High correlation between Chagas' disease serology and PCR-based detection of Trypanosoma cruzi kinetoplast DNA in bolivian children living in an endemic area

Submitted by sandra infurna ([email protected]) on 2016-06-29T15:31:55Z No. of bitstreams: 1 carlos20_morel_etal_IOC_1994.pdf: 578671 bytes, checksum: 49c1bfe1a3334487aede673ca532654a (MD5)Approved for entry into archive by sandra infurna ([email protected]) on 2016-06-29T15:43:03Z (GMT) No. of bitstreams: 1 carlos20_morel_etal_IOC_1994.pdf: 578671 bytes, checksum: 49c1bfe1a3334487aede673ca532654a (MD5)Made available in DSpace on 2016-06-29T15:43:03Z (GMT). No. of bitstreams: 1 carlos20_morel_etal_IOC_1994.pdf: 578671 bytes, checksum: 49c1bfe1a3334487aede673ca532654a (MD5) Previous issue date: 1994Submitted by Angelo Silva ([email protected]) on 2016-07-07T11:16:53Z No. of bitstreams: 3 carlos20_morel_etal_IOC_1994.pdf.txt: 19093 bytes, checksum: d5ec7ae508e9468c358833ecf7cf1076 (MD5) carlos20_morel_etal_IOC_1994.pdf: 578671 bytes, checksum: 49c1bfe1a3334487aede673ca532654a (MD5) license.txt: 2991 bytes, checksum: 5a560609d32a3863062d77ff32785d58 (MD5)Approved for entry into archive by sandra infurna ([email protected]) on 2016-07-07T12:13:56Z (GMT) No. of bitstreams: 3 license.txt: 2991 bytes, checksum: 5a560609d32a3863062d77ff32785d58 (MD5) carlos20_morel_etal_IOC_1994.pdf: 578671 bytes, checksum: 49c1bfe1a3334487aede673ca532654a (MD5) carlos20_morel_etal_IOC_1994.pdf.txt: 19093 bytes, checksum: d5ec7ae508e9468c358833ecf7cf1076 (MD5)Made available in DSpace on 2016-07-07T12:13:56Z (GMT). No. of bitstreams: 3 license.txt: 2991 bytes, checksum: 5a560609d32a3863062d77ff32785d58 (MD5) carlos20_morel_etal_IOC_1994.pdf: 578671 bytes, checksum: 49c1bfe1a3334487aede673ca532654a (MD5) carlos20_morel_etal_IOC_1994.pdf.txt: 19093 bytes, checksum: d5ec7ae508e9468c358833ecf7cf1076 (MD5) Previous issue date: 1994Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Departamento de Bioquímica e Biologia Molecular. Laboratório de Biologia Molecular e Doenças Endêmicas. Rio de Janeiro, RJ, Brasil.UMR CNRS/ ORSTOM, Génétique Moléculaire des Parasites et des Vecteurs. CP 9214, La Paz, Bolivia.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Departamento de Bioquímica e Biologia Molecular. Laboratório de Biologia Molecular e Doenças Endêmicas. Rio de Janeiro, RJ, Brasil.Universidad Mayor de San Andres. Instituto Boliviano de Biologia de Altura. La Paz, Bolivia.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Departamento de Bioquímica e Biologia Molecular. Laboratório de Biologia Molecular e Doenças Endêmicas. Rio de Janeiro, RJ, Brasil.Fundação Oswaldo Cruz. Instituto Oswaldo Cruz. Departamento de Bioquímica e Biologia Molecular. Laboratório de Biologia Molecular e Doenças Endêmicas. Rio de Janeiro, RJ, Brasil.UMR CNRS/ ORSTOM, Génétique Moléculaire des Parasites et des Vecteurs. CP 9214, La Paz, Bolivia.The detection of Tr)tpunosomu crirzi kinetoplast DNA by polymerase chain reaction (PCR) amplification is a potentially powerful tool for the parasitological diagnosis of Chagas’ disease. We have applied this technique in a field situation in Bolivia, where 45 children from a primary school were subjected to serological testing, buffy coat analysis and PCR diagnosis. 26 of the 28 serology-positive individuals were also positive by PCR. In addition, two serology-negative children gave a positive result by PCR, including one who was positive in the buffy coat test. These results suggest that PCR detection of T. cruzi DNA in blood can be a very useful complement to serology in Chagas’ disease diagnosis in Bolivia

Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria

Background: The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the different Synechococcus clades (based on 16S rRNA gene markers) suggest the occurrence of two major lifestyles ('opportunists'/'specialists'), corresponding to two distinct broad habitats ('coastal'/'open ocean'). Yet, the genetic basis of niche partitioning is still poorly understood in this ecologically important group. Results: Here, we compare the genomes of 11 marine Synechococcus isolates, representing 10 distinct lineages. Phylogenies inferred from the core genome allowed us to refine the taxonomic relationships between clades by revealing a clear dichotomy within the main subcluster, reminiscent of the two aforementioned lifestyles. Genome size is strongly correlated with the cumulative lengths of hypervariable regions (or 'islands'). One of these, encompassing most genes encoding the light-harvesting phycobilisome rod complexes, is involved in adaptation to changes in light quality and has clearly been transferred between members of different Synechococcus lineages. Furthermore, we observed that two strains (RS9917 and WH5701) that have similar pigmentation and physiology have an unusually high number of genes in common, given their phylogenetic distance. Conclusion: We propose that while members of a given marine Synechococcus lineage may have the same broad geographical distribution, local niche occupancy is facilitated by lateral gene transfers, a process in which genomic islands play a key role as a repository for transferred genes. Our work also highlights the need for developing picocyanobacterial systematics based on genome-derived parameters combined with ecological and physiological data

