The electrophotonic silicon biosensor

The emergence of personalized and stratified medicine requires label-free and low-cost diagnostic technology capable of monitoring multiple disease biomarkers in parallel. Silicon photonic biosensors combine high sensitivity analysis with scalable, low-cost manufacturing technology but they tend to measure only a single biomarker and provide no information about their (bio)chemical activity. Here, we introduce an electrochemical silicon photonic sensor capable of highly sensitive and multiparameter profiling of biomolecules. Our electro-photonic technology consists of microring resonators optimally n-doped to support high Q resonances alongside electrochemical processes in situ. The inclusion of electrochemical processes enables site selective immobilization of different biomolecules, here single stranded DNA, onto individual microrings within a sensor array. The combination of photonic and electrochemical characterization of molecules bound to the sensor surface also provides direct quantification of binding density and unique insight into chemical reactivity that is unavailable with photonic detection alone. By exploiting both the photonic and the electrical properties of silicon, the sensor opens new modalities for sensing on the micro-scale

TreeDyn: towards dynamic graphics and annotations for analyses of trees

BACKGROUND: Analyses of biomolecules for biodiversity, phylogeny or structure/function studies often use graphical tree representations. Many powerful tree editors are now available, but existing tree visualization tools make little use of meta-information related to the entities under study such as taxonomic descriptions or gene functions that can hardly be encoded within the tree itself (if using popular tree formats). Consequently, a tedious manual analysis and post-processing of the tree graphics are required if one needs to use external information for displaying or investigating trees. RESULTS: We have developed TreeDyn, a tool using annotations and dynamic graphical methods for editing and analyzing multiple trees. The main features of TreeDyn are 1) the management of multiple windows and multiple trees per window, 2) the export of graphics to several standard file formats with or without HTML encapsulation and a new format called TGF, which enables saving and restoring graphical analysis, 3) the projection of texts or symbols facing leaf labels or linked to nodes, through manual pasting or by using annotation files, 4) the highlight of graphical elements after querying leaf labels (or annotations) or by selection of graphical elements and information extraction, 5) the highlight of targeted trees according to a source tree browsed by the user, 6) powerful scripts for automating repetitive graphical tasks, 7) a command line interpreter enabling the use of TreeDyn through CGI scripts for online building of trees, 8) the inclusion of a library of packages dedicated to specific research fields involving trees. CONCLUSION: TreeDyn is a tree visualization and annotation tool which includes tools for tree manipulation and annotation and uses meta-information through dynamic graphical operators or scripting to help analyses and annotations of single trees or tree collections

Additional Haplogroups of Toxoplasma gondii out of Africa: Population Structure and Mouse-Virulence of Strains from Gabon

Prevalence of human toxoplasmosis in tropical African countries usually exceeds 50%. Its role as a major opportunistic infection of AIDS patients is regularly described. Due to the lack of investigation, congenital infection is certainly underestimated in Africa. Incidence of Toxoplasma ocular disease is higher in Africa and South America than in Europe. Severe cases in immunocompetent patients were described after infection acquired in Amazonia, but nothing is known about such cases in Africa. Several studies argued for a role of genotypes in the clinical expression of human toxoplasmosis, and for a geographical structuration of Toxoplasma across continents. Genetic data concerning isolates from Africa are scarce. Here, apart from the worldwide Type III, we described two main haplogroups, Africa 1 and 3. We detected genetic exchanges between urban centers favored by trade exchange and transportation. It shows how important human influence is, even in shaping the genetic structure of a zoonotic disease agent. Finding of identical haplogroups in South America suggested that these African and American strains share a common ancestor. As a higher pathogenicity in human of South American genotypes has been described, this similarity of genotypes should encourage further clinical studies with genotype analysis in Africa

Disc-based microarrays: principles and analytical applications

[EN] The idea of using disk drives to monitor molecular biorecognition events on regular optical discs has received considerable attention during the last decade. CDs, DVDs, Blu-ray discs and other new optical discs are universal and versatile supports with the potential for development of protein and DNA microarrays. Besides, standard disk drives incorporated in personal computers can be used as compact and affordable optical reading devices. Consequently, a CD technology, resulting from the audio-video industry, has been used to develop analytical applications in health care, environmental monitoring, food safety and quality assurance. The review presents and critically evaluates the current state of the art of disc-based microarrays with illustrative examples, including past, current and future developments. Special mention is made of the analytical developments that use either chemically activated or raw standard CDs where proteins, oligonucleotides, peptides, haptens or other biological probes are immobilized. The discs are also used to perform the assays and must maintain their readability with standard optical drives. The concept and principle of evolving disc-based microarrays and the evolution of disk drives as optical detectors are also described. The review concludes with the most relevant uses ordered chronologically to provide an overview of the progress of CD technology applications in the life sciences. Also, it provides a selection of important references to the current literature.This work was supported by the Spanish Ministry of Economy and Competitiveness (project CTQ2013-45875-R) and Generalitat Valenciana (PROMETEO II 2014/040 and ACOMP 2012/158). All authors were partially sponsored by the European Regional Development Fund.Morais, S.; Puchades, R.; Maquieira Catala, Á. 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Transmission Of Leishmania Infantum In The Canine Leishmaniasis Focus Of Mont-Rolland, Senegal: Ecological, Parasitological And Molecular Evidence For A Possible Role Of Sergentomyia Sand Flies

