262 results on '"Rioux, D."'
Search Results
102. Scanning Tunneling Microscopy of Deoxyribonucleic-Acid During Replication
- Author
-
Destasio, G., Rioux, D., Margaritondo, G., Mercanti, D., Trasatti, L., and Moore, C.
- Subjects
PROSPECTS ,DNA ,BIOMOLECULES ,MOLECULAR-STRUCTURE - Abstract
Scanning tunneling microscopy was used to produce topographic images of uncoated and unlabeled deoxyribonucleic acid (DNA) in air, on a graphite substrate. The images show for the first time a DNA molecule that had been isolated while it was replicating.
103. Valence State of Copper in Nd2-Xcexcuo4
- Author
-
Hwu, Y, Marsi, M, Terrasi, Antonio, Rioux, D, Chang, Y, Mckinley, Jt, Onellion, M, Margaritondo, G, Capozi, M, Quaresima, C, Campo, A, Ottaviani, C, Perfetti, P, Stoffel, Ng, and Wang, E.
- Subjects
Condensed Matter::Materials Science ,Condensed Matter::Superconductivity ,Condensed Matter::Strongly Correlated Electrons ,CHARGE-CARRIERS ,PHOTOEMISSION ,CU - Abstract
New photoemission data are presented for a series of Ce-doped or undoped, reduced or nonreduced, Nd cuprates. The data, taken with high signal-to-noise level in the constant-initial-state mode, demonstrate the presence of Cu+, in contrast with previous photoemission and electron-energy-loss studies.
104. Extracellular sheath formation by Sphaeropsis hypodermia and association with its infection in elm trees
- Author
-
Bernier, L., Bussieres, G., Simard, M., Rioux, D., and Ouellette, G. B.
- Subjects
FUNGI ,PLANT diseases - Abstract
Sphaeropsis hypodermia, isolated from a cankered American elm branch, was grown on agar medium (PDA), on autoclaved wiping paper (Kimwipes), and American elm (Ulmus americana) wood chips, or inoculated intogreenhouse-grown American elm saplings. Samples from each treatment were double-fixed with glutaraldehyde and osmium tetroxide and examined with the light and the transmission electron microscopes. Ultrastructurally, the hyphae on PDA and inert substrates appeared surroundedby large extracellular sheaths which were delimited by rigid opaque bands of various thicknesses. The sheaths extended appreciable distances from the fungal cells, as evidenced by their adherence to rigid substrates. Individual or aggregated opaque bodies, even as large masses on elm wood chips, were the main components of the sheath. This opaque material was often associated with penetration and ruptures of the wood cells. Inoculated into elm trees, the fungus rapidly caused pronounced alterations of cambial tissues and colonized the adjoining bark and xylem cells. The prominent penetration and breakdown of the inner and outer bark cells by the fungus were associated with opaque material, particularly in cortical fibres. The material was structurally similar to the sheath formed on the rigid sterilized substrates. In the xylem, only the walls of the recently deposited cells were visibly altered, and although mature fibres were generally colonized, the passage of the fungus from one fibre to another was rarely observed, contrary to the passage from vessel and ray cells to adjoining cells. In that instance, only bands of opaque material present in the walls of fibres were connected with fungal cells in their lumen. In the inner bark and cambial regions, cell hypertrophy and hyperplasia occurred next to host walls that were altered and contained similar opaque material. The extracellular sheath of S. hypodermia under in vitro conditions and the; opaque material associated with host wall alteratio [ABSTRACT FROM AUTHOR]
- Published
- 2000
105. Photoemission study of an In diffusion barrier in ZnSe/InP(100) heterostructures
- Author
-
Rioux, D. and Hoechst, H.
- Published
- 1994
- Full Text
- View/download PDF
106. Valence band discontinuity at the ZnTe/CdTe interface: Making ohmic contact to [ital P]-type CdTe
- Author
-
Rioux, D [Synchrotron Radiation Center, 3731 Schneider Drive, Stoughton, Wisconsin 53589 (United States)]
- Published
- 1992
107. Unravelling large-scale patterns and drivers of biodiversity in dry rivers.
- Author
-
Foulquier A, Datry T, Corti R, von Schiller D, Tockner K, Stubbington R, Gessner MO, Boyer F, Ohlmann M, Thuiller W, Rioux D, Miquel C, Albariño R, Allen DC, Altermatt F, Arce MI, Arnon S, Banas D, Banegas-Medina A, Beller E, Blanchette ML, Blessing J, Boëchat IG, Boersma K, Bogan M, Bonada N, Bond N, Brintrup K, Bruder A, Burrows R, Cancellario T, Canhoto C, Carlson S, Cid N, Cornut J, Danger M, de Freitas Terra B, De Girolamo AM, Del Campo R, Díaz Villanueva V, Dyer F, Elosegi A, Febria C, Figueroa Jara R, Four B, Gafny S, Gómez R, Gómez-Gener L, Guareschi S, Gücker B, Hwan J, Jones JI, Kubheka PS, Laini A, Langhans SD, Launay B, Le Goff G, Leigh C, Little C, Lorenz S, Marshall J, Martin Sanz EJ, McIntosh A, Mendoza-Lera C, Meyer EI, Miliša M, Mlambo MC, Morais M, Moya N, Negus P, Niyogi D, Pagán I, Papatheodoulou A, Pappagallo G, Pardo I, Pařil P, Pauls SU, Polášek M, Rodríguez-Lozano P, Rolls RJ, Sánchez-Montoya MM, Savić A, Shumilova O, Sridhar KR, Steward A, Taleb A, Uzan A, Valladares Y, Vander Vorste R, Waltham NJ, Zak DH, and Zoppini A
- Subjects
- Animals, Fungi classification, Fungi genetics, Geologic Sediments microbiology, Bacteria classification, Bacteria genetics, Invertebrates classification, DNA Barcoding, Taxonomic, Plants classification, Archaea classification, Archaea genetics, Biodiversity, Rivers microbiology
- Abstract
More than half of the world's rivers dry up periodically, but our understanding of the biological communities in dry riverbeds remains limited. Specifically, the roles of dispersal, environmental filtering and biotic interactions in driving biodiversity in dry rivers are poorly understood. Here, we conduct a large-scale coordinated survey of patterns and drivers of biodiversity in dry riverbeds. We focus on eight major taxa, including microorganisms, invertebrates and plants: Algae, Archaea, Bacteria, Fungi, Protozoa, Arthropods, Nematodes and Streptophyta. We use environmental DNA metabarcoding to assess biodiversity in dry sediments collected over a 1-year period from 84 non-perennial rivers across 19 countries on four continents. Both direct factors, such as nutrient and carbon availability, and indirect factors such as climate influence the local biodiversity of most taxa. Limited resource availability and prolonged dry phases favor oligotrophic microbial taxa. Co-variation among taxa, particularly Bacteria, Fungi, Algae and Protozoa, explain more spatial variation in community composition than dispersal or environmental gradients. This finding suggests that biotic interactions or unmeasured ecological and evolutionary factors may strongly influence communities during dry phases, altering biodiversity responses to global changes., (© 2024. The Author(s).)
- Published
- 2024
- Full Text
- View/download PDF
108. Ectopic ACTH Cushing's syndrome caused by a large-cell neuroendocrine lung carcinoma responding to desmopressin.
- Author
-
Larose S, Rioux D, Albadine R, and Lacroix A
- Abstract
Ectopic adrenocorticotrophic hormone (ACTH) secretion (EAS) is a rare cause of ACTH-dependent Cushing's syndrome (CS), most often caused by a thoracic neuroendocrine tumor (NET). Large-cell neuroendocrine carcinomas (LCNEC) with EAS are rare and usually present a more severe ACTH secretion and hypercortisolism. We report a 44-year-old non-smoker man, who presented clinical and biochemical evidence of ACTH-dependent CS. Desmopressin 10 μg i.v. produced a 157% increase in ACTH and a 25% increase in cortisol from baseline; there was no stimulation of ACTH or cortisol during the corticotropin-releasing hormone (CRH) test and no suppression with high dose dexamethasone. Pituitary MRI identified a 5 mm lesion, but inferior petrosal venous sinus sampling under desmopressin did not identify a central ACTH source. Thorax and abdominal imaging identified a left lung micronodule. Surgery confirmed a lung LCNEC with strongly positive ACTH immunohistochemistry (IHC) in the primary and lymph node metastasis. The patient was in CS remission after surgery and adjuvant chemotherapy but developed a recurrence 9.5 years later, with LCNEC pulmonary left hilar metastases, ectopic CS, and positive ACTH IHC. This is the first report of LCNEC, with morphologic feature of carcinoid tumor of the lung with ectopic ACTH stimulated by desmopressin. Long delay prior to metastatic recurrence indicates relatively indolent NET. This case report indicates that response to desmopressin, which usually occurs in Cushing's disease or benign NETs, can occur in malignant LCNEC., Competing Interests: The authors have no disclosures related to this report and no competing interests to declare., (© the author(s).)
- Published
- 2023
- Full Text
- View/download PDF
109. Demographic inferences and climatic niche modelling shed light on the evolutionary history of the emblematic cold-adapted Apollo butterfly at regional scale.
- Author
-
Kebaïli C, Sherpa S, Rioux D, and Després L
- Subjects
- Animals, Biological Evolution, Demography, Ecosystem, Europe, Genetic Variation, Phylogeny, Butterflies genetics
- Abstract
Cold-adapted species escape climate warming by latitudinal and/or altitudinal range shifts, and currently occur in Southern Europe in isolated mountain ranges within "sky islands". Here, we studied the genetic structure of the Apollo butterfly in five such sky islands (above 1,000 m) in France, and infer its demographic history since the last interglacial, using single nucleotide polymorphisms (ddRADseq SNPs). The Auvergne and Alps populations show strong genetic differentiation but not alpine massifs, although separated by deep valleys. Combining three complementary demographic inference methods and species distribution models (SDMs) we show that the LIG period was highly unfavourable for Apollo that probably survived in small population in the highest summits of Auvergne. The population shifted downslope and expanded eastward between LIG and LGM throughout the large climatically suitable Rhône valley between the glaciated summits of Auvergne and Alps. The Auvergne and Alps populations started diverging before the LGM but remained largely connected till the mid-Holocene. Population decline in Auvergne was more gradual but started before (~7 kya vs. 800 ya), and was much stronger with current population size ten times lower than in the Alps. In the Alps, the low genetic structure and limited evidence for isolation by distance suggest a nonequilibrium metapopulation functioning. The core Apollo population experienced cycles of contraction-expansion with climate fluctuations with largely interconnected populations overtime according to a "metapopulation-pulsar" functioning. This study demonstrates the power of combining demographic inferences and SDMs to determine past and future evolutionary trajectories of an endangered species at a regional scale., (© 2021 John Wiley & Sons Ltd.)
