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Breaking the 1000-gene barrier for Mimivirus using ultra-deep genome and transcriptome sequencing
Matthieu Legendre, Sébastien Santini, Alain Rico, Chantal Abergel, Jean-Michel Claverie
Virology Journal , 2011, DOI: 10.1186/1743-422x-8-99
Abstract: We now report a much deeper analysis using the SOLiD? technology combining RNA-Seq of the Mimivirus transcriptome during the infectious cycle (202.4 Million reads), and a complete genome re-sequencing (45.3 Million reads). This study corrected the genome sequence and identified several single nucleotide polymorphisms. Our results also provided clear evidence of previously overlooked transcription units, including an important RNA polymerase subunit distantly related to Euryarchea homologues. The total Mimivirus gene count is now 1018, 11% greater than the original annotation.This study highlights the huge progress brought about by ultra-deep sequencing for the comprehensive annotation of virus genomes, opening the door to a complete one-nucleotide resolution level description of their transcriptional activity, and to the realistic modeling of the viral genome expression at the ultimate molecular level. This work also illustrates the need to go beyond bioinformatics-only approaches for the annotation of short protein and non-coding genes in viral genomes.Mimivirus, a nucleocytoplasmic large double stranded DNA virus infecting Acanthamoeba species, is the largest virus identified to date. Its icosahedral fibrillated capsid has a diameter of 750 nm. Besides its outstanding particle size, the genome of Mimivirus is also exceptional both in size and complexity. The initial sequencing revealed a linear genome of 1,181,404 nt (roughly the size of the spirochaete bacterium Treponema pallidum genome) harboring 911 protein coding genes and 6 tRNAs [1]. Some of these genes were observed for the first time in a virus, the most salient being those involved in protein translation and DNA repair. These unique features reawaked conceptual discussions on the nature of viruses and the frontier between viruses and cellular organisms [2-4].We recently reported the first RNA-Seq study of a large DNA virus using the 454-Flex technology [5]. The transcriptome analysis of Mimivirus during
Reticulamoeba Is a Long-Branched Granofilosean (Cercozoa) That Is Missing from Sequence Databases
David Bass, Akinori Yabuki, Sébastien Santini, Sarah Romac, Cédric Berney
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049090
Abstract: We sequenced the 18S ribosomal RNA gene of seven isolates of the enigmatic marine amoeboflagellate Reticulamoeba Grell, which resolved into four genetically distinct Reticulamoeba lineages, two of which correspond to R. gemmipara Grell and R. minor Grell, another with a relatively large cell body forming lacunae, and another that has similarities to both R. minor and R. gemmipara but with a greater propensity to form cell clusters. These lineages together form a long-branched clade that branches within the cercozoan class Granofilosea (phylum Cercozoa), showing phylogenetic affinities with the genus Mesofila. The basic morphology of Reticulamoeba is a roundish or ovoid cell with a more or less irregular outline. Long and branched reticulopodia radiate from the cell. The reticulopodia bear granules that are bidirectionally motile. There is also a biflagellate dispersal stage. Reticulamoeba is frequently observed in coastal marine environmental samples. PCR primers specific to the Reticulamoeba clade confirm that it is a frequent member of benthic marine microbial communities, and is also found in brackish water sediments and freshwater biofilm. However, so far it has not been found in large molecular datasets such as the nucleotide database in NCBI GenBank, metagenomic datasets in Camera, and the marine microbial eukaryote sampling and sequencing consortium BioMarKs, although closely related lineages can be found in some of these datasets using a highly targeted approach. Therefore, although such datasets are very powerful tools in microbial ecology, they may, for several methodological reasons, fail to detect ecologically and evolutionary key lineages.
