Genetic diversity and population structure of Leishmania infantum from Southeastern France : evaluation using Multi-Locus Microsatellite Typing

In the south of France, Leishmania infantum is responsible for numerous cases of canine leishmaniasis (CanL), sporadic cases of human visceral leishmaniasis (VL) and rare cases of cutaneous and muco-cutaneous leishmaniasis (CL and MCL, respectively). Several endemic areas have been clearly identified in the south of France including the Pyrenees-Orientales, Cevennes (CE), Provence (P), Alpes-Maritimes (AM) and Corsica (CO). Within these endemic areas, the two cities of Nice (AM) and Marseille (P), which are located 150 km apart, and their surroundings, concentrate the greatest number of French autochthonous leishmaniasis cases. In this study, 270 L. infantum isolates from an extended time period (1978-2011) from four endemic areas, AM, P, CE and CO, were assessed using Multi-Locus Microsatellite Typing (MLMT). MLMT revealed a total of 121 different genotypes with 91 unique genotypes and 30 repeated genotypes. Substantial genetic diversity was found with a strong genetic differentiation between the Leishmania populations from AM and P. However, exchanges were observed between these two endemic areas in which it seems that strains spread from AM to P. The genetic differentiations in these areas suggest strong epidemiological structuring. A model-based analysis using STRUCTURE revealed two main populations: population A (consisting of samples primarily from the P and AM endemic areas with MON-1 and non-MON-1 strains) and population B consisting of only MON-1 strains essentially from the AM endemic area. For four patients, we observed several isolates from different biological samples which provided insight into disease relapse and re-infection. These findings shed light on the transmission dynamics of parasites in humans. However, further data are required to confirm this hypothesis based on a limited sample set. This study represents the most extensive population analysis of L. infantum strains using MLMT conducted in France

Thermal Phase Mixing During First Order Phase Transitions

The dynamics of first order phase transitions are studied in the context of (3+1)-dimensional scalar field theories. Particular attention is paid to the question of quantifying the strength of the transition, and how `weak' and `strong' transitions have different dynamics. We propose a model with two available low temperature phases separated by an energy barrier so that one of them becomes metastable below the critical temperature $T_c$. The system is initially prepared in this phase and is coupled to a thermal bath. Investigating the system at its critical temperature, we find that `strong' transitions are characterized by the system remaining localized within its initial phase, while `weak' transitions are characterized by considerable phase mixing. Always at $T_c$, we argue that the two regimes are themselves separated by a (second order) phase transition, with an order parameter given by the fractional population difference between the two phases and a control parameter given by the strength of the scalar field's quartic self-coupling constant. We obtain a Ginzburg-like criterion to distinguish between `weak' and `strong' transitions, in agreement with previous results in (2+1)-dimensions.Comment: 28 pages RevTeX, 9 postscript figures, IMPERIAL/TP/93-94/58, DART-HEP-94/0

Impact of Iron-site defects on Superconductivity in LiFeAs

PW acknowledges funding from the MPG-UBC center and financial support from EPSRC (EP/I031014/1).In conventional s-wave superconductors, only magnetic impurities exhibit impurity bound states, whereas for an s order parameter they can occur for both magnetic and non-magnetic impurities. Impurity bound states in superconductors can thus provide important insight into the order parameter. Here, we present a combined experimental and theoretical study of native and engineered iron-site defects in LiFeAs. Detailed comparison of tunneling spectra measured on impurities with spin fluctuation theory reveals a continuous evolution from negligible impurity bound state features for weaker scattering potential to clearly detectable states for somewhat stronger scattering potentials. All bound states for these intermediate strength potentials are pinned at or close to the gap edge of the smaller gap, a phenomenon that we explain and ascribe to multi-orbital physics.PostprintPeer reviewe

Adaptive fast multipole methods on the GPU

We present a highly general implementation of fast multipole methods on graphics processing units (GPUs). Our two-dimensional double precision code features an asymmetric type of adaptive space discretization leading to a particularly elegant and flexible implementation. All steps of the multipole algorithm are efficiently performed on the GPU, including the initial phase which assembles the topological information of the input data. Through careful timing experiments we investigate the effects of the various peculiarities of the GPU architecture.Comment: Software available at http://user.it.uu.se/~stefane/freeware.htm

REACTIONS OF 1, 2, 4-TRIAZINES WITH 4, 5-DIMETHYL-1, 2-DEHYDROBENZENE

Arynes are known intermediates in reactions with azaheterocycles. However, the reactions of fist ones with 1, 2, 4-trriazines are not well studied so far. In continuation of our studies on interactions of 3, 5-substituted-1, 2, 4-triazines with arynes we wish to report herein our results observed in reactions of these heterocycles with 4, 5-dimethyl-1, 2-dehydrobenzene. This dimethyl-aryne was generated in situ from the corresponding anthranilic acid as precursor by the reaction with iso-Amyl-ONO in 1, 4-dioxane and the following reaction with 5, 6-diaryl-3-(pyridyl-2)-1, 2, 4-trazines 1 in refluxed toluene for 2 hours. In all the cases the reaction afforded the domino-products, namely pyrido[1, 2-a]indoles 2, as major products, while the “classical” ID Diels-Alder products, such as iso-quinolines 3, were obtained only in trace amounts.This work was supported by Russian Science Foundation (Grant # 18-13-00365) and Russian Foundation for Basic Researches (Grant # 19-53-55002)

The landscape of extreme genomic variation in the highly adaptable Atlantic killifish