- Published
- 2022
- Full Text
- View/download PDF
110. Altitudinal Zonation of Green Algae Biodiversity in the French Alps.
- Author
-
Stewart A, Rioux D, Boyer F, Gielly L, Pompanon F, Saillard A, Thuiller W, Valay JG, Maréchal E, and Coissac E
- Abstract
Mountain environments are marked by an altitudinal zonation of habitat types. They are home to a multitude of terrestrial green algae, who have to cope with abiotic conditions specific to high elevation, e.g., high UV irradiance, alternating desiccation, rain and snow precipitations, extreme diurnal variations in temperature and chronic scarceness of nutrients. Even though photosynthetic green algae are primary producers colonizing open areas and potential markers of climate change, their overall biodiversity in the Alps has been poorly studied so far, in particular in soil, where algae have been shown to be key components of microbial communities. Here, we investigated whether the spatial distribution of green algae followed the altitudinal zonation of the Alps, based on the assumption that algae settle in their preferred habitats under the pressure of parameters correlated with elevation. We did so by focusing on selected representative elevational gradients at distant locations in the French Alps, where soil samples were collected at different depths. Soil was considered as either a potential natural habitat or temporary reservoir of algae. We showed that algal DNA represented a relatively low proportion of the overall eukaryotic diversity as measured by a universal Eukaryote marker. We designed two novel green algae metabarcoding markers to amplify the Chlorophyta phylum and its Chlorophyceae class, respectively. Using our newly developed markers, we showed that elevation was a strong correlate of species and genus level distribution. Altitudinal zonation was thus determined for about fifty species, with proposed accessions in reference databases. In particular, Planophila laetevirens and Bracteococcus ruber related species as well as the snow alga Sanguina genus were only found in soil starting at 2,000 m above sea level. Analysis of environmental and bioclimatic factors highlighted the importance of pH and nitrogen/carbon ratios in the vertical distribution in soil. Capacity to grow heterotrophically may determine the Trebouxiophyceae over Chlorophyceae ratio. The intensity of freezing events (freezing degree days), proved also determinant in Chlorophyceae distribution. Guidelines are discussed for future, more robust and precise analyses of environmental algal DNA in mountain ecosystems and address green algae species distribution and dynamics in response to environmental changes., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2021 Stewart, Rioux, Boyer, Gielly, Pompanon, Saillard, Thuiller, Valay, Maréchal and Coissac.)
- Published
- 2021
- Full Text
- View/download PDF
111. Double-digest RAD-sequencing: do pre- and post-sequencing protocol parameters impact biological results?
- Author
-
Cumer T, Pouchon C, Boyer F, Yannic G, Rioux D, Bonin A, and Capblancq T
- Subjects
- Alleles, Animals, Computational Biology methods, DNA Restriction Enzymes metabolism, Genetics, Population, Polymorphism, Single Nucleotide, Reproducibility of Results, Butterflies genetics, Fagus genetics, High-Throughput Nucleotide Sequencing methods, Sequence Analysis, DNA methods
- Abstract
Next-generation sequencing technologies have opened a new era of research in population genetics. Following these new sequencing opportunities, the use of restriction enzyme-based genotyping techniques, such as restriction site-associated DNA sequencing (RAD-seq) or double-digest RAD-sequencing (ddRAD-seq), has dramatically increased in the last decade. From DNA sampling to SNP calling, the laboratory and bioinformatic parameters of enzyme-based techniques have been investigated in the literature. However, the impact of those parameters on downstream analyses and biological results remains less documented. In this study, we investigated the effects of sevral pre- and post-sequencing settings on ddRAD-seq results for two biological systems: a complex of butterfly species (Coenonympha sp.) and several populations of common beech (Fagus sylvatica). Our results suggest that pre-sequencing parameters (i.e., DNA quantity, number of PCR cycles during library preparation) have a significant impact on the number of recovered reads and SNPs, on the number of unique alleles and on individual heterozygosity. In the same way, we found that post-sequencing settings (i.e., clustering and minimum coverage thresholds) influenced loci reconstruction (e.g., number of loci, mean coverage) and SNP calling (e.g., number of SNPs; heterozygosity) but had only a marginal impact on downstream analyses (e.g., measure of genetic differentiation, estimation of individual admixture, and demographic inferences). In addition, replication analyses confirmed the reproducibility of the ddRAD-seq procedure. Overall, this study assesses the degree of sensitivity of ddRAD-seq data to pre- and post-sequencing protocols, and illustrates its robustness when studying population genetics.
- Published
- 2021
- Full Text
- View/download PDF
112. Antibacterial activity of geraniin from sugar maple leaves: an ultrastructural study with the phytopathogen Xanthomonas campestris pv. vitians .
- Author
-
Delisle-Houde M, Blais M, Tweddell RJ, and Rioux D
- Abstract
Effect of geraniin extracted from sugar maple ( Acer saccharum ) leaves on the viability of the phytopathogen Xanthomonas campestris pv. vitians was evaluated with the SYTOX Green nucleic acid stain, penetrating only compromised membranes, and plate counts. In parallel, structural changes of treated bacteria were examined in transmission electron microscopy (TEM). Based on SYTOX Green and plate counts, geraniin at the minimum bactericidal concentration (3.125 mg/ml) increased mortality after 45 min by 37% and 62%, respectively, when compared with controls. According to observations in TEM, geraniin caused morphological alterations of these rod-shaped bacteria, including degradation of their envelopes, as also suggested by the incorporation of SYTOX. These alterations were often accompanied by cytoplasm leakage and the formation of more pronounced whitish areas in the cytoplasm similar to vacuolization. Moreover, multi-membranous and/or -wall systems were at times formed in the treated bacteria. The presence of some extracellular electron-dense material was frequently noted around the treated bacteria. The matrix surrounding control bacteria tended to disappear after geraniin treatment. This study highlights for the first time the effect of geraniin on bacterial ultrastructure, thus contributing to a better understanding of the mechanism by which this molecule exerts antibacterial activity., (© Società Italiana di Patologia Vegetale (S.I.Pa.V.) 2021.)
- Published
- 2021
- Full Text
- View/download PDF
113. Increasing Undergraduate Exposure to Oncology: the Role of Oncology Interest Groups.
- Author
-
Sherwood M, Rioux D, Knight R, LeBlanc M, Betsch T, Giuliani M, and Caissie A
- Subjects
- Canada, Curriculum, Group Processes, Humans, Medical Oncology standards, Medical Oncology statistics & numerical data, Surveys and Questionnaires, Education, Medical, Undergraduate methods, Medical Oncology education, Mentors psychology, Societies statistics & numerical data, Students, Medical psychology
- Abstract
This study describes a medical school oncology interest group (OIG) and assesses its influence on student perceptions of oncology, interest in pursuing oncology as a career, and comfort levels with oncology topics such as breaking bad news. From 2015 to 2017, the OIG annual event took place at a satellite campus of a larger Canadian undergraduate medical school. The event provided a question and answer period with a panel of physicians from multiple oncology specialties-discussions focused around lifestyle, training, clinical work, lifestyle, and career focus. Small physician-led groups taught breaking bad news using the SPIKES framework. The interest group also provided a mentoring and networking opportunity to interested students. Pre- and post-event surveys were distributed to students and physicians. For three consecutive years, the student-run, and physician-mentored OIG successfully recruited student and physician participants, providing a clinical skill teaching session as well as mentorship opportunities to students. Pre-event surveys found that only 20% of students believed their current curriculum was adequate as it relates to oncology education. In pre-session, 13% (6/45) of students indicated comfort with the skill of breaking bad news, compared with that in post-session with 81% (34/42) of students feeling comfortable. When asked "How likely are you to pursue a future elective opportunity in oncology?" 49% (20/41) of students indicated "likely" as their response in the pre-session. This response increased post-session to 70% (28/40). The event highlighted the potential for OIGs to increase student interest in pursuing oncology electives and student-perceived comfort with breaking bad news. OIGs are important in promoting interest in the field of oncology and in improving confidence in breaking bad news. This medical student-created, run and maintained oncology interest group supplemented standard curriculum by providing relevant educational and mentorship opportunities to students. This study highlights the feasibility of implementing a self-sustaining medical school oncology interest group and its potential to positively impact student learning and interest in oncology.
- Published
- 2020
- Full Text
- View/download PDF
114. Olfaction: Receptor Antagonistes.
- Author
-
Rioux D and Carlson JR
- Subjects
- Animals, Mammals, Odorants, Receptors, Odorant genetics
- Abstract
Odor receptors of the mammalian olfactory system have long been known to be activated in combinatorial fashion by odorants. A large-scale study now reveals that inhibition of receptors by odorants is comparably prevalent and combinatorial., (Copyright © 2020 Elsevier Inc. All rights reserved.)
