Fast and reliable method to estimate global DNA methylation in plants and fungi with high-pressure liquid chromatography (HPLC)-ultraviolet detection and even more sensitive one with HPLC-mass spectrometry

DNA (Deoxyribonucleic acid) methylation is one of the epigenetic modifications of DNA, acting as a bridge between genotype and phenotype. Thus, disruption of DNA methylation pattern has tremendous consequences for organism development. Current methods to determine DNA methylation suffer from methodological drawbacks like high requirement of DNA and poor reproducibility of chromatograms. Here we provide a fast and reliable method using high-pressure liquid chromatography (HPLC)-ultraviolet (UV) detector and even more sensitive one with HPLC- mass spectrometry (MS) and we test this method with various plant and fungal DNA isolates. We optimized the preparation of the DNA degradation step to decrease background noise, we improved separation conditions to provide reliable and reproducible chromatograms and conditions to measure nucleotides in HPLC-MS. We showed that global DNA methylation level can be accurately and reproducibly measured with as little as 0.2 µM for HPLC-UV and 0.02 µM for HPLC-MS of methylated cytosine.

Identification of a bio-signature for barley resistance against Pyrenophora teres infection based on physiological, molecular and sensor-based phenotyping

Necrotic and chlorotic symptoms induced during Pyrenophora teres infection in barley leaves indicate a compatible interaction that allows the hemi-biotrophic fungus Pyrenophora teres to colonise the host. However, it is unexplored how this fungus affects the physiological responses of resistant and susceptible cultivars during infection. To assess the degree of resistance in four different cultivars, we quantified visible symptoms and fungal DNA and performed expression analyses of genes involved in plant defence and ROS scavenging. To obtain insight into the interaction between fungus and host, we determined the activity of 19 key enzymes of carbohydrate and antioxidant metabolism. The pathogen impact was also phenotyped non-invasively by sensor-based multireflectance and -fluorescence imaging. Symptoms, regulation of stress-related genes and pathogen DNA content distinguished the cultivar Guld as being resistant. Severity of net blotch symptoms was also strongly correlated with the dynamics of enzyme activities already within the first day of infection. In contrast to the resistant cultivar, the three susceptible cultivars showed a higher reflectance over seven spectral bands and higher fluorescence intensities at specific excitation wavelengths. The combination of semi high-throughput physiological and molecular analyses with non-invasive phenotyping enabled the identification of bio-signatures that discriminates the resistant from susceptible cultivars.

Comparison of methods for isolating fungal DNA

Objectives

The main aim of this work was to compare the methods of DNA isolation in the moulds of genus Mucorales with special regard to the amount and purity of the DNA acquired. The acquired DNA was then amplified by specific real-time PCR.

Design

Five DNA extraction procedures were carried out in a Class 2 Biosafety cabinet in a dedicated room with suitable biosafety precautions and appropriate biowaste disposal methods. A total of 6 Mucorales clinical strains were used.

Results

From the viewpoint of concentration and purity, methods A shown abundant amount of fungal DNA whereas methods E report a pure fungal DNA with R260/280 of 1.7 near the optimal 1.8. The DNA quantity reach statistically difference at ANOVA test with p value 0.0005

Conclusion

Overall, the E method was the most efficient method in the extraction of DNA from fungal cultures compared to the other methods considering time, cost, technical expertise, and instrumentation. Use of this assay will allow researchers to obtain DNA from fungi quickly for use in molecular assays

Safe DNA-extraction Protocol Suitable for Studying Tree-fungus Interactions

We present a safe and low-cost method suitable for DNA extraction from mycelium and tree tissue samples. After sample preparation, the extraction takes about 60 min. Method performance was tested by extracting DNA from various tree tissue samples and from mycelium grown on solid and liquid media. DNA was extracted from juvenile and mature host material (Picea abies, Populus trichocarpa, Pseudotsuga menziesii) infected with different pathogens (Heterobasidion annosum, Heterobasidion parviporum, Leptographium wagenerii, Sphaerulina musiva). Additionally, DNA was extracted from pure cultures of the pathogens and several endophytic fungi. PCR success rate was 100% for young poplar material and fungal samples, and 48-72% for conifer and mature broadleaved plant samples. We recommend using 10-50 mg of fresh sample for the best results. The method offers a safe and low-cost DNA extraction alternative to study tree-fungus interactions, and is a potential resource for teaching purposes.

Fungal-Grade Reagents and Materials for Molecular Analysis

Fungal DNA is present at very low loads in clinical specimens. Molecular detection by amplification assays generally is a challenge because of a potentially multiple input of contaminating DNA from exogenous sources. Besides airborne, handling and cross-contamination, materials and reagents used in the molecular laboratory can contain microbial DNA which is a long underestimated potential source of false positive results. In this contribution decontamination procedures of materials and reagents and the selection of certified microbial DNA-free components for sample collection, DNA extraction, and PCR amplification are discussed with respect to the aim of building up a reliable molecular system for the diagnosis of fungal organisms at the limit of detection.

Ocular symptoms and tear film break up time (BUT) among junior high school students in Penang, Malaysia - Associations with fungal DNA in school dust

BACKGROUND

There are few studies on ocular effects of indoor mould exposure in schools, especially in the tropics OBJECTIVE: To study associations between eye symptoms and tear film break up time (BUT) in students and demographic data and fungal DNA in schools.

