Capturing next-generation genome wide molecular markers in cassava helps to untangle the crop's genetic improvement history [W144]

The release of the cassava reference genome by Prochnik et al. in 2012 has allowed cassava geneticists identifying tens of thousands genome-wide sequence variations across multiple cultivars. These genomic variations have helped to develop a new generation of molecular markers for the crop's genetics research either by re-sequencing using restriction-site associated DNA-sequencing (RAD-seq) or by the SNPtype™ allele-specific PCR assays technology. Today CIAT's cassava program using these technologies has characterized at the DNA level more than 3000 cassava cultivars used by farmers in South East Asia or Latin America; including improved cultivars, LAC landraces, and its potential wild close relatives conserved at the world's largest collections of the crop. These next generation molecular markers along with the analytical methods implemented in the Cassava Genome Hub has allowed to analyze the crop's genetic diversity, performed population and family structure analyses, unravel the crop's phylogenetic and phylogeographic history and confirm its recent introduction histories in Africa and South East Asia. Also, using these genomic and bioinformatics resources, the SNPtype™ technology has allowed us to examine the factors affecting the adoption of improved cassava varieties in the Cauca Department in southwest Colombia, as well as, six regions of Vietnam where most of the cassava is grown. These analytical approaches have showed the power of our next-generation sequencing analytical methods could have in identifying both historical population structure and recent colonization history along with the identification of clones recently adopted including its pedigree. But more importantly, it is guiding our efforts to understand the nature of complex traits in cassava such as whitefly resistance, post-harvest physiological deterioration of the roots, starch stability and content and its resistance to diseases such as frog skin disease. (Résumé d'auteur

Population structure of wild and cultivated plants shows hierarchical organization of cassava germplasm diversity. [P0324]

Cultivated cassava diversity has been shaped and is influenced by its wild relatives gene pools. Its primary gene pool (GP-1) consists of the flabellifolia-peruviana subspecies complex that cross easily with domesticated plants. Its secondary gene pool (GP-2) spans Manihot wild species that have a limited ability to interbreed with cassava. RAD sequencing of 640 accessions from the core collection at CIAT, with increased sampling of GP-1 and GP-2, shows a kinship connectivity of 9% and 175 nonrelated individuals. GP-2 sources of cultivated material include but are not limited M. glaziovii. A clear subdivision of the flabellifolia complex is not congruent with the previously postulated peruviana-flabellifolia-tristis taxonomic division. At least 5 different genetically isolated populations around the Amazon Basin could be founding stocks of current cultivated Manihot esculenta. Phylogenetic and pedigree analysis show a hierarchical structure of the populations in Latin America and the Caribbean in both wild and cultivated cassava with extensive gene flow and admixture. This hierarchical structure is dominated by kinship relations, with 95% of the sequenced samples having a third degree relative, and 75 % belonging to a single 1st degree cluster. We propose that this pedigree structure most likely is the result of modern breeding programs carried out by institutions like CIAT and EMBRAPA. Nevertheless strong phylogenetic signal can be detected from the unrelated accession set that could go back to the columbian exchange and holocene domestication. Consequences on breeding and the study of the domestication process are further discussed. (Résumé d'auteur

The impact of histopathology and NAB2-STAT6 fusion subtype in classification and grading of meningeal solitary fibrous tumor/hemangiopericytoma.

