Ecoregional Dominance in Spatial Distribution of Avian Influenza (H5N1) Outbreaks

Recent articles in Emerging Infectious Diseases (1,2) and elsewhere (3,4) have highlighted the role of Anatidae migration in dispersal of the H5N1 subtype of highly pathogenic avian influenza (HPAI) virus. Although these articles point out that identifying the geographic origin of migrating waterfowl is needed to understand and predict pathogen dispersal, study analyses have been limited to pathways with nominal reference to climatic and vegetation patterns that control spatiotemporal patterns of this migration

Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes

Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images.Abbreviations: 3D FISH: three-dimensional fluorescence in situ hybridization; 3D: three-dimensional; ASY1: ASYNAPTIC 1; CC: chromocenters; CO: Crossover; DAPI: 4',6-diamidino-2-phenylindole; DMC1: DNA MEIOTIC RECOMBINASE 1; DSB: Double-Strand Break; FISH: fluorescence in situ hybridization; GFP: GREEN FLUORESCENT PROTEIN; HEI10: HUMAN ENHANCER OF INVASION 10; NCO: Non-Crossover; NE: Nuclear Envelope; Oligo-FISH: oligonucleotide fluorescence in situ hybridization; RNPII: RNA Polymerase II; SC: Synaptonemal Complex; SIM: structured illumination microscopy; ZMM (ZIP: MSH4: MSH5 and MER3 proteins); ZYP1: ZIPPER-LIKE PROTEIN 1

Extending nanoscale patterning with multipolar surface plasmon resonances.

Plasmonic excitation of metallic nanoparticles can trigger chemical reactions at the nanoscale. Such optical effects can also be employed to selectively and locally graft photopolymer layers at the nanostructure surface, and, when combined with a surface functionalization agent, new pathways can be explored to modify the surface of a plasmonic nanoparticle. Among these approaches, diazonium salt chemistry is seen as an attractive strategy due to the high photoinduced reactivity of these salts. In this work, we demonstrate that it is possible to trigger the site-selective grafting of aryl films derived from diazonium salts on distinct nano-localized area of single gold nanotriangles, by taking advantage of their multipolar localized surface plasmon modes. It is shown the aryl film will preferentially graft in areas where the electric field enhancement is maximum, independently of the considered excited surface plasmon mode. These experimental findings are in very good qualitative agreement with the calculations of the local electric field, using the finite-difference time-domain (FDTD) method. We believe that this plasmonic-based approach will not only pave a new way for the spatially controlled surface functionalization of plasmonic nanoparticles, but also provide a general strategy to attach distinct molecules to hot spot regions on a single nanoparticle, opening promising prospects in sensing and multiplexing, and optically nano-scale patterning of functional groups

Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes

Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images

Completing the TRB family: newly characterized members show ancient evolutionary origins and distinct localization, yet similar interactions

Telomere repeat binding proteins (TRBs) belong to a family of proteins possessing a Myb-like domain which binds to telomeric repeats. Three members of this family (TRB1, TRB2, TRB3) from Arabidopsis thaliana have already been described as associated with terminal telomeric repeats (telomeres) or short interstitial telomeric repeats in gene promoters (telo-boxes). They are also known to interact with several protein complexes: telomerase, Polycomb repressive complex 2 (PRC2) E(z) subunits and the PEAT complex (PWOs-EPCRs-ARIDs-TRBs). Here we characterize two novel members of the TRB family (TRB4 and TRB5). Our wide phylogenetic analyses have shown that TRB proteins evolved in the plant kingdom after the transition to a terrestrial habitat in Streptophyta, and consequently TRBs diversified in seed plants. TRB4-5 share common TRB motifs while differing in several others and seem to have an earlier phylogenetic origin than TRB1-3. Their common Myb-like domains bind long arrays of telomeric repeats in vitro, and we have determined the minimal recognition motif of all TRBs as one telo-box. Our data indicate that despite the distinct localization patterns of TRB1-3 and TRB4-5 in situ, all members of TRB family mutually interact and also bind to telomerase/PRC2/PEAT complexes. Additionally, we have detected novel interactions between TRB4-5 and EMF2 and VRN2, which are Su(z)12 subunits of PRC2

Reconstruction accuracy dependence with induced-shear-wave magnitude in Magnetic Resonance Elastography

Congrès sous l’égide de la Société Française de Génie Biologique et Médical (SFGBM)National audienceSince 1996, Magnetic Resonance Elastography (MRE) holds the promise for absolute quantitation of the mechanical parameters of living tissues [1]. The reproducibility of the technique was challenged [2] while the measurement precision was determined by the uncertainty of the recorded MR-signal phase onto which the inferred motion is encoded [3]. We assumed that the ratio of the resulting total wave amplitude to its related uncertainty, AT/ΔAT,_ _should be considered to validate the acquired set of MRE data. Nevertheless, as long as this ratio is greater than unity, the validity of the extracted mechanical parameters might not be questioned. Here, we extract the complex shear modulus, G=G′+G′′, by inversion of the three-dimensional equation of motion [4] for a wide range of inferred wave amplitude, starting from zero, in a breast phantom. The shear dynamic, G′, and loss, G′′, moduli were found to increase with the wave amplitude before reaching a plateau at ratios AT/ΔAT much greater than one. Experiments were carried with standard motion-sensitized refocused field echo (RFE) [1] and motion fractional-encoding fast field echo (FFE) [5], for which sensitivities largely differ, so the relevance of a MRE-validity threshold based on the ratio AT/ΔAT could be exhibited

CD4 recovery following antiretroviral treatment interruptions in children and adolescents with HIV infection in Europe and Thailand

Objectives: The aim of the study was to explore factors associated with CD4 percentage (CD4%) reconstitution following treatment interruptions (TIs) of antiretroviral therapy (ART). Methods: Data from paediatric HIV-infected cohorts across 17 countries in Europe and Thailand were pooled. Children on combination ART (cART; at least three drugs from at least two classes) for > 6 months before TI of ≥ 30 days while aged < 18 years were included. CD4% at restart of ART (r-ART) and in the long term (up to 24 months after r-ART) following the first TI was modelled using asymptotic regression. Results: In 779 children with at least one TI, the median age at first TI was 10.1 [interquartile range (IQR) 6.4, 13.6] years and the mean CD4% was 27.3% [standard deviation (SD) 11.0%]; the median TI duration was 9.0 (IQR 3.5, 22.5) months. In regression analysis, the mean CD4% was 19.2% [95% confidence interval (CI) 18.3, 20.1%] at r-ART, and 27.1% (26.2, 27.9%) in the long term, with half this increase in the first 6 months. r-ART and long-term CD4% values were highest in female patients and in children aged < 3 years at the start of TI. Long-term CD4% was highest in those with a TI lasting 1 to <3 months, those with r-ART after year 2000 and those with a CD4% nadir ≥ 25% (all P < 0.001). The effect of CD4% nadir during the TI differed significantly (P = 0.038) by viral suppression at the start of the TI; in children with CD4% nadir < 15% during TI, recovery was better in those virally suppressed prior to the TI; viral suppression was not associated with recovery in children with CD4% nadir ≥ 25%. Conclusions: After restart of ART following TI, most children reconstituted well immunologically. Nevertheless, several factors predicted better immunological reconstitution, including younger age and higher nadir CD4% during TI