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Taxonomic study on the molluscs collected during the Marion-Dufresne expedition (MD55) off SE Brazil: the Naticidae (Mollusca: Caenogastropoda)

Luiz Ricardo L. Simone
2014 Zoosystema  
., had their phenotypic characters coded and inserted in a wider cladistic analysis (Simone 2011), with no inclusion of new characters.  ...  KEY WOrDs Brazil, Anatomy, Naticidae, Caenogastropoda, Deep-water, new genus, new species. résumé Étude taxonomique des mollusques collectés pendant la campagne Marion-Dufresne (MD55) au large du sud est  ...  Simone L. L. R.  ... 
doi:10.5252/z2014n3a2 fatcat:t72wlig3dvgohph7o37x6ohhnq

Taxonomic study on the molluscs collected in Marion-Dufresne expedition (MD55) to SE Brazil: Xenophoridae, Cypraeoidea, mitriforms and Terebridae (Caenogastropoda)

Luiz Ricardo L. Simone, Carlo M. Cunha
2012 Zoosystema  
Complement: Deep-water caenogastropods of Marion-Dufresne expedition (MD55)ZOOSYSTEMA • 2012 • 34 (4)  ...  1999 (Simone , 2000 Simone & Gracia 2006) .  ... 
doi:10.5252/z2012n4a6 fatcat:3yldydrqmjg2ffagmzpvmz6ana

Cerithiidae, Litiopidae, Modulidae and Planaxidae (Gastropoda, Cerithioidea) collected by the Marion Dufresne MD55 expedition in southeastern Brazil

Daniel Caracanhas Cavallari, Sérgio Mendonça Almeida, Luiz Ricardo L. Simone
2020 Papéis Avulsos de Zoologia  
Several deep-water mollusks collected during the Marion Dufresne MD55 expedition off SE Brazil have been studied in recent papers.  ...  The malacologists onboard of the R/V Marion DuFresne, namely Philippe Bouchet, José H.  ...  Remarkably, they brood eggs in a special head-foot concavity (Simone, 2001) .  ... 
doi:10.11606/1807-0205/2020.60.35 fatcat:iafoiql5ujciblcwiczo6uubyu

Membranoproliferative glomerulonephritis in a patient with chronic Q fever

Simon Leclerc, Virginie Royal, Simon Frédéric Dufresne, Blandine Mondésert, Louis-Philippe Laurin
2020 Kidney International Reports  
doi:10.1016/j.ekir.2020.09.038 pmid:33305139 pmcid:PMC7710843 fatcat:yruexvobfvgtvltg3jrgykasuu

Draft Genome Sequences of Azole-Resistant and Azole-Susceptible Aspergillus turcosus Clinical Isolates Recovered from Bronchoalveolar Lavage Fluid Samples

Maxime Parent-Michaud, Philippe J. Dufresne, Éric Fournier, Christine Martineau, Sandrine Moreira, Vincent Perkins, Louis de Repentigny, Simon F. Dufresne, Christina Cuomo
2019 Microbiology Resource Announcements  
We present the draft genome sequences of two clinical strains of Aspergillus turcosus, one azole-susceptible (strain HMR-AF-23/LSPQ-01275) and the other azole-resistant (strain HMR-AF-1038/LSPQ-01280), isolated from bronchoalveolar lavage fluid of two adult patients. These two strains are the first reported clinical isolates of A. turcosus.
doi:10.1128/mra.01446-18 pmid:30637396 pmcid:PMC6318367 fatcat:egtnhcqngffztjlq4s5dcntwze

Lymphocytic Vasculitis Associated With Mild Rejection in a Vascularized Composite Allograft Recipient

Simon F. Roy, Vimal Krishnan, Vincent Quoc-Huy Trinh, Suzon Collette, Simon F. Dufresne, Daniel E. Borsuk, Delphine Désy
2020 Transplantation  
Histologic criteria for diagnosing acute rejection in vascularized composite tissue allograft (VCA) have been established by the Banff 2007 Working Classification of Skin-Containing Composite Tissue Allograft, but the role of early vascular lesions in graft rejection warrants additional analysis. We performed a retrospective study of 34 skin biopsies performed over 430 days for rejection surveillance, in Canada's first face allotransplant recipient. Three observers reviewed all biopsies to
more » ... s the nature and intensity of the inflammatory skin infiltrate. A complete histological and immunohistochemical review of the vascular components was performed with a focus on lymphocytic vasculitis, intravascular fibrin, vessel caliber, extent of injury, C4d positivity and inflammatory cell phenotyping. We then correlated these data points to clinical and immunosuppression parameters. Acute vascular damage in biopsies that would be classified as mild acute rejection correlates with troughs in immunosuppression and subside when immunosuppressive Tacrolimus doses are increased. Grade 0 Banff rejection and Grade I without lymphocytic vasculitis were almost indistinguishable, whilst Grade I with lymphocytic vasculitis was an easy and reproducible histologic finding. Our results highlight the possible relevance of vascular injury in the context of VCA, as its presence might underlie a more aggressive form of immune rejection. If these findings are validated in other VCA patients, vascular injury in mild rejection might warrant a different clinical approach.
doi:10.1097/tp.0000000000003241 pmid:32235257 fatcat:zlrhhrihbfbptjjdyofguq3cye

