provision. Discussion This study has been developed because of the need for a new way of working for pharmacists and pharmacies; it is the first trial of any community pharmacy-based pharmaceutical care intervention in Italy. The results will inform future policy and practice in Italian community pharmacy. Trial registration number ISRCTN72438848. Keywords Asthma – Medicines use review – Cluster randomised controlled trial (RCT) – Community pharmac

A cluster randomised control trial to evaluate the effectiveness and cost-effectiveness of the Italian medicines use review (I-MUR) for asthma patients

Background The economic burden of asthma, which relates to the degree of control, is €5 billion annually in Italy. Pharmacists could help improve asthma control, reducing this burden. This study aimed to evaluate the effectiveness and cost-effectiveness of Medicines Use Reviews provided by community pharmacists in asthma. Methods This cluster randomised, multi-centre, controlled trial in adult patients with asthma was conducted in 15 of the 20 regions of Italy between September 2014 and July 2015. After stratification by region, community pharmacists were randomly allocated to group A (trained in and delivered the intervention at baseline) or B (training and delivery 3 months later), using computerised random number generation in blocks of 10. Each recruited up to five patients, with both groups followed for 9 months. The intervention consisted of a systematic, structured face-to-face consultation with a pharmacist, covering asthma symptoms, medicines used, attitude towards medicines and adherence, recording pharmacist-identified pharmaceutical care issues (PCIs). The primary outcome was asthma control, assessed using the Asthma-Control-Test (ACT) score (ACT ≥ 20 represents good control). Secondary outcomes were: number of active ingredients, adherence, cost-effectiveness compared with usual care. Although blinding was not possible for either pharmacists or patients, assessment of outcomes was conducted by researchers blind to group allocation. Results Numbers of pharmacists and patients enrolled were 283 (A = 136; B = 147) and 1263 (A = 600; B = 663), numbers completing were 201 (A = 97; B = 104) and 816 (A = 400; B = 416), respectively. Patients were similar in age and gender and 56.13% (458/816) had poor/partial asthma control. Pharmacists identified 1256 PCIs (mean 1.54/patient), mostly need for education, monitoring and potentially ineffective therapy. Median ACT score at baseline differed between groups (A = 19, B = 18; p < 0.01). Odds ratio for improved asthma control was 1.76 (95% CI 1.33–2.33) and number needed to treat 10 (95% CI 6–28). Number of active ingredients reduced by 7.9% post-intervention (p < 0.01). Adherence improved by 35.4% 3 months post-intervention and 40.0% at 6 months (p < 0.01). The probability of the intervention being more cost-effective than usual care was 100% at 9 months. Conclusions This community pharmacist-based intervention demonstrated both effectiveness and cost-effectiveness. It has since been implemented as the first community pharmacy cognitive service in Italy

Venture capital-backed firms, unavoidable value-destroying trade sales, and fair value protections

This paper investigates the implications of the fair value protections contemplated by the standard corporate contract (i.e., the standard contract form for which corporate law provides) for the entrepreneur–venture capitalist relationship, focusing, in particular, on unavoidable value-destroying trade sales. First, it demonstrates that the typical entrepreneur–venture capitalist contract does institutionalize the venture capitalist’s liquidity needs, allowing, under some circumstances, for counterintuitive instances of contractually-compliant value destruction. Unavoidable value-destroying trade sales are the most tangible example. Next, it argues that fair value protections can prevent the entrepreneur and venture capitalist from allocating the value that these transactions generate as they would want. Then, it shows that the reality of venture capital-backed firms calls for a process of adaptation of the standard corporate contract that has one major step in the deactivation or re-shaping of fair value protections. Finally, it argues that a standard corporate contract aiming to promote social welfare through venture capital should feature flexible fair value protections.info:eu-repo/semantics/publishedVersio

Comprehensive assessment of sequence variation within the copy number variable defensin cluster on 8p23 by target enriched in-depth 454 sequencing

<p>Abstract</p> <p>Background</p> <p>In highly copy number variable (CNV) regions such as the human defensin gene locus, comprehensive assessment of sequence variations is challenging. PCR approaches are practically restricted to tiny fractions, and next-generation sequencing (NGS) approaches of whole individual genomes e.g. by the 1000 Genomes Project is confined by an affordable sequence depth. Combining target enrichment with NGS may represent a feasible approach.</p> <p>Results</p> <p>As a proof of principle, we enriched a ~850 kb section comprising the CNV defensin gene cluster DEFB, the invariable DEFA part and 11 control regions from two genomes by sequence capture and sequenced it by 454 technology. 6,651 differences to the human reference genome were found. Comparison to HapMap genotypes revealed sensitivities and specificities in the range of 94% to 99% for the identification of variations.</p> <p>Using error probabilities for rigorous filtering revealed 2,886 unique single nucleotide variations (SNVs) including 358 putative novel ones. DEFB CN determinations by haplotype ratios were in agreement with alternative methods.</p> <p>Conclusion</p> <p>Although currently labor extensive and having high costs, target enriched NGS provides a powerful tool for the comprehensive assessment of SNVs in highly polymorphic CNV regions of individual genomes. Furthermore, it reveals considerable amounts of putative novel variations and simultaneously allows CN estimation.</p

Genomic deletions of MSH2 and MLH1 in colorectal cancer families detected by a novel mutation detection approach

Hereditary non-polyposis colorectal cancer is an autosomal dominant condition due to germline mutations in DNA-mismatch-repair genes, in particular MLH1, MSH2 and MSH6. Here we describe the application of a novel technique for the detection of genomic deletions in MLH1 and MSH2. This method, called multiplex ligation-dependent probe amplification, is a quantitative multiplex PCR approach to determine the relative copy number of each MLH1 and MSH2 exon. Mutation screening of genes was performed in 126 colorectal cancer families selected on the basis of clinical criteria and in addition, for a subset of families, the presence of microsatellite instability (MSI-high) in tumours. Thirty-eight germline mutations were detected in 37 (29.4%) of these kindreds, 31 of which have a predicted pathogenic effect. Among families with MSI-high tumours 65.7% harboured germline gene defects. Genomic deletions accounted for 54.8% of the pathogenic mutations. A complete deletion of the MLH1 gene was detected in two families. The multiplex ligation-dependent probe amplification approach is a rapid method for the detection of genomic deletions in MLH1 and MSH2. In addition, it reveals alterations that might escape detection using conventional diagnostic techniques. Multiplex ligation-dependent probe amplification might be considered as an early step in the molecular diagnosis of hereditary non-polyposis colorectal cancer