8,858 research outputs found

    The rolling circle amplification and next generation sequencing approaches reveal genome wide diversity of Kenyan cassava mosaic geminivirus

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    Rolling circle amplification is a simple approach of enriching populations of single-stranded DNA plant begomovirus genomes (genus, Begomovirus; family,  Geminiviridae). This is an innovative approach that utilizes the robustness of the bacteriophage phi29 DNA polymerase used in circle amplification, together with deep sequencing using Illumina Miseq and bioinformatics to assess population  diversity of begomoviruses in naturally infected cassava. The approach is suitable for detecting rare members in a population in begomoviral populations in situation where mixtures of isolates, strains, and multiple species occur. The main objectives were to increase the sensitivity of detection of next generation sequencing by enriching it using rolling circle amplification then determination of the diversity of  the cassava mosaic geminivirus. This was done by total nucleic acids isolated from symptomatic, field cassava infected plants, then using rolling circle amplification to multiply the less abundant viral  sequences. Enriched and non-enriched virus-libraries were subjected to deep sequencing using Illumina Miseq. Using  bioinformatic CLC Genomics 5.5.1 software programs the quality assessment of reads and contig assembly of viral sequences. This was done through de novo and reference-guided assembly. The identity and diversities of the begomoviral sequences were compared with sequences in Sanger sequencing of viral components deposited in the NCBI Gene Bank. In this study we have demonstrated that RCA increases the chances of detecting the virus by approximately 10 to 1000 fold and wide genome diversity of cassava mosaic geminivirus in various cassava growing zones in Kenya were detected. In conclusion, this approach described herein is simple and will enhance the exploration of begomovirus diversities from cassava infected plants, irrespective of their viral abundance. This will make it possible for routine screening of field samples as the cost of deep sequencing NGS is decreasing and the advances of bioinformatic software development become enhanced. This is the first report of the RCA-Illumina-NGS approach to explore cassava infected with begomoviruses under field conditions and their diversities. Key words: Illumina Miseq sequencing, geminivirus, ssDNA viruses, viral sequence enrichment, de novo genome assembly, rolling cycle amplification (RCA)

    High yield synthesis of graphene quantum dots from biomass waste as a highly selective probe for Fe3+ sensing

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    Graphene quantum dots (GQDs), a novel type of zero-dimensional fluorescent materials, have gained considerable attention owing to their unique optical properties, size and quantum confinement. However, their high cost and low yield remain open challenges for practical applications. In this work, a low cost, green and renewable biomass resource is utilised for the high yield synthesis of GQDs via microwave treatment. The synthesis approach involves oxidative cutting of short range ordered carbon derived from pyrolysis of biomass waste. The GQDs are successfully synthesised with a high yield of over 84%, the highest value reported to date for biomass derived GQDs. As prepared GQDs are highly hydrophilic and exhibit unique excitation independent photoluminescence emission, attributed to their single-emission fluorescence centre. As prepared GQDs are further modified by simple hydrothermal treatment and exhibit pronounced optical properties with a high quantum yield of 0.23. These modified GQDs are used for the highly selective and sensitive sensing of ferric ions (Fe3+). A sensitive sensor is prepared for the selective detection of Fe3+ ions with a detection limit of as low as 2.5 × 10–6 M. The utilisation of renewable resource along with facile microwave treatment paves the way to sustainable, high yield and cost-effective synthesis of GQDs for practical applications

    Expression of Estrogen Alpha and Beta Receptors in Prostate Cancer and Hyperplasia: Immunohistochemical Analysis

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    Objectives: Estrogen receptors are believed to play a significant role in the pathogenesis of prostate carcinoma (PCa). The aim of this study is to evaluate the expression of ER-α and ER-β in human benign and malignant prostatic tissue.Patients and Methods: The archival materials of 100 prostatic specimens (65 PCa, 35 BPH) were collected from the Department of Pathology, King Abdul-Aziz University Hospital, Jeddah, Saudi Arabia. Seven PCa cases contained foci of high-grade prostate intraepithelial neoplasia (HGPIN). Immunohistochemistry was used to test the protein expression of ER-α and ER-β utilizing monoclonal mouse antihuman antibodies.Results: Among the 65 cases of PCa, ER-α was expressed in 3 cases (4.6%) in epithelial cells and 4 cases (6.1%) in stromal cells. ER-α was not expressed in any of the HGPIN foci. Additionally, ER-α was not expressed in either luminal or basal cells in any of the 35 BPH cases. However it was expressed in 4 cases (11.4%) in stromal cells of BPH. In PCa, ER-β was expressed in 61 cases (93.8%) and 35 cases (53.8%) in the epithelial and stromal cells respectively. ER-β was expressed only in 2 cases (28.5%) out of 7 HGPIN foci. It was expressed in 33 cases (94.3%) of epithelialand stromal cells of BPH. Conclusion: The majority of PCa and BPH exhibited nuclear immunoreactivity for ER-β in both tumor and stromal cells and they are usually negative for ER-α. There is probably partial loss of ER-β in HGPIN. ER-β may have a role in the process of prostatic hyperplasia and malignancy.Key Words: ER-α, ER-β, prostate, hyperplasia, premalignant, cancer,  immunohistochemistr

