A common molecular signature of patients with sickle cell disease revealed by microarray meta-analysis and a genome-wide association study

<div><p>A chronic inflammatory state to a large extent explains sickle cell disease (SCD) pathophysiology. Nonetheless, the principal dysregulated factors affecting this major pathway and their mechanisms of action still have to be fully identified and elucidated. Integrating gene expression and genome-wide association study (GWAS) data analysis represents a novel approach to refining the identification of key mediators and functions in complex diseases. Here, we performed gene expression meta-analysis of five independent publicly available microarray datasets related to homozygous SS patients with SCD to identify a consensus SCD transcriptomic profile. The meta-analysis conducted using the MetaDE R package based on combining p values (maxP approach) identified 335 differentially expressed genes (DEGs; 224 upregulated and 111 downregulated). Functional gene set enrichment revealed the importance of several metabolic pathways, of innate immune responses, erythrocyte development, and hemostasis pathways. Advanced analyses of GWAS data generated within the framework of this study by means of the atSNP R package and SIFT tool identified 60 regulatory single-nucleotide polymorphisms (rSNPs) occurring in the promoter of 20 DEGs and a deleterious SNP, affecting CAMKK2 protein function. This novel database of candidate genes, transcription factors, and rSNPs associated with SCD provides new markers that may help to identify new therapeutic targets.</p></div

Designing a course model for distance-based online bioinformatics training in Africa: The H3ABioNet experience

This publication hasn't any creative commons license associated.This deposit is composed by the main article plus the supplementary materials of the publication.This deposit is composed by a publication in which the IGC's authors have had the role of collaboration (it's a collaboration publication). This type of deposit in ARCA is in restrictedAccess (it can't be in open access to the public), and can only be accessed by two ways: either by requesting a legal copy from the author (the email contact present in this deposit) or by visiting the following link: http://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005715#sec022Africa is not unique in its need for basic bioinformatics training for individuals from a diverse range of academic backgrounds. However, particular logistical challenges in Africa, most notably access to bioinformatics expertise and internet stability, must be addressed in order to meet this need on the continent. H3ABioNet (www.h3abionet.org), the Pan African Bioinformatics Network for H3Africa, has therefore developed an innovative, free-of-charge "Introduction to Bioinformatics" course, taking these challenges into account as part of its educational efforts to provide on-site training and develop local expertise inside its network. A multiple-delivery-mode learning model was selected for this 3-month course in order to increase access to (mostly) African, expert bioinformatics trainers. The content of the course was developed to include a range of fundamental bioinformatics topics at the introductory level. For the first iteration of the course (2016), classrooms with a total of 364 enrolled participants were hosted at 20 institutions across 10 African countries. To ensure that classroom success did not depend on stable internet, trainers pre-recorded their lectures, and classrooms downloaded and watched these locally during biweekly contact sessions. The trainers were available via video conferencing to take questions during contact sessions, as well as via online "question and discussion" forums outside of contact session time. This learning model, developed for a resource-limited setting, could easily be adapted to other settings.National Human Genome Research Institute; Office of the Director; National Institutes of Health grant: (U41HG006941).info:eu-repo/semantics/publishedVersio

The Governance of Animal Care and Use for Scientific Purposes in Africa and the Middle East

Animals are commonly used for scientific purposes in Africa and the Middle East. However, this field is often inadequately regulated, with many countries lacking national legislation, policies, or guidelines for the care and use of animals used for research, testing, or education. This results in an essentially uncontrolled system where scientific quality and animal wellbeing cannot robustly be guaranteed, which may hinder acceptance (i.e., publication) of results by the scientific community and limit public confidence. Though accepted international guidelines and best practice recommendations exist that could be adopted or adapted to meet local needs, the responsible conduct of research and animal welfare may not be prioritized in regions that are affected by instability, poverty, disease, or malnutrition. Some notable exceptions do, however, exist in individual countries or institutions where ethical review processes, oversight of animal health and welfare, the competence of personnel, and other scientific standards are appropriately regulated and implemented. These countries and institutions represent nodes of expertise that could act as platforms of support for surrounding regions in terms of the provision of education, training, and sharing of experience and resources. To make such regional capacitystrengthening efforts sustainable will require regional cooperation, the establishment of regional networks, harmonization of policies, pooled resources, and long-term investment in education, training, and infrastructure. An overarching system is needed to oversee the efficient promotion of scientific and ethical standards and the dissemination of information on laboratory animal science in Africa and the Middle East, while each country should remain able to maintain a system of oversight that reflects its own cultures, traditions, religions, laws, and regulations. This article provides an overview of the governance of the care and use of animals for scientific purposes in different regions of Africa and the Middle East as a foundation for coordinated future advancement.</p