Re-purposing Ac/Ds transgenic system for CRISPR/dCas9 modulation of enhancers and non-coding RNAs in zebrafish

Due to its genetic amenability coupled with recent advances in genome editing, the zebrafish serves as an excellent model to examine the function of both coding and non-coding elements. Recently, the non-coding genome has gained prominence due to its critical role in development and disease. Here, we have re-purposed the Ac/Ds maize transposition system to reliably screen and efficiently characterise zebrafish enhancers, with or without germline propagation. We further utilised the system to stably express guide RNAs in microinjected embryos enabling tissue-specific CRISPR/dCas9-interference (CRISPRi) knockdown of lncRNA and enhancer activity without disrupting the underlying genetic sequence. Our study highlights the utility of Ac/Ds transposition for transient epigenome modulation of non-coding elements in zebrafish

Low cost GIS data base solution for water utility network in Sri Lanka

In 1999 National Water Supply and Drainage Board (NWSDB) commenced developing a Water Utility GIS for the Greater Colombo(GC) area with the objective of improving its operations and maintenance activities. National Survey Department of Sri Lanka was contracted out to produce 1:1000 scale 3D digital base maps from Air Photographs. Available water utility maps were digitized using Autocad Map GIS and updated using Global Positioning Systems and other survey methods. Due to voluminous nature of base maps and utility data it is impractical to store them as a one seamless coverage. Storing these data as separate map tiles leads to several practical constraints such as updating difficulties, searching delays and data retrieval problems. Therefore it is required to develop a Geo-database to efficiently manage these data. It is not feasible to utilize available commercial Geo-databases for this purpose due to their high purchasing and maintenance costs. As a solution PostgreSql, a free Open Source Object Relational Database Management System(ORDBMS) was selected. PostgreSql has a module called PostGIS which handles spatial data and is used by hundreds of similar organization around the world. The software successfully runs on Linux Operating System, which also is a freeware. Geo-database was established in PostgreSQL ORDBMS with necessary table structures, relations etc., to store and manage geometric/attribute data of water features including 3D basemap data. A user friendly interface was developed within Autocad Map GIS to handle data uploading and retrievals. All necessary procedures were introduced to the organization for the efficient management of the Geo-database. Further, an Intranet Web Map Browser was developed to browse the data. Currently the system has 18 themes with total objects of around 800,000 and successfully used by all Water Manager Regions in GC area for their day-to-day activities. This implemented solution provides an excellent platform for the NWSDB to do advance geo data management for low cost

Association of endometriosis and p53 gene codon 72 polymorphism in a group of Sri Lankan women

Objectives: To evaluate the association between endometriosis and the p53 gene polymorphism in a group of Sri Lankan women.Methods: A case control study was conducted in a tertiary care hospital where women with endometriosis (N=25) were compared with women without endometriosis (N=25), both confirmed by laparoscopy or laparotomy. Genotype distribution of the p53 codon 72 polymorphism was analyzed by allele specific polymerase chain reaction and direct sequencing. Allele frequency was compared using chi square test to determine the association.Results: Allele frequencies of the three p53 genotypes, Arg/Arg, Arg/Pro and Pro/Pro in the study population (26%, 60% and 14% respectively) conformed with the Hardy-Weinberg equilibrium. There was no statistically significant difference (p = 0.155) in the frequency of proline allele between the cases and controls {odds ratio of 1.5 (95% CI 0.83- 2.73)}. However among the women with endometriosis the proline allele frequency was 36.7% in stage IV and 50% in stage III compared to 25% and 16.7% respectively in stages II and I.Conclusions: In this group of Sri Lankan women, p53 codon 72 polymorphism was not associated with endometriosis although a higher frequency of proline allele was observed in advanced stages of the disease.

Novel role of extracellular matrix protein 1 (ECM1) in cardiac aging and myocardial infarction

© 2019 Hardy 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. Introduction The prevalence of heart failure increases in the aging population and following myocardial infarction (MI), yet the extracellular matrix (ECM) remodeling underpinning the development of aging- and MI-associated cardiac fibrosis remains poorly understood. A link between inflammation and fibrosis in the heart has long been appreciated, but has mechanistically remained undefined. We investigated the expression of a novel protein, extracellular matrix protein 1 (ECM1) in the aging and infarcted heart. Methods Young adult (3-month old) and aging (18-month old) C57BL/6 mice were assessed. Young mice were subjected to left anterior descending artery-ligation to induce MI, or transverse aortic constriction (TAC) surgery to induce pressure-overload cardiomyopathy. Left ventricle (LV) tissue was collected early and late post-MI/TAC. Bone marrow cells (BMCs) were isolated from young healthy mice, and subject to flow cytometry. Human cardiac fibroblast (CFb), myocyte, and coronary artery endothelial & smooth muscle cell lines were cultured; human CFbs were treated with recombinant ECM1. Primary mouse CFbs were cultured and treated with recombinant angiotensin-II or TGF-β1. Immunoblotting, qPCR and mRNA fluorescent in-situ hybridization (mRNA-FISH) were conducted on LV tissue and cells. Results ECM1 expression was upregulated in the aging LV, and in the infarct zone of the LV early post-MI. No significant differences in ECM1 expression were found late post-MI or at any time-point post-TAC. ECM1 was not expressed in any resident cardiac cells, but ECM1 was highly expressed in BMCs, with high ECM1 expression in granulocytes. Flow cytometry of bone marrow revealed ECM1 expression in large granular leucocytes. mRNA-FISH revealed that ECM1 was indeed expressed by inflammatory cells in the infarct zone at day-3 post-MI. ECM1 stimulation of CFbs induced ERK1/2 and AKT activation and collagen-I expression, suggesting a pro-fibrotic role. Conclusions ECM1 expression is increased in ageing and infarcted hearts but is not expressed by resident cardiac cells. Instead it is expressed by bone marrow-derived granulocytes. ECM1 is sufficient to induce cardiac fibroblast stimulation in vitro. Our findings suggest ECM1 is released from infiltrating inflammatory cells, which leads to cardiac fibroblast stimulation and fibrosis in aging and MI. ECM1 may be a novel intermediary between inflammation and fibrosis

