The Poetry of Giacomo da Lentino, Sicilian Poet of the Thirteenth Century

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Meiosis-specific gene discovery in plants: RNA-Seq applied to isolated Arabidopsis male meiocytes

<p>Abstract</p> <p>Background</p> <p>Meiosis is a critical process in the reproduction and life cycle of flowering plants in which homologous chromosomes pair, synapse, recombine and segregate. Understanding meiosis will not only advance our knowledge of the mechanisms of genetic recombination, but also has substantial applications in crop improvement. Despite the tremendous progress in the past decade in other model organisms (e.g., <it>Saccharomyces cerevisiae </it>and <it>Drosophila melanogaster</it>), the global identification of meiotic genes in flowering plants has remained a challenge due to the lack of efficient methods to collect pure meiocytes for analyzing the temporal and spatial gene expression patterns during meiosis, and for the sensitive identification and quantitation of novel genes.</p> <p>Results</p> <p>A high-throughput approach to identify meiosis-specific genes by combining isolated meiocytes, RNA-Seq, bioinformatic and statistical analysis pipelines was developed. By analyzing the studied genes that have a meiosis function, a pipeline for identifying meiosis-specific genes has been defined. More than 1,000 genes that are specifically or preferentially expressed in meiocytes have been identified as candidate meiosis-specific genes. A group of 55 genes that have mitochondrial genome origins and a significant number of transposable element (TE) genes (1,036) were also found to have up-regulated expression levels in meiocytes.</p> <p>Conclusion</p> <p>These findings advance our understanding of meiotic genes, gene expression and regulation, especially the transcript profiles of MGI genes and TE genes, and provide a framework for functional analysis of genes in meiosis.</p

Can a quality improvement project impact maternal and child health outcomes at scale in northern Ghana?

Background Quality improvement (QI) interventions are becoming more common in low- and middle-income countries, yet few studies have presented impact evaluations of these approaches. In this paper, we present an impact evaluation of a scale-up phase of ‘Project Fives Alive!’, a QI intervention in Ghana that aims to improve maternal and child health outcomes. ‘Project Fives Alive!’ employed a QI methodology to recognize barriers to care-seeking and care provision at the facility level and then to identify, test and implement simple and low-cost local solutions that address the barriers. Methods A quasi-experimental design, multivariable interrupted time series analysis, with data coming from 744 health facilities and controlling for potential confounding factors, was used to study the effect of the project. The key independent variables were the change categories (interventions implemented) and implementation phase – Wave 2a (early phase) versus Wave 2b (later phase). The outcomes studied were early antenatal care (ANC), skilled delivery, facility-level under-five mortality and attendance of underweight infants at child welfare clinics. We stratified the analysis by facility type, namely health posts, health centres and hospitals. Results Several of the specific change categories were significantly associated with improved outcomes. For example, three of five change categories (early ANC, four or more ANC visits and skilled delivery/immediate postnatal care (PNC)) for health posts and two of five change categories (health education and triage) for hospitals were associated with increased skilled delivery. These change categories were associated with increases in skilled delivery varying from 28% to 58%. PNC changes for health posts and health centres were associated with greater attendance of underweight infants at child welfare clinics. The triage change category was associated with increased early antenatal care in hospitals. Intensity, the number of change categories tested, was associated with increased skilled delivery in health centres and reduced under-five mortality in hospitals. Conclusions Using an innovative evaluation technique we determined that ‘Project Fives Alive!’ demonstrated impact at scale for the outcomes studied. The QI approach used by this project should be considered by other low- and middle-income countries in their efforts to improve maternal and child health

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Journal of Computer Science &amp; Systems Biology- Open Access www.omicsonline.com Research Article JCSB/Vol.1 2008 Management of High-Throughput DNA Sequencing Projects: Alpheus

Copyright: © 2008 Neil A. Miller et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. High-throughput DNA sequencing has enabled systems biology to begin to address areas in health, agricultural and basic biological research. Concomitant with the opportunities is an absolute necessity to manage significant volumes of high-dimensional and inter-related data and analysis. Alpheus is an analysis pipeline, database and visualization software for use with massively parallel DNA sequencing technologies that feature multigigabase throughput characterized by relatively short reads, such as Illumina-Solexa (sequencing-by-synthesis), Roche-454 (pyrosequencing) and Applied Biosystem’s SOLiD (sequencing-by-ligation). Alpheus enables alignmen