Rapid and easy method to extract and preserve DNA from Cryptococcus neoformans and other pathogenic yeasts

Fungal Endophyte Communities of Crucifer Crops Are Seasonally Dynamic and Structured by Plant Identity, Plant Tissue and Environmental Factors

Endophytic fungi are important in diverse plant functions but knowledge of the factors that shape assemblages of these symbionts is lacking. Here, using a culture-dependent approach, we report 4,178 endophytic fungal isolates representing 16 orders isolated from stems, roots and leaves of three cruciferous plant species, Chinese cabbage (Brassica rapa L.), radish (Raphanus sativus L.) and white cabbage (B. olerocea L.), collected from 21 focal fields with different landscape contexts and pesticide uses during four seasons (summer, autumn, winter and spring). The colonization rate of fungi was found to be most strongly affected by season, plant identity and plant tissue. The colonization was highest during autumn, followed by summer, spring and lowest during winter. The colonization was highest in B. olerocea (53.2%), followed by B. rapa (42.6%), and lowest in R. sativus (35.0%). The colonization was highest in stems (51.9%) in all plant types, followed by leaves (42.4%) and roots (37.5%). Hypocreales was the dominant order (33.3% of all the isolates), followed by Glomerellales (26.5%), Eurotiales (12.1%), Pleosporales (9.8%) and Capnodiales (6.0%). Fungal endophyte abundance (number of isolates) followed the same pattern as colonization rate, while species richness varied with season and host plant tissue. Ordination analyses showed that the abundance and richness of Hypocreales, Eurotiales and Sordariales were associated with plant roots, while Capnodiales, Pleosporales and Trichosphaeriales were associated with spring. Other environmental factors, elevation, and the proportions of grassland, forest, orchard and waterbodies in the surrounding landscape also exerted effects within some categories of other main effects or for certain fungal taxa. Our results indicate that while fungal endophyte communities of crucifer crops vary strongly with the season, they are also strongly structured by plant identity and plant tissue, to a lesser extent by pesticide use and only weakly by landscape composition. The understanding of the ecological roles of fungal endophytes could contribute to habitat management and consequently improve crop pest management.

Draft Genome Sequence of the Oleaginous Yeast Cryptococcus curvatus ATCC 20509

Cryptococcus curvatus ATCC 20509 is a commonly used nonmodel oleaginous yeast capable of converting a variety of carbon sources into fatty acids. Here, we present the draft genome sequence of this popular organism to provide a means for more in-depth studies of its fatty acid production potential.

Draft Genome Sequence of Cryptococcus terricola JCM 24523, an Oleaginous Yeast Capable of Expressing Exogenous DNA

Cryptococcus terricola JCM 24523 has recently been identified as an oleaginous yeast capable of converting starch into fatty acids. This draft genome sequence provides a platform for elucidating its fatty acid production potential and supporting comparisons with other oleaginous species.

Simple and rapid method for the detection of Filobasidiella neoformans in a probiotic dairy product by using loop-mediated isothermal amplification

Yeast contamination is a serious problem in the food industry and a major cause of food spoilage. Several yeasts, such as Filobasidiella neoformans, which cause cryptococcosis in humans, are also opportunistic pathogens, so a simple and rapid method for monitoring yeast contamination in food is essential. Here, we developed a simple and rapid method that utilizes loop-mediated isothermal amplification (LAMP) for the detection of F. neoformans. A set of five specific LAMP primers was designed that targeted the 5.8S-26S rDNA internal transcribed spacer 2 region of F. neoformans, and the primer set's specificity was confirmed. In a pure culture of F. neoformans, the LAMP assay had a lower sensitivity threshold of 10(2)cells/mL at a runtime of 60min. In a probiotic dairy product artificially contaminated with F. neoformans, the LAMP assay also had a lower sensitivity threshold of 10(2)cells/mL, which was comparable to the sensitivity of a quantitative PCR (qPCR) assay. We also developed a simple two-step method for the extraction of DNA from a probiotic dairy product that can be performed within 15min. This method involves initial protease treatment of the test sample at 45°C for 3min followed by boiling at 100°C for 5min under alkaline conditions. In a probiotic dairy product artificially contaminated with F. neoformans, analysis by means of our novel DNA extraction method followed by LAMP with our specific primer set had a lower sensitivity threshold of 10(3)cells/mL at a runtime of 60min. In contrast, use of our novel method of DNA extraction followed by qPCR assay had a lower sensitivity threshold of only 10(5)cells/mL at a runtime of 3 to 4h. Therefore, unlike the PCR assay, our LAMP assay can be used to quickly evaluate yeast contamination and is sensitive even for crude samples containing bacteria or background impurities. Our study provides a powerful tool for the primary screening of large numbers of food samples for yeast contamination.

