Ten Simple Rules for Developing a Short Bioinformatics Training Course

This is an open-access article under the Creative Commonset.-- et al.This paper considers what makes a short course in bioinformatics successful. In today’s research environment, exposure to bioinformatics training is something that anyone embarking on life sciences research is likely to need at some point. Furthermore, as research technologies evolve, this need will continue to grow. In fact, as a consequence of the introduction of high-throughput technologies, there has already been an increase in demand for training relating to the use of computational resources and tools designed for high-throughput data storage, retrieval, and analysis. Biologists and computational scientists alike are seeking postgraduate learning opportunities in various bioinformatics topics that meet the needs and time restrictions of their schedules. Short, intensive bioinformatics courses (typically from a couple of days to a week in length, and covering a variety of topics) are available throughout the world, and more continue to be developed to meet the growing training needs.This work was partly supported by the Intramural Research Program of the NIH, NLM, NCBI, and by funds awarded to the EMBL-European Bioinformatics Institute by the European Commission under SLING, grant agreement number 226073 (Integrating Activity) within Research Infrastructures of the FP7 Capacities Specific Programme EMBL-EBI.Peer reviewe

Open access essentials: how you can go open access with CIAT?

What is Open Access? Are you uncertain as to what it’s all about and what you can you do to enhance access to your research results? This seminar will give you an overview and update of CGIAR and CIAT’s open access policy, legal context, issues and considerations related to open access, progress made in managing different types of data and further opportunities and plans to strengthen open access in CIAT. There will be time for discussion where we look forward to hear your suggestions and experiences related to open access

Widespread environmental contamination with Mycobacterium tuberculosis complex revealed by a molecular detection protocol

Environmental contamination with Mycobacterium tuberculosis complex (MTC) has been considered crucial for bovine tuberculosis persistence in multi-host-pathogen systems. However, MTC contamination has been difficult to detect due to methodological issues. In an attempt to overcome this limitation we developed an improved protocol for the detection of MTC DNA. MTC DNA concentration was estimated by the Most Probable Number (MPN) method. Making use of this protocol we showed that MTC contamination is widespread in different types of environmental samples from the Iberian Peninsula, which supports indirect transmission as a contributing mechanism for the maintenance of bovine tuberculosis in this multi-host-pathogen system. The proportion of MTC DNA positive samples was higher in the bovine tuberculosis-infected than in presumed negative area (0.32 and 0.18, respectively). Detection varied with the type of environmental sample and was more frequent in sediment from dams and less frequent in water also from dams (0.22 and 0.05, respectively). The proportion of MTC-positive samples was significantly higher in spring (p<0.001), but MTC DNA concentration per sample was higher in autumn and lower in summer. The average MTC DNA concentration in positive samples was 0.82 MPN/g (CI95 0.70-0.98 MPN/g). We were further able to amplify a DNA sequence specific of Mycobacterium bovis/caprae in 4 environmental samples from the bTB-infected area

Bilateral asynchronous acute epidural hematoma : a case report

BACKGROUND: Bilateral extradural hematomas have only rarely been reported in the literature. Even rarer are cases where the hematomas develop sequentially, one after removal of the other. Among 187 cases of operated epidural hematomas during past 4 years in our hospital, we found one case of sequentially developed bilateral epidural hematoma. CASE PRESENTATION: An 18-year-old conscious male worker was admitted to our hospital after a fall. After deterioration of his consciousness, an emergency brain CT scan showed a right temporoparietal epidural hematoma. The hematoma was evacuated, but the patient did not improve afterwards. Another CT scan showed contralateral epidural hematoma and the patient was reoperated. Postoperatively, the patient recovered completely. CONCLUSIONS: This case underlines the need for monitoring after an operation for an epidural hematoma and the need for repeat brain CT scans if the patient does not recover quickly after removal of the hematoma, especially if the first CT scan has been done less than 6 hours after the trauma. Intraoperative brain swelling can be considered as a clue for the development of contralateral hematoma

Delegation and coordination with multiple threshold public goods: experimental evidence