A rare variant of the superficial ulnar artery, and its clinical implications: a case report

The superficial ulnar artery is a rare variation of the upper limb arterial system that arises from the brachial or axillary artery and runs superficial to the muscles arising from the medial epicondyle [1-3]. The incidence is about 0.7 to 7% [1,4,5]. In our routine dissections we found a superficial ulnar artery, which crossed the cubital fossa superficial to the bicipital aponeurosis making it highly vulnerable to intra-arterial injection. This is a rare variation that every medical and nursing staff member should know about

From Pioneer to Repressor: Bimodal foxd3 Activity Dynamically Remodels Neural Crest Regulatory Landscape In Vivo

The neural crest (NC) is a transient embryonic stem cell-like population characterized by its multipotency and broad developmental potential. Here, we perform NC-specific transcriptional and epigenomic profiling of foxd3-mutant cells in vivo to define the gene regulatory circuits controlling NC specification. Together with global binding analysis obtained by foxd3 biotin-ChIP and single cell profiles of foxd3-expressing premigratory NC, our analysis shows that, during early steps of NC formation, foxd3 acts globally as a pioneer factor to prime the onset of genes regulating NC specification and migration by re-arranging the chromatin landscape, opening cis-regulatory elements and reshuffling nucleosomes. Strikingly, foxd3 then gradually switches from an activator to its well-described role as a transcriptional repressor and potentially uses differential partners for each role. Taken together, these results demonstrate that foxd3 acts bimodally in the neural crest as a switch from "permissive" to "repressive" nucleosome and chromatin organization to maintain multipotency and define cell fates

Prevalence and risk factors for impaired kidney function in the district of Anuradhapura, Sri Lanka: a cross-sectional population-representative survey in those at risk of chronic kidney disease of unknown aetiology

BACKGROUND: Over the last 20 years there have been reports of a form of chronic kidney disease of unknown cause (CKDu) affecting rural communities in the North Central Province of Sri Lanka. Valid prevalence estimates, using a standardised methodology, are needed to assess the burden of disease, assess secular trends, and perform international comparisons. METHODS: We conducted a cross-sectional representative population survey in five study areas with different expected prevalences of CKDu. We used a proxy definition of CKDu involving a single measure of impaired kidney function (eGFR< 60 mL/min/1.7m2, using the CKD-Epi formula) in the absence of hypertension, diabetes or heavy proteinuria. RESULTS: A total of 4803 participants (88.7%) took part in the study and 202 (6.0%; 95% CI 5.2-6.8) had a low eGFR in the absence of hypertension, diabetes and heavy proteinuria and hence met the criteria for proxy CKDu. The proportion of males (11.2%; 95% CI 9.2-13.1) were triple than the females (3.7%; 95% CI 2.9-4.5). Advancing age and history of CKD among parents or siblings were risk factors for low GFR among both males and females while smoking was found to be a risk factor among males. CONCLUSIONS: These data, collected using a standardised methodology demonstrate a high prevalence of impaired kidney function, not due to known causes of kidney disease, in the selected study areas of the Anuradhapura district of Sri Lanka. The aetiology of CKDu in Sri Lanka remains unclear and there is a need for longitudinal studies to describe the natural history and to better characterise risk factors for the decline in kidney function

Tracking Official Development Assistance for Reproductive Health in Conflict-Affected Countries

Preeti Patel and colleagues report inequity in the disbursement of official development assistance for reproductive health between countries affected by conflict and those unaffected

Influenza vaccine effectiveness against hospitalisation with confirmed influenza in the 2010-11 seasons: a test-negative observational study

Immunisation programs are designed to reduce serious morbidity and mortality from influenza, but most evidence supporting the effectiveness of this intervention has focused on disease in the community or in primary care settings. We aimed to examine the effectiveness of influenza vaccination against hospitalisation with confirmed influenza. We compared influenza vaccination status in patients hospitalised with PCR-confirmed influenza with patients hospitalised with influenza-negative respiratory infections in an Australian sentinel surveillance system. Vaccine effectiveness was estimated from the odds ratio of vaccination in cases and controls. We performed both simple multivariate regression and a stratified analysis based on propensity score of vaccination. Vaccination status was ascertained in 333 of 598 patients with confirmed influenza and 785 of 1384 test-negative patients. Overall estimated crude vaccine effectiveness was 57% (41%, 68%). After adjusting for age, chronic comorbidities and pregnancy status, the estimated vaccine effectiveness was 37% (95% CI: 12%, 55%). In an analysis accounting for a propensity score for vaccination, the estimated vaccine effectiveness was 48.3% (95% CI: 30.0, 61.8%). Influenza vaccination was moderately protective against hospitalisation with influenza in the 2010 and 2011 seasons.Allen C. Cheng, Mark Holmes, Louis B. Irving, Simon G. A. Brown, Grant W. Waterer, Tony M. Korman, N. Deborah Friedman, Sanjaya Senanayake, Dominic E. Dwyer, Stephen Brady, Grahame Simpson, Richard Wood-Baker, John Upham, David Paterson, Christine Jenkins, Peter Wark, Paul M. Kelly, Tom Kotsimbo