The Conserved Candida albicans CA3427 Gene Product Defines a New Family of Proteins Exhibiting the Generic Periplasmic Binding Protein Structural Fold
Sébastien Santini,Jean-Michel Claverie,Nicolas Mouz,Tristan Rousselle,Caroline Maza,Vincent Monchois,Chantal Abergel
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0018528
Abstract: Nosocomial diseases due to Candida albicans infections are in constant rise in hospitals, where they cause serious complications to already fragile intensive care patients. Antifungal drug resistance is fast becoming a serious issue due to the emergence of strains resistant to currently available antifungal agents. Thus the urgency to identify new potential protein targets, the function and structure of which may guide the development of new antifungal drugs. In this context, we initiated a comparative genomics study in search of promising protein coding genes among the most conserved ones in reference fungal genomes. The CA3427 gene was selected on the basis of its presence among pathogenic fungi contrasting with its absence in the non pathogenic Saccharomyces cerevisiae. We report the crystal 3D-structure of the Candida albicans CA3427 protein at 2.1 ? resolution. The combined analysis of its sequence and structure reveals a structural fold originally associated with periplasmic binding proteins. The CA3427 structure highlights a binding site located between the two protein domains, corresponding to a sequence segment conserved among fungi. Two crystal forms of CA3427 were found, suggesting that the presence or absence of a ligand at the proposed binding site might trigger a “Venus flytrap” motion, coupled to the previously described activity of bacterial periplasmic binding proteins. The conserved binding site defines a new subfamily of periplasmic binding proteins also found in many bacteria of the bacteroidetes division, in a choanoflagellate (a free-living unicellular and colonial flagellate eukaryote) and in a placozoan (the closest multicellular relative of animals). A phylogenetic analysis suggests that this gene family originated in bacteria before its horizontal transfer to an ancestral eukaryote prior to the radiation of fungi. It was then lost by the Saccharomycetales which include Saccharomyces cerevisiae.
Structural characterization of CA1462, the Candida albicans thiamine pyrophosphokinase
Sébastien Santini, Vincent Monchois, Nicolas Mouz, Cécile Sigoillot, Tristan Rousselle, Jean-Michel Claverie, Chantal Abergel
BMC Structural Biology , 2008, DOI: 10.1186/1472-6807-8-33
Abstract: We report the enzymatic characterization and the crystallographic structure of the Candida albicans Thiamine pyrophosphokinase. The protein was co-crystallized with thiamine or thiamine-PNP.The presence of an inorganic phosphate in the crystallographic structure opposite the known AMP binding site relative to the thiamine moiety suggests that a second AMP molecule could be accommodated in the C. albicans structure. Together with the crystallographic structures of the enzyme/substrate complexes this suggests the existence of a secondary, less specific, nucleotide binding site in the Candida albicans thiamine pyrophosphokinase which could transiently serve during the release or the binding of ATP. The structures also highlight a conserved Glutamine residue (Q138) which could interact with the ATP α-phosphate and act as gatekeeper. Finally, the TPK/Thiamine-PNP complex is consistent with a one step mechanism of pyrophosphorylation.Our laboratory runs a structural genomics project (PROFUN [1]) targeting fungal protein-coding genes in search of new anti-fungal targets. The main goal of this project is to quantitatively express the selected Saccharomyces cerevisiae and Candida albicans genes products to characterize them functionally and structurally as well as explore their potential as new drug targets. The genes selected in Candida albicans are of two types: 1) they have orthologous genes in Saccharomyces cerevisiae that are essential or 2) they are conserved in pathogenic fungal genomes and can be absent from the non-pathogenic yeast Saccharomyces cerevisiae.Candida albicans is a diploid organism with eight sets of homologous chromosomes and a genome size of about 32 Mb. This pathogen is part of the normal microflora of the human gastrointestinal tract or oropharynx and is responsible for various nosocomial infections, potentially lethal in immunocompromised patients or patients in the intensive care unit. The CA1462 protein is encoded by a gene conserved across all k
New insights on early evolution of spiny-rayed fishes (Teleostei: Acanthomorpha)
Wei-Jen Chen,Francesco Santini,Jhen-Nien Chen,Shu-Hui Liu,Sébastien Lavoué