- Published
- 2020
- Full Text
- View/download PDF
115. Hyperspectral Imaging as a Tool to Study Optical Anisotropy in Lanthanide-Based Molecular Single Crystals.
- Author
-
Rodrigues EM, Rutajoga N, Rioux D, Yvon-Leroux J, and Hemmer E
- Subjects
- Anisotropy, Luminescence, Lanthanoid Series Elements chemistry, Optical Imaging, Optical Phenomena
- Abstract
In this work, we describe a protocol for a novel application of hyperspectral imaging (HSI) in the analysis of luminescent lanthanide (Ln
3+ )-based molecular single crystals. As representative example, we chose a single crystal of the heterodinuclear Ln-based complex [TbEu(bpm)(tfaa)6] (bpm=2,2'-bipyrimidine, tfaa- =1,1,1-trifluoroacetylacetonate) exhibiting bright visible emission under UV excitation. HSI is an emerging technique that combines 2-dimensional spatial imaging of a luminescent structure with spectral information from each pixel of the obtained image. Specifically, HSI on single crystals of the [Tb-Eu] complex provided local spectral information unveiling variation of the luminescence intensity at different points along the studied crystals. These changes were attributed to the optical anisotropy present in the crystal, which results from the different molecular packing of Ln3+ ions in each one of the directions of the crystal structure. The HSI herein described is an example of the suitability of such technique for spectro-spatial investigations of molecular materials. Yet, importantly, this protocol can be easily extended for other types of luminescent materials (such as micron-sized molecular crystals, inorganic microparticles, nanoparticles in biological tissues, or labelled cells, among others), opening many possibilities for deeper investigation of structure-property relationships. Ultimately, such investigations will provide knowledge to be leveraged into the engineering of advanced materials for a wide range of applications from bioimaging to technological applications, such as waveguides or optoelectronic devices.- Published
- 2020
- Full Text
- View/download PDF
116. Convergence and divergence: An analysis of mechanical restraints.
- Author
-
Jacob JD, Holmes D, Rioux D, Corneau P, and MacPhee C
- Subjects
- Humans, Interviews as Topic methods, Ontario, Psychiatric Nursing ethics, Psychiatric Nursing methods, Qualitative Research, Nurses psychology, Patients psychology, Restraint, Physical ethics
- Abstract
Background: Psychiatric nurses are regularly confronted with the uses and effects of control interventions such as mechanical restraints. Although there are evident tensions in the literature regarding the use of mechanical restraints, very little research has focused on the lived and embodied experience of their use, whether from the patient's perspective or the perspective of nursing staff responsible for their application., Research Aims: (1) to gain access to the bodily phenomenon of being placed in mechanical restraints; (2) to give voice to the intimate experiential understanding of this experience; and (3) through phenomenological interpretation, to understand the subjective processes and meaning-making of this experience., Research Design: For this research, we adopted a distinctly ethics-oriented application of the methodology known as interpretative phenomenological analysis, that is, the interpretive dimension of the research focused on ethical practice in mental healthcare - one that is informed by experiential accounts of the lived body., Participants and Research Context: A total of 40 in-depth semi-structured, nondirected interviews with both nurses (n = 21) and patients (n = 19) we conducted to meet the aims of this article. Participants were recruited from an inpatient psychiatric unit of a Canadian general hospital., Ethical Considerations: The research received research ethics board clearance from both the hospital where the study took place and the University of Ottawa., Findings: The comparative analysis is presented under the following headings: (1) context of care, (2) meaning of quality of care, (3) emotional reactions and nurse-patient relationship, (4) meeting the needs and (5) need for alternatives., Discussion/conclusions: The research findings are discussed in light of current literature and implications for practice.
- Published
- 2019
- Full Text
- View/download PDF
117. Speciation with gene flow: Evidence from a complex of alpine butterflies ( Coenonympha , Satyridae).
- Author
-
Capblancq T, Mavárez J, Rioux D, and Després L
- Abstract
Until complete reproductive isolation is achieved, the extent of differentiation between two diverging lineages is the result of a dynamic equilibrium between genetic isolation and mixing. This is especially true for hybrid taxa, for which the degree of isolation in regard to their parental species is decisive in their capacity to rise as a new and stable entity. In this work, we explored the past and current patterns of hybridization and divergence within a complex of closely related butterflies in the genus Coenonympha in which two alpine species, C. darwiniana and C. macromma , have been shown to result from hybridization between the also alpine C. gardetta and the lowland C. arcania . By testing alternative scenarios of divergence among species, we show that gene flow has been uninterrupted throughout the speciation process, although leading to different degrees of current genetic isolation between species in contact zones depending on the pair considered. Nonetheless, at broader geographic scale, analyses reveal a clear genetic differentiation between hybrid lineages and their parental species, pointing out to an advanced stage of the hybrid speciation process. Finally, the positive correlation observed between ecological divergence and genetic isolation among these butterflies suggests a potential role for ecological drivers during their speciation processes., Competing Interests: None declared.
- Published
- 2019
- Full Text
- View/download PDF
118. Unravelling the invasion history of the Asian tiger mosquito in Europe.
- Author
-
Sherpa S, Blum MGB, Capblancq T, Cumer T, Rioux D, and Després L
- Subjects
- Aedes genetics, Animals, Bayes Theorem, Europe, Genetics, Population, Italy, Polymorphism, Single Nucleotide, Population Density, Aedes physiology, Genetic Variation, Introduced Species
- Abstract
Multiple introductions are key features for the establishment and persistence of introduced species. However, little is known about the contribution of genetic admixture to the invasive potential of populations. To address this issue, we studied the recent invasion of the Asian tiger mosquito (Aedes albopictus) in Europe. Combining genome-wide single nucleotide polymorphisms and historical knowledge using an approximate Bayesian computation framework, we reconstruct the colonization routes and establish the demographic dynamics of invasion. The colonization of Europe involved at least three independent introductions in Albania, North Italy and Central Italy that subsequently acted as dispersal centres throughout Europe. We show that the topology of human transportation networks shaped demographic histories with North Italy and Central Italy being the main dispersal centres in Europe. Introduction modalities conditioned the levels of genetic diversity in invading populations, and genetically diverse and admixed populations promoted more secondary introductions and have spread farther than single-source invasions. This genomic study provides further crucial insights into a general understanding of the role of genetic diversity promoted by modern trade in driving biological invasions., (© 2019 John Wiley & Sons Ltd.)
- Published
- 2019
- Full Text
- View/download PDF
119. Body size determines soil community assembly in a tropical forest.
- Author
-
Zinger L, Taberlet P, Schimann H, Bonin A, Boyer F, De Barba M, Gaucher P, Gielly L, Giguet-Covex C, Iribar A, Réjou-Méchain M, Rayé G, Rioux D, Schilling V, Tymen B, Viers J, Zouiten C, Thuiller W, Coissac E, and Chave J
- Subjects
- Animals, Bacteria, DNA Barcoding, Taxonomic, Food Chain, French Guiana, Fungi, Plants, Soil Microbiology, Biodiversity, Biota, Body Size, Rainforest, Tropical Climate
- Abstract
Tropical forests shelter an unparalleled biological diversity. The relative influence of environmental selection (i.e., abiotic conditions, biotic interactions) and stochastic-distance-dependent neutral processes (i.e., demography, dispersal) in shaping communities has been extensively studied for various organisms, but has rarely been explored across a large range of body sizes, in particular in soil environments. We built a detailed census of the whole soil biota in a 12-ha tropical forest plot using soil DNA metabarcoding. We show that the distribution of 19 taxonomic groups (ranging from microbes to mesofauna) is primarily stochastic, suggesting that neutral processes are prominent drivers of the assembly of these communities at this scale. We also identify aluminium, topography and plant species identity as weak, yet significant drivers of soil richness and community composition of bacteria, protists and to a lesser extent fungi. Finally, we show that body size, which determines the scale at which an organism perceives its environment, predicted the community assembly across taxonomic groups, with soil mesofauna assemblages being more stochastic than microbial ones. These results suggest that the relative contribution of neutral processes and environmental selection to community assembly directly depends on body size. Body size is hence an important determinant of community assembly rules at the scale of the ecological community in tropical soils and should be accounted for in spatial models of tropical soil food webs., (© 2018 John Wiley & Sons Ltd.)
- Published
- 2019
- Full Text
- View/download PDF
120. Differences in the fungal communities nursed by two genetic groups of the alpine cushion plant, Silene acaulis .
- Author
-
Roy J, Bonneville JM, Saccone P, Ibanez S, Albert CH, Boleda M, Gueguen M, Ohlmann M, Rioux D, Clément JC, Lavergne S, and Geremia RA
- Abstract
Foundation plants shape the composition of local biotic communities and abiotic environments, but the impact of a plant's intraspecific variations on these processes is poorly understood. We examined these links in the alpine cushion moss campion ( Silene acaulis ) on two neighboring mountain ranges in the French Alps. Genotyping of cushion plants revealed two genetic clusters matching known subspecies. The exscapa subspecies was found on both limestone and granite, while the longiscapa one was only found on limestone. Even on similar limestone bedrock, cushion soils from the two S. acaulis subspecies deeply differed in their impact on soil abiotic conditions. They further strikingly differed from each other and from the surrounding bare soils in fungal community composition. Plant genotype variations accounted for a large part of the fungal composition variability in cushion soils, even when considering geography or soil chemistry, and particularly for the dominant molecular operational taxonomic units (MOTUs). Both saprophytic and biotrophic fungal taxa were related to the MOTUs recurrently associated with a single plant genetic cluster. Moreover, the putative phytopathogens were abundant, and within the same genus ( Cladosporium ) or species ( Pyrenopeziza brassicae ), MOTUs showing specificity for each plant subspecies were found. Our study highlights the combined influences of bedrock and plant genotype on fungal recruitment into cushion soils and suggests the coexistence of two mechanisms, an indirect selection resulting from the colonization of an engineered soil by free-living saprobes and a direct selection resulting from direct plant-fungi interactions.
- Published
- 2018
- Full Text
- View/download PDF
121. First Extensive Microscopic Study of Butternut Defense Mechanisms Following Inoculation with the Canker Pathogen Ophiognomonia clavigignenti-juglandacearum Reveals Compartmentalization of Tissue Damage.