    Concise synthesis of rare pyrido[1,2-a]pyrimidin-2-ones and related nitrogen-rich bicyclic scaffolds with a ring-junction nitrogen.

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    Pyrido[1,2-a]pyrimidin-2-ones represent a pharmaceutically interesting class of heterocycles. The structurally related pyrido[1,2-a]pyrimidin-4-ones are associated with a broad range of useful biological properties. Furthermore, quinolizinone-type scaffolds of these sorts with a bridgehead nitrogen are expected to display interesting physico-chemical properties. However, pyrido[1,2-a]pyrimidin-2-ones are largely under-represented in current small molecule screening libraries and the physical and biological properties of the pyrido[1,2-a]pyrimidin-2-one scaffold have been poorly explored (indeed, the same can be said for unsaturated bicyclic compounds with a bridgehead nitrogen in general). Herein, we report the development of a new strategy for the concise synthesis of substituted pyrido[1,2-a]pyrimidin-2-ones from readily available starting materials. The synthetic route involved the acylation of the lithium amide bases of 2-aminopyridines with alkynoate esters to form alkynamides, which were then cyclised under thermal conditions. The use of lithium amide anions ensured excellent regioselectivity for the 2-oxo-isomer over the undesired 4-oxo-isomer, which offers a distinct advantage over some existing methods for the synthesis of pyrido[1,2-a]pyrimidin-2-ones. Notably, different aminoazines could also be employed in this approach, which enabled access to several very unusual bicyclic systems with higher nitrogen contents. This methodology thus represents an important contribution towards the synthesis of pyrido[1,2-a]pyrimidin-2-ones and other rare azabicycles with a ring-junction nitrogen. These heterocycles represent attractive structural templates for drug discovery.The research leading to these results has received funding from the European Research Council under the European Union's Seventh Framework Programme (FP7/2007-2013) / ERC grant agreement n° [279337/DOS]. The authors also thank AstraZeneca, the European Union (EU), the Engineering and Physical Sciences Research Council (EPSRC), the Biotechnology and Biological Sciences Research Council (BBSRC), the Medical Research Council (MRC), and the Wellcome Trust for funding. Data accessibility: all data supporting this study are provided as Supplementary Information accompanying this paper.This is the final version of the article. It was first available from Royal Society of Chemistry via http://dx.doi.org/10.1039/c5ob01784

    Utilization of services provided by village based ethnic minority midwives in mountainous villages of Vietnam

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    Introduction: Since 2011, the Vietnam’s Ministry of Health implemented the ethnic minority midwives (EMMs) scheme in order to increase the utilization of maternal health services by women from ethnic minorities and those living in hard-to-reach mountainous areas. This paper analyzes the utilization of antenatal, delivery, and postpartum care provided by EMMs and reports the key determinants of utilization of EMM services as perceived by service users. Methods: A structured questionnaire was administered in 2015 to all mothers (n=320) who gave birth to a live-born during a 1-year period in 31 villages which had EMM in two provinces, Dien Bien and Kon Tum. A multivariate logistic regression model was used to examine the association between all potential factors and the use of services provided by EMMs. Results: We found that EMMs provided more antenatal care and postnatal care as compared with delivery services, which corresponded to their job descriptions. The results also showed that utilization of antenatal care provided by EMMs was lower than that of postnatal care. The proportion of those who never heard about EMM was high (24%). Among the mothers who knew about EMM services, 33.4% had antenatal checkups, 20.1% were attended during home deliveries, and 57.3% had postnatal visits by an EMM. Key factors that determined the use of EMM services included knowledge of the location of EMM’s house, being aware about EMMs by health workers, trust in services provided by EMMs, and perception that many others mothers in a village also knew about EMM services. Conclusion: EMM seems to be an important mechanism to ensure assistance during home births and postnatal care for ethnic minority groups, who are often resistant to attend health facilities. Building trust and engaging with communities are the key facilitators to increase the utilization of services provided by EMMs. Communication campaigns to raise awareness about EMMs and to promote their services in the village, particularly by other health workers, represent an important strategy to further improve effectiveness of EMM scheme