METHODS

A school environment study was performed among randomly selected students in eight randomly selected secondary schools in Penang, Malaysia. Information on eye symptoms and demographic data was collected by a standardised questionnaire. BUT was measured by two methods, self-reported BUT (SBUT) and by the non-invasive Tearscope (NIBUT). Dust was collected by vacuuming in 32 classrooms and analysed for five fungal DNA sequences. Geometric mean (GM) for total fungal DNA was 7.31*10⁴ target copies per gram dust and for Aspergillus/Penicillium DNA 3.34*10⁴ target copies per gram dust. Linear mixed models and 3-level multiple logistic regression were applied adjusting for demographic factors.

RESULTS

A total of 368 students (58%) participated and 17.4% reported weekly eye symptoms the last 3 months. The median SBUT and TBUT were 15 and 12s, respectively. Students wearing glasses (OR 2.41, p=0.01) and with a history of atopy (OR=2.67; p=0.008) had more eye symptoms. Girls had less eye symptoms than boys (OR=0.34; p=0.006) Indoor carbon dioxide in the classrooms was low (range 380-720ppm), temperature was 25-30°C and relative air humidity 70-88%. Total fungal DNA in vacuumed dust was associated with shorter SBUT (4s shorter per 10⁵ target copies per gram dust; p=0.04) and NIBUT (4s shorter per 10⁵ target copies per gram dust; p<0.001). Aspergillus/Penicillium DNA was associated with shorter NIBUT (5s shorter per 10⁵ target copies per gram dust; p=0.01).

CONCLUSION

Fungal contamination in schools in a tropical country can be a risk factor for impaired tear film stability among students.

Respiratory symptoms and fractional exhaled nitric oxide (FeNO) among students in Penang, Malaysia in relation to signs of dampness at school and fungal DNA in school dust

Few health studies exist on dampness and mould in schools in the tropics. We studied associations between fraction of exhaled nitric oxide (FeNO), respiratory symptoms and airway infections among students and dampness and fungal DNA in schools in Malaysia. A total of 368 randomly selected students from 32 classrooms in 8 secondary schools in Penang, Malaysia, participated (58% participation rate). Information on current respiratory symptoms and the home environment was collected by a standardised questionnaire. FeNO was measured by NIOX MINO (50ml/min). The classrooms were inspected and dust was collected by vacuuming on special filters and was analysed for five fungal DNA sequences by quantitative PCR. Linear mixed models and 3-level multiple logistic regression (school, classroom, student) were applied adjusting for demographic data and the home environment. Totally 10.3% reported doctor's diagnosed asthma, 15.1% current wheeze, 12.4% current asthma, 37.3% daytime breathlessness, 10.2% nocturnal breathlessness, 38.9% airway infections and 15.5% had pollen or furry pet allergy. The geometric mean of FeNO was 19.9ppb and 45% had elevated FeNO (>20ppb). Boys had higher levels of FeNO. Chinese had less daytime breathlessness than Malay (OR=0.30: p<0.001). Indoor carbon dioxide levels were low (380-720ppm). Dampness was observed in 18% of the classrooms and was associated with respiratory infections (OR=3.70; 95% CI 1.14-12.1) and FeNO (p=0.04). Aspergillus versicolor DNA was detected in 67% of the classrooms. Higher numbers of Aspergillus versicolor DNA in classroom dust were associated with wheeze (p=0.006), current asthma (p=0.002), respiratory infections (p=0.005) and elevated FeNO levels (p=0.02). In conclusion, respiratory symptoms were common among the students and the high FeNO levels indicate ongoing airway inflammation. Building dampness and the mould Aspergillus versicolor in schools in Malaysia can be risk factors for impaired respiratory health among the students.

Endotoxin, ergosterol, muramic acid and fungal DNA in dust from schools in Johor Bahru, Malaysia--Associations with rhinitis and sick building syndrome (SBS) in junior high school students

This paper studied associations between ocular symptoms, rhinitis, throat and dermal symptoms, headache and fatigue in students by ethnicity and in relation to exposure to chemical microbial markers and fungal DNA in vacuumed dust in schools in Malaysia. A total of 462 students from 8 randomly selected secondary schools in Johor Bahru, Malaysia, participated (96% response rate). Dust was vacuumed from 32 classrooms and analysed for levels of five types of endotoxin as 3-hydroxy fatty acids (C10, C12, C14, C16 and C18 3-OH), muramic acid, ergosterol and five sequences of fungal DNA. Multiple logistic regression was applied. Totally 11.9% reported weekly ocular symptoms, 18.8% rhinitis, 15.6% throat and 11.1% dermal symptoms, 20.6% headache and 22.1% tiredness. Totally 21.1% reported pollen or furry pet allergy (atopy) and 22.0% parental asthma or allergy. Chinese students had less headache than Malay and Indian had less rhinitis and less tiredness than Malay. Parental asthma/allergy was a risk factor for ocular (odds ratio=3.79) and rhinitis symptoms (OR=3.48). Atopy was a risk factor for throat symptoms (OR=2.66), headache (OR=2.13) and tiredness (OR=2.02). There were positive associations between amount of fine dust in the dust samples and ocular symptoms (p<0.001) and rhinitis (p=0.006). There were positive associations between C14 3-OH and rhinitis (p<0.001) and between C18 3-OH and dermal symptoms (p=0.007). There were negative (protective) associations between levels of total endotoxin (LPS) (p=0.004) and levels of ergosterol (p=0.03) and rhinitis and between C12 3-OH and throat symptoms (p=0.004). In conclusion, the amount of fine dust in the classroom was associated with rhinitis and other SBS symptoms and improved cleaning of the schools is important. Endotoxin in the school dust seems to be mainly protective for rhinitis and throat symptoms but different types of endotoxin could have different effects. The ethnic differences in symptoms among the students deserve further attention.