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Search Results: 1 - 10 of 32709 matches for " Daniel Brami "
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Metagenomic Exploration of Viruses throughout the Indian Ocean
Shannon J. Williamson, Lisa Zeigler Allen, Hernan A. Lorenzi, Douglas W. Fadrosh, Daniel Brami, Mathangi Thiagarajan, John P. McCrow, Andrey Tovchigrechko, Shibu Yooseph, J. Craig Venter
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0042047
Abstract: The characterization of global marine microbial taxonomic and functional diversity is a primary goal of the Global Ocean Sampling Expedition. As part of this study, 19 water samples were collected aboard the Sorcerer II sailing vessel from the southern Indian Ocean in an effort to more thoroughly understand the lifestyle strategies of the microbial inhabitants of this ultra-oligotrophic region. No investigations of whole virioplankton assemblages have been conducted on waters collected from the Indian Ocean or across multiple size fractions thus far. Therefore, the goals of this study were to examine the effect of size fractionation on viral consortia structure and function and understand the diversity and functional potential of the Indian Ocean virome. Five samples were selected for comprehensive metagenomic exploration; and sequencing was performed on the microbes captured on 3.0-, 0.8- and 0.1 μm membrane filters as well as the viral fraction (<0.1 μm). Phylogenetic approaches were also used to identify predicted proteins of viral origin in the larger fractions of data from all Indian Ocean samples, which were included in subsequent metagenomic analyses. Taxonomic profiling of viral sequences suggested that size fractionation of marine microbial communities enriches for specific groups of viruses within the different size classes and functional characterization further substantiated this observation. Functional analyses also revealed a relative enrichment for metabolic proteins of viral origin that potentially reflect the physiological condition of host cells in the Indian Ocean including those involved in nitrogen metabolism and oxidative phosphorylation. A novel classification method, MGTAXA, was used to assess virus-host relationships in the Indian Ocean by predicting the taxonomy of putative host genera, with Prochlorococcus, Acanthochlois and members of the SAR86 cluster comprising the most abundant predictions. This is the first study to holistically explore virioplankton dynamics across multiple size classes and provides unprecedented insight into virus diversity, metabolic potential and virus-host interactions.
A reforma tributária do governo Lula: continuísmo e injusti?a fiscal
Brami-Celentano, Alexandrine;Carvalho, Carlos Eduardo;
Revista Katálysis , 2007, DOI: 10.1590/S1414-49802007000100006
Abstract: the tax reform proposed by the lula government in 2003, quickly approved by congress, remained at the limits of the proposals of the previous government of president fernando henrique cardoso and his social democratic party (psdb), inspired by neoliberal ideology. the small advances in reducing regressivity, such as exemptions for basic consumer products, have not altered the role of the tax structure in the concentration of wealth, with a predominance of indirect taxes and their regressive effects. taxation has deserved little attention in the broad debate about social policies in brazil, which concentrates on the allocation of public expenses and the efficiency of spending, without proper attention to the role of the tax structure in the concentration of income and wealth in the country. the article presents the regressive profile of the brazilian tax structure, preserved by the reform of 2003 and discusses the neoliberal agenda that guides the initiatives of the lula government in this field.
A Metagenomic Framework for the Study of Airborne Microbial Communities
Shibu Yooseph, Cynthia Andrews-Pfannkoch, Aaron Tenney, Jeff McQuaid, Shannon Williamson, Mathangi Thiagarajan, Daniel Brami, Lisa Zeigler-Allen, Jeff Hoffman, Johannes B. Goll, Douglas Fadrosh, John Glass, Mark D. Adams, Robert Friedman, J. Craig Venter
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0081862
Abstract: Understanding the microbial content of the air has important scientific, health, and economic implications. While studies have primarily characterized the taxonomic content of air samples by sequencing the 16S or 18S ribosomal RNA gene, direct analysis of the genomic content of airborne microorganisms has not been possible due to the extremely low density of biological material in airborne environments. We developed sampling and amplification methods to enable adequate DNA recovery to allow metagenomic profiling of air samples collected from indoor and outdoor environments. Air samples were collected from a large urban building, a medical center, a house, and a pier. Analyses of metagenomic data generated from these samples reveal airborne communities with a high degree of diversity and different genera abundance profiles. The identities of many of the taxonomic groups and protein families also allows for the identification of the likely sources of the sampled airborne bacteria.
