50 research outputs found
Incorporating molecular data in fungal systematics: a guide for aspiring researchers
The last twenty years have witnessed molecular data emerge as a primary
research instrument in most branches of mycology. Fungal systematics, taxonomy,
and ecology have all seen tremendous progress and have undergone rapid,
far-reaching changes as disciplines in the wake of continual improvement in DNA
sequencing technology. A taxonomic study that draws from molecular data
involves a long series of steps, ranging from taxon sampling through the
various laboratory procedures and data analysis to the publication process. All
steps are important and influence the results and the way they are perceived by
the scientific community. The present paper provides a reflective overview of
all major steps in such a project with the purpose to assist research students
about to begin their first study using DNA-based methods. We also take the
opportunity to discuss the role of taxonomy in biology and the life sciences in
general in the light of molecular data. While the best way to learn molecular
methods is to work side by side with someone experienced, we hope that the
present paper will serve to lower the learning threshold for the reader.Comment: Submitted to Current Research in Environmental and Applied Mycology -
comments most welcom
Research Notes : United States : Superoxide dismutase (SOD) in soybean
We are using vertical polyacrylamide gel electrophoresis (Davis, 1964) and a staining system modified after Beauchamp and Fridovich (1971) to study superoxide dismutase polymorphisms in the subgenus soja. This staining system generates superoxide radical; hence, it is specific for SOD activity. We re-solve up to 9 SOD bands in dry or germinating soybean cotyledons, and in leaves
A chemical survey of exoplanets with ARIEL
Thousands of exoplanets have now been discovered with a huge range of masses, sizes and orbits: from rocky Earth-like planets to large gas giants grazing the surface of their host star. However, the essential nature of these exoplanets remains largely mysterious: there is no known, discernible pattern linking the presence, size, or orbital parameters of a planet to the nature of its parent star. We have little idea whether the chemistry of a planet is linked to its formation environment, or whether the type of host star drives the physics and chemistry of the planetâs birth, and evolution. ARIEL was conceived to observe a large number (~1000) of transiting planets for statistical understanding, including gas giants, Neptunes, super-Earths and Earth-size planets around a range of host star types using transit spectroscopy in the 1.25â7.8 ÎŒm spectral range and multiple narrow-band photometry in the optical. ARIEL will focus on warm and hot planets to take advantage of their well-mixed atmospheres which should show minimal condensation and sequestration of high-Z materials compared to their colder Solar System siblings. Said warm and hot atmospheres are expected to be more representative of the planetary bulk composition. Observations of these warm/hot exoplanets, and in particular of their elemental composition (especially C, O, N, S, Si), will allow the understanding of the early stages of planetary and atmospheric formation during the nebular phase and the following few million years. ARIEL will thus provide a representative picture of the chemical nature of the exoplanets and relate this directly to the type and chemical environment of the host star. ARIEL is designed as a dedicated survey mission for combined-light spectroscopy, capable of observing a large and well-defined planet sample within its 4-year mission lifetime. Transit, eclipse and phase-curve spectroscopy methods, whereby the signal from the star and planet are differentiated using knowledge of the planetary ephemerides, allow us to measure atmospheric signals from the planet at levels of 10â100 part per million (ppm) relative to the star and, given the bright nature of targets, also allows more sophisticated techniques, such as eclipse mapping, to give a deeper insight into the nature of the atmosphere. These types of observations require a stable payload and satellite platform with broad, instantaneous wavelength coverage to detect many molecular species, probe the thermal structure, identify clouds and monitor the stellar activity. The wavelength range proposed covers all the expected major atmospheric gases from e.g. H2O, CO2, CH4 NH3, HCN, H2S through to the more exotic metallic compounds, such as TiO, VO, and condensed species. Simulations of ARIEL performance in conducting exoplanet surveys have been performed â using conservative estimates of mission performance and a full model of all significant noise sources in the measurement â using a list of potential ARIEL targets that incorporates the latest available exoplanet statistics. The conclusion at the end of the Phase A study, is that ARIEL â in line with the stated mission objectives â will be able to observe about 1000 exoplanets depending on the details of the adopted survey strategy, thus confirming the feasibility of the main science objectives.Peer reviewedFinal Published versio
Retrospective French nationwide survey of childhood aggressive vascular anomalies of bone, 1988-2009
<p>Abstract</p> <p>Objective</p> <p>To document the epidemiological, clinical, histological and radiological characteristics of aggressive vascular abnormalities of bone in children.</p> <p>Study design</p> <p>Correspondents of the French Society of Childhood Malignancies were asked to notify all cases of aggressive vascular abnormalities of bone diagnosed between January 1988 and September 2009.</p> <p>Results</p> <p>21 cases were identified; 62% of the patients were boys. No familial cases were observed, and the disease appeared to be sporadic. Mean age at diagnosis was 8.0 years [0.8-16.9 years]. Median follow-up was 3 years [0.3-17 years]. The main presenting signs were bone fracture (n = 4) and respiratory distress (n = 7), but more indolent onset was observed in 8 cases. Lung involvement, with lymphangiectasies and pleural effusion, was the most frequent form of extraosseous involvement (10/21). Bisphosphonates, alpha interferon and radiotherapy were used as potentially curative treatments. High-dose radiotherapy appeared to be effective on pleural effusion but caused major late sequelae, whereas antiangiogenic drugs like alpha interferon and zoledrenate have had a limited impact on the course of pulmonary complications. The impact of bisphosphonates and alpha interferon on bone lesions was also difficult to assess, owing to insufficient follow-up in most cases, but it was occasionally positive. Six deaths were observed and the overall 10-year mortality rate was about 30%. The prognosis depended mainly on pulmonary and spinal complications.</p> <p>Conclusion</p> <p>Aggressive vascular abnormalities of bone are extremely rare in childhood but are lifethreatening. The impact of anti-angiogenic drugs on pulmonary complications seems to be limited, but they may improve bone lesions.</p
