Towards the understanding of the cocoa transcriptome: Production and analysis of an exhaustive dataset of ESTs of Theobroma cacao L. generated from various tissues and under various conditions

Theobroma cacao L., is a tree originated from the tropical rainforest of South America. It is one of the major cash crops for many tropical countries. T. cacao is mainly produced on smallholdings, providing resources for 14 million farmers. Disease resistance and T. cacao quality improvement are two important challenges for all actors of cocoa and chocolate production. T. cacao is seriously affected by pests and fungal diseases, responsible for more than 40% yield losses and quality improvement, nutritional and organoleptic, is also important for consumers. An international collaboration was formed to develop an EST genomic resource database for cacao. Fifty-six cDNA libraries were constructed from different organs, different genotypes and different environmental conditions. A total of 149,650 valid EST sequences were generated corresponding to 48,594 unigenes, 12,692 contigs and 35,902 singletons. A total of 29,849 unigenes shared significant homology with public sequences from other species. Gene Ontology (GO) annotation was applied to distribute the ESTs among the main GO categories. A specific information system (ESTtik) was constructed to process, store and manage this EST collection allowing the user to query a database. To check the representativeness of our EST collection, we looked for the genes known to be involved in two different metabolic pathways extensively studied in other plant species and important for T. cacao qualities: the flavonoid and the terpene pathways. Most of the enzymes described in other crops for these two metabolic pathways were found in our EST collection. A large collection of new genetic markers was provided by this ESTs collection. This EST collection displays a good representation of the T. cacao transcriptome, suitable for analysis of biochemical pathways based on oligonucleotide microarrays derived from these ESTs. It will provide numerous genetic markers that will allow the construction of a high density gene map of T. cacao. This EST collection represents a unique and important molecular resource for T. cacao study and improvement, facilitating the discovery of candidate genes for important T. cacao trait variation. (Résumé d'auteur

A multi-stakeholder strategy to identify conservation priorities in Peninsular Malaysia

Malaysia, with its rapidly growing economy, exemplifies the tensions between conservation and development faced by many tropical nations. Here we present the results of a multi-stakeholder engagement exercise conducted to (1) define conservation priorities in Peninsular Malaysia and (2) explore differences in perceptions among and within stakeholder groups (i.e. government, academia, NGOs and the private sector). Our data collection involved two workshops and two online surveys where participants identified seven general conservation themes and ranked the top five priority issues within each theme. The themes were: (1) policy and management, (2) legislation and enforcement, (3) finance and resource allocation, (4) knowledge, research and development, (5) socio-economic issues, (6) public awareness and participation and (7) rights of nature. In spite of their very different backgrounds and agendas, the four stakeholder groups showed general agreement in their priority preferences except for two issues. Respondents from government and private sector differed the most from each other in their priority choices while academia and NGO showed the highest degree of similarity. This ranked list of 35 conservation priorities is expected to influence the work of policy-makers and others in Peninsular Malaysia and can be used as a model to identify conservation priorities elsewhere

Hyperglycaemia lowering activity and hypoglycaemic risk assessment of Sarenta, an Ivorian traditional herbal remedy

Background: Diabetes remains a major public health problem for which traditional medicine is a better therapeutic alternative for low-income populations, including African populations. The aim of this work was to evaluate the effect of Sarenta, an herbal preparation used in Ivorian traditional medicine as anti-diabetic, on hyperglycaemia and on basic glycaemia.Methods: Hyperglycaemia lowering activity was led in rats receiving glucose at 5 g/kg body weight by gavage after oral pre-treatment with either Sarenta at 125, 206 or 209.5 mg/kg b. wt., either glibenclamide at 10 mg/kg b. wt., or physiological saline solution. Hypoglycaemic risk was assessed by administering the same doses of Sarenta to native i.e. NaCl-treated rats. For both tests, blood glucose was measured before any substance was administered and then every hour for 4 hours.Results: After 4 hours, Sarenta at 206 mg/kg b. wt. and 209.5 mg/kg b. wt. significantly reduced the induced hyperglycaemia in rats by 33.87% and 37.39%, respectively. The degree of the hyperglycaemia lowering effect of the remedy at these two doses was not significantly different from that of glibenclamide. In addition, Sarenta at 209.5 mg/kg b. wt. resulted in a significant reduction of basic blood sugar to 29.78% four hours after administration.Conclusions: The remedy Sarenta has a hyperglycaemia lowering activity that could partially justify its traditional use in the treatment of diabetes. However, considering its hypoglycemic effect, precautions should be taken when using this traditional medicine