Detection of Light Images by Simple Tissues as Visualized by Photosensitized Magnetic Resonance Imaging
Catherine Tempel-Brami, Iddo Pinkas, Avigdor Scherz, Yoram Salomon
PLOS ONE , 2007, DOI: 10.1371/journal.pone.0001191
Abstract: In this study, we show how light can be absorbed by the body of a living rat due to an injected pigment circulating in the blood stream. This process is then physiologically translated in the tissue into a chemical signature that can be perceived as an image by magnetic resonance imaging (MRI). We previously reported that illumination of an injected photosynthetic bacteriochlorophyll-derived pigment leads to a generation of reactive oxygen species, upon oxygen consumption in the blood stream. Consequently, paramagnetic deoxyhemoglobin accumulating in the illuminated area induces changes in image contrast, detectable by a Blood Oxygen Level Dependent (BOLD)-MRI protocol, termed photosensitized (ps)MRI. Here, we show that laser beam pulses synchronously trigger BOLD-contrast transients in the tissue, allowing representation of the luminous spatiotemporal profile, as a contrast map, on the MR monitor. Regions with enhanced BOLD-contrast (7-61 fold) were deduced as illuminated, and were found to overlap with the anatomical location of the incident light. Thus, we conclude that luminous information can be captured and translated by typical oxygen exchange processes in the blood of ordinary tissues, and made visible by psMRI (Fig. 1). This process represents a new channel for communicating environmental light into the body in certain analogy to light absorption by visual pigments in the retina where image perception takes place in the central nervous system. Potential applications of this finding may include: non-invasive intra-operative light guidance and follow-up of photodynamic interventions, determination of light diffusion in opaque tissues for optical imaging and possible assistance to the blind.
Kinematic cues for the categorization of pointing movements made by hemiparetic stroke patients
Roby-Brami Agnès,Borjas Lorena,Hanneton Sylvain
BIO Web of Conferences , 2011, DOI: 10.1051/bioconf/20110100076
Abstract: Our visual sensitivity to human movements is illustrated by our ability to recognize actions even with a minimal visual display. The present study investigates if professional expertise influences the precision of recognition and the visual cues used. We presented movements made by hemiparetic stroke patients and healthy subjects to expert (physicians and physiotherapists) and naive observers. Since stroke induces perturbations of hand trajectory and interjoint coordination, we presented two types of computer animation (one dot representing the hand and stick diagram of the upper body). The observers had to score the pathological character of the movements. The observers were able to differentiate patients according to their impairment level. The experts responded faster but, surprisingly, their responses did not differ from those of na ve observers. The subjective judgment relied mainly on the quality of hand trajectory. The weak influence of postural information should be confirmed with more realistic displays.
Analyse cinématique de l'épaule chez des patients hémiparétiques lors de la saisie d'objets pesants
Svetlana Dedobbeler,Sylvain Hanneton,Agnès Roby-Brami
Quantitative Biology , 2006,
Abstract: The aim of this study is to produce a kinematic analysis of movements of the shoulder complex when hemiparetic patients achieve the grasping of weighted objects. We propose to describe the influence of the weight on kinematic characteristics of the gesture and to establish the relevance of several quantitative indexes concerning the quality of the grasping gesture.
Functional Tradeoffs Underpin Salinity-Driven Divergence in Microbial Community Composition
Chris L. Dupont, John Larsson, Shibu Yooseph, Karolina Ininbergs, Johannes Goll, Johannes Asplund-Samuelsson, John P. McCrow, Narin Celepli, Lisa Zeigler Allen, Martin Ekman, Andrew J. Lucas, ?ke Hagstr?m, Mathangi Thiagarajan, Bj?rn Brindefalk, Alexander R. Richter, Anders F. Andersson, Aaron Tenney, Daniel Lundin, Andrey Tovchigrechko, Johan A. A. Nylander, Daniel Brami, Jonathan H. Badger, Andrew E. Allen, Douglas B. Rusch, Jeff Hoffman, Erling Norrby, Robert Friedman, Jarone Pinhassi, J. Craig Venter, Birgitta Bergman
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0089549
Abstract: Bacterial community composition and functional potential change subtly across gradients in the surface ocean. In contrast, while there are significant phylogenetic divergences between communities from freshwater and marine habitats, the underlying mechanisms to this phylogenetic structuring yet remain unknown. We hypothesized that the functional potential of natural bacterial communities is linked to this striking divide between microbiomes. To test this hypothesis, metagenomic sequencing of microbial communities along a 1,800 km transect in the Baltic Sea area, encompassing a continuous natural salinity gradient from limnic to fully marine conditions, was explored. Multivariate statistical analyses showed that salinity is the main determinant of dramatic changes in microbial community composition, but also of large scale changes in core metabolic functions of bacteria. Strikingly, genetically and metabolically different pathways for key metabolic processes, such as respiration, biosynthesis of quinones and isoprenoids, glycolysis and osmolyte transport, were differentially abundant at high and low salinities. These shifts in functional capacities were observed at multiple taxonomic levels and within dominant bacterial phyla, while bacteria, such as SAR11, were able to adapt to the entire salinity gradient. We propose that the large differences in central metabolism required at high and low salinities dictate the striking divide between freshwater and marine microbiomes, and that the ability to inhabit different salinity regimes evolved early during bacterial phylogenetic differentiation. These findings significantly advance our understanding of microbial distributions and stress the need to incorporate salinity in future climate change models that predict increased levels of precipitation and a reduction in salinity.
