Oct 07

TSS seq based core promoter architecture in blood feeding Tsetse fly…

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TSS seq based core promoter architecture in blood feeding Tsetse fly (Glossina morsitans morsitans) vector of Trypanosomiasis

Background

mwangi_fig1Transcription initiation regulation is mediated by sequence-specific interactions between DNA-binding proteins (transcription factors) and cis-elements, where BRE, TATA, INR, DPE and MTE motifs constitute canonical core motifs for basal transcription initiation of genes. Accurate identification of transcription start site (TSS) and their corresponding promoter regions is critical for delineation of these motifs. To this end, the genome scale analysis of core promoter architecture in insects has been confined to Drosophila. The recently sequenced Tsetse fly genome provides a unique opportunity to analyze transcription initiation regulation machinery in blood-feeding insects.

 

Results

mwangi_fig4A computational method for identification of TSS in newly sequenced Tsetse fly genome was evaluated, using TSS seq tags sampled from two developmental stages namely; larvae and pupae. There were 3134 tag clusters among which 45.4 % (1424) of the tag clusters mapped to first coding exons or their proximal predicted 5′UTR regions and 1.0 % (31) tag clusters mapping to transposons, within a threshold of 100 tags per cluster. These 1393 non transposon-derived core promoters had best online casinos propensity for AT nucleotides. The −1/+1 and 1/+1 positions in D. melanogaster, and G. m. morsitans had propensity for CA and AA dinucleotides respectively. The 1393 tag clusters comprised narrow promoters (5 %), broad with peak promoters (23 %) and broad without peak promoters (72 %). Two-way motif co-occurrence analysis showed that the MTE-DPE pair is over-represented in broad core promoters. The frequently occurring triplet motifs in all promoter classes are the INR-MTE-DPE, TATA-MTE-DPE and TATA-INR-DPE. Promoters without the TATA motif had higher frequency of the MTE and INR motifs than those observed in Drosophila, where the DPE motif occur more frequently in promoters without TATA motif. Gene ontology terms associated with developmental processes were overrepresented in the narrow and broad with peak promoters.

Conclusions

The study has identified different motif combinations associated with broad promoters in a blood-feeding insect. In the case of TATA-less core promoters, G.m. morsitans uses the MTE to compensate for the lack of a TATA motif. The increasing availability of TSS seq data allows for revision of existing gene annotation datasets with the potential of identifying new transcriptional units.

Full paper here.

Aug 24

B3Africa: Bridging Biobanking and Biomedical Research Across Europe and Africa

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Kicking off groundbreaking Africa-EU partnership in biomedical sciences: Foundation of a global research infrastructure for biobanking.

The University of the Western Cape, Cape Town (South Africa) is hosting the first meeting of the newly launched project “B3Africa – Bridging Biobanking and Biomedical Research across Europe and Africa” on 24-25 August 2015. The rapidly evolving African biobanks are invaluable for biomedical research because the African population has the greatest genomic diversity on the planet and represents an incredible resource of information to advance fundamental understanding of health and disease.

“We have no time to lose”, says Alan Christoffels, from the University of the Western Cape and the South African National Bioinformatics Institute. “Connecting bio-resources from Africa and Europe and providing adequate technology will revolutionise how we perform research. The easy-to-use technical solutions will allow the participation of research from different regions regardless the level of development and networking capabilities. It will make possible to include many research institutions as equal partners in the global effort to improve health and wellbeing”.

Eleven partners from African and European countries will jointly develop a collaboration framework and an informatics infrastructure that will accelerate and facilitate biomedical research across the continents to address global health challenges together. Via the Horizon 2020 work programme the European Commission provides a budget of ~ 2 Million Euro over the period of 3 years for the B3Africa initiative that involves a highly motivated group that is ready to get to work.

Biological specimens have been collected for decades, but only since the late 1990s have biobanks been established in a more systematic way. Biobanks collect and store a variety of (mostly human) samples from tissue, cells, blood, saliva, plasma, or DNA. These samples are essential in biomedical research to understand disease mechanisms and develop new therapies. “Access to high quality biological samples is the number one requirement to advance biomedical research. The technology exists”, explains Jan-Eric Litton, one of the initiators of the European Biobanking infrastructure BBMRI-ERIC, “but policymakers will have to learn to view biological samples as key raw material for 21st century medical science.”

B3Africa has two strategic aims:

  1. Create a harmonised ethical and legal framework between European and African partner institutions: A common ethical and legal framework is essential for a trustable informatics platform that will allow sharing bio-resources and data and also consolidate the Africa-EU biobank cooperation.
  2. Provide an “out-of-the-box” informatics solution that facilitates data management, processing and sharing and can also be used under challenging networking conditions in Africa and Europe.

Partners in B3Africa are: Sveriges Lantbruksuniversitet (SLU), Biobanking and Biomolecular Resources Research Infrastructure Consortium (BBMRI-ERIC), Karolinska Institutet (KI), Centre for Research Ethics & Bioethics (CRB) at Uppsala University, University of the Western Cape (UWC), Makerere University (MAK), Stellenbosch University (SU), International Agency for Research on Cancer (IARC), International Live Stock Research Institute (ILRI), Medizinische Universitat Graz (MUG), Institute of Human Virology Nigeria (IHVN).

Aug 20

SANBI hosts colloquium on databases

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On the 20th of August 2015, SANBI hosted a colloquium entitled Store, Query and Analyze @ SANBI (programme here) where six SANBI researchers presented on storing, analysing and presenting data using databases. After an introduction by Peter van Heusden, Hocine Bendou presented on using Django to build a web application to integrate sample data drawn from a number of Biobanks. Lunga Sizani introduced ZODB, the Zope Object database, an object database that allows Python coders to directly store Python objects in persistent storage. After a brief tea break Junaid Gamieldien presented his work on using the Neo4J graph database to store and query a large scale semantic network for biological data.

Mario Jonas took a turn towards sequence oriented data and presented the JBrowse gene browser and its use of JSON and AJAX for highly responsible navigation of gene feature data. Samuel Egieyeh walked us through KNIME  (demo) and DataWarrior as a tools for chemoinformatics. Finally Werner Veldsman presented his work on a JSON database (based on Typicode JSON Server) for exploring and presenting literature associated with particular SNPs.