- Author
-
Rioux D, Blais M, Nadeau-Thibodeau N, Lagacé M, DesRochers P, Klimaszewska K, and Bernier L
- Subjects
- Cell Wall ultrastructure, Cellulose analogs & derivatives, Cellulose metabolism, Juglans metabolism, Juglans microbiology, Juglans ultrastructure, Phenols metabolism, Plant Diseases microbiology, Plant Dormancy, Seedlings immunology, Seedlings microbiology, Seedlings ultrastructure, Xylem immunology, Xylem microbiology, Xylem ultrastructure, Ascomycota physiology, Disease Resistance, Juglans immunology, Plant Diseases immunology
- Abstract
Ophiognomonia clavigignenti-juglandacearum endangers the survival of butternut (Juglans cinerea) throughout its native range. While screening for disease resistance, we found that artificial inoculations of 48 butternut seedlings with O. clavigignenti-juglandacearum induced the expression of external symptoms, but only after a period of dormancy. Before dormancy, compartmentalized tissues such as necrophylactic periderms (NPs) and xylem reaction zones (RZs) contributed to limiting pathogen invasion. Phenols were regularly detected in RZs, often in continuity with NPs during wound closure, and confocal microscopy revealed their presence in parenchyma cells, vessel plugs and cell walls. Vessels were blocked with tyloses and gels, particularly those present in RZs. Suberin was also detected in cells formed over the affected xylem by the callus at the inoculation point, in a few tylosis walls, and in longitudinal tubes that formed near NPs. Following dormancy, in all inoculated seedlings but one, defensive barriers were breached by O. clavigignenti-juglandacearum and then additional ones were produced in response to this new invasion. The results of this histopathological study indicate that trees inoculated in selection programs to test butternut canker resistance should go through at least one period of dormancy and that asymptomatic individuals should be dissected to better assess how they defend themselves against O. clavigignenti-juglandacearum.
- Published
- 2018
- Full Text
- View/download PDF
122. Humidity response depends on the small soluble protein Obp59a in Drosophila .
- Author
-
Sun JS, Larter NK, Chahda JS, Rioux D, Gumaste A, and Carlson JR
- Subjects
- Animals, Climate Change, Drosophila melanogaster physiology, Receptors, Odorant genetics, Receptors, Odorant physiology, Sensilla physiology, Carrier Proteins genetics, Drosophila Proteins genetics, Drosophila melanogaster genetics, Humidity
- Abstract
Hygrosensation is an essential sensory modality that is used to find sources of moisture. Hygroreception allows animals to avoid desiccation, an existential threat that is increasing with climate change. Humidity response, however, remains poorly understood. Here we find that humidity-detecting sensilla in the Drosophila antenna express and rely on a small protein, Obp59a. Mutants lacking this protein are defective in three hygrosensory behaviors, one operating over seconds, one over minutes, and one over hours. Remarkably, loss of Obp59a and humidity response leads to an increase in desiccation resistance. Obp59a is an exceptionally well-conserved, highly localized, and abundantly expressed member of a large family of secreted proteins. Antennal Obps have long been believed to transport hydrophobic odorants, and a role in hygroreception was unexpected. The results enhance our understanding of hygroreception, Obp function, and desiccation resistance, a process that is critical to insect survival., Competing Interests: JS, NL, JC, DR, AG, JC No competing interests declared, (© 2018, Sun et al.)
- Published
- 2018
- Full Text
- View/download PDF
123. Diet shifts by adult flightless dung beetles Circellium bacchus, revealed using DNA metabarcoding, reflect complex life histories.
- Author
-
Kerley GIH, Landman M, Ficetola GF, Boyer F, Bonin A, Rioux D, Taberlet P, and Coissac E
- Subjects
- Animals, Biodiversity, DNA, Diet, Feces, Coleoptera
- Abstract
Life history changes may change resource use. Such shifts are not well understood in the dung beetles, despite recognised differences in larval and adult feeding ability. We use the flightless dung beetle Circellium bacchus to explore such shifts, identifying dung sources of adults using DNA metabarcoding, and comparing these with published accounts of larval dung sources. C. bacchus is traditionally considered to specialise on the dung of large herbivores for both larval and adult feeding. We successfully extracted mammal DNA from 151 adult C. bacchus fecal samples, representing 16 mammal species (ranging from elephants to small rodents), many of which are hitherto undescribed in the diet. Adult C. bacchus showed clear dung source preferences, especially for large herbivores inhabiting dense-cover vegetation. Our approach also confirmed the presence of cryptic taxa in the study area, and we propose that this may be used for biodiversity survey and monitoring purposes. Murid rodent feces were the most commonly fed-upon dung source (77.5%) for adult C. bacchus, differing markedly from the large and megaherbivore dung sources used for larval rearing. These findings support the hypothesis of life history-specific shifts in resource use in dung beetles, and reveal a hitherto unsuspected, but ecologically important, role of these dung beetles in consuming rodent feces. The differences in feeding abilities of the larval and adult life history stages have profound consequences for their resource use and foraging strategies, and hence the ecological role of dung beetles. This principle and its ecological consequences should be explored in other scarabaeids.
- Published
- 2018
- Full Text
- View/download PDF
124. An Overview of Canadian Research Activities on Diseases Caused by Phytophthora ramorum: Results, Progress, and Challenges.
- Author
-
Shamoun SF, Rioux D, Callan B, James D, Hamelin RC, Bilodeau GJ, Elliott M, Lévesque CA, Becker E, McKenney D, Pedlar J, Bailey K, Brière SC, Niquidet K, and Allen E
- Subjects
- Antibiosis physiology, Canada, Fungicides, Industrial pharmacology, Geography, Host-Pathogen Interactions drug effects, Phytophthora drug effects, Plant Diseases economics, Research economics, Trees classification, Phytophthora physiology, Plant Diseases microbiology, Research statistics & numerical data, Trees microbiology
- Abstract
International trade and travel are the driving forces behind the spread of invasive plant pathogens around the world, and human-mediated movement of plants and plant products is now generally accepted as the primary mode of their introduction, resulting in huge disturbance to ecosystems and severe socio-economic impact. These problems are exacerbated under the present conditions of rapid climatic change. We report an overview of the Canadian research activities on Phytophthora ramorum. Since the first discovery and subsequent eradication of P. ramorum on infected ornamentals in nurseries in Vancouver, British Columbia, in 2003, a research team of Canadian government scientists representing the Canadian Forest Service, Canadian Food Inspection Agency, and Agriculture and Agri-Food Canada worked together over a 10-year period and have significantly contributed to many aspects of research and risk assessment on this pathogen. The overall objectives of the Canadian research efforts were to gain a better understanding of the molecular diagnostics of P. ramorum, its biology, host-pathogen interactions, and management options. With this information, it was possible to develop pest risk assessments and evaluate the environmental and economic impact and future research needs and challenges relevant to P. ramorum and other emerging forest Phytophthora spp.
- Published
- 2018
- Full Text
- View/download PDF
125. Factors Influencing the Regional Dynamics of Butternut Canker.
- Author
-
Sambaraju KR, DesRochers P, and Rioux D
- Subjects
- Quebec, Seasons, Weather, Ascomycota physiology, Juglans microbiology, Plant Diseases microbiology
- Abstract
Butternut (Juglans cinerea) is an important component of native biodiversity in eastern North America. Of urgent concern is the survival of butternut, whose populations are declining rapidly, in large part due to an exotic pathogen, Ophiognomonia clavigignenti-juglandacearum, that causes butternut canker. The disease presently occurs throughout the range of butternut in North America, causing branch and stem cankers, dieback, and tree mortality. Despite the existential threat posed by O. clavigignenti-juglandacearum to butternut, a detailed understanding of the factors that drive cross-scale disease patterns is lacking. Therefore, we investigated the association of a range of factors, including tree attributes, topography, and weather, with butternut canker spatial dynamics at different scales using data collected in the province of Quebec, Canada. Trunk canker damage and dieback showed distinct geographic patterns. Bark phenotype was not significantly associated with trunk canker damage. Results suggest that open or dominant trees may show less dieback than intermediate or suppressed trees. Probability of the presence of trunk canker and percent dieback were proportional to the tree diameter at breast height. Temperature was positively associated with disease severity at a 1-km
2 scale. Our results provide strong evidence that multiple factors, notably weather, influence butternut canker epidemiology.- Published
- 2018
- Full Text
- View/download PDF
126. Genetic diversity and distribution differ between long-established and recently introduced populations in the invasive mosquito Aedes albopictus.
- Author
-
Sherpa S, Rioux D, Pougnet-Lagarde C, and Després L
- Subjects
- Analysis of Variance, Animals, Gene Flow, Geography, Introduced Species, Phylogeny, Polymorphism, Single Nucleotide, Population Dynamics, Aedes classification, Aedes genetics, Genetic Markers, Genetic Variation, Genetics, Population
- Abstract
The Asian tiger mosquito Aedes albopictus, native to South-eastern Asia, is currently the most invasive mosquito in the world. The spatio-temporal dynamics of its expansion through the genetic characterization of invasive populations has been challenged so far by the limited number of genetic markers variable enough to infer the genetic structure in recently invaded areas. Here we applied the double-digest Restriction-site Associated DNA sequencing method (ddRADseq) to mosquitoes collected in two invaded areas, Reunion Island (12 localities) and Europe (18 localities). Analyses of genetic diversity, Bayesian clustering, Maximum Likelihood inference and isolation-by-distance tests based on 1561 genome-wide distributed Single Nucleotide Polymorphisms (SNPs) revealed that Reunion Island and Europe form two distinct genetic clusters, supporting no contemporary gene flow and suggesting two different and independent invasion histories. Long-established populations (Reunion Island) were more genetically diverse than recently introduced European populations. The largest part of genetic variance was found at the intra-individual level (>85%) and most F
IS values were positive, suggesting inbreeding at the local scale. The two invaded areas showed contrasting patterns of genetic structure. Significant isolation-by-distance was found among Reunion Island populations, suggesting that these populations are at the drift-migration equilibrium. In contrast, long-distance human-assisted transport is probably the main dispersal mechanism in Europe., (Copyright © 2017 Elsevier B.V. All rights reserved.)- Published
- 2018
- Full Text
- View/download PDF
127. At the Origin of a Worldwide Invasion: Unraveling the Genetic Makeup of the Caribbean Bridgehead Populations of the Dengue Vector Aedes aegypti.