Meningeal solitary fibrous tumor (SFT)/hemangiopericytoma (HPC) is a rare tumor with propensity for recurrence and metastasis. Although multiple classification schemes have been proposed, optimal risk stratification remains unclear, and the prognostic impact of fusion status is uncertain. We compared the 2016 WHO CNS tumor grading scheme (CNS-G), a three-tier system based on histopathologic phenotype and mitotic count, to the 2013 WHO soft-tissue counterpart (ST-G), a two-tier system based on mitotic count alone, in a cohort of 133 patients [59 female, 74 male; mean age 54 years (range 20-87)] with meningeal SFT/HPC. Tumors were pathologically confirmed through review of the first tumor resection (n = 97), local recurrence (n = 35), or distant metastasis (n = 1). A STAT6 immunostain showed nuclear expression in 132 cases. NAB2-STAT6 fusion was detected in 99 of 111 successfully tested tumors (89%) including the single STAT6 immunonegative tumor. Tumors were classified by CNS-G as grade 1 (n = 43), 2 (n = 41), or 3 (n = 49), and by ST-G as SFT (n = 84) or malignant SFT (n = 49). Necrosis was present in 16 cases (12%). On follow-up, 42 patients had at least one subsequent recurrence or metastasis (7 metastasis only, 33 recurrence only, 2 patients had both). Twenty-nine patients died. On univariate analysis, necrosis (p = 0.002), CNS-G (p = 0.01), and ST-G (p = 0.004) were associated with recurrence-free (RFS) but not overall survival (OS). NAB2-STAT6 fusion type was not significantly associated with RFS or OS, but was associated with phenotype. A modified ST-G incorporating necrosis showed higher correlation with RFS (p = 0.0006) and remained significant (p = 0.02) when considering only the primary tumors. From our data, mitotic rate and necrosis appear to stratify this family of tumors most accurately and could be incorporated in a future grading scheme

Characterization of surface and porous properties of synthetic hybrid lamellar silica

Synthetic lamellar silica and hybrid lamellar silicas have been prepared by liquid crystal templating, template extraction and silanization. The samples have been characterized by thermogravimetric analysis (TGA), carbon analysis, spectroscopy, X-ray diffraction (XRD) and nitrogen adsorption. The XRD analyses have shown that the lamellar periodic stacking is preserved for all samples. The quantity and type of organic molecules at the silica surface have been evaluated by carbon analysis, TGA and spectroscopy. The covalent grafting of the solvent used for extraction of the initial surfactant has been highlighted by these analyses. The nitrogen adsorption analyses have revealed three categories of pores and two types of samples. The initial lamellar silica exhibits a very low specific surface area and plate-like type of pores. The second type of samples is made up of the hybrid samples and the initial substrate from whom the surfactant has been extracted. These samples show a significantly higher specific surface area with interlamellar spaces corresponding to narrow-slit like mesopores around 4 nm. The nitrogen adsorption data analysis has highlighted the presence of micropores within the silica sheets. The difference of the specific surface is due to pore blocking by the surfactant impeding the access to nitrogen into interlamellar spaces and by the silanes covering the pores once the surface modified. The presence of micro and mesopores combined to a high BET specific surface of 612 m²/g makes these lamellar silicas interesting materials for catalysis applications.Peer reviewe

DNA methylation-based classification of central nervous system tumours.

Accurate pathological diagnosis is crucial for optimal management of patients with cancer. For the approximately 100 known tumour types of the central nervous system, standardization of the diagnostic process has been shown to be particularly challenging-with substantial inter-observer variability in the histopathological diagnosis of many tumour types. Here we present a comprehensive approach for the DNA methylation-based classification of central nervous system tumours across all entities and age groups, and demonstrate its application in a routine diagnostic setting. We show that the availability of this method may have a substantial impact on diagnostic precision compared to standard methods, resulting in a change of diagnosis in up to 12% of prospective cases. For broader accessibility, we have designed a free online classifier tool, the use of which does not require any additional onsite data processing. Our results provide a blueprint for the generation of machine-learning-based tumour classifiers across other cancer entities, with the potential to fundamentally transform tumour pathology

Measurement of the cosmic ray spectrum above 4×10184{\times}10^{18} eV using inclined events detected with the Pierre Auger Observatory

A measurement of the cosmic-ray spectrum for energies exceeding $4{\times}10^{18}$ eV is presented, which is based on the analysis of showers with zenith angles greater than $60^{\circ}$ detected with the Pierre Auger Observatory between 1 January 2004 and 31 December 2013. The measured spectrum confirms a flux suppression at the highest energies. Above $5.3{\times}10^{18}$ eV, the "ankle", the flux can be described by a power law $E^{-\gamma}$ with index $\gamma=2.70 \pm 0.02 \,\text{(stat)} \pm 0.1\,\text{(sys)}$ followed by a smooth suppression region. For the energy ($E_\text{s}$) at which the spectral flux has fallen to one-half of its extrapolated value in the absence of suppression, we find $E_\text{s}=(5.12\pm0.25\,\text{(stat)}^{+1.0}_{-1.2}\,\text{(sys)}){\times}10^{19}$ eV.Comment: Replaced with published version. Added journal reference and DO