Frontiers in Marine Science , 2014, DOI: 10.3389/fmars.2014.00053
Abstract: The Acanthomorpha is the largest group of teleost fishes with about one third of extant vertebrate species. In the course of its evolution this lineage experienced several episodes of radiation, leading to a large number of descendant lineages differing profoundly in morphology, ecology, distribution and behavior. Although Acanthomorpha was recognized decades ago, we are only now beginning to decipher its large-scale, time-calibrated phylogeny, a prerequisite to test various evolutionary hypotheses explaining the tremendous diversity of this group. In this study, we provide new insights into the early evolution of the acanthomorphs and the euteleost allies based on the phylogenetic analysis of a newly developed dataset combining nine nuclear and mitochondrial gene markers. Our inferred tree is time-calibrated using 15 fossils, some of which have not been used before. While our phylogeny strongly supports a monophyletic Neoteleostei, Ctenosquamata (i.e., Acanthomorpha plus Myctophiformes), and Acanthopterygii, we find weak support (bootstrap value < 48%) for the traditionally defined Acanthomorpha, as well as evidence of non-monophyly for the traditional Paracanthopterygii, Beryciformes, and Percomorpha. We corroborate the new Paracanthopterygii sensu Miya et al. (2005) including Polymixiiformes, Zeiformes, Gadiformes, Percopsiformes, and likely the enigmatic Stylephorus chordatus. Our timetree largely agrees with other recent studies based on nuclear loci in inferring an Early Cretaceous origin for the acanthomorphs followed by a Late Cretaceous/Early Paleogene radiation of major lineages. This is in contrast to mitogenomic studies mostly inferring Jurassic or even Triassic ages for the origin of the acanthomorphs. We compare our results to those of previous studies, and attempt to address some of the issues that may have led to incongruence between the fossil record and the molecular clock studies, as well as between the different molecular timetrees.
Montefeltro seismicity: from Serpieri's seismograph to the RSNC seismograph station
S. Santini
Annals of Geophysics , 2000, DOI: 10.4401/ag-3653
Abstract: In recent years, the recovery of some historical documents has permitted us to operate the seismographs used by Alessandro Serpieri (1823-1885) at the Observatory of the University of Urbino in the XIX century. The space-time concept of sensor network was already clear to Serpieri and he tried to apply this concept to the analysis of seismic phenomena in Italy. This paper reviews the history of the Urbino Observatory from Serpieri's age to present times. The historical region of Montefeltro, where Urbino is the main town, is affected by seismicity with typical magnitudes between 2.2 and 2.5. Most of these events occur in the upper 15 km of the crust. The seismicity of the neighbouring regions is mainly concentrated in three zones: Northern Rimini, the Apennine belt and the Sibillini Mountain area. From the overall data, it is possible to infer that there is a basin characterised by microseismicity and essentially dominated by a compressive tectonic regime in the Montefeltro area. Furthermore seismological data seem to show a "quiet" segment, separating the extension area from the compression area, characterised by a low concentration of seismic events.
A note on Northern Marche seismicity: new focal mechanisms and seismological evidence
S. Santini
Annals of Geophysics , 2003, DOI: 10.4401/ag-4374
Abstract: A geodynamic interpretation of the Northern Marche region is diffi cult, the zone being characterized by complex structures which cannot be defi ned in the form of a simple, standard model. It is unquestionable that the geodynamic setting, whatever it is, bears a strong infl uence on the seismic hazard assessment of a region, and this is the background reason for the present note. In order to obtain a more detailed picture of seismological evidence in this zone, 11 new fault plane solutions of crustal events with 2.9 < M < 4.3 were calculated, using data recorded by the national seismic network of the Istituto Nazionale di Geofi sica e Vulcanologia in the period 1990-2000. The aim is to add local information to the previous studies by Frepoli and Amato (1997, 2000). A possible result of this new study is the division of the Northern Marche region into three areas with different focal mechanism categories: the inner area of the Apenninic belt, the Adriatic on-shore and the Adriatic off-shore. This note is intended to be a contribution to update seismological evidence in the Northern Marche region.