- Author
-
Sherpa S, Rioux D, Goindin D, Fouque F, François O, and Després L
- Subjects
- Animals, Caribbean Region epidemiology, Dengue epidemiology, Genetic Variation, Humans, Insecticide Resistance, Polymorphism, Single Nucleotide, Aedes genetics, Dengue transmission, Mosquito Vectors genetics
- Abstract
Human-driven global environmental changes have considerably increased the risk of biological invasions, especially the spread of human parasites and their vectors. Among exotic species that have major impacts on public health, the dengue fever mosquito Aedes aegypti originating from Africa has spread worldwide during the last three centuries. Although considerable progress has been recently made in understanding the history of this invasion, the respective roles of human and abiotic factors in shaping patterns of genetic diversity remain largely unexplored. Using a genome-wide sample of genetic variants (3,530 ddRAD SNPs), we analyzed the genetic structure of Ae. aegypti populations in the Caribbean, the first introduced territories in the Americas. Fourteen populations were sampled in Guyane and in four islands of the Antilles that differ in climatic conditions, intensity of urbanization, and vector control history. The genetic diversity in the Caribbean was low (He = 0.14-0.17), as compared with a single African collection from Benin (He = 0.26) and site-frequency spectrum analysis detected an ancient bottleneck dating back ∼300 years ago, supporting a founder event during the introduction of Ae. aegypti. Evidence for a more recent bottleneck may be related to the eradication program undertaken on the American continent in the 1950s. Among 12 loci detected as FST-outliers, two were located in candidate genes for insecticide resistance (cytochrome P450 and voltage-gated sodium channel). Genome-environment association tests identified additional loci associated with human density and/or deltamethrin resistance. Our results highlight the high impact of human pressures on the demographic history and genetic variation of Ae. aegypti Caribbean populations., (© The Author 2017. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)
- Published
- 2018
- Full Text
- View/download PDF
128. Corrigendum to "Evolution and taxonomy of the wild species of the genus Ovis (Mammalia, Artiodactyla, Bovidae)" [Mol. Phylogenet. Evol. 54(2) (2010) 315-326].
- Author
-
Rezaei HR, Naderi S, Chintauan-Marquier IC, Jordan S, Taberlet P, Virk AT, Naghash HR, Rioux D, Kaboli M, Luikart G, and Pompanon F
- Published
- 2017
- Full Text
- View/download PDF
129. [Understanding the use of mechanical restraints in psychiatry: phenomenological study of nurses’lived experience].
- Author
-
Corneau P, Jacob JD, Holmes D, and Rioux D
- Subjects
- Attitude of Health Personnel, Canada, Comprehension, Health Knowledge, Attitudes, Practice, Humans, Life Change Events, Practice Patterns, Nurses', Psychiatric Nursing methods, Nurses psychology, Restraint, Physical psychology, Stress, Psychological etiology, Stress, Psychological prevention & control
- Abstract
The use of mechanical restraints in psychiatric settings is currently the subject of ethical controversy. However, both patients' and nurses' voices are absent in the debate over this controversial intervention. The objective of this qualitative study was to examine the experience of psychiatric nurses using mechanical restraints. Twentyone nurses working on either the acute psychiatric inpatient unit and/or the emergency psychiatric unit of a university affiliated Canadian hospital participated in semi-structured interviews, which were then transcribed, coded and analyzed using the interpretative phenomenological analysis (IPA) method. Three main themes were identified : 1) Practice setting ; 2) Mechanical restraint process ; and 3) Resorting to mechanical restraints. These results highlight the organizational and emotional challenges faced by psychiatric nurses. Foucault and Goffman's work were the primary theoretical sources that guided the critical analysis of this qualitative research.
- Published
- 2017
- Full Text
- View/download PDF
130. 3D multiplexed immunoplasmonics microscopy.
- Author
-
Bergeron É, Patskovsky S, Rioux D, and Meunier M
- Subjects
- Biomarkers analysis, Cell Line, Tumor, Humans, Membrane Proteins analysis, Microscopy, Fluorescence, Silver, Antibodies, Microscopy methods, Nanospheres, Nanotubes
- Abstract
Selective labelling, identification and spatial distribution of cell surface biomarkers can provide important clinical information, such as distinction between healthy and diseased cells, evolution of a disease and selection of the optimal patient-specific treatment. Immunofluorescence is the gold standard for efficient detection of biomarkers expressed by cells. However, antibodies (Abs) conjugated to fluorescent dyes remain limited by their photobleaching, high sensitivity to the environment, low light intensity, and wide absorption and emission spectra. Immunoplasmonics is a novel microscopy method based on the visualization of Abs-functionalized plasmonic nanoparticles (fNPs) targeting cell surface biomarkers. Tunable fNPs should provide higher multiplexing capacity than immunofluorescence since NPs are photostable over time, strongly scatter light at their plasmon peak wavelengths and can be easily functionalized. In this article, we experimentally demonstrate accurate multiplexed detection based on the immunoplasmonics approach. First, we achieve the selective labelling of three targeted cell surface biomarkers (cluster of differentiation 44 (CD44), epidermal growth factor receptor (EGFR) and voltage-gated K(+) channel subunit KV1.1) on human cancer CD44(+) EGFR(+) KV1.1(+) MDA-MB-231 cells and reference CD44(-) EGFR(-) KV1.1(+) 661W cells. The labelling efficiency with three stable specific immunoplasmonics labels (functionalized silver nanospheres (CD44-AgNSs), gold (Au) NSs (EGFR-AuNSs) and Au nanorods (KV1.1-AuNRs)) detected by reflected light microscopy (RLM) is similar to the one with immunofluorescence. Second, we introduce an improved method for 3D localization and spectral identification of fNPs based on fast z-scanning by RLM with three spectral filters corresponding to the plasmon peak wavelengths of the immunoplasmonics labels in the cellular environment (500 nm for 80 nm AgNSs, 580 nm for 100 nm AuNSs and 700 nm for 40 nm × 92 nm AuNRs). Third, the developed technology is simple and compatible with standard epi-fluorescence microscopes used in biological and clinical laboratories. Thus, 3D multiplexed immunoplasmonics microscopy is ready for clinical applications as a cost-efficient alternative to immunofluorescence.
- Published
- 2016
- Full Text
- View/download PDF
131. Is There Any Evidence for Rapid, Genetically-Based, Climatic Niche Expansion in the Invasive Common Ragweed?
- Author
-
Gallien L, Thuiller W, Fort N, Boleda M, Alberto FJ, Rioux D, Lainé J, and Lavergne S
- Subjects
- Acclimatization genetics, Altitude, Ambrosia adverse effects, Ambrosia immunology, Climate, Ecosystem, Evolution, Molecular, France, Gene Flow, Genetic Variation, Humans, Models, Biological, Phenotype, Selection, Genetic, Ambrosia genetics, Introduced Species
- Abstract
Climatic niche shifts have been documented in a number of invasive species by comparing the native and adventive climatic ranges in which they occur. However, these shifts likely represent changes in the realized climatic niches of invasive species, and may not necessarily be driven by genetic changes in climatic affinities. Until now the role of rapid niche evolution in the spread of invasive species remains a challenging issue with conflicting results. Here, we document a likely genetically-based climatic niche expansion of an annual plant invader, the common ragweed (Ambrosia artemisiifolia L.), a highly allergenic invasive species causing substantial public health issues. To do so, we looked for recent evolutionary change at the upward migration front of its adventive range in the French Alps. Based on species climatic niche models estimated at both global and regional scales we stratified our sampling design to adequately capture the species niche, and localized populations suspected of niche expansion. Using a combination of species niche modeling, landscape genetics models and common garden measurements, we then related the species genetic structure and its phenotypic architecture across the climatic niche. Our results strongly suggest that the common ragweed is rapidly adapting to local climatic conditions at its invasion front and that it currently expands its niche toward colder and formerly unsuitable climates in the French Alps (i.e. in sites where niche models would not predict its occurrence). Such results, showing that species climatic niches can evolve on very short time scales, have important implications for predictive models of biological invasions that do not account for evolutionary processes.
- Published
- 2016
- Full Text
- View/download PDF
132. Hybridization promotes speciation in Coenonympha butterflies.
- Author
-
Capblancq T, Després L, Rioux D, and Mavárez J
- Subjects
- Animals, Bayes Theorem, Biological Evolution, France, Genetics, Population, Italy, Polymorphism, Single Nucleotide, Sequence Analysis, DNA, Switzerland, Butterflies genetics, Genetic Speciation, Hybridization, Genetic
- Abstract
Hybridization has become a central element in theories of animal evolution during the last decade. New methods in population genomics and statistical model testing now allow the disentangling of the complexity that hybridization brings into key evolutionary processes such as local adaptation, colonization of new environments, species diversification and extinction. We evaluated the consequences of hybridization in a complex of three alpine butterflies in the genus Coenonympha, by combining morphological, genetic and ecological analyses. A series of approximate Bayesian computation procedures based on a large SNP data set strongly suggest that the Darwin's Heath (Coenonympha darwiniana) originated through hybridization between the Pearly Heath (Coenonympha arcania) and the Alpine Heath (Coenonympha gardetta) with different parental contributions. As a result of hybridization, the Darwin's Heath presents an intermediate morphology between the parental species, while its climatic niche seems more similar to the Alpine Heath. Our results also reveal a substantial genetic and morphologic differentiation between the two geographically disjoint Darwin's Heath lineages leading us to propose the splitting of this taxon into two different species., (© 2015 John Wiley & Sons Ltd.)
- Published
- 2015
- Full Text
- View/download PDF
133. Upscaling the niche variation hypothesis from the intra- to the inter-specific level.
- Author
-
Bison M, Ibanez S, Redjadj C, Boyer F, Coissac E, Miquel C, Rioux D, Said S, Maillard D, Taberlet P, Yoccoz NG, and Loison A
- Subjects
- Animals, Behavior, Animal, DNA Barcoding, Taxonomic, Deer genetics, Diet, Herbivory, Population Dynamics, Rupicapra genetics, Seasons, Sheep, Domestic genetics, Social Behavior, Species Specificity, Deer physiology, Ecosystem, Rupicapra physiology, Sheep, Domestic physiology
- Abstract
The "niche variation hypothesis" (NVH) predicts that populations with wider niches should display higher among-individual variability. This prediction originally stated at the intra-specific level may be extended to the inter-specific level: individuals of generalist species may differ to a greater extent than individuals of a specialist species. We tested the NVH at intra- and inter-specific levels based on a large diet database of three large herbivore feces collected in the field and analyzed using DNA metabarcoding. The three herbivores (roe deer Capreolus capreolus, chamois Rupicapra rupicapra and mouflon Ovis musimon) are highly contrasted in terms of sociality (solitary to highly gregarious) and diet. The NVH at the intraspecific level was tested by relating, for the same population, diet breadth and inter-individual variation across the four seasons. Compared to null models, our data supported the NVH both at the intra- and inter-specific levels. Inter-individual variation of the diet of solitary species was not larger than in social species, although social individuals feed together and could therefore have more similar diets. Hence, the NVH better explained diet breadth than other factors such as sociality. The expansion of the population niche of the three species was driven by resource availability, and achieved by an increase in inter-individual variation, and the level of inter-individual variability was larger in the generalist species (mouflon) than in the specialist one (roe deer). This mechanism at the base of the NVH appears at play at different levels of biological organization, from populations to communities.