    Psychometrics of new scales of parenting practices to encourage or discourage Hispanic preschool children's physical activity

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    Conference Theme: Promoting Healthy Eating and activity worldwidePoster - Personal and environmental determinants of physical activity in children and adolescents: abstract P077PURPOSE: Develop and assess the psychometrics of a new instrument for parenting practices (PP) that encourage or discourage physical activity (PA) in Hispanic preschool children. METHOD: Cross--‐sectional study of 240 Hispanic parents who reported their demographics and frequency of using PP that encourage (structure and encouragement) or discourage (promoting inactivity, psychological control, safety …postprin

    The impact of gender on difficulty of classical open cholecystectomy

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    Background: Cholecystectomy demands attention, and expectation of abnormal anatomy in the veins, arteries or ducts. Prediction of difficult cholecystectomy does not only helpin patient counseling but also helps the surgeon to prepare better for the technical difficulties that may be encountered1-3.The aim: To find out whether there is impact of gender on the difficulty of surgery during open cholecystectomy.Patients and methods: This is a prospective hospital based study. Patients who presented to Ibn Sina Hospital for open cholecystectomy during the period from April 2011 to April 2012 were included in this study. Special emphasis was put on gender, the operative time, difficulty of surgeryand complications of open cholecystectomy. A pre-tested questionnaire was filled during interview of patients and operating surgeons.Results: A total 327 operations were included in the study. Of them there were 34(64.2%) males and 99(36.1%) females presented early i.e. after the first diagnosis was made. The mean operative time was 44.6 min for males and 43.57 min for females. Difficult surgery was described in 6(11.3%) of male and 23(8.4%) females.Conclusion: There was no significant statistical difference in the operative time, difficulty of operation and complication rate between males and females.Key words: Open cholecystectomy, difficulty, gender

    A recent whole-genome duplication divides populations of a globally-distributed microsporidian

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    This is the final version of the article. Available from Oxford University Press via the DOI in this record.The Microsporidia are a major group of intracellular fungi and important parasites of animals including insects, fish, and immunocompromised humans. Microsporidian genomes have undergone extreme reductive evolution but there are major differences in genome size and structure within the group: some are prokaryote-like in size and organisation (<3 Mb of gene-dense sequence) whilst others have more typically eukaryotic genome architectures. To gain fine-scale, population-level insight into the evolutionary dynamics of these tiny eukaryotic genomes, we performed the broadest microsporidian population genomic study to date, sequencing geographically isolated strains of Spraguea, a marine microsporidian infecting goosefish worldwide. Our analysis revealed that population structure across the Atlantic Ocean is associated with a conserved difference in ploidy, with American and Canadian isolates sharing an ancestral whole genome duplication that was followed by widespread pseudogenisation and sorting-out of paralogue pairs. Whilst past analyses have suggested de novo gene formation of microsporidian-specific genes, we found evidence for the origin of new genes from noncoding sequence since the divergence of these populations. Some of these genes experience selective constraint, suggesting the evolution of new functions and local host adaptation. Combining our data with published microsporidian genomes, we show that nucleotide composition across the phylum is shaped by a mutational bias favouring A and T nucleotides, which is opposed by an evolutionary force favouring an increase in genomic GC content. This work reveals ongoing dramatic reorganisation of genome structure and the evolution of new gene functions in modern microsporidians despite extensive genomic streamlining in their common ancestor.The authors would like to thank John Brookfield and David Studholme for helpful discussions. This work was supported by a Marie Curie Intra-European postdoctoral fellowship (T.A.W.) and the European Research Council Advanced Investigator Programme and the Wellcome Trust (grant numbers ERC- 2010- AdG-268701 045404 to T.M.E.) It is also supported by a Royal Society University Research Fellowship (B.A.P.W.)

    RI4 AN ECONOMIC ANALYSIS OF RAPID TESTS AND ANTIVIRAL TREATMENTS FOR INFLUENZA IN CHILDREN

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