Multi-locus sequence typing and phylogenetics of Cryptococcus neoformans AD hybrids

Hybrid AD strains of the human pathogenic Cryptococcus neoformans species complex have been reported from many parts of the world. However, their origin, diversity, and evolution are incompletely understood. In this study, we analyzed 102 AD hybrid strains representing 21 countries on five continents. For each strain, we obtained its mating type and its allelic sequences at each of the seven loci that have been used for genotyping haploid serotypes A and D strains of the species complex by the Cryptococcus research community. Our results showed that most AD hybrids exhibited loss of heterozygosity at one or more of the seven analyzed loci. Phylogenetic and population genetic analyses of the allelic sequences revealed multiple origins of the hybrids within each continent, dating back to one million years ago in Africa and up to the present in other continents. We found evidence for clonal reproduction and long-distance dispersal of these hybrids in nature. Comparisons with the global haploid serotypes A and D strains identified new alleles and new haploid multi-locus genotypes in AD hybrids, consistent with the presence of yet-to-be discovered genetic diversity in haploid populations of this species complex in nature. Together, our results indicate that AD hybrids can be effectively genotyped using the same multi-locus sequencing type approach as that established for serotypes A and D strains. Our comparisons of the AD hybrids among each other as well as with the global haploid serotypes A and D strains revealed novel genetic diversity as well as evidence for multiple origins and dynamic evolution of these hybrids in nature.

A low cost, safe, disposable, rapid and self-sustainable paper-based platform for diagnostic testing: lab-on-paper

There is a strong interest in the use of biopolymers in the electronic and biomedical industries, mainly towards low-cost applications. The possibility of developing entirely new kinds of products based on cellulose is of current interest, in order to enhance and to add new functionalities to conventional paper-based products. We present our results towards the development of paper-based microfluidics for molecular diagnostic testing. Paper properties were evaluated and compared to nitrocellulose, the most commonly used material in lateral flow and other rapid tests. Focusing on the use of paper as a substrate for microfluidic applications, through an eco-friendly wax-printing technology, we present three main and distinct colorimetric approaches: (i) enzymatic reactions (glucose detection); (ii) immunoassays (antibodies anti-Leishmania detection); (iii) nucleic acid sequence identification (Mycobacterium tuberculosis complex detection). Colorimetric glucose quantification was achieved through enzymatic reactions performed within specific zones of the paper-based device. The colouration achieved increased with growing glucose concentration and was highly homogeneous, covering all the surface of the paper reaction zones in a 3D sensor format. These devices showed a major advantage when compared to the 2D lateral flow glucose sensors, where some carryover of the coloured products usually occurs. The detection of anti-Leishmania antibodies in canine sera was conceptually achieved using a paper-based 96-well enzyme-linked immunosorbent assay format. However, optimization is still needed for this test, regarding the efficiency of the immobilization of antigens on the cellulose fibres. The detection of Mycobacterium tuberculosis nucleic acids integrated with a non-cross-linking gold nanoprobe detection scheme was also achieved in a wax-printed 384-well paper-based microplate, by the hybridization with a species-specific probe. The obtained results with the above-mentioned proof-of-concept sensors are thus promising towards the future development of simple and cost-effective paper-based diagnostic devices.

Gold nanoprobe assay for the identification of mycobacteria of the Mycobacterium tuberculosis complex

Members of the Mycobacterium tuberculosis complex (MTC) are causative agents of human and animal tuberculosis. This complex encompasses several phylogenetically related species, including M. tuberculosis, the main aetiological agent of human tuberculosis, and Mycobacterium bovis, the causative agent of bovine tuberculosis, a relevant worldwide zoonosis. Clear epidemiological evaluation of appropriate and effective treatment requires unambiguous differentiation between MTC members. Routine diagnosis has been increasingly relying on the molecular identification of MTC members. In the present study, we report the use of a gold nanoparticle-based approach for the sensitive, specific and fast identification of MTC and for the differentiation of M. bovis and M. tuberculosis using the gyrB locus as target. This gold nanoprobe strategy relies on the colorimetric differentiation of specific DNA sequences based on differential aggregation profiles in the presence or absence of specific target hybridization. Three nanoprobes were designed and successfully used for the specific identification of members of MTC, M. bovis and M. tuberculosis.

