Cryptococcus gattii sero-mating type allelic pattern determined by multiplex PCR

AbstractMolecular methods to differentiate serotypes, mating types and molecular types of Cryptococcus neoformans and C. gattii are important tools to understand epidemiology and pathogenesis of these pathogens. In this study, a multiplex polymerase chain reaction (PCR) approach was applied to sero-mating typing of C. gattii strains. Four pairs of primers were designed to target 4 allele-specific genes located in the mating-type locus. Twenty-three C. gattii strains, presenting different mating types and serotypes, were tested to validate the method. The method was able to identify all sero-mating allelic patterns including hybrid combinations, and therefore, it represents a simple one-step PCR for sero-mating typing of C. gattii strains

Global Molecular Epidemiology of Cryptococcus neoformans and Cryptococcus gattii : an Atlas of the Molecular Types

Cryptococcosis is a fungal disease affecting more than one million people per year worldwide. The main etiological agents of cryptococcosis are the two sibling species Cryptococcus neoformans and Cryptococcus gattii that present numerous differences in geographical distribution, ecological niches, epidemiology, pathobiology, clinical presentation and molecular characters. Genotyping of the two Cryptococcus species at subspecies level supplies relevant information to understand how this fungus has spread worldwide, the nature of its population structure, and how it evolved to be a deadly pathogen. At present, nine major molecular types have been recognized: VNI, VNII, VNB, VNIII, and VNIV among C. neoformans isolates, and VGI, VGII, VGIII, and VGIV among C. gattii isolates. In this paper all the information available in the literature concerning the isolation of the two Cryptococcus species has been collected and analyzed on the basis of their geographical origin, source of isolation, level of identification, species, and molecular type. A detailed analysis of the geographical distribution of the major molecular types in each continent has been described and represented on thematic maps. This study represents a useful tool to start new epidemiological surveys on the basis of the present knowledge

EXTRACTION of DEMS and ORTHOIMAGES from ARCHIVE AERIAL IMAGERY to SUPPORT PROJECT PLANNING in CIVIL ENGINEERING

Archive aerial photos represent a valuable heritage to provide information about land content and topography in the past years. Today, the availability of low-cost and open-source solutions for photogrammetric processing of close-range and drone images offers the chance to provide outputs such as DEM's and orthoimages in easy way. This paper is aimed at demonstrating somehow and to which level of accuracy digitized archive aerial photos may be used within a such kind of low-cost software (Agisoft Photoscan Professional®) to generate photogrammetric outputs. Different steps of the photogrammetric processing workflow are presented and discussed. The main conclusion is that this procedure may come to provide some final products, which however do not feature the high accuracy and resolution that may be obtained using high-end photogrammetric software packages specifically designed for aerial survey projects. In the last part a case study is presented about the use of four-epoch archive of aerial images to analyze the area where a tunnel has to be excavated

Soil enables mating and sporulation of Cryptococcus neoformans species complex

The pathogenic yeasts of Cryptococcus neoformans species complex have been isolated in the environment from bird excreta, soil, trees, and decaying wood. Although previous studies showed the ability of C. neoformans species complex to grow and mate on bird excreta and plant materials, there are no studies on soil. Therefore, the aim of the present study is to verify if C. neoformans species complex is able to grow on media containing soil and if it is able to sexually reproduce on this substrate. Soil media were prepared using four different soil samples collected in four different Italian regions, and the two reference strains JEC20 and JEC21 were tested to verify their ability to mate on these media. All the media supported the growth and sexual reproduction confirming that soil represents a realized niche for C. neoformans species complex

Pebble Bed Reactor Dust Production Model

The operation of pebble bed reactors, including fuel circulation, can generate graphite dust, which in turn could be a concern for internal components; and to the near field in the remote event of a break in the coolant circuits. The design of the reactor system must, therefore, take the dust into account and the operation must include contingencies for dust removal and for mitigation of potential releases. Such planning requires a proper assessment of the dust inventory. This paper presents a predictive model of dust generation in an operating pebble bed with recirculating fuel. In this preliminary work the production model is based on the use of the assumption of proportionality between the dust production and the normal force and distance traveled. The model developed in this work uses the slip distances and the inter-pebble forces computed by the authors’ PEBBLES. The code, based on the discrete element method, simulates the relevant static and kinetic friction interactions between the pebbles as well as the recirculation of the pebbles through the reactor vessel. The interaction between pebbles and walls of the reactor vat is treated using the same approach. The amount of dust produced is proportional to the wear coefficient for adhesive wear (taken from literature) and to the slip volume, the product of the contact area and the slip distance. The paper will compare the predicted volume with the measured production rates. The simulation tallies the dust production based on the location of creation. Two peak production zones from intra pebble forces are predicted within the bed. The first zone is located near the pebble inlet chute due to the speed of the dropping pebbles. The second peak zone occurs lower in the reactor with increased pebble contact force due to the weight of supported pebbles. This paper presents the first use of a Discrete Element Method simulation of pebble bed dust production