The Culicoides species (Diptera : Ceratopogonidae) of Senegal: towards identifying the vectors of African horse sickness virus, 40 years after the first studies

African Horse Sickness (AHS) has been described for the first time in Senegal in the 1880s. Since then, it is an endemic disease, with occasional epizootic outbreaks, which caused significant economic losses. The last outbreak occurred in 2007 and caused the death of 1,169 horses in several regions, with a total cost estimated at 900 million CFA, of which the half was due to mortality and morbidity. Today, the unique available control strategy for AHS virus is mass vaccination. The vector species responsible for AHS virus transmission belong to the genus Culicoides. In Senegal, studies on the fauna of Culicoides have been conducted four decades ago and failed to highlight the species of veterinary interest involved in the virus transmission. If Culicoides imicola is historically recognized as the main Afrotropical vector species, its role in the transmission has never been established in Senegal. Under the framework of the EDENext project (European FP7 project), several studies were initiated in 2011 to update the Culicoides diversity of Senegal and to allow a better understanding of the species role in the transmission of AHS virus. The Culicoides population dynamics was followed up monthly for one year, using OVI traps and horse-baited traps in five sites along a transect Dakar-Thies, in western Senegal. Captured individuals were identified morphologically at the species level, or with molecular identification tools for the C. schultzei group. The data obtained in this survey were then confronted with the reported incidences of the 2007 AHS outbreaks. This preliminary work allows updating the list of Culicoides of Senegal, helps clarifying the species delimitation for the C. schultzei group and contributes to identify potential vector species of African horse sickness virus in Senegal. It also allows choosing the candidate vectors to rear in the insectarium to unable vector competence studies. (Texte intégral

A first step in the understanding of the cocoa transcriptome: Analysis of an exhaustive dataset of ESTs on Theobroma cacao generated from various tissues and under various conditions

To better understand the cocoa transcriptome and to provide a framework for future investigations on cocoa functional genomics, approximately 175 000 cocoa clones from 52 cDNA libraries were sequenced. These libraries were constructed with RNA isolated from 13 genotypes (mainly from the two genotypes Scavina6 and ISC1) and from various tissues and organs (flowers, seeds, cherels, pod, shoot, root or embryos) under various conditions (fermentation, abiotic and biotic stresses). Suppression subtractive hybridisation (SSH) libraries were also produced under various plant pathogen interactions and from flowers pollinated by self compatible or incompatible pollen. From these cDNA libraries, 149 650 good quality ESTs were generated and analyzed using our "in house" bioinformatics pipeline. The assembly process produced 13837 contigs and 66746 singletons that represent 80583 different potential transcripts. These unigenes were assigned with BLASTX and BLASTN similarities, Gene Ontology annotation and protein domains. A comparison with public ESTs cocoa sequences already already available in public domain indicates that 80% of the unigenes may not have been described in public databases. (Texte intégral

On the Reconstruction of Palaeo-Ice Sheets: Recent Advances and Future Challenges

Reconstructing the growth and decay of palaeo-ice sheets is critical to understanding mechanisms of global climate change and associated sea-level fluctuations in the past, present and future. The significance of palaeo-ice sheets is further underlined by the broad range of disciplines concerned with reconstructing their behaviour, many of which have undergone a rapid expansion since the 1980s. In particular, there has been a major increase in the size and qualitative diversity of empirical data used to reconstruct and date ice sheets, and major improvements in our ability to simulate their dynamics in numerical ice sheet models. These developments have made it increasingly necessary to forge interdisciplinary links between sub-disciplines and to link numerical modelling with observations and dating of proxy records. The aim of this paper is to evaluate recent developments in the methods used to reconstruct ice sheets and outline some key challenges that remain, with an emphasis on how future work might integrate terrestrial and marine evidence together with numerical modelling. Our focus is on pan-ice sheet reconstructions of the last deglaciation, but regional case studies are used to illustrate methodological achievements, challenges and opportunities. Whilst various disciplines have made important progress in our understanding of ice-sheet dynamics, it is clear that data-model integration remains under-used, and that uncertainties remain poorly quantified in both empirically-based and numerical ice-sheet reconstructions. The representation of past climate will continue to be the largest source of uncertainty for numerical modelling. As such, palaeo-observations are critical to constrain and validate modelling. State-of-the-art numerical models will continue to improve both in model resolution and in the breadth of inclusion of relevant processes, thereby enabling more accurate and more direct comparison with the increasing range of palaeo-observations. Thus, the capability is developing to use all relevant palaeo-records to more strongly constrain deglacial (and to a lesser extent pre-LGM) ice sheet evolution. In working towards that goal, the accurate representation of uncertainties is required for both constraint data and model outputs. Close cooperation between modelling and data-gathering communities is essential to ensure this capability is realised and continues to progress