When multiple charities, social programs and community projects simultaneously vie for funding, donors risk mis-coordinating their contributions leading to an inefficient distribution of funding across projects. Community chests and other intermediary organizations facilitate coordination among donors and reduce such risks. To study this, we extend a threshold public goods framework to allow donors to contribute through an intermediary rather than directly to the public goods. Through a series of experiments, we show that the presence of an intermediary increases public good success and subjects’ earnings only when the intermediary is formally committed to direct donations to socially beneficial goods. Without such a restriction, the presence of an intermediary has a negative impact, complicating the donation environment, decreasing contributions and public good success.When multiple charities, social programs and community projects simultaneously vie for funding, donors risk mis-coordinating their contributions leading to an inefficient distribution of funding across projects. Community chests and other intermediary organizations facilitate coordination among donors and reduce such risks. To study this, we extend a threshold public goods framework to allow donors to contribute through an intermediary rather than directly to the public goods. Through a series of experiments, we show that the presence of an intermediary increases public good success and subjects’ earnings only when the intermediary is formally committed to direct donations to socially beneficial goods. Without such a restriction, the presence of an intermediary has a negative impact, complicating the donation environment, decreasing contributions and public good success

Fossil Carder Bee's nest from the Hominin locality of Taung, South Africa

The Buxton-Norlim Limeworks southwest of Taung, South Africa, is renowned for the discovery of the first Australopithecus africanus fossil, the ‘Taung Child’. The hominin was recovered from a distinctive pink calcrete that contains an abundance of invertebrate ichnofauna belonging to the Coprinisphaera ichnofacies. Here we describe the first fossil bee’s nest, attributed to the ichnogenus Celliforma, from the Plio-Pleistocene of Africa. Petrographic examination of a cell lining revealed the preservation of an intricate organic matrix lined with the calcitic casts of numerous plant trichomes–a nesting behaviour unique to the modern-day carder bees (Anthidiini). The presence of Celliforma considered alongside several other recorded ichnofossils can be indicative of a dry, savannah environment, in agreement with recent work on the palaeoenvironment of Plio-Pleistocene southern Africa. Moreover, the occurrence of ground-nesting bees provides further evidence that the pink calcrete deposits are of pedogenic origin, rather than speleogenic origin as has previously been assumed. This study demonstrates the potential value of insect trace fossils as palaeoenvironmental indicators

A Crucial Role of Flagellin in the Induction of Airway Mucus Production by Pseudomonas aeruginosa

Pseudomonas aeruginosa is an opportunistic pathogen involved in nosocomial infections. Flagellin is a P. aeruginosa virulence factor involved in host response to this pathogen. We examined the role of flagellin in P. aeruginosa-induced mucus secretion. Using a mouse model of pulmonary infection we showed that PAK, a wild type strain of P. aeruginosa, induced airway mucus secretion and mucin muc5ac expression at higher levels than its flagellin-deficient mutant (ΔFliC). PAK induced expression of MUC5AC and MUC2 in both human airway epithelial NCI-H292 cell line and in primary epithelial cells. In contrast, ΔFliC infection had lower to no effect on MUC5AC and MUC2 expressions. A purified P. aeruginosa flagellin induced MUC5AC expression in parallel to IL-8 secretion in NCI-H292 cells. Accordingly, ΔFliC mutant stimulated IL-8 secretion at significantly lower levels compared to PAK. Incubation of NCI-H292 cells with exogenous IL-8 induced MUC5AC expression and pre-incubation of these cells with an anti-IL-8 antibody abrogated flagellin-mediated MUC5AC expression. Silencing of TLR5 and Naip, siRNA inhibited both flagellin-induced MUC5AC expression and IL-8 secretion. Finally, inhibition of ERK abolished the expression of both PAK- and flagellin-induced MUC5AC. We conclude that: (i) flagellin is crucial in P. aeruginosa-induced mucus hyper-secretion through TLR5 and Naip pathways; (ii) this process is mediated by ERK and amplified by IL-8. Our findings help understand the mechanisms involved in mucus secretion during pulmonary infectious disease induced by P. aeruginosa, such as in cystic fibrosis