Cryptococcus neoformans and Cryptococcus gattii Species Complex Isolates on the Slopes of Mount Etna, SICILY, Italy

This study investigated the presence of Cryptococcus neoformans and Cryptococcus gattii species complex isolates on olive trees growing in the Eastern part of Sicily (Italy) characterized by the presence of the volcano Etna and the ability of these fungal pathogens to sexually reproduce on medium containing volcanic soil. Samples from 124 olive trees were collected from 14 different sites around Mount Etna. Eighteen trees (14.5%) resulted colonized by C. neoformans VNI-\u3b1A isolates, one (0.8%) by VNIV-\u3b1D isolates, and two (1.6%) by C. gattii VGI-\u3b1B isolates. The ability of environmental and reference strains belonging to VNI, VNIV, and VGI molecular types to sexually reproduce on a medium containing volcanic soil was also tested. VNI and VNIV strains were able to produce filaments and basiodiospores more vigorously than on the control medium, whereas VGI strains were not fertile. In conclusion, the present study identified which C. neoformans and C. gattii species complex genotypes are circulating in Eastern Sicily and confirmed the ecological role of olive trees as environmental reservoir of these pathogens. It also showed that Cryptococcus is able to colonize and sexually reproduce in inhospitable environments such as the slopes of a volcano

Development Status of the PEBBLES Code for Pebble Mechanics: Improved Physical Models and Speed-up

PEBBLES is a code for simulating the motion of all the pebbles in a pebble bed reactor. Since pebble bed reactors are packed randomly and not precisely placed, the location of the fuel elements in the reactor is not deterministically known. Instead, when determining operating parameters the motion of the pebbles can be simulated and stochastic locations can be found. The PEBBLES code can output information relevant for other simulations of the pebble bed reactors such as the positions of the pebbles in the reactor, packing fraction change in an earthquake, and velocity profiles created by recirculation. The goal for this level three milestone was to speedup the PEBBLES code through implementation on massively parallel computer. Work on this goal has resulted in speeding up both the single processor version and creation of a new parallel version of PEBBLES. Both the single processor version and the parallel running capability of the PEBBLES code have improved since the fiscal year start. The hybrid MPI/OpenMP PEBBLES version was created this year to run on the increasingly common cluster hardware profile that combines nodes with multiple processors that share memory and a cluster of nodes that are networked together. The OpenMP portions use the Open Multi-Processing shared memory parallel processing model to split the task across processors in a single node that shares memory. The Message Passing Interface (MPI) portion uses messages to communicate between different nodes over a network. The following are wall clock speed up for simulating an NGNP-600 sized reactor. The single processor version runs 1.5 times faster compared to the single processor version at the beginning of the fiscal year. This speedup is primarily due to the improved static friction model described in the report. When running on 64 processors, the new MPI/OpenMP hybrid version has a wall clock speed up of 22 times compared to the current single processor version. When using 88 processors, a speed up of 23 times is achieved. This speedup and other improvements of PEBBLES combine to make PEBBLES more capable and more useful for simulation of a pebble bed reactor. This report details the implementation and effects of the speedup work done over the course of the fiscal year

PEBBLES: A COMPUTER CODE FOR MODELING PACKING, FLOW AND RECIRCULATIONOF PEBBLES IN A PEBBLE BED REACTOR

A comprehensive, high fidelity model for pebble flow has been developed and embodied in the PEBBLES computer code. In this paper, a description of the physical artifacts included in the model is presented and some results from using the computer code for predicting the features of pebble flow and packing in a realistic pebble bed reactor design are shown. The sensitivity of models to various physical parameters is also discussed

A disulfide bridge allows for site-selective binding in liver bile acid binding protein thereby stabilising the orientation of key amino acid side chains

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