Diagnosis of common dermatophyte infections by a novel multiplex real-time polymerase chain reaction detection/identification scheme

BACKGROUND

In the absence of a functional dermatophyte-specific polymerase chain reaction (PCR), current diagnosis of dermatophytoses, which constitute the commonest communicable diseases worldwide, relies on microscopy and culture. This combination of techniques is time-consuming and notoriously low in sensitivity.

OBJECTIVES

Recent dermatophyte gene sequence records were used to design a real-time PCR assay for detection and identification of dermatophytes in clinical specimens in less than 24 h.

PATIENTS AND METHODS

Two assays based on amplification of ribosomal internal transcribed spacer regions and on the use of probes specific to relevant species and species-complexes were designed, optimised and clinically evaluated. One assay was for detecting the Trichophyton mentagrophytes species complex plus T. tonsurans and T. violaceum. The second assayed for the T. rubrum species complex, Microsporum canis and M. audouinii.

RESULTS

The analytical sensitivity of both assays was 0.1 pg DNA per reaction, corresponding to 2.5-3.3 genomes per sample. The protocol was clinically evaluated over 6 months by testing 92 skin, nail and hair specimens from 67 patients with suspected dermatophytosis. Real-time PCR detected and correctly identified the causal agent in specimens from which T. rubrum, T. interdigitale, M. audouinii or T. violaceum grew in culture, and also identified a dermatophyte species in an additional seven specimens that were negative in microscopy and culture.

CONCLUSIONS

This highly sensitive assay also proved to have high positive and negative predictive values (95.7% and 100%), facilitating the accurate, rapid diagnosis conducive to targeted rather than empirical therapy for dermatophytoses.

MfLIP1, a gene encoding an extracellular lipase of the lipid-dependent fungus Malassezia furfur

Malassezia furfur is a dimorphic fungus and a member of the normal cutaneous microflora of humans. However, it is also a facultative pathogen, associated with a wide range of skin diseases. One unusual feature of M. furfur is an absolute dependency on externally provided lipids which the fungus hydrolyses by lipolytic activity to release fatty acids necessary for both growth and pathogenicity. In this study, the cloning and characterization of the first gene encoding a secreted lipase of M. furfur possibly associated with this activity are reported. The gene, MfLIP1, shows high sequence similarity to other known extracellular lipases, but is not a member of a lipase gene family in M. furfur. MfLIP1 consists of 1464 bp, encoding a protein with a molecular mass of 54·3 kDa, a conserved lipase motif and an N-terminal signal peptide of 26 aa. By using a genomic library, two other genes were identified flanking MfLIP1, one of them encoding a putative secreted catalase, the other a putative amine oxidase. The cDNA of MfLIP1 was expressed in Pichia pastoris and the biochemical properties of the recombinant lipase were analysed. MfLip1 is most active at 40 °C and the pH optimum was found to be 5·8. The lipase hydrolysed lipids, such as Tweens, frequently used as the source of fatty acids in M. furfur media, and had minor esterase activity. Furthermore, the lipase is inhibited by different bivalent metal ions. This is the first molecular description of a secreted lipase from M. furfur.

Rapid methods to extract DNA and RNA from Cryptococcus neoformans

Extraction of nucleic acids from the pathogenic yeast Cryptococcus neoformans is normally hampered by a thick and resistant capsule, accounting for at least 70% of the whole cellular volume. This paper presents procedures based on mechanical cell breakage to extract DNA and RNA from C. neoformans and other capsulated species. The proposed system for DNA extraction involves capsule relaxation by means of a short urea treatment and bead beating. These two steps allow a consistent extraction even from strains resistant to other procedures. Yield and quality of DNA obtained with the proposed method were higher than those obtained with two earlier described methods. This protocol can be extended to every yeast species and particularly to those difficult to handle for the presence of a capsule. RNA purification is accomplished using an original lysing matrix and the FastPrep System (Bio101) after a preliminary bead beating treatment. Yields range around 1 mg RNA from 15 ml overnight culture (10(9) cells), RNA appears undegraded, making it suitable for molecular manipulations.

Molecular differentiation of seven Malassezia species

A system based on PCR and restriction endonuclease analysis was developed to distinguish the seven currently recognized Malassezia species. Seventy-eight strains, including authentic culture collection strains and routine clinical isolates, were investigated for variation in the ribosomal DNA repeat units. Two genomic regions, namely, the large subunit of the ribosomal gene and the internal transcribed spacer (ITS) region, were amplified by PCR, and products were digested with restriction endonucleases. The patterns generated were useful in identification of five out of seven Malassezia species. M. sympodialis was readily distinguishable in that its ITS region yielded a 700-bp amplified fragment, whereas the other six species yielded an 800-bp fragment. M. globosa and M. restricta were very similar in the regions studied and could be distinguished only by performing a hot start-touchdown PCR on primers for the beta-tubulin gene. Primers based on the conserved areas of the Candida cylindracea lipase gene, which were used in an attempt to amplify Malassezia lipases, yielded an amplification product after annealing at 55 degrees C only with M. pachydermatis. This specific amplification may facilitate the rapid identification of this organism.