230 research outputs found

    RNA deep sequencing reveals differential MicroRNA expression during development of sea urchin and sea star

    Get PDF
    microRNAs (miRNAs) are small (20-23 nt), non-coding single stranded RNA molecules that act as post-transcriptional regulators of mRNA gene expression. They have been implicated in regulation of developmental processes in diverse organisms. The echinoderms, Strongylocentrotus purpuratus (sea urchin) and Patiria miniata (sea star) are excellent model organisms for studying development with well-characterized transcriptional networks. However, to date, nothing is known about the role of miRNAs during development in these organisms, except that the genes that are involved in the miRNA biogenesis pathway are expressed during their developmental stages. In this paper, we used Illumina Genome Analyzer (Illumina, Inc.) to sequence small RNA libraries in mixed stage population of embryos from one to three days after fertilization of sea urchin and sea star (total of 22,670,000 reads). Analysis of these data revealed the miRNA populations in these two species. We found that 47 and 38 known miRNAs are expressed in sea urchin and sea star, respectively, during early development (32 in common). We also found 13 potentially novel miRNAs in the sea urchin embryonic library. miRNA expression is generally conserved between the two species during development, but 7 miRNAs are highly expressed in only one species. We expect that our two datasets will be a valuable resource for everyone working in the field of developmental biology and the regulatory networks that affect it. The computational pipeline to analyze Illumina reads is available at http://www.benoslab.pitt.edu/services.html. © 2011 Kadri et al

    Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

    Get PDF
    DNA supercoiling is an inherent consequence of twisting DNA and is critical for regulating gene expression and DNA replication. However, DNA supercoiling at a genomic scale in human cells is uncharacterized. To map supercoiling we used biotinylated-trimethylpsoralen as a DNA structure probe to show the genome is organized into supercoiling domains. Domains are formed and remodeled by RNA polymerase and topoisomerase activities and are flanked by GC-AT boundaries and CTCF binding sites. Under-wound domains are transcriptionally active, enriched in topoisomerase I, “open” chromatin fibers and DNaseI sites, but are depleted of topoisomerase II. Furthermore DNA supercoiling impacts on additional levels of chromatin compaction as under-wound domains are cytologically decondensed, topologically constrained, and decompacted by transcription of short RNAs. We suggest that supercoiling domains create a topological environment that facilitates gene activation providing an evolutionary purpose for clustering genes along chromosomes

    Long non-coding RNAs and cancer: a new frontier of translational research?

    Get PDF
    Author manuscriptTiling array and novel sequencing technologies have made available the transcription profile of the entire human genome. However, the extent of transcription and the function of genetic elements that occur outside of protein-coding genes, particularly those involved in disease, are still a matter of debate. In this review, we focus on long non-coding RNAs (lncRNAs) that are involved in cancer. We define lncRNAs and present a cancer-oriented list of lncRNAs, list some tools (for example, public databases) that classify lncRNAs or that scan genome spans of interest to find whether known lncRNAs reside there, and describe some of the functions of lncRNAs and the possible genetic mechanisms that underlie lncRNA expression changes in cancer, as well as current and potential future applications of lncRNA research in the treatment of cancer.RS is supported as a fellow of the TALENTS Programme (7th R&D Framework Programme, Specific Programme: PEOPLE—Marie Curie Actions—COFUND). MIA is supported as a PhD fellow of the FCT (Fundação para a Ciência e Tecnologia), Portugal. GAC is supported as a fellow by The University of Texas MD Anderson Cancer Center Research Trust, as a research scholar by The University of Texas System Regents, and by the Chronic Lymphocytic Leukemia Global Research Foundation. Work in GAC’s laboratory is supported in part by the NIH/ NCI (CA135444); a Department of Defense Breast Cancer Idea Award; Developmental Research Awards from the Breast Cancer, Ovarian Cancer, Brain Cancer, Multiple Myeloma and Leukemia Specialized Programs of Research Excellence (SPORE) grants from the National Institutes of Health; a 2009 Seena Magowitz–Pancreatic Cancer Action Network AACR Pilot Grant; the Laura and John Arnold Foundation and the RGK Foundation

    Healthy Firms: Constraints to Growth among Private Health Sector Facilities in Ghana and Kenya