Evaluation of RTS,S/AS02A and RTS,S/AS01B in Adults in a High Malaria Transmission Area

This study advances the clinical development of the RTS,S/AS01B candidate malaria vaccine to malaria endemic populations. As a primary objective it compares the safety and reactogenicity of RTS,S/AS01B to the more extensively evaluated RTS,S/AS02A vaccine.A Phase IIb, single centre, double-blind, controlled trial of 6 months duration with a subsequent 6 month single-blind follow-up conducted in Kisumu West District, Kenya between August 2005 and August 2006. 255 healthy adults aged 18 to 35 years were randomized (1ratio1ratio1) to receive 3 doses of RTS,S/AS02A, RTS,S/AS01B or rabies vaccine (Rabipur; Chiron Behring GmbH) at months 0, 1, 2. The primary objective was the occurrence of severe (grade 3) solicited or unsolicited general (i.e. systemic) adverse events (AEs) during 7 days follow up after each vaccination.Both candidate vaccines had a good safety profile and were well tolerated. One grade 3 systemic AE occurred within 7 days of vaccination (RTS,S/AS01B group). No unsolicited AEs or SAEs were related to vaccine. A marked increase in anti-CS antibody GMTs was observed post Dose 2 of both RTS,S/AS01B (31.6 EU/mL [95% CI: 23.9 to 41.6]) and RTS,S/AS02A (16.7 EU/mL [95% CI: 12.9 to 21.7]). A further increase was observed post Dose 3 in both the RTS,S/AS01B (41.4 EU/mL [95% CI: 31.7 to 54.2]) and RTS,S/AS02A (21.4 EU/mL [95% CI: 16.0 to 28.7]) groups. Anti-CS antibody GMTs were significantly greater with RTS,S/AS01B compared to RTS,S/AS02A at all time points post Dose 2 and Dose 3. Both candidate vaccines produced strong anti-HBs responses. Vaccine efficacy in the RTS,S/AS01B group was 29.5% (95% CI: -15.4 to 56.9, p = 0.164) and in the RTS,S/AS02A group 31.7% (95% CI: -11.6 to 58.2, p = 0.128).Both candidate malaria vaccines were well tolerated over a 12 month surveillance period. A more favorable immunogenicity profile was observed with RTS,S/AS01B than with RTS,S/AS02A.Clinicaltrials.gov NCT00197054

Antioxidant and Antiradical Activities of Manihot esculenta Crantz (Euphorbiaceae) Leaves and Other Selected Tropical Green Vegetables Investigated on Lipoperoxidation and Phorbol-12-myristate-13-acetate (PMA) Activated Monocytes

Abelmoschus esculentus (Malvaceae), Hibiscus acetosella (Malvaceae), Manihot esculenta Crantz (Euphorbiaceae) and Pteridium aquilinum (Dennstaedtiaceae) leaves are currently consumed as vegetables by migrants from sub-Saharan Africa living in Western Europe and by the people in the origin countries, where these plants are also used in the folk medicine. Manihot leaves are also eaten in Latin America and some Asian countries. This work investigated the capacity of aqueous extracts prepared from those vegetables to inhibit the peroxidation of a linoleic acid emulsion. Short chain, volatile C-compounds as markers of advanced lipid peroxidation were measured by gas chromatography by following the ethylene production. The generation of lipid hydroperoxides, was monitored by spectroscopy using N-N′-dimethyl-p-phenylene-diamine (DMPD). The formation of intermediate peroxyl, and other free radicals, at the initiation of the lipid peroxidation was investigated by electron spin resonance, using α-(4-pyridyl-1-oxide)-N-tert-butylnitrone as spin trap agent. The ability of the extracts to decrease the cellular production of reactive oxygen species (ROS) in “inflammation like” conditions was studied by fluorescence technique using 2′,7′-dichlorofluorescine-diacetate as fluorogenic probe, in a cell model of human monocytes (HL-60 cells) activated with phorbol ester. Overall the extracts displayed efficient concentration-dependent inhibitory effects. Their total polyphenol and flavonoid content was determined by classic colorimetric methods. An HPLC-UV/DAD analysis has clearly identified the presence of some polyphenolic compounds, which explains at least partially the inhibitions observed in our models. The role of these plants in the folk medicine by sub-Saharan peoples as well as in the prevention of oxidative stress and ROS related diseases requires further consideration