Direct and specific identification of Cryptococcus neoformans in biological samples using fluorescently labelled DNA probes

Fluorescence in situ hybridisation (FISH) is a suitable technique for the rapid, reliable and cultivation-independent identification of microbial pathogens. This study describes the development of fluorescently labelled rRNA-targeted oligonucleotides and a FISH assay to detect and identify Cryptococcus neoformans in culture and biological samples. All C. neoformans reference and clinical isolates gave positive signals with the specific oligonucleotide probes, whereas all non-target yeast species gave negative reactions with the same probes. The assay was also successfully applied to the detection of C. neoformans cells in cerebrospinal samples from patients with clinical diagnosis of cryptococcosis. The described FISH-based assay revealed to be practical, sensitive and specific for the detection and identification of C. neoformans yeasts.

Application of fluorescence in situ hybridisation (FISH) to the analysis of yeast population dynamics in winery and laboratory grape must fermentations

To analyse the yeast population diversity during wine fermentations, specific fluorescein-labelled oligonucleotide probes targeted to the D1/D2 region of the 26S rRNA of different yeast species known to occur frequently in this environment were designed and tested with reference strains. The probes were then used to identify wine must isolates and to follow, in combination with plate counts, the evolution of yeast populations in two winery fermentations of white and red grape musts. In both cases, a high diversity of non-Saccharomyces yeast species was detected, including Candida stellata, Hanseniaspora uvarum, H. guilliermondii, Kluyveromyces marxianus, K. thermotolerans and Torulaspora delbrueckii. Some of these species (e.g., K. marxianus, K. thermotolerans and T. delbrueckii) were present in significant amounts during the tumultuous fermentation stage, despite the predominance of Saccharomyces cerevisiae cells following the inoculation of the wine musts with a starter strain. To further clarify the yeast population dynamics at the late phase of the fermentations, and because winery conditions do not allow a reliable control of experimental variables, strains isolated from the industrial musts were used to conduct two laboratory microvinifications in synthetic grape juice, using different ratios of S. cerevisiae/non-Saccharomyces in the inocula. Under these conditions, the results were similar to those obtained in the winery, showing a yeast profile with mixed species throughout the first fermentation stage, i.e. until about 40-50% of the total sugar was consumed. Non-Saccharomyces yeasts were outgrown by S. cerevisiae only after ethanol reached concentrations around 4-5% (v/v), which argues in favour of a potential important role of non-Saccharomyces in the final organoleptic characteristics of the wine.

Emendation of the basidiomycetous yeast genus Kondoa and the description of Kondoa aeria sp. nov

The genus Kondoa Y. Yamada, Nakagawa & Banno was erected to accommodate a single taxon, K. malvinella (Fell & Hunter) Y. Yamada, Nakagawa & Banno, which was transferred from the teliospore-forming genus Rhodosporidium Banno based on pronounced differences in the 5S and 26S ribosomal RNA (rRNA) nucleotide sequences to R. toruloides Banno. In contrast with the original description, reinvestigation of K. malvinella revealed the formation of transversely septate (auricularioid) basidia that did not arise on teliospores, but formed directly on the dikaryotic mycelium. The four-celled basidia developed sterigmata on which forcibly discharged asymmetric basidiospores (ballistospores) were produced. Additionally, a new taxon emerged from the study of recent isolates, for which the name K. aeria sp. nov. is proposed. This new species produced two-celled auricularioid basidia on hyphae with incomplete clamp connections. Ballistospores arose on the basidia at the tip of sterigmata and, after ejection, germinated by budding. These observations led us to present an emended diagnosis for the genus Kondoa. Analysis of the sequence data from the D1/D2 region of the 26S rRNA gene showed a very close resemblance between K. aeria and K. malvinella in a cluster that also contained several Bensingtonia species. Taxa in this cluster share specific physiological traits and produce characteristic pinkish-cream to mauve colonies; in contrast, formation of ballistoconidia is only observed in the Bensingtonia species. Sequence data supported placement of K. malvinella and K. aeria in the 'Agaricostilbum clade' of the Urediniomycetes.

Is MUC1 polymorphism associated with female infertility?

The transmembrane mucin glycoprotein (MUC1) has an anti-adhesive role, and functions to maintain a non-receptive uterine state. A polymorphic variation of the MUC1 gene has been associated with female infertility due to suspected failure of embryo implantation, based on the significant greater size of the lower allele observed in infertile women. The aim of this study was to confirm this preliminary observation using long polymerase chain reaction (PCR), which has amplified the 60-bp polymorphic variable number of tandem repeat (VNTR) associated to the binding domain of the MUC1 glycoprotein. DNA samples were obtained from 20 women, 10 fertile and 10 infertile, and the VNTR region was amplified through a long PCR procedure. The VNTR size range from 1.6 to 2.9 kb (22-44 motifs). The average size for the lower allele was 1.69 kb for both groups, and for the upper allele was 2.35 and 2.49 kb (P > 0.05) for fertile and infertile groups respectively. The VNTR polymorphism of the MUC1 gene was not associated with female infertility, although its significance cannot be discarded. It is suggested that other regulatory molecules and signals may interact with the MUC1 gene variations, favouring endometrial receptivity and embryo attachment.