    Get PDF
    Background: Health outcomes in developing countries continue to lag the developed world, and many countries are not on target to meet the Millennium Development Goals. The private health sector provides much of the care in many developing countries (e.g., approximately 50 percent in Sub-Saharan Africa), but private providers are often poorly integrated into the health system. Efforts to improve health systems performance will need to include the private sector and increase its contributions to national health goals. However, the literature on constraints private health care providers face is limited. Methodology/Principal Findings: We analyze data from a survey of private health facilities in Kenya and Ghana to evaluate growth constraints facing private providers. A significant portion of facilities (Ghana: 62 percent; Kenya: 40 percent) report limited access to finance as the most significant barrier they face; only a small minority of facilities report using formal credit institutions to finance day to day operations (Ghana: 6 percent; Kenya: 11 percent). Other important barriers include corruption, crime, limited demand for goods and services, and poor public infrastructure. Most facilities have paper-based rather than electronic systems for patient records (Ghana: 30 percent; Kenya: 22 percent), accounting (Ghana: 45 percent; Kenya: 27 percent), and inventory control (Ghana: 41 percent; Kenya: 24 percent). A majority of clinics in both countries report undertaking activities to improve provider skills and to monitor the level and quality of care they provide. However, only a minority of pharmacies report undertaking such activities

    The Prevention and Control of HIV/AIDS, TB and Vector-borne Diseases in Informal Settlements: Challenges, Opportunities and Insights

    Get PDF
    Today’s urban settings are redefining the field of public health. The complex dynamics of cities, with their concentration of the poorest and most vulnerable (even within the developed world) pose an urgent challenge to the health community. While retaining fidelity to the core principles of disease prevention and control, major adjustments are needed in the systems and approaches to effectively reach those with the greatest health risks (and the least resilience) within today’s urban environment. This is particularly relevant to infectious disease prevention and control. Controlling and preventing HIV/AIDS, tuberculosis and vector-borne diseases like malaria are among the key global health priorities, particularly in poor urban settings. The challenge in slums and informal settlements is not in identifying which interventions work, but rather in ensuring that informal settlers: (1) are captured in health statistics that define disease epidemiology and (2) are provided opportunities equal to the rest of the population to access proven interventions. Growing international attention to the plight of slum dwellers and informal settlers, embodied by Goal 7 Target 11 of the Millennium Development Goals, and the considerable resources being mobilized by the Global Fund to fight AIDS, TB and malaria, among others, provide an unprecedented potential opportunity for countries to seriously address the structural and intermediate determinants of poor health in these settings. Viewed within the framework of the “social determinants of disease” model, preventing and controlling HIV/AIDS, TB and vector-borne diseases requires broad and integrated interventions that address the underlying causes of inequity that result in poorer health and worse health outcomes for the urban poor. We examine insights into effective approaches to disease control and prevention within poor urban settings under a comprehensive social development agenda

    Econometric analysis to evaluate the effect of community-based health insurance on reducing informal self-care in Burkina Faso

    Get PDF
    Objective This study examines the role of community-based health insurance (CBHI) in influencing health-seeking behaviour in Burkina Faso, West Africa. Community-based health insurance was introduced in Nouna district, Burkina Faso, in 2004 with the goal to improve access to contracted providers based at primary- and secondary-level facilities. The paper specifically examines the effect of CBHI enrolment on reducing the prevalence of seeking modern and traditional methods of self-treatment as the first choice in care among the insured population

    The Prevalence and Regulation of Antisense Transcripts in Schizosaccharomyces pombe

    Get PDF
    A strand-specific transcriptome sequencing strategy, directional ligation sequencing or DeLi-seq, was employed to profile antisense transcriptome of Schizosaccharomyces pombe. Under both normal and heat shock conditions, we found that polyadenylated antisense transcripts are broadly expressed while distinct expression patterns were observed for protein-coding and non-coding loci. Dominant antisense expression is enriched in protein-coding genes involved in meiosis or stress response pathways. Detailed analyses further suggest that antisense transcripts are independently regulated with respect to their sense transcripts, and diverse mechanisms might be potentially involved in the biogenesis and degradation of antisense RNAs. Taken together, antisense transcription may have profound impacts on global gene regulation in S. pombe
    corecore