Identification of Candida auris using the updated 8.01 VITEK®2 yeast identification system: a multi-laboratory evaluation study

Georges Ambaraghassi, Philippe J. Dufresne, Simon F. Dufresne, Émilie Vallières, José F. Muñoz, Christina A. Cuomo, Elizabeth L. Berkow, Shawn R. Lockhart, Me-Linh Luong
2019 Journal of Clinical Microbiology  
Introduction Candida auris is an emerging multidrug-resistant yeast that has been systematically incorrectly identified by phenotypic methods in clinical microbiology laboratories. VITEK®2 automated identification system (bioMérieux) recently included C. auris in its database (version 8.01). Material and methods We evaluated the performance of VITEK®2 (YST ID Card) to identify C. auris and related species. A panel of 44 isolates of Candida species (C. auris, n=35; C. haemulonii, n=5; C.
more » ... emulonii, n=4) were tested by three different hospital-based microbiology laboratories. Results Among 35 isolates of C. auris, VITEK®2 yielded correct identification in an average of 52% of tested samples. Low discrimination results were obtained in an average of 27% with inability to distinguish between C. auris, C. duobushaemulonii and C. famata. Incorrect identification results were obtained in an average of 21%, the majority (91%) of which were reported as C. duobushaemulonii and 9% as C. lusitaniae/C. duobushaemulonii. Proportion of correct identification was not statistically different across different centers (p=0,78). Stratification by genetic clades demonstrated that 100% (n=8) of the strains of the South American clade were correctly identified, compared to 7% (n=10) and 0% (n=4) from the African and East Asian clade respectively. None of the non-auris Candida strains (n=9) were incorrectly identified as C. auris. Conclusion Our results show that VITEK®2 (version 8.01) yeast identification system has a limited ability to correctly identify C. auris. This data suggests that an identification result for C. duobushaemulonii should warrant further testing to rule out C. auris. Overall performance of VITEK®2 seems to differ according to C. auris genetic clade with the South American isolates yielding the most accurate result.
doi:10.1128/jcm.00884-19 pmid:31413079 pmcid:PMC6812989 fatcat:6cqcbg5uirdmdeo3wgsxtk3bie

Diversity and comparative genomics of chimeric viruses inSphagnum-dominated peatlands

Achim Quaiser, Mart Krupovic, Alexis Dufresne, André-Jean Francez, Simon Roux
2016 Virus Evolution  
A new group of viruses carrying naturally chimeric single-stranded (ss) DNA genomes that encompass genes derived from eukaryotic ssRNA and ssDNA viruses has been recently identified by metagenomic studies. The host range, genomic diversity, and abundance of these chimeric viruses, referred to as cruciviruses, remain largely unknown. In this article, we assembled and analyzed thirty-seven new crucivirus genomes from twelve peat viromes, representing twenty-four distinct genome organizations, and
more » ... nearly tripling the number of available genomes for this group. All genomes possess the two characteristic genes encoding for the conserved capsid protein (CP) and a replication protein. Additional ORFs were conserved only in nearly identical genomes with no detectable similarity to known genes. Two cruciviruses possess putative introns in their replication-associated genes. Sequence and phylogenetic analyses of the replication proteins revealed intragene chimerism in at least eight chimeric genomes. This highlights the large extent of horizontal gene transfer and recombination events in the evolution of ssDNA viruses, as previously suggested. Read mapping analysis revealed that members of the 'Cruciviridae' group are particularly prevalent in peat viromes. Sequences matching the CP ranged from 0.6 up to 10.9 percent in the twelve peat viromes. In contrast, from sixty-nine available viromes derived from other environments, only twenty-four contained cruciviruses, which on average accounted for merely 0.2 percent of sequences. Overall, this study provides new genome information and insights into the diversity of chimeric viruses, a necessary first step in progressing toward an accurate quantification and host range identification of these new viruses.
doi:10.1093/ve/vew025 pmid:29492276 pmcid:PMC5822885 fatcat:rtf4mvwrrvcg3i3wcvng6gfm6u