Neoplastic cells are a rare component in human glioblastoma microvasculature

Microvascular proliferation is a key biological and diagnostic hallmark of human glioblastoma, one of the most aggressive forms of human cancer. It has recently been suggested that stem-like glioblastoma cells have the capacity to differentiate into functional endothelial cells, and that a significant proportion of the vascular lining in tumors has a neoplastic origin. In principle, this finding could significantly impact the efficacy and development of antiangiogenic therapies targeting the vasculature. While the potential of stem-like cancer cells to form endothelium in culture seems clear, in our clinical experience using a variety of molecular markers, neoplastic cells do not contribute significantly to the endothelial-lined vasculature of primary human glioblastoma. We sought to confirm this impression by analyzing vessels in glioblastoma previously examined using chromogenic in situ hybridization (CISH) for EGFR and immunohistochemistry for mutant IDH1. Vessels containing cells expressing these definitive neoplastic markers were identified in a small fraction of tumors, but only 10% of vessel profiles examined contained such cells and when identified these cells comprised less than 10% of the vascular cellularity in the cross section. Interestingly, these rare intravascular cells showing EGFR amplification by CISH or mutant IDH1 protein by immunohistochemistry were located in the middle or outer portions of vessel walls, but not amongst the morphologic boundaries of the endothelial lining. To more directly address the capacity of glioblastoma cells to contribute to the vascular endothelium, we performed double labeling (Immunofluorescence/FISH) for the endothelial marker CD34 and EGFR gene locus. Although rare CD34 positive neoplastic cells unassociated with vessels were identified (<1%), this analysis did not identify EGFR amplified cells within vascular linings, and further supports our observations that incorporation of glioblastoma cells into the tumor vessels is at best extremely rare, and therefore of questionable clinical or therapeutic significance

A Latin American approach to mediatization: specificities and contributions to a global discussion about how the media shape contemporary societies

Theories on mediatization have been developed in Latin America in parallel to those flourishing in the Global North. This article analyzes the former while keeping an eye on the more available theoretical production in English-speaking publications. The main part of the article covers Eliseo Verón’s initial reflections on the semantization of violence to his later development of an evolutionary approach to mediatization. The article then introduces the contributions made by Latin American researchers who have followed in Verón’s wake during the last decade. The article concludes with an overview of the parallelisms between the two theoretical strands, and considers their complementarities as well as the possible exchanges between them

Energy Estimation of Cosmic Rays with the Engineering Radio Array of the Pierre Auger Observatory

The Auger Engineering Radio Array (AERA) is part of the Pierre Auger Observatory and is used to detect the radio emission of cosmic-ray air showers. These observations are compared to the data of the surface detector stations of the Observatory, which provide well-calibrated information on the cosmic-ray energies and arrival directions. The response of the radio stations in the 30 to 80 MHz regime has been thoroughly calibrated to enable the reconstruction of the incoming electric field. For the latter, the energy deposit per area is determined from the radio pulses at each observer position and is interpolated using a two-dimensional function that takes into account signal asymmetries due to interference between the geomagnetic and charge-excess emission components. The spatial integral over the signal distribution gives a direct measurement of the energy transferred from the primary cosmic ray into radio emission in the AERA frequency range. We measure 15.8 MeV of radiation energy for a 1 EeV air shower arriving perpendicularly to the geomagnetic field. This radiation energy -- corrected for geometrical effects -- is used as a cosmic-ray energy estimator. Performing an absolute energy calibration against the surface-detector information, we observe that this radio-energy estimator scales quadratically with the cosmic-ray energy as expected for coherent emission. We find an energy resolution of the radio reconstruction of 22% for the data set and 17% for a high-quality subset containing only events with at least five radio stations with signal.Comment: Replaced with published version. Added journal reference and DO