Chætognath transcriptome reveals ancestral and unique features among bilaterians

Background: The chætognaths (arrow worms) have puzzled zoologists for years because of their astonishing morphological and developmental characteristics. Despite their deuterostome-like development, phylogenomic studies recently positioned the chætognath phylum in protostomes, most likely in an early branching. This key phylogenetic position and the peculiar characteristics of chætognaths prompted further investigation of their genomic features. / Results: Transcriptomic and genomic data were collected from the chætognath Spadella cephaloptera through the sequencing of expressed sequence tags and genomic bacterial artificial chromosome clones. Transcript comparisons at various taxonomic scales emphasized the conservation of a core gene set and phylogenomic analysis confirmed the basal position of chætognaths among protostomes. A detailed survey of transcript diversity and individual genotyping revealed a past genome duplication event in the chætognath lineage, which was, surprisingly, followed by a high retention rate of duplicated genes. Moreover, striking genetic heterogeneity was detected within the sampled population at the nuclear and mitochondrial levels but cannot be explained by cryptic speciation. Finally, we found evidence for trans-splicing maturation of transcripts through splice-leader addition in the chætognath phylum and we further report that this processing is associated with operonic transcription. / Conclusion: These findings reveal both shared ancestral and unique derived characteristics of the chætognath genome, which suggests that this genome is likely the product of a very original evolutionary history. These features promote chætognaths as a pivotal model for comparative genomics, which could provide new clues for the investigation of the evolution of animal genomes

Patterns of eukaryotic diversity from the surface to the deep-ocean sediment

Remote deep-ocean sediment (DOS) ecosystems are among the least explored biomes on Earth. Genomic assessments of their biodiversity have failed to separate indigenous benthic organisms from sinking plankton. Here, we compare global-scale eukaryotic DNA metabarcoding datasets (18S-V9) from abyssal and lower bathyal surficial sediments and euphotic and aphotic ocean pelagic layers to distinguish plankton from benthic diversity in sediment material. Based on 1685 samples collected throughout the world ocean, we show that DOS diversity is at least threefold that in pelagic realms, with nearly two-thirds represented by abundant yet unknown eukaryotes. These benthic communities are spatially structured by ocean basins and particulate organic carbon (POC) flux from the upper ocean. Plankton DNA reaching the DOS originates from abundant species, with maximal deposition at high latitudes. Its seafloor DNA signature predicts variations in POC export from the surface and reveals previously overlooked taxa that may drive the biological carbon pump

Ecogenomics and biogeochemical impacts of uncultivated globally abundant ocean viruses

Ocean microbes drive global-scale biogeochemical cycling, but do so under constraints imposed by viruses on host community composition, metabolism, and evolutionary trajectories. Due to sampling and cultivation challenges, genome-level viral diversity remains poorly described and grossly understudied in nature such that <1% of observed surface ocean viruses, even those that are abundant and ubiquitous, are ′known′. Here we analyze a global map of abundant, double stranded DNA (dsDNA) viruses and viral-encoded auxiliary metabolic genes (AMGs) with genomic and ecological contexts through the Global Ocean Viromes (GOV) dataset, which includes complete genomes and large genomic fragments from both surface and deep ocean viruses sampled during the Tara Oceans and Malaspina research expeditions. A total of 15,222 epi- and mesopelagic viral populations were identified that comprised 867 viral clusters (VCs, approximately genus-level groups). This roughly triples known ocean viral populations, doubles known candidate bacterial and archaeal virus genera, and near-completely samples epipelagic communities at both the population and VC level. Thirty-eight of the 867 VCs were identified as the most impactful dsDNA viral groups in the oceans, as these were locally or globally abundant and accounted together for nearly half of the viral populations in any GOV sample. Most of these were predicted in silico to infect dominant, ecologically relevant microbes, while two thirds of them represent newly described viruses that lacked any cultivated representative. Beyond these taxon-specific ecological observations, we identified 243 viral-encoded AMGs in GOV, only 95 of which were known. Deeper analyses of 4 of these AMGs revealed that abundant viruses directly manipulate sulfur and nitrogen cycling, and do so throughout the epipelagic ocean. Together these data provide a critically-needed organismal catalog and functional context to begin meaningfully integrating viruses into ecosystem models as key players in nutrient cycling and trophic networks

Genome analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38–39 Mb genomes include 11,860–14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared t

PCR-based diagnosis for Chagas' disease in bolivian children living in an active transmission area : comparison with conventional serological and parasitological diagnosis

A large field study has been performed in the Cochabamba region of Bolivia with the aim of comparing the polymerase chain reaction (PCR) with other diagnosis methods for Chagas' disease. The amplification of #Trypanosoma cruzi$-specific kinetoplast DNA sequences in blood samples was compared with classical serological methods, specific IgM detection and direct parasite visualization for 268 school children in a single village where Chagas' disease transmission is active. Of 113 children positive by classical serology or buffy coat examination, 106 were detected by PCR (sensitivity : 93,8%). We did not observe any significant difference of PCR sensitivity between initial (IgM and/or buffy coat positive) and indeterminate stage (only IgG positive) patients. Among the remaining 155 children unconfirmed as chagasic (who were either only IgM positive, or IgG-, IgM-, and buffy coat -negative) only one case was PCR positive. This case may be due to DNA contamination, or to a very recent infection not detected otherwise, or to specific immune depression. These results show that PCR is a very sensitive parasitological test for Chagas' disease in active transmission regions. The future follow-up of the possibly infected patients who were only IgM-positive should clarify the interest of PCR and IgM tests in the detection of starting infections. (Résumé d'auteur