Draft Genome Sequence of Azole-Resistant Aspergillus thermomutatus (Neosartorya pseudofischeri) Strain HMR-AF-39, Isolated from a Human Nasal Septum Abscess Aspirate

Maxime Parent-Michaud, Philippe J. Dufresne, Éric Fournier, Christine Martineau, Sandrine Moreira, Vincent Perkins, Louis de Repentigny, Simon F. Dufresne, Antonis Rokas
2019 Microbiology Resource Announcements  
Here, we present the draft genome sequence of Aspergillus thermomutatus (formerly known as Neosartorya pseudofischeri; strain HMR-AF-39/LSPQ-01276), a cryptic species of Aspergillus section Fumigati. This species is intrinsically resistant to antifungal azoles and is recognized as an agent of invasive aspergillosis among immunocompromised hosts.
doi:10.1128/mra.01444-18 pmid:30637395 pmcid:PMC6318366 fatcat:hv6yai2grzhvpij6awmdjvqr6u

Self-assembly of amorphous biophotonic nanostructures by phase separation

Eric R. Dufresne, Heeso Noh, Vinodkumar Saranathan, Simon G. J. Mochrie, Hui Cao, Richard O. Prum
2009 Soft Matter  
Some of the most vivid colors in the animal kingdom are created not by pigments, but by wavelength-selective scattering of light from nanostructures. Here we investigate quasi-ordered nanostructures of avian feather barbs which produce vivid non-iridescent colors. These b-keratin and air nanostructures are found in two basic morphologies: tortuous channels and amorphous packings of spheres. Each class of nanostructure is isotropic and has a pronounced characteristic length scale of variation in
more » ... composition. These local structural correlations lead to strong backscattering over a narrow range of optical frequencies and little variation with angle of incidence. Such optical properties play important roles in social and sexual communication. To be effective, birds need to precisely control the development of these nanoscale structures, yet little is known about how they grow. We hypothesize that multiple lineages of birds have convergently evolved to exploit phase separation and kinetic arrest to self-assemble spongy color-producing nanostructures in feather barbs. Observed avian nanostructures are strikingly similar to those self-assembled during the phase separation of fluid mixtures; the channel and sphere morphologies are characteristic of phase separation by spinodal decomposition and nucleation and growth, respectively. These unstable structures are locked-in by the kinetic arrest of the b-keratin matrix, likely through the entanglement or cross-linking of supermolecular bkeratin fibers. Using the power of self-assembly, birds can robustly realize a diverse range of nanoscopic morphologies with relatively small physical and chemical changes during feather development. In contrast to pigmentary colors, structural colors are produced by optical interactions with nanoscale variations in refractive index. 1,2 Organismal structural colors can be produced by photonic crystals. 2 In addition to these highly periodic structures, biological photonic nanostructures also include amorphous, or quasi-ordered, dielectric nanostructures where there are local correlations but little long-range order. 3 An important fundamental question for understanding the function and evolution of structural coloration of organisms is how these nanostructures develop during individual growth. Variations in the dimensions of a nanostructure will produce visible variations in color that may result in ineffective social or sexual communication signals. Thus, nanostructure development must be precisely controlled to produce appropriate color phenotypes. Inside the body of butterfly scales, color-producing air-chitin nanostructures develop from a biological template produced by complex growth of the cellular Fig. 1 (A) Male Eastern Bluebird (Sialia sialis, Turdidae). (B) Male Plum-throated Cotinga (Cotinga maynana, Cotingidae). (C) Channeltype b-keratin and air nanostructure from back contour feather barbs of S. sialis. (D) Sphere-type b-keratin and air nanostructure from back contour feather barbs of C. maynana. (E) Small-angle X-ray scattering data from channel-type feather barb of S. sialis.. (F) Small-angle X-ray scattering data from sphere-type feather barb of C. maynana. Scale bars (C-D) 500 nm, (E-F) 0.025 nm À1 of spatial frequency. Photo credits: (B) Ken Thomas (image in the public domain); (B) Thomas Valqui (reproduced with permission).
doi:10.1039/b902775k fatcat:bwscf4ioa5fqflwoi65oa7pg3a

Diversity and comparative genomics of Microviridae in Sphagnum- dominated peatlands