- Published
- 2015
- Full Text
- View/download PDF
134. Mechanisms and Mediators That Drive Arthritis Pain.
- Author
-
Krustev E, Rioux D, and McDougall JJ
- Subjects
- Arthralgia etiology, Arthritis complications, Humans, Neurogenic Inflammation pathology, Pain Management, Arthralgia physiopathology, Arthritis physiopathology
- Abstract
There are over 100 different types of arthritis and each can differ greatly in their aetiology and pathophysiology; however, one characteristic that is common to all arthritic conditions is joint pain. Musculoskeletal pain is the leading cause of disability in the world, and the number one reason arthritis patients visit their primary care physician. Despite the prevalence and burden of arthritis pain, current analgesics lack sufficient efficacy and are plagued by multiple adverse side effects. In this review, we outline the current landscape of research concerning joint pain, drawing from both preclinical and clinical studies. Specifically, this review is a discussion of the different neurophysiological processes that occur during joint disease and how inflammatory and neuropathic aspects contribute to the development of arthritis pain.
- Published
- 2015
- Full Text
- View/download PDF
135. Wide-field hyperspectral 3D imaging of functionalized gold nanoparticles targeting cancer cells by reflected light microscopy.
- Author
-
Patskovsky S, Bergeron E, Rioux D, and Meunier M
- Subjects
- Antibodies, Monoclonal chemistry, Antibodies, Monoclonal immunology, Breast Neoplasms metabolism, Cell Line, Tumor, Equipment Design, Gene Expression Regulation, Neoplastic, Humans, Hyaluronan Receptors immunology, Hyaluronan Receptors metabolism, Imaging, Three-Dimensional instrumentation, Microscopy instrumentation, Polyethylene Glycols chemistry, Breast Neoplasms pathology, Gold chemistry, Imaging, Three-Dimensional methods, Metal Nanoparticles, Microscopy methods
- Abstract
We present a new hyperspectral reflected light microscopy system with a scanned broadband supercontinuum light source. This wide-field and low phototoxic hyperspectral imaging system has been successful for performing spectral three-dimensional (3D) localization and spectroscopic identification of CD44-targeted PEGylated AuNPs in fixed cell preparations. Such spatial and spectral information is essential for the improvement of nanoplasmonic-based imaging, disease detection and treatment in complex biological environment. The presented system can be used for real-time 3D NP tracking as spectral sensors, thus providing new avenues in the spatio-temporal characterization and detection of bioanalytes. 3D image of the distribution of functionalized AuNPs attached to CD44-expressing MDA-MB-231 human cancer cells., (© 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)
- Published
- 2015
- Full Text
- View/download PDF
136. Variation in stem morphology and movement of amyloplasts in white spruce grown in the weightless environment of the International Space Station.
- Author
-
Rioux D, Lagacé M, Cohen LY, and Beaulieu J
- Subjects
- Cell Nucleus metabolism, Endoplasmic Reticulum metabolism, Extraterrestrial Environment, Plant Stems metabolism, Plastids ultrastructure, Seedlings growth & development, Seedlings metabolism, Space Flight, Starch metabolism, Gravitropism physiology, Gravity Sensing physiology, Picea growth & development, Plant Leaves growth & development, Plant Shoots growth & development, Plant Stems growth & development, Plastids metabolism, Weightlessness
- Abstract
One-year-old white spruce (Picea glauca) seedlings were studied in microgravity conditions in the International Space Station (ISS) and compared with seedlings grown on Earth. Leaf growth was clearly stimulated in space whereas data suggest a similar trend for the shoots. Needles on the current shoots of ground-based seedlings were more inclined towards the stem base than those of seedlings grown in the ISS. Amyloplasts sedimented in specialized cells of shoots and roots in seedlings grown on Earth while they were distributed at random in similar cells of seedlings tested in the ISS. In shoots, such amyloplasts were found in starch sheath cells located between leaf traces and cortical cells whereas in roots they were constituents of columella cells of the cap. Nuclei were regularly observed just above the sedimented amyloplasts in both organs. It was also frequent to detect vacuoles with phenolic compounds and endoplasmic reticulum (ER) close to the sedimented amyloplasts. The ER was mainly observed just under these amyloplasts. Thus, when amyloplasts sediment, the pressure exerted on the ER, the organelle that can for instance secrete proteins destined for the plasma membrane, might influence their functioning and play a role in signaling pathways involved in gravity-sensing white spruce cells., (Crown Copyright © 2015. Published by Elsevier Ltd. All rights reserved.)
- Published
- 2015
- Full Text
- View/download PDF
137. Hyperspectral reflected light microscopy of plasmonic Au/Ag alloy nanoparticles incubated as multiplex chromatic biomarkers with cancer cells.
- Author
-
Patskovsky S, Bergeron E, Rioux D, Simard M, and Meunier M
- Subjects
- Cell Line, Tumor, Gold chemistry, Humans, Neoplasms metabolism, Neoplasms pathology, Silver chemistry, Alloys chemistry, Biomarkers, Tumor analysis, Chemistry Techniques, Analytical methods, Metal Nanoparticles chemistry, Microscopy
- Abstract
A hyperspectral microscopy system based on a reflected light method for plasmonic nanoparticle (NP) imaging was designed and compared with a conventional darkfield method for spatial localization and spectroscopic identification of single Au, Ag and Au/Ag alloy NPs incubated with fixed human cancer cell preparations. A new synthesis protocol based on co-reduction of Au and Ag salts combined with the seeded growth technique was used for the fabrication of monodispersed alloy NPs with sizes ranging from 30 to 100 nm in diameter. We validated theoretically and experimentally the performance of 60 nm Au, Ag and Au/Ag (50 : 50) NPs as multiplexed biological chromatic markers for biomedical diagnostics and optical biosensing. The advantages of the proposed reflected light microscopy method are presented for NP imaging in a complex and highly diffusing medium such as a cellular environment. The obtained information is essential for the development of a high throughput, selective and efficient strategy for cancer detection and treatment.
- Published
- 2014
- Full Text
- View/download PDF
138. A novel β-adrenergic response element regulates both basal and agonist-induced expression of cyclin-dependent kinase 1 gene in cardiac fibroblasts.
- Author
-
Gaspard GJ, MacLean J, Rioux D, and Pasumarthi KB
- Subjects
- Adrenergic beta-Agonists pharmacology, Animals, CCAAT-Binding Factor genetics, CDC2 Protein Kinase biosynthesis, CDC2 Protein Kinase genetics, Cell Proliferation, Cells, Cultured, DNA-Binding Proteins genetics, Fibroblasts metabolism, Fibrosis, Isoproterenol, Male, Mice, Promoter Regions, Genetic genetics, RNA, Messenger biosynthesis, Response Elements, CCAAT-Binding Factor metabolism, CDC2 Protein Kinase metabolism, Myocardium enzymology, Myocardium pathology
- Abstract
Cardiac fibrosis, a known risk factor for heart disease, is typically caused by uncontrolled proliferation of fibroblasts and excessive deposition of extracellular matrix proteins in the myocardium. Cyclin-dependent kinase 1 (CDK1) is involved in the control of G2/M transit phase of the cell cycle. Here, we showed that isoproterenol (ISO)-induced cardiac fibrosis is associated with increased levels of CDK1 exclusively in fibroblasts in the adult mouse heart. Treatment of primary embryonic ventricular cell cultures with ISO (a nonselective β-adrenergic receptor agonist) increased CDK1 protein expression in fibroblasts and promoted their cell cycle activity. Quantitative PCR analysis confirmed that ISO increases CDK1 transcription in a transient manner. Further, the ISO-responsive element was mapped to the proximal -100-bp sequence of the CDK1 promoter region using various 5'-flanking sequence deletion constructs. Sequence analysis of the -100-bp CDK1 minimal promoter region revealed two putative nuclear factor-Y (NF-Y) binding elements. Overexpression of the NF-YA subunit in primary ventricular cultures significantly increased the basal activation of the -100-bp CDK1 promoter construct but not the ISO-induced transcription of the minimal promoter construct. In contrast, dominant negative NF-YA expression decreased the basal activity of the minimal promoter construct and ISO treatment fully rescued the dominant negative effects. Furthermore, site-directed mutagenesis of the distal NF-Y binding site in the -100-bp CDK1 promoter region completely abolished both basal and ISO-induced promoter activation of the CDK1 gene. Collectively, our results raise an exciting possibility that targeting CDK1 or NF-Y in the diseased heart may inhibit fibrosis and subsequently confer cardioprotection.