© The Author(s), 2017. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 9 (2017): 659-676, doi:10.1093/gbe/evx023.Understanding and predicting the fate of populations in changing environments require knowledge about the mechanisms that support phenotypic plasticity and the adaptive value and evolutionary fate of genetic variation within populations. Atlantic killifish (Fundulus heteroclitus) exhibit extensive phenotypic plasticity that supports large population sizes in highly fluctuating estuarine environments. Populations have also evolved diverse local adaptations. To yield insights into the genomic variation that supports their adaptability, we sequenced a reference genome and 48 additional whole genomes from a wild population. Evolution of genes associated with cell cycle regulation and apoptosis is accelerated along the killifish lineage, which is likely tied to adaptations for life in highly variable estuarine environments. Genome-wide standing genetic variation, including nucleotide diversity and copy number variation, is extremely high. The highest diversity genes are those associated with immune function and olfaction, whereas genes under greatest evolutionary constraint are those associated with neurological, developmental, and cytoskeletal functions. Reduced genetic variation is detected for tight junction proteins, which in killifish regulate paracellular permeability that supports their extreme physiological flexibility. Low-diversity genes engage in more regulatory interactions than high-diversity genes, consistent with the influence of pleiotropic constraint on molecular evolution. High genetic variation is crucial for continued persistence of species given the pace of contemporary environmental change. Killifish populations harbor among the highest levels of nucleotide diversity yet reported for a vertebrate species, and thus may serve as a useful model system for studying evolutionary potential in variable and changing environments.This work was primarily supported by a grant from the National Science Foundation (collaborative research grants DEB-1265282, DEB-1120512, DEB-1120013, DEB-1120263, DEB-1120333, DEB-1120398 to J.K.C., D.L.C., M.E.H., S.I.K., M.F.O., J.R.S., W.W., and A.W.). Further support was provided by the National Institute of Environmental Health Sciences (1R01ES021934-01 to A.W., P42ES7373 to T.H.H., P42ES007381 to M.E.H., and R01ES019324 to J.R.S.), the National Institute of General Medical Sciences (P20GM103423 and P20GM104318 to B.L.K.), and the National Science Foundation (DBI-0640462 and XSEDE-MCB100147 to D.G.)

Tear fluid biomarkers in ocular and systemic disease: potential use for predictive, preventive and personalised medicine

In the field of predictive, preventive and personalised medicine, researchers are keen to identify novel and reliable ways to predict and diagnose disease, as well as to monitor patient response to therapeutic agents. In the last decade alone, the sensitivity of profiling technologies has undergone huge improvements in detection sensitivity, thus allowing quantification of minute samples, for example body fluids that were previously difficult to assay. As a consequence, there has been a huge increase in tear fluid investigation, predominantly in the field of ocular surface disease. As tears are a more accessible and less complex body fluid (than serum or plasma) and sampling is much less invasive, research is starting to focus on how disease processes affect the proteomic, lipidomic and metabolomic composition of the tear film. By determining compositional changes to tear profiles, crucial pathways in disease progression may be identified, allowing for more predictive and personalised therapy of the individual. This article will provide an overview of the various putative tear fluid biomarkers that have been identified to date, ranging from ocular surface disease and retinopathies to cancer and multiple sclerosis. Putative tear fluid biomarkers of ocular disorders, as well as the more recent field of systemic disease biomarkers, will be shown

Computational Prototyping Tools and Techniques

Contains reports on five research projects.Industry Consortium (Mobil, Statoil, DNV Software, Shell, OTRC, Petrobras, NorskHydro, Exxon, Chevron, SAGA, NSWC)U.S. Navy - Office of Naval ResearchAnalog DevicesDefense Advanced Research Projects Agency Contract J-FBI-95-215Cadence Design SystemsHarris SemiconductorMAFET ConsortiumMotorola SemiconductorDefense Advanced Research Projects AgencyMultiuniversity Research InitiativeSemiconductor Research CorporationIBM Corporatio

Improvement of Aroma in Transgenic Potato As a Consequence of Impairing Tuber Browning

Sensory analysis studies are critical in the development of quality enhanced crops, and may be an important component in the public acceptance of genetically modified foods. It has recently been established that odor preferences are shared between humans and mice, suggesting that odor exploration behavior in mice may be used to predict the effect of odors in humans. We have previously found that mice fed diets supplemented with engineered nonbrowning potatoes (-PPO) consumed more potato than mice fed diets supplemented with wild-type potatoes (WT). This prompted us to explore a possible role of potato odor in mice preference for nonbrowning potatoes. Taking advantage of two well established neuroscience paradigms, the “open field test” and the “nose-poking preference test”, we performed experiments where mice exploration behavior was monitored in preference assays on the basis of olfaction alone. No obvious preference was observed towards -PPO or WT lines when fresh potato samples were tested. However, when oxidized samples were tested, mice consistently investigated -PPO potatoes more times and for longer periods than WT potatoes. Congruently, humans discriminated WT from -PPO samples with a considerably better performance when oxidized samples were tested than when fresh samples were tested in blind olfactory experiments. Notably, even though participants ranked all samples with an intermediate level of pleasantness, there was a general consensus that the -PPO samples had a more intense odor and also evoked the sense-impression of a familiar vegetable more often than the WT samples. Taken together, these findings suggest that our previous observations might be influenced, at least in part, by differential odors that are accentuated among the lines once oxidative deterioration takes place. Additionally, our results suggest that nonbrowning potatoes, in addition to their extended shelf life, maintain their odor quality for longer periods of time than WT potatoes. To our knowledge this is the first report on the use of an animal model applied to the sensory analysis of a transgenic crop