Leishmania (L.) infantum is the causative agent in an endemic focus of canine leishmaniasis in the Mont-Rolland district (Thiès, Senegal). In this area, the transmission cycle is well established and more than 30% of dogs and 20% of humans are seropositive for L. infantum. However, the sand fly species involved in L. infantum transmission cycle are still unknown. Between 2007 and 2010, 3654 sand flies were collected from different environments (indoor, peridomestic, farming and sylvatic areas) to identify the main L. infantum vector(s). Nine sand fly species were identified. The Phlebotomus genus (n = 54 specimens; Phlebotomus (Ph) duboscqi and Phlebotomus (Ph). rodhaini) was markedly under-represented in comparison to the Sergentomyia genus (n = 3600 specimens; Sergentomyia (Se) adleri, Se. clydei, Se. antennata, Se. buxtoni, Se. dubia, Se. schwetzi and Se. magna). Se. dubia and Se. schwetzi were the dominant species indoor and in peridomestic environments, near humans and dogs. Blood-meal analysis indicated their anthropophilic behavior. Some Se. schwetzi specimens fed also on dogs. The dissection of females in the field allowed isolating L. infantum from sand flies of the Sergentomyia genus (0.4% of Se. dubia and 0.79% of Se. schwetzi females). It is worth noting that one Se. dubia female not engorged and not gravid revealed highly motile metacyclic of L. infantum in the anterior part of the midgut. PCR-based diagnosis and sequencing targeting Leishmania kinetoplast DNA (kDNA) highlighted a high rate of L. infantum-positive females (5.38% of Se. dubia, 4.19% of Se. schwetzi and 3.64% of Se. magna). More than 2% of these positive females were unfed, suggesting the parasite survival after blood-meal digestion or egg laying. L. infantum prevalence in Se. schwetzi was associated with its seroprevalence in dogs and humans and L. infantum prevalence in Se. dubia was associated with its seroprevalence in humans. These evidences altogether strongly suggest that species of the Sergentomyia genus are probably the vectors of canine leishmaniasis in the Mont-Rolland area and challenge one more time the dogma that in the Old World, leishmaniasis is exclusively transmitted by species of the Phlebotomus genus., Leishmaniases, neglected tropical vector-borne diseases, remain today a problem of public health. Classically, the sand flies involved in Leishmania transmission belong either to the Phlebotomus genus (Old World) or to the Lutzomyia genus (New World). In the rural community of Mont-Rolland (Senegal, West Africa), Leishmania infantum is the causative agent in an endemic focus of canine leishmaniasis. Recent surveys revealed more than 30% of dogs and 20% of humans with a positive serological test for Leishmania in this community. However, the sand fly species involved in L. infantum transmission were still unknown. Between 2007 and 2010, we carried out a study in this community to identify the sand fly species responsible for L. infantum transmission. We collected nine species belonging mainly to Sergentomyia genus and in low proportion to Phlebotomus genus. The abundance around dogs and humans, the detection of live and mature parasites in anterior midgut, the high rate of L. infantum-positive females using molecular analyses and the identification of dog and human blood in the fed females incriminates Se. schwetzi and Se. dubia as possible vectors of L. infantum. This hypothesis is strongly supported by statistical analyses performed to compare the prevalence of infected sand flies with the seroprevalence data in humans and dogs.PubMedWoSScopu

Elemental composition of arbuscular mycorrhizal fungi at high salinity.

We investigated the elemental composition of spores and hyphae of arbuscular mycorrhizal fungi (AMF) collected from two saline sites at the desert border in Tunisia, and of Glomus intraradices grown in vitro with or without addition of NaCl to the medium, by proton-induced X-ray emission. We compared the elemental composition of the field AMF to those of the soil and the associated plants. The spores and hyphae from the saline soils showed strongly elevated levels of Ca, Cl, Mg, Fe, Si, and K compared to their growth environment. In contrast, the spores of both the field-derived AMF and the in vitro grown G. intraradices contained lower or not elevated Na levels compared to their growth environment. This resulted in higher K:Na and Ca:Na ratios in spores than in soil, but lower than in the associated plants for the field AMF. The K:Na and Ca:Na ratios of G. intraradices grown in monoxenic cultures were also in the same range as those of the field AMF and did not change even when those ratios in the growth medium were lowered several orders of magnitude by adding NaCl. These results indicate that AMF can selectively take up elements such as K and Ca, which act as osmotic equivalents while they avoid uptake of toxic Na. This could make them important in the alleviation of salinity stress in their plant hosts