Achim Quaiser, Alexis Dufresne, Flore Ballaud, Simon Roux, Yvan Zivanovic, Jonathan Colombet, Télesphore Sime-Ngando, André-Jean Francez
2015 Frontiers in Microbiology  
Microviridae, a family of bacteria-infecting ssDNA viruses, is one of the still poorly characterized bacteriophage groups, even though it includes phage PhiX174, one of the main models in virology for genomic and capsid structure studies. Recent studies suggest that they are diverse and well represented in marine and freshwater virioplankton as well as in human microbiomes. However, their diversity, abundance, and ecological role are completely unknown in soil ecosystems. Here we present the
more » ... parative analysis of 17 completely assembled Microviridae genomes from 12 viromes of a Sphagnum-dominated peatland. Phylogenetic analysis of the conserved major capsid protein sequences revealed the affiliation to Gokushovirinae and Pichovirinae as well as to two newly defined subfamilies, the Aravirinae and Stokavirinae. Additionally, two new distinct prophages were identified in the genomes of Parabacteroides merdae and Parabacteroides distasonis representing a potential new subfamily of Microviridae. The differentiation of the subfamilies was confirmed by gene order and similarity analysis. Relative abundance analysis using the affiliation of the major capsid protein (VP1) revealed that Gokushovirinae, followed by Aravirinae, are the most abundant Microviridae in 11 out of 12 peat viromes. Sequences matching the Gokushovirinae and Aravirinae VP1 matching sequences, respectively, accounted for up to 4.19 and 0.65% of the total number of sequences in the corresponding virome, respectively. In this study we provide new genome information of Microviridae and pave the way toward quantitative estimations of Microviridae subfamilies.
doi:10.3389/fmicb.2015.00375 pmid:25972855 pmcid:PMC4412055 fatcat:mxmlh56xdfbgfflouzkwim5rmm

How non-iridescent colors are generated by quasi-ordered structures of bird feathers [article]

Heeso Noh, Seng Fatt Liew, Vinodkumar Saranathan, Rickchard O. Prum, Simon G. I. Mochrie, Eric R. Dufresne, Hui Cao
2009 arXiv   pre-print
We investigated the mechanism of structural coloration by quasi-ordered nanostructures in bird feather barbs. Small-angle X-ray scattering (SAXS) data reveal the structures are isotropic and have short-range order on length scales comparable to optical wavelengths. We performed angle-resolved reflection and scattering spectrometry to fully characterize the colors under directional and omni-directional illumination of white light. Under directional lighting, the colors change with the angle
more » ... en the directions of illumination and observation. The angular dispersion of the primary peaks in the scattering/reflection spectra can be well explained by constructive interference of light that is scattered only once in the quasi-ordered structures. Using the Fourier power spectra of structure from the SAXS data we calculated optical scattering spectra and explained why light scattering peak is the highest in the backscattering direction. Under omni-directional lighting, colors from the quasi-ordered structures are invariant with the viewing angle. The non-iridescent coloration results from isotropic nature of structures instead of strong backscattering. By comparing the data to those of an periodic structure, we demonstrated the difference in structural coloration between the quasi-ordered structures and ordered structures.
arXiv:0912.4487v1 fatcat:ofkmi63mija4nkfkw74yyc2ivu

Successful Treatment of DisseminatedAnncaliia algeraeMicrosporidial Infection With Combination Fumagillin and Albendazole

Mélissa Boileau, José Ferreira, Imran Ahmad, Christian Lavallée, Yvonne Qvarnstrom, Simon F. Dufresne
2016 Open Forum Infectious Diseases  
Anncaliia algerae myositis is a life-threatening, emerging microsporidiosis among immunocompromised hosts. We report a case of disseminated A algerae infection in a man previously treated with alemtuzumab. Due to failure of albendazolebased therapy, fumagillin was added as a novel approach to management, with a good clinical response and patient survival.
doi:10.1093/ofid/ofw158 pmid:27704013 pmcid:PMC5047403 fatcat:xvvy5ybenjc57nbrji3hfmzhsq

Biomimetic isotropic nanostructures for structural coloration [article]

Jason D. Forster, Heeso Noh, Seng Fatt Liew, Vinodkumar Saranathan, Carl F. Schreck, Lin Yang, Jin-Gyu Park, Richard O. Prum, Corey S. O'Hern, Simon G. J. Mochrie, Hui Cao, Eric R. Dufresne
2010 arXiv   pre-print
SAXS measurements of the feathers were carried out at beamline 8-ID-I at the APS, Argonne National Labs, as described in Dufresne et al.  ... 
arXiv:0912.4290v2 fatcat:xathd7efgrbkvaawsdy7cwckny
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