- Published
- 2014
- Full Text
- View/download PDF
139. Fifty thousand years of Arctic vegetation and megafaunal diet.
- Author
-
Willerslev E, Davison J, Moora M, Zobel M, Coissac E, Edwards ME, Lorenzen ED, Vestergård M, Gussarova G, Haile J, Craine J, Gielly L, Boessenkool S, Epp LS, Pearman PB, Cheddadi R, Murray D, Bråthen KA, Yoccoz N, Binney H, Cruaud C, Wincker P, Goslar T, Alsos IG, Bellemain E, Brysting AK, Elven R, Sønstebø JH, Murton J, Sher A, Rasmussen M, Rønn R, Mourier T, Cooper A, Austin J, Möller P, Froese D, Zazula G, Pompanon F, Rioux D, Niderkorn V, Tikhonov A, Savvinov G, Roberts RG, MacPhee RD, Gilbert MT, Kjær KH, Orlando L, Brochmann C, and Taberlet P
- Subjects
- Animals, Arctic Regions, Bison physiology, Cold Climate, Freezing, High-Throughput Nucleotide Sequencing, Horses physiology, Mammoths physiology, Poaceae genetics, Poaceae growth & development, Soil, Time Factors, Yukon Territory, Biodiversity, Diet, Herbivory, Nematoda classification, Nematoda genetics, Nematoda isolation & purification, Plants classification, Plants genetics
- Abstract
Although it is generally agreed that the Arctic flora is among the youngest and least diverse on Earth, the processes that shaped it are poorly understood. Here we present 50 thousand years (kyr) of Arctic vegetation history, derived from the first large-scale ancient DNA metabarcoding study of circumpolar plant diversity. For this interval we also explore nematode diversity as a proxy for modelling vegetation cover and soil quality, and diets of herbivorous megafaunal mammals, many of which became extinct around 10 kyr bp (before present). For much of the period investigated, Arctic vegetation consisted of dry steppe-tundra dominated by forbs (non-graminoid herbaceous vascular plants). During the Last Glacial Maximum (25-15 kyr bp), diversity declined markedly, although forbs remained dominant. Much changed after 10 kyr bp, with the appearance of moist tundra dominated by woody plants and graminoids. Our analyses indicate that both graminoids and forbs would have featured in megafaunal diets. As such, our findings question the predominance of a Late Quaternary graminoid-dominated Arctic mammoth steppe.
- Published
- 2014
- Full Text
- View/download PDF
140. Multi-stemmed trees of Nothofagus pumilio second-growth forest in Patagonia are formed by highly related individuals.
- Author
-
Till-Bottraud I, Fajardo A, and Rioux D
- Subjects
- Amplified Fragment Length Polymorphism Analysis, Biomarkers analysis, Chile, DNA, Plant genetics, Fires, Genotype, Magnoliopsida growth & development, Plant Leaves genetics, Plant Leaves growth & development, Plant Stems genetics, Plant Stems growth & development, Trees, Magnoliopsida genetics, Polymorphism, Genetic genetics
- Abstract
Background and Aims: Multi-stemmed trees (tree clusters) in Nothofagus pumilio, a dominant tree species in Patagonia, are very uncommon and are restricted to the edge of second-growth forests following human-provoked fires. No vegetative reproduction has been reported so far. The genetic structure of multi-stemmed trees of this species was investigated and it was hypothesized that genets within a cluster were more closely related than average in the population., Methods: Fifteen clusters (composed of at least three purported stems) and 15 single trees were sampled at the edge of a second-growth forest and genotyped using two amplified fragment length polymorphism (AFLP) primer pairs. We obtained 119 polymorphic markers that allowed clonality to be determined, together with sibship structure and relatedness among samples., Key Results: Clonality was detected in seven clusters but all clusters had at least two different genotypes. Full sibs were found exclusively within clusters and in all clusters. Within a cluster, stems that were not identified as full sibs were often half sibs. Relatedness values for the full sibs and half sibs were higher than the theoretical values of 0·5 and 0·25 but the relatedness between clusters was very low., Conclusions: Tree clusters that are merged at the edge of the second-growth forest of N. pumilio are composed of stems of the same genotype and of other genotypes that are highly related (but not always). It is suggested that this peculiar genetic structure results from a combination of several causes, including selection for merging of related individuals.
- Published
- 2012
- Full Text
- View/download PDF
141. Soil sampling and isolation of extracellular DNA from large amount of starting material suitable for metabarcoding studies.
- Author
-
Taberlet P, Prud'Homme SM, Campione E, Roy J, Miquel C, Shehzad W, Gielly L, Rioux D, Choler P, Clément JC, Melodelima C, Pompanon F, and Coissac E
- Subjects
- Animals, Biodiversity, DNA analysis, Ecosystem, Fungi genetics, Oligochaeta genetics, Plants genetics, Polymerase Chain Reaction, DNA isolation & purification, DNA Barcoding, Taxonomic methods, Soil chemistry, Soil Microbiology
- Abstract
DNA metabarcoding refers to the DNA-based identification of multiple species from a single complex and degraded environmental sample. We developed new sampling and extraction protocols suitable for DNA metabarcoding analyses targeting soil extracellular DNA. The proposed sampling protocol has been designed to reduce, as much as possible, the influence of local heterogeneity by processing a large amount of soil resulting from the mixing of many different cores. The DNA extraction is based on the use of saturated phosphate buffer. The sampling and extraction protocols were validated first by analysing plant DNA from a set of 12 plots corresponding to four plant communities in alpine meadows, and, second, by conducting pilot experiments on fungi and earthworms. The results of the validation experiments clearly demonstrated that sound biological information can be retrieved when following these sampling and extraction procedures. Such a protocol can be implemented at any time of the year without any preliminary knowledge of specific types of organisms during the sampling. It offers the opportunity to analyse all groups of organisms using a single sampling/extraction procedure and opens the possibility to fully standardize biodiversity surveys., (© 2012 Blackwell Publishing Ltd.)
- Published
- 2012
- Full Text
- View/download PDF
142. Tracking genes of ecological relevance using a genome scan in two independent regional population samples of Arabis alpina.
- Author
-
Poncet BN, Herrmann D, Gugerli F, Taberlet P, Holderegger R, Gielly L, Rioux D, Thuiller W, Aubert S, and Manel S
- Subjects
- Alleles, Amplified Fragment Length Polymorphism Analysis, DNA, Plant genetics, Environment, France, Linkage Disequilibrium, Models, Statistical, Switzerland, Adaptation, Physiological genetics, Arabis genetics, Genetics, Population, Genome, Plant
- Abstract
Understanding the genetic basis of adaptation in response to environmental variation is fundamental as adaptation plays a key role in the extension of ecological niches to marginal habitats and in ecological speciation. Based on the assumption that some genomic markers are correlated to environmental variables, we aimed to detect loci of ecological relevance in the alpine plant Arabis alpina L. sampled in two regions, the French (99 locations) and the Swiss (109 locations) Alps. We used an unusually large genome scan [825 amplified fragment length polymorphism loci (AFLPs)] and four environmental variables related to temperature, precipitation and topography. We detected linkage disequilibrium among only 3.5% of the considered AFLP loci. A population structure analysis identified no admixture in the study regions, and the French and Swiss Alps were differentiated and therefore could be considered as two independent regions. We applied generalized estimating equations (GEE) to detect ecologically relevant loci separately in the French and Swiss Alps. We identified 78 loci of ecological relevance (9%), which were mainly related to mean annual minimum temperature. Only four of these loci were common across the French and Swiss Alps. Finally, we discuss that the genomic characterization of these ecologically relevant loci, as identified in this study, opens up new perspectives for studying functional ecology in A. alpina, its relatives and other alpine plant species.
- Published
- 2010
- Full Text
- View/download PDF
143. Selection criteria for scoring amplified fragment length polymorphisms (AFLPs) positively affect the reliability of population genetic parameter estimates.
- Author
-
Herrmann D, Poncet BN, Manel S, Rioux D, Gielly L, Taberlet P, and Gugerli F
- Subjects
- Amplified Fragment Length Polymorphism Analysis standards, Arabis genetics, DNA, Plant genetics, Genetic Markers genetics, Genetics, Population standards, Polymerase Chain Reaction, Reproducibility of Results, Algorithms, Amplified Fragment Length Polymorphism Analysis methods, Computational Biology methods, Genetics, Population methods
- Abstract
A reliable data set is a fundamental prerequisite for consistent results and conclusions in population genetic studies. However, marker scoring of genetic fingerprints such as amplified fragment length polymorphisms (AFLPs) is a highly subjective procedure, inducing inconsistencies owing to personal or laboratory-specific criteria. We applied two alternative marker selection algorithms, the newly developed script scanAFLP and the recently published AFLPScore, to a large AFLP genome scan to test how population genetic parameters and error rates were affected. These results were confronted with replicated random selections of marker subsets. We show that the newly developed marker selection criteria reduced the mismatch error rate and had a notable influence on estimates of genetic diversity and differentiation. Both effects are likely to influence biological inference. For example, genetic diversity (HS) was 29% lower while genetic differentiation (FST) was 8% higher when applying scanAFLP compared with AFLPScore. Likewise, random selections of markers resulted in substantial deviations of population genetic parameters compared with the data sets including specific selection criteria. These randomly selected marker sets showed surprisingly low variance among replicates. We conclude that stringent marker selection and phenotype calling reduces noise in the data set while retaining patterns of population genetic structure.
- Published
- 2010
- Full Text
- View/download PDF
144. Evolution and taxonomy of the wild species of the genus Ovis (Mammalia, Artiodactyla, Bovidae).
- Author
-
Rezaei HR, Naderi S, Chintauan-Marquier IC, Jordan S, Taberlet P, Virk AT, Naghash HR, Rioux D, Kaboli M, Luikart G, and Pompanon F
- Subjects
- Animals, Bayes Theorem, Cell Nucleus genetics, Cytochromes b genetics, DNA, Mitochondrial genetics, Likelihood Functions, Sequence Alignment, Sequence Analysis, DNA, Sheep classification, Evolution, Molecular, Phylogeny, Sheep genetics
- Abstract
New insights for the systematic and evolution of the wild sheep are provided by molecular phylogenies inferred from Maximum parsimony, Bayesian, Maximum likelihood, and Neighbor-Joining methods. The phylogeny of the wild sheep was based on cytochrome b sequences of 290 samples representative of most of the sub-species described in the genus Ovis. The result was confirmed by a combined tree based on cytochrome b and nuclear sequences for 79 Ovis samples representative of the robust clades established with mitochondrial data. Urial and mouflon, which are either considered as a single or two separate species, form two monophyletic groups (O. orientalis and O. vignei). Their hybrids appear in one or the other group, independently from their geographic origin. The European mouflon O. musimon is clearly in the O. orientalis clade. The others species, O. dalli, O. canadensis, O. nivicola, and O. ammon are monophyletic. The results support an Asiatic origin of the genus Ovis, followed by a migration to North America through North-Eastern Asia and the Bering Strait and a diversification of the genus in Eurasia less than 3 million years ago. Our results show that the evolution of the genus Ovis is a striking example of successive speciation events occurring along the migration routes propagating from the ancestral area., (Copyright (c) 2009. Published by Elsevier Inc.)