Comparative genomics of the pathogenic ciliate Ichthyophthirius multifiliis, its free-living relatives and a host species provide insights into adoption of a parasitic lifestyle and prospects for disease control
Robert S Coyne, Linda Hannick, Dhanasekaran Shanmugam, Jessica B Hostetler, Daniel Brami, Vinita S Joardar, Justin Johnson, Diana Radune, Irtisha Singh, Jonathan H Badger, Ujjwal Kumar, Milton Saier, Yufeng Wang, Hong Cai, Jianying Gu, Michael W Mather, Akhil B Vaidya, David E Wilkes, Vidyalakshmi Rajagopalan, David J Asai, Chad G Pearson, Robert C Findly, Harry W Dickerson, Martin Wu, Cindy Martens, Yves Van de Peer, David S Roos, Donna M Cassidy-Hanley, Theodore G Clark
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-10-r100
Abstract: We report the sequencing, assembly and annotation of the Ich macronuclear genome. Compared with its free-living relative T. thermophila, the Ich genome is reduced approximately two-fold in length and gene density and three-fold in gene content. We analyzed in detail several gene classes with diverse functions in behavior, cellular function and host immunogenicity, including protein kinases, membrane transporters, proteases, surface antigens and cytoskeletal components and regulators. We also mapped by orthology Ich's metabolic pathways in comparison with other ciliates and a potential host organism, the zebrafish Danio rerio.Knowledge of the complete protein-coding and metabolic potential of Ich opens avenues for rational testing of therapeutic drugs that target functions essential to this parasite but not to its fish hosts. Also, a catalog of surface protein-encoding genes will facilitate development of more effective vaccines. The potential to use T. thermophila as a surrogate model offers promise toward controlling 'white spot' disease and understanding the adaptation to a parasitic lifestyle.The ciliates are an ancient and diverse phylogenetic group related to the largely parasitic apicomplexans, but consisting mostly of free-living heterotrophs. Some ciliates, however, have adopted a parasitic lifestyle. By far the most important of these is Ichthyophthirius multifiliis (which we will refer to by its common name of Ich), an endoparasite that causes white spot disease in freshwater fish [1,2]. With an extremely broad host-range, Ich is responsible for large-scale die-offs in natural populations and poses a significant threat to the growing worldwide aquaculture industry. Ich has a simple life cycle with no intermediate hosts (Figure 1). The free-swimming theront form invades the epidermis of susceptible fish, feeding on host tissue and growing up to 0.5 mm in diameter. Host-associated trophonts become visible as individual white spots for which this disease is n
Ears on the hand: reaching 3D audio targets
Forma Vincent,Hoellinger Thomas,Auvray Malika,Roby-Brami Agnès
BIO Web of Conferences , 2011, DOI: 10.1051/bioconf/20110100026
Abstract: We studied the ability of right-handed participants to reach 3D audio targets with their right hand. Our immersive audio environment was based on the OpenAL library and Fastrak magnetic sensors for motion capture. Participants listen the target through a “virtual” listener linked to a sensor fixed either on the head or on the hand. We compare three experimental conditions in which the virtual listener is on the head, on the left hand, and on the right hand (that reach the target). We show that (1) participants are able to learn the task but (2) with a low success rate and high durations, (3) the individual levels of performance are very variable, (4) the best performances are achieved when the listener is on the right hand. Consequently, we concluded that our participants were able to learn to locate 3D audio sources even if their ears are transposed on their hand, but we found of behavioral differences between the three experimental conditions.
Motor Rehabilitation after Stroke
Ching-yi Wu,Keh-chung Lin,Steven L. Wolf,Agnès Roby-Brami
Stroke Research and Treatment , 2012, DOI: 10.1155/2012/810706
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