First Dating of a Recombination Event in Mammalian Tick-Borne Flaviviruses
The mammalian tick-borne flavivirus group (MTBFG) contains viruses associated with important human and animal diseases such as encephalitis and hemorrhagic fever. In contrast to mosquito-borne flaviviruses where recombination events are frequent, the evolutionary dynamic within the MTBFG was believed to be essentially clonal. This assumption was challenged with the recent report of several homologous recombinations within the Tick-borne encephalitis virus (TBEV). We performed a thorough analysis of publicly available genomes in this group and found no compelling evidence for the previously identified recombinations. However, our results show for the first time that demonstrable recombination (i.e., with large statistical support and strong phylogenetic evidences) has occurred in the MTBFG, more specifically within the Louping ill virus lineage. Putative parents, recombinant strains and breakpoints were further tested for statistical significance using phylogenetic methods. We investigated the time of divergence between the recombinant and parental strains in a Bayesian framework. The recombination was estimated to have occurred during a window of 282 to 76 years before the present. By unravelling the temporal setting of the event, we adduce hypotheses about the ecological conditions that could account for the observed recombination
Revisiting Recombination Signal in the Tick-Borne Encephalitis Virus: A Simulation Approach
<div><p>The hypothesis of wide spread reticulate evolution in Tick-Borne Encephalitis virus (TBEV) has recently gained momentum with several publications describing past recombination events involving various TBEV clades. Despite a large body of work, no consensus has yet emerged on TBEV evolutionary dynamics. Understanding the occurrence and frequency of recombination in TBEV bears significant impact on epidemiology, evolution, and vaccination with live vaccines. In this study, we investigated the possibility of detecting recombination events in TBEV by simulating recombinations at several locations on the virusâ phylogenetic tree and for different lengths of recombining fragments. We derived estimations of rates of true and false positive for the detection of past recombination events for seven recombination detection algorithms. Our analytical framework can be applied to any investigation dealing with the difficult task of distinguishing genuine recombination signal from background noise. Our results suggest that the problem of false positives associated with low detection <i>P</i>-values in TBEV, is more insidious than generally acknowledged. We reappraised the recombination signals present in the empirical data, and showed that reliable signals could only be obtained in a few cases when highly genetically divergent strains were involved, whereas false positives were common among genetically similar strains. We thus conclude that recombination among wild-type TBEV strains may occur, which has potential implications for vaccination with live vaccines, but that these events are surprisingly rare.</p></div
Collection localities for the E-sequences used to build the tree in Fig I in S1 file.
<p>Strains origins for three clades of interest (W1, FE4 and FE5) are indicated with arrows. Because strain origins are reported with various levels of precision (from local to national level), this map should only be used as an indication of the patchy record of TBEV genetic diversity. This map also shows that the territory comprised between the Irkutsk and Zabaikalsky regions represent a hot spot of genetic diversity with the co-circulation of X1-, X2-, FE- and S-strains. Some well known foci such as the presence of the S-TBEV in Finland and the isolation of all three sub-types in Estonia and Latvia are not included on the map as the associated sequences are too short to yield reliable phylogenetic signal. Sampling intensity is given in number of sequences collected in the same locality. The map was generated using an equidistant cylindrical projection with the Basemap toolkit available from the python package Matplotlib (<a href="http://matplotlib.org/basemap/users/cyl.html?highlight=cylindrical" target="_blank">http://matplotlib.org/basemap/users/cyl.html?highlight=cylindrical</a>).</p
Synoptic diagram presenting the methods and analytical framework deployed during in the simulation.
<p>The analytical protocol designed to estimate the rates of true and false positive for the detection of recombination in simulated data consists in several steps: STEPS 1â3 derive the parameters for the simulation from empirical sequence alignments. STEPS 4â8 simulate alignments that are similar to the empirical data in term of tree topology, divergence dates, number of strains, number of sites and rate heterogeneity among sites. Several stochastic processes are added in order to model lineage specific substitution rate variation (STEP 4) and model the effect of purifying selection (STEP 6). The simulated datasets with and without recombinations are finally analyzed with RDP4 (STEP 9).</p
Range of durations between the recombination tMRCA of the donor and receiver clades for the simulated events.
<p>Range of durations between the recombination tMRCA of the donor and receiver clades for the simulated events.</p