Ixodes ricinus Tick Lipocalins: Identification, Cloning, Phylogenetic Analysis and Biochemical Characterization
Jér?me Beaufays, Beno?t Adam, Yves Decrem, Pierre-Paul Prév?t, Sébastien Santini, Robert Brasseur, Michel Brossard, Laurence Lins, Luc Vanhamme, Edmond Godfroid
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003941
Abstract: Background During their blood meal, ticks secrete a wide variety of proteins that interfere with their host's defense mechanisms. Among these proteins, lipocalins play a major role in the modulation of the inflammatory response. Methodology/Principal Findings Screening a cDNA library in association with RT-PCR and RACE methodologies allowed us to identify 14 new lipocalin genes in the salivary glands of the Ixodes ricinus hard tick. A computational in-depth structural analysis confirmed that LIRs belong to the lipocalin family. These proteins were called LIR for “Lipocalin from I. ricinus” and numbered from 1 to 14 (LIR1 to LIR14). According to their percentage identity/similarity, LIR proteins may be assigned to 6 distinct phylogenetic groups. The mature proteins have calculated pM and pI varying from 21.8 kDa to 37.2 kDa and from 4.45 to 9.57 respectively. In a western blot analysis, all recombinant LIRs appeared as a series of thin bands at 50–70 kDa, suggesting extensive glycosylation, which was experimentally confirmed by treatment with N-glycosidase F. In addition, the in vivo expression analysis of LIRs in I. ricinus, examined by RT-PCR, showed homogeneous expression profiles for certain phylogenetic groups and relatively heterogeneous profiles for other groups. Finally, we demonstrated that LIR6 codes for a protein that specifically binds leukotriene B4. Conclusions/Significance This work confirms that, regarding their biochemical properties, expression profile, and sequence signature, lipocalins in Ixodes hard tick genus, and more specifically in the Ixodes ricinus species, are segregated into distinct phylogenetic groups suggesting potential distinct function. This was particularly demonstrated by the ability of LIR6 to scavenge leukotriene B4. The other LIRs did not bind any of the ligands tested, such as 5-hydroxytryptamine, ADP, norepinephrine, platelet activating factor, prostaglandins D2 and E2, and finally leukotrienes B4 and C4.
Euler, Reader of Newton: Mechanics and Algebraic Analysis  [PDF]
Sébastien Maronne, Marco Panza
Advances in Historical Studies (AHS) , 2014, DOI: 10.4236/ahs.2014.31003
Abstract: We follow two of the many paths leading from Newton’s to Euler’s scientific productions, and give an account of Euler’s role in the reception of some of Newton’s ideas, as regards two major topics: mechanics and algebraic analysis. Euler contributed to a re-appropriation of Newtonian science, though transforming it in many relevant aspects. We study this re-appropriation with respect to the mentioned topics and show that it is grounded on the development of Newton’s conceptions within a new conceptual frame also influenced by Descartes’s views sand Leibniz’s formalism.
Simulation of the long-term behaviour of a fault with two asperities
M. Dragoni,S. Santini
Nonlinear Processes in Geophysics (NPG) , 2010,
Abstract: A system made of two sliding blocks coupled by a spring is employed to simulate the long-term behaviour of a fault with two asperities. An analytical solution is given for the motion of the system in the case of blocks having the same friction. An analysis of the phase space shows that orbits can reach a limit cycle only after entering a particular subset of the space. There is an infinite number of different limit cycles, characterized by the difference between the forces applied to the blocks or, as an alternative, by the recurrence pattern of block motions. These results suggest that the recurrence pattern of seismic events produced by the equivalent fault system is associated with a particular stress distribution which repeats periodically. Admissible stress distributions require a certain degree of inhomogeneity, which depends on the geometry of fault system. Aperiodicity may derive from stress transfers from neighboring faults.
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