Genome-wide identification and in silico characterization of major RNAi gene families in date palm (Phoenix dactylifera).

BACKGROUND: Dates contain various minerals that are essential for good health. The major RNA interference (RNAi) gene families play a vital role in plant growth and development by controlling the expression of protein-coding genes against different biotic and abiotic stresses. However, these gene families for date palm are not yet studied. Therefore, this study has explored major RNAi genes and their characteristics in date palm. RESULTS: We have identified 4 PdDCLs, 7 PdAGOs, and 3 PdRDRs as RNAi proteins from the date palm genome by using AtRNAi genes as query sequences in BLASTp search. Domain analysis of predicted RNAi genes has revealed the Helicase_C, Dicer_dimer, PAZ, RNase III, and Piwi domains that are associated with the gene silencing mechanisms. Most PdRNAi proteins have been found in the nucleus and cytosol associated with the gene silencing actions. The gene ontology (GO) enrichment analysis has revealed some important GO terms including RNA interference, dsRNA fragmentation, and ribonuclease_III activity that are related to the protein-coding gene silencing mechanisms. Gene regulatory network (GRN) analysis has identified PAZ and SNF2 as the transcriptional regulators of PdRNAi genes. Top-ranked 10 microRNAs including Pda-miR156b, Pda-miR396a, Pda-miR166a, Pda-miR167d, and Pda-miR529a have been identified as the key post-transcriptional regulators of PdRNAi genes that are associated with different biotic/abiotic stresses. The cis-acting regulatory element analysis of PdRNAi genes has detected some vital cis-acting elements including ABRE, MBS, MYB, MYC, Box-4, G-box, I-box, and STRE that are linked with different abiotic stresses. CONCLUSION: The results of this study might be valuable resources for the improvement of different characteristics in date palm by further studies in wet-lab.

Association of climate factors with dengue incidence in Bangladesh, Dhaka City: A count regression approach.

Background: In Bangladesh, particularly in Dhaka city, dengue fever is a major factor in serious sickness and hospitalization. The weather influences the temporal and geographical spread of the vector-borne disease dengue in Dhaka. As a result, rainfall and ambient temperature are considered macro factors influencing dengue since they have a direct impact on Aedes aegypti population density, which changes seasonally dependent on these critical variables. This study aimed to clarify the relationship between climatic variables and the incidence of dengue disease. Methods: A total of 2253 dengue and climate data were used for this study. Maximum and minimum temperature (°C), humidity (grams of water vapor per kilogram of air g.kg-1), rainfall (mm), sunshine hour (in (average) hours per day), and wind speed (knots (kt)) in Dhaka were considered as the independent variables for this study which trigger the dengue incidence in Dhaka city, Bangladesh. Missing values were imputed using multiple imputation techniques. Descriptive and correlation analyses were performed for each variable and stationary tests were observed using Dicky Fuller test. However, initially, the Poisson model, zero-inflated regression model, and negative binomial model were fitted for this problem. Finally, the negative binomial model is considered the final model for this study based on minimum AIC values. Results: The mean of maximum and minimum temperature, wind speed, sunshine hour, and rainfall showed some fluctuations over the years. However, a mean number of dengue cases reported a higher incidence in recent years. Maximum and minimum temperature, humidity, and wind speed were positively correlated with dengue cases. However, rainfall and sunshine hours were negatively associated with dengue cases. The findings showed that factors such as maximum temperature, minimum temperature, humidity, and windspeed are crucial in the transmission cycles of dengue disease. On the other hand, dengue cases decreased with higher levels of rainfall. Conclusion: The findings of this study will be helpful for policymakers to develop a climate-based warning system in Bangladesh.

Vegetative Growth of Four Strains of Hericium erinaceus Collected from Different Habitats.

Vegetative growth of four different strains of Hericium erinaceus was observed. The temperature suitable for optimal mycelial growth was determined to be 25℃, with growth observed in the extend temperature range of 20~30℃. The different strains of this mushroom showed distinct pH requirements for their optimum vegetative growth, with the most favorable growth observed at pH 6. Considering vegetative mycelial growth, PDA, YM, Hennerberg, Hamada, and Glucose peptone were the most favorable media, and Czapek Dox, Hoppkins, Glucose tryptone, and Lilly were the most unfavorable media for these mushroom strains. With the exception of lactose, most of the carbon sources assayed demonstrated favorable vegetative growth of H. erinaceus. For mycelial growth, the most suitable nitrogen source was alanine and the most unsuitable was histidine. Oak sawdust medium supplemented with 10~20% rice bran was the best for mycelial growth of the mushroom.