Estimation and diversity of phylloplane mycobiota on selected plants in a Mediterranean-type ecosystem in Portugal

Mediterranean ecosystems have not been consistently investigated as natural habitats for microbes in general, and fungi in particular. Here we present the results of a survey of epiphytic mycobiota (filamentous fungi and yeasts) on the phylloplane of selected plants in the Arrábida Natural Park, an ecosystem of Mediterranean characteristics in Portugal, using conventional culture-dependent isolation methods. Leaves from the species Acer monspessulanum and Quercus faginea (deciduous trees) and Cistus albidus, Pistacia lentiscus, and Osyris quadripartita (evergreen shrubs) were collected twice a year for two consecutive years, at two distinct locations of Serra da Arrábida: the more humid northern slope and the drier southern slope. A total of 1029 strains of filamentous fungi and 540 strains of yeasts were isolated, which represented at least 36 and 46 distinct species, respectively. Total counts were higher on the plants from the northern slope and there was a general increase from spring to autumn, notably on the deciduous trees for the yeasts. Plant species that had higher numbers of leaf colonists (A. monspessulanum, C. albidus, and Q. faginea) also yielded a wider range of species. Among the filamentous fungi there was a predominance of species of ascomycetous affinity, whereas basidiomycetous species dominated among yeast isolates. Some of the taxa recovered were common to other phylloplane studies (e.g., ubiquitous molds and yeasts such as Cladosporium spp. and Cryptococcus spp., respectively), but less common species were also found, some of which appeared to represent undescribed taxa. Interestingly, a few species seemed to be associated with a particular plant, notably in the case of the evergreen shrub C. albidus. However, for a considerable number of fungi and yeasts the same taxon was recovered throughout the year from more than one plant and at both sites, suggesting that such species might be genuine phylloplane inhabitants (or at least of aerial plant surfaces) even though they appeared not to display host specificity.

Intravenous hydroxyethylrutosides combined with long-term oral anticoagulation in atherosclerotic nonreconstructable critical leg ischemia: a retrospective study

OBJECTIVE

To evaluate in a group of seriously diseased patients with nonreconstructable chronic critical leg ischemia (CLI), treated by a combination of i.v. hydroxyethylrutosides (HR)* and oral anticoagulation (AC) by warfarin, the short-term effects on the cutaneous microvascular blood perfusion of the soles of feet and especially the long-term clinical outcome in terms of amputation and death.

DESIGN

A retrospective comparison between two groups of patients, HR + AC and a comparable reference group, fulfilling the same inclusion and exclusion criteria corresponding to the definition of CLI according to the Second European Consensus Document (1991). Clinical follow-up in both groups was made after 1, 3, 6, 12, and 24 months.

SETTING

Patients were examined at university departments of clinical physiology with special interest in peripheral vascular disease, in cooperation with colleagues at university departments of surgery, internal medicine and dermatology of Karolinska Hospital, Södersjukhuset and Huddinge Hospital.

PATIENTS

A total of seventy patients with CLI according to the definition of the Second European Consensus Document, 1991, ie, besides severe rest pain or ischemic lesions also a toe blood pressure < 30 mg Hg. Group with HR + anticoagulation (AC): 42 patients (19 diabetics, 23 nondiabetics). Reference group: 28 patients (18 diabetics, 10 nondiabetics). For distribution of age and toe blood pressure at baseline, see Table I.

INTERVENTIONS

Therapy group: besides ordinary standard therapy, daily HR infusions for a mean period of 3.6 weeks + oral anticoagulation continued to the end of the study at 24 months. A comparable reference group on the same basic therapy but without the combination HR + AC. PARAMETERS IN EVALUATION: Short-term parameters: clinical data, skin temperature, and fluorescein imaging. Long-term outcome: amputation or death.

RESULTS

Short-term and long-term results with HR + AC indicated that patients with severe CLI and very poor prognosis benefited in terms of survival and limb salvage from initial therapy with HR infusion combined with long-term oral anticoagulation. Results of this combined treatment seem at least comparable with those with i.v. prostacyclin analogies.