- Published
- 2010
- Full Text
- View/download PDF
145. History or ecology? Substrate type as a major driver of spatial genetic structure in Alpine plants.
- Author
-
Alvarez N, Thiel-Egenter C, Tribsch A, Holderegger R, Manel S, Schönswetter P, Taberlet P, Brodbeck S, Gaudeul M, Gielly L, Küpfer P, Mansion G, Negrini R, Paun O, Pellecchia M, Rioux D, Schüpfer F, Van Loo M, Winkler M, and Gugerli F
- Subjects
- DNA Fingerprinting, Geography, Phylogeny, Plant Development, Plants classification, Species Specificity, Time Factors, Biodiversity, Climate, Plants genetics, Soil
- Abstract
Climatic history and ecology are considered the most important factors moulding the spatial pattern of genetic diversity. With the advent of molecular markers, species' historical fates have been widely explored. However, it has remained speculative what role ecological factors have played in shaping spatial genetic structures within species. With an unprecedented, dense large-scale sampling and genome-screening, we tested how ecological factors have influenced the spatial genetic structures in Alpine plants. Here, we show that species growing on similar substrate types, largely determined by the nature of bedrock, displayed highly congruent spatial genetic structures. As the heterogeneous and disjunctive distribution of bedrock types in the Alps, decisive for refugial survival during the ice ages, is temporally stable, concerted post-glacial migration routes emerged. Our multispecies study demonstrates the relevance of particular ecological factors in shaping genetic patterns, which should be considered when modelling species projective distributions under climate change scenarios.
- Published
- 2009
- Full Text
- View/download PDF
146. Fungal colonization and host defense reactions in Ulmus americana callus cultures inoculated with Ophiostoma novo-ulmi.
- Author
-
Aoun M, Rioux D, Simard M, and Bernier L
- Subjects
- Host-Pathogen Interactions, Ophiostoma genetics, Ophiostoma growth & development, Ophiostoma pathogenicity, Phenols metabolism, Plant Diseases microbiology, Reverse Transcriptase Polymerase Chain Reaction, Starch metabolism, Ulmus immunology, Ophiostoma isolation & purification, Ulmus microbiology
- Abstract
The host-pathogen interaction leading to Dutch elm disease was analyzed using histo- and cyto-chemical tests in an in vitro system. Friable and hard susceptible Ulmus americana callus cultures were inoculated with the highly aggressive pathogen Ophiostoma novo-ulmi. Inoculated callus tissues were compared with water-treated callus tissues and studied with light microscopy (LM), transmission-electron microscopy (TEM), and scanning-electron microscopy (SEM). New aspects of this interaction are described. These include the histological observation, for the first time in plant callus cultures, of suberin with its typical lamellar structure in TEM and the intracellular presence of O. novo-ulmi. Expression of the phenylalanine ammonia lyase gene, monitored by real-time quantitative polymerase chain reaction, was correlated with the accumulation of suberin, phenols, and lignin in infected callus cultures. This study validates the potential use of the in vitro system for genomic analyses aimed at identifying genes expressed during the interaction in the Dutch elm disease pathosystem.
- Published
- 2009
- Full Text
- View/download PDF
147. Silicon nanoparticles produced by femtosecond laser ablation in water as novel contamination-free photosensitizers.
- Author
-
Rioux D, Laferrière M, Douplik A, Shah D, Lilge L, Kabashin AV, and Meunier MM
- Subjects
- Drug Contamination prevention & control, Materials Testing, Nanoparticles radiation effects, Nanoparticles therapeutic use, Particle Size, Photosensitizing Agents therapeutic use, Lasers, Nanoparticles chemistry, Nanoparticles ultrastructure, Photosensitizing Agents chemistry, Water chemistry
- Abstract
We report the synthesis of novel inorganic contamination-free photosensitizers based on colloidal silicon nanoparticles prepared by laser ablation in pure deionized water. We show that such nanoparticles are capable of generating singlet oxygen ((1)O(2)) under laser irradiation with a yield estimated at 10% of that of photofrin, which makes them a potential candidate for therapeutics, antiseptics, or disinfectants. We also discuss a model of (1)O(2) generation and the possibility for optimizing its release. Potential advantages of such novel inorganic photosensitizers include stable and nonphotobleaching (1)O(2) release, easy removal, and low dark toxicity.
- Published
- 2009
- Full Text
- View/download PDF
148. Post-glacial history of the dominant alpine sedge Carex curvula in the European Alpine System inferred from nuclear and chloroplast markers.
- Author
-
Puşcaş M, Choler P, Tribsch A, Gielly L, Rioux D, Gaudeul M, and Taberlet P
- Subjects
- Europe, Genotype, Geography, Sequence Analysis, DNA, Cyperaceae genetics, DNA, Chloroplast genetics, DNA, Plant genetics, Phylogeny, Polymorphism, Single Nucleotide
- Abstract
The alpine sedge Carex curvula ssp. curvula is a clonal, dominant graminoid found in the European Alps, the Carpathians, the Pyrenees and in some of the Balkan Mountains. It is a late-successional species of acidophilous alpine meadows that occurs on sites that were covered by ice during the last glacial maximum (LGM). By applying the amplified fragment length polymorphism (AFLP) fingerprinting and chloroplast DNA (cpDNA) sequencing, we attempted to identify the recolonization routes followed by the species after the last ice retreat. We relied on the genetic diversity of 37 populations covering the entire distributional range of the species. As a wind-pollinated species, C. curvula is characterized by a low level of population genetic differentiation. Nuclear and chloroplast data both support the hypothesis of a long-term separation of Eastern (Balkans and Carpathians) and Western (Alps and Pyrenees) lineages. In the Alps, a continuum of genetic depauperation from the east to the west may be related to a recolonization wave originating in the eastern-most parts of the chain, where the main glacial refugium was likely located. The Pyrenean populations are nested within the western Alps group and show a low level of genetic diversity, probably due to recent long-distance colonization. In contrast to the Alps, we found no phylogeographical structure in the Carpathians. The combination of reduced ice extension during the Würm period and the presence of large areas of siliceous substrate at suitable elevation suggest that in contrast to populations in the Alps, the species in the Carpathians underwent a local vertical migration rather than extinction and recolonization over long distance.
- Published
- 2008
- Full Text
- View/download PDF
149. CE-SSCP and CE-FLA, simple and high-throughput alternatives for fungal diversity studies.
- Author
-
Zinger L, Gury J, Alibeu O, Rioux D, Gielly L, Sage L, Pompanon F, and Geremia RA
- Subjects
- DNA Fingerprinting methods, DNA, Fungal analysis, DNA, Fungal isolation & purification, Ecosystem, Fungi genetics, Fungi isolation & purification, Reproducibility of Results, Sensitivity and Specificity, Biodiversity, Electrophoresis, Capillary methods, Fungi classification, Polymorphism, Restriction Fragment Length, Polymorphism, Single-Stranded Conformational, Soil Microbiology
- Abstract
Fungal communities are key components of soil, but the study of their ecological significance is limited by a lack of appropriated methods. For instance, the assessment of fungi occurrence and spatio-temporal variation in soil requires the analysis of a large number of samples. The molecular signature methods provide a useful tool to monitor these microbial communities and can be easily adapted to capillary electrophoresis (CE) allowing high-throughput studies. Here we assess the suitability of CE-FLA (Fragment Length Polymorphism, denaturing conditions) and CE-SSCP (Single-Stranded Conformation Polymorphism, native conditions) applied to environmental studies since they require a short molecular marker and no post-PCR treatments. We amplified the ITS1 region from 22 fungal strains isolated from an alpine ecosystem and from total genomic DNA of alpine and infiltration basin soils. The CE-FLA and CE-SSCP separated 17 and 15 peaks respectively from a mixture of 19 strains. For the alpine soil-metagenomic DNA, the FLA displayed more peaks than the SSCP and the converse result was found for infiltration basin sediments. We concluded that CE-FLA and CE-SSCP of ITS1 region provided complementary information. In order to improve CE-SSCP sensitivity, we tested its resolution according to migration temperature and found 32 degrees C to be optimal. Because of their simplicity, quickness and reproducibility, we found that these two methods were promising for high-throughput studies of soil fungal communities.
- Published
- 2008
- Full Text
- View/download PDF
150. The vegetative life-cycle of the clover pathogen Cymadothea trifolii as revealed by transmission electron microscopy.
- Author
-
Simon UK, Bauer R, Rioux D, Simard M, and Oberwinkler F
- Subjects
- Ascomycota ultrastructure, Hyphae metabolism, Microscopy, Electron, Transmission, Ascomycota physiology, Plant Diseases microbiology
- Abstract
The vegetative life-cycle of Cymadothea trifolii (anamorph Polythrincium trifolii), causing sooty blotch of clover, is described using chemically as well as cryofixed and freeze-substituted samples. The pathogen enters the leaf through stomata and proliferates intercellularly. Nutrients are assumedly obtained via an interaction apparatus produced within the pathogen's hyphae, opposite to which the host cell is triggered to invaginate its plasmalemma. Rare attempts of 'self-parasitism' were also seen. Entering the conidial stage, stromata are laid down under the lower epidermis. The dying tissue above may explain the necrotic spots observed on infected leaflets. Foot cells in the conidial stromata produce thick-walled conidiophores, which grow sympodially. New conidiophores may grow into empty shells of old ones. Conidia are detached after pores between them and conidiophores have become plugged by organelles resembling Woronin bodies. Conidia are usually two-celled and their walls contain chitin and beta-1,3-glucans as indicated by labelling with gold-conjugated wheat germ agglutinin and anti-beta-1,3-glucan antibodies. Both conidiophores and conidia contain a structure which we regard as a new organelle with as yet unknown function.
- Published
- 2005
- Full Text
- View/download PDF
Catalog
Discovery Service for Jio Institute Digital Library
For full access to our library's resources, please sign in.