Risk Factors and Immunity in a Nationally Representative Population following the 2009 Influenza A(H1N1) Pandemic

Understanding immunity, incidence and risk factors of the 2009 influenza A(H1N1) pandemic (2009 H1N1) through a national seroprevalence study is necessary for informing public health interventions and disease modelling.We collected 1687 serum samples and individual risk factor data between November-2009 to March-2010, three months after the end of the 2009 H1N1 wave in New Zealand. Participants were randomly sampled from selected general practices countrywide and hospitals in the Auckland region. Baseline immunity was measured from 521 sera collected during 2004 to April-2009. Haemagglutination inhibition (HI) antibody titres of ≥1∶40 against 2009 H1N1 were considered seroprotective as well as seropositive. The overall community seroprevalence was 26.7% (CI:22.6–29.4). The seroprevalence varied across age and ethnicity. Children aged 5–19 years had the highest seroprevalence (46.7%;CI:38.3–55.0), a significant increase from the baseline (14%;CI:7.2–20.8). Older adults aged ≥60 had no significant difference in seroprevalence between the serosurvey (24.8%;CI:18.7–30.9) and baseline (22.6%;CI:15.3–30.0). Pacific peoples had the highest seroprevalence (49.5%;CI:35.1–64.0). There was no significant difference in seroprevalence between both primary (29.6%;CI:22.6–36.5) and secondary healthcare workers (25.3%;CI:20.8–29.8) and community participants. No significant regional variation was observed. Multivariate analysis indicated age as the most important risk factor followed by ethnicity. Previous seasonal influenza vaccination was associated with higher HI titres. Approximately 45.2% of seropositive individuals reported no symptoms.Based on age and ethnicity standardisation to the New Zealand Population, about 29.5% of New Zealanders had antibody titers at a level consistent with immunity to 2009 H1N1. Around 18.3% of New Zealanders were infected with the virus during the first wave including about one child in every three. Older people were protected due to pre-existing immunity. Age was the most important factor associated with infection followed by ethnicity. Healthcare workers did not appear to have an increased risk of infection compared with the general population

Polyphenol Content and Modulatory Activities of Some Tropical Dietary Plant Extracts on the Oxidant Activities of Neutrophils and Myeloperoxidase

Young leaves of Manihot esculenta Crantz (Euphorbiaceae), Abelmoschus esculentus (Malvaceae), Hibiscus acetosella (Malvaceae) and Pteridium aquilinum (Dennstaedtiaceae) are currently consumed as green vegetables by peoples in sub-Saharan Africa, Latin America, Asia and their migrants living in Western Europe. Sub-Saharan peoples use Manihot, Abelmoschus and Hibiscus also in the folk medicine to alleviate fever and pain, in the treatment of conjunctivitis, rheumatism, hemorrhoid, abscesses, ... The present study investigates the effects of aqueous extracts of those plants on the production of reactive oxygen species (ROS) and the release of myeloperoxidase (MPO) by equine neutrophils activated with phorbol 12-myristate 13-acetate (PMA). The ROS production was measured by lucigenin-enhanced chemiluminescence (CL), and the release of total MPO by an ELISA method. The study also investigates the effect of the extracts on the activity of MPO by studying its nitration activity on tyrosine and by using a new technique called SIEFED (Specific Immunological Extraction Followed by Enzymatic Detection) that allows studying the direct interaction of compounds with the enzyme. In all experiments, the aqueous extracts of the plants developed concentration-dependent inhibitory effects. A moderate heat treatment did not significantly modify the inhibitory capacity of the extracts in comparison to not heated ones. Total polyphenol and flavonoid contents were determined with an HPLC-UV/DAD analysis and a spectroscopic method using Folin-Ciocalteu reagent. Some polyphenols with well-known antioxidant activities (caffeic acid, chlorogenic acid, hyperoside, rosmarinic acid and rutin) were found in the extracts and may partly explain the inhibitory activities observed. The role of those dietary and medicinal plants in the treatment of ROS-dependent inflammatory diseases could have new considerations for health