Degradation of three aromatic dyes by white rot fungi and the production of ligninolytic enzymes.

This study was conducted to evaluate the degradation of aromatic dyes and the production of ligninolytic enzymes by 10 white rot fungi. The results of this study revealed that Pycnoporus cinnabarinus, Pleurotus pulmonarius, Ganoderma lucidum, Trametes suaveolens, Stereum ostrea and Fomes fomentarius have the ability to efficiently degrade congo red on solid media. However, malachite green inhibited the mycelial growth of these organisms. Therefore, they did not effectively decolorize malachite green on solid media. However, P. cinnabarinus and P. pulmonarius were able to effectively decolorize malachite green on solid media. T. suaveolens and F. rosea decolorized methylene blue more effectively than any of the other fungi evaluated in this study. In liquid culture, G. lucidum, P. cinnabarinus, Naematoloma fasciculare and Pycnoporus coccineus were found to have a greater ability to decolorize congo red. In addition, P. cinnabarinus, G. lucidum and T. suaveolens decolorized methylene blue in liquid media more effectively than any of the other organisms evaluated in this study. Only F. fomentarius was able to decolorize malachite green in liquid media, and its ability to do so was limited. To investigate the production of ligninolytic enzymes in media containing aromatic compounds, fungi were cultured in naphthalene supplemented liquid media. P. coccineus, Coriolus versicolor and P. cinnabarinus were found to produce a large amount of laccase when grown in medium that contained napthalene.

Favorable Culture Conditions for Mycelial Growth of Korean Wild Strains in Ganoderma lucidum.

Ganoderma lucidum (Fr.) Karst (Polyporaceae), belonging to basidiomycota, is one of the most famous medicinal mushrooms. This study was carried out to investigate favorable mycelial growth conditions, such as pH, temperature, growth media, carbon sources and nitrogen sources of Korean strains in G. lucidum. The most suitable temperature for the mycelial growth was obtained at 30℃. In general, optimal temperature range for the mycelial growth was found at 25~30℃. This Mushroom has a broad pH range (5~9) for its mycelial growth and mostly favorable growth was found at pH 5. Generally, Hamada, Glucose peptone, YM, Mushroom complete and Lilly media were the most suitable for the mycelial growth of G. lucidum. Among 10 different carbon sources, dextrin, galactose and fructose were best but the rest of other carbon sources also facilitated the growth of mycelia. The most suitable nitrogen sources were ammonium acetate, glycine, arginine and calcium nitrate, but to a certain extent, all of the supplemented nitrogen sources also stimulated the mycelial growth.

Physicochemical Requirement for the Vegetative Growth of Schizophyllum commune Collected from Different Ecological Origins.

Schizophyllum commune is an edible and medicinal mushroom widely distributed in the world. The optimal growth conditions for the mycelia of 10 strains of the fungus were investigated. The temperature suitable for the mycelial growth and density was obtained at 30~35℃. Among the tested conditions, the minimum mycelial growth was found at 15℃. In case of pH, the most favorable growth was found at pH 5. The results indicated that this mushroom well adapted to high temperature and low pH for its mycelial growth. Considering growth phenotype of mycelia, Hamada, Hennerberg, PDA and YM were the most suitable and Lilly, Glucose triptone, Glucose peptone and Hoppkins were the most unfavorable among tested media for the mycelial growth of S. commune. Out of tested carbon sources, dextrin and fructose were the most suitable and lactose, mannose and sorbitol were the unsuitable for the fungus. Compact mycelial density was obtained from most of the carbon sources. Among used nitrogen sources, calcium nitrate, potassium nitrate and alanine were the most appropriate and the most incompatible were ammonium phosphate, histidine, urea and arginine for mycelial growth of S. commune on the culture media. Calcium nitrate, histidine and potassium nitrate showed moderately thin or thin, and rest of nitrogen sources showed compact or moderately compact mycelial density.

Suitable Conditions for Mycelial Growth of Phellinus spp.

The fungus Phellinus is a mushroom that is widely used medicinally. The optimal conditions for mycelial growth of 13 strains of the fungus were investigated. Mycelial growth was optimal at 25℃ and was uniformly minimal at 15℃ and 35℃. Growth was optimal at pH 6~7. The mycelial phenotype was best promoted by growth using Potato Dextrose agar, Hamada, Glucose peptone, and Yeast-Malt media, whereas Czapek Dox, Hennerberg, and Lilly media were the most unfavorable for the mycelial growth of Phellinus spp. Glucose, sucrose, fructose, and dextrin were the most suitable carbon sources for mycelial growth, while lactose, maltose, and galactose were unsuitable. Among tested nitrogen sources, ammonium phosphate, potassium nitrate, and arginine best promoted mycelial growth, while alanine, urea, and histidine least promoted mycelial growth.

Antibacterial and Antifungal Activities of Stereum ostrea, an Inedible Wild Mushroom.

Antibacterial and antifungal activities of liquid culture filtrate, water and ethanol extract (solid culture) of Stereum ostrea were evaluated against 5 bacteria and 3 plant pathogenic fungi. To determine the minimal inhibitory concentration (MIC), we studied 5~300 mg/ml concentrations against bacteria and fungi separately. The MIC was 10 mg/ml for Bacillus subtilis and 40 mg/ml for Colletotrichum gloeosporioides and Colletotrichum miyabeanus. Liquid culture filtrate was more effective against Gram positive than Gram negative bacteria, and Staphylococcus aureus was the most inhibited (20.3 mm) bacterium. Water and ethanol extracts were effective against both Gram positive and Gram negative bacteria, and water extract was better than ethanol extract. In water and ethanol extract, inhibition zones were 23.6 and 21.0 mm (S. aureus) and 26.3 and 22.3 mm (Pseudomonas aeruginosa), respectively. For plant pathogenic fungi, the highest and lowest percent inhibition of mycelial growth (PIMG) was found 82.8 and 14.4 against C. miyabeanus and Botrytis cinerea in liquid culture filtrate, respectively. In water extract, the PIMG was found to be the highest 85.2 and lowest 41.7 for C. miyabeanus and C. gloeosporioides, respectively. The inhibitory effect of ethanol extract was better against C. miyabeanus than C. gloeosporioides and B. cinerea. Among 3 samples, water extract was the best against tested pathogenic fungi. This study offers that the extracts isolated from S. ostrea contain potential compounds which inhibit the growth of both bacteria and fungi.

The Artificial Cultivation of Oudemansiella mucida on the Oak Sawdust Medium.

To produce fruiting bodies of Oudemansiella mucida, porcelain fungus, on the oak sawdust medium, additives suitable for the mycelial growth and fruiting body formation were screened. In general, the mycelial growth of the three strains of O. mucida used in this study have been good on oak sawdust mixed rice bran of 20~30%. The mycelia incubated in potato dextrose broth for 7 days were inoculated on oak sawdust medium supplemented with various ratios of rice bran and incubated for 30 days at 25℃ in the dark condition until the mycelia of O. mucida fully colonized the media from top to bottom. Then, top surface of the media in the bottles were horizontally scratched with a spatula and filled with tap water for 3 hours. To induce the primordial formation of O. mucida, the bottles were transferred to the mushroom cultivating room under 12 hrs of light (350 lux) and dark condition with relative humidity of 95% at 17℃. The primordia of O. mucida were formed on the surface of oak sawdust media after 7 days of incubation. The mature fruiting bodies were observed 5 days after primordial formation. The fruiting bodies O. mucida were formed on oak sawdust medium mixed with 5 to 30% rice bran. However, abundant fruiting-bodies of O. mucida were produced in oak sawdust medium supplemented with 20% rice bran. This is the first report associated with an artificial fruiting body production of O. mucida in Korea.

Effect of Fungicides and Plant Extracts on the Conidial Germination of Colletotrichum gloeosporioides Causing Mango Anthracnose.

In Northern Bangladesh, generally mango trees are planted as agroforest that gives higher Net Present Value (NPV) than traditional agriculture. Mango anthracnose caused by Colletotrichum gloeosporioides Penz. is seen as a very destructive and widely distributed disease, which results in poor market value. Five fungicides such as Cupravit, Bavistin, Dithane M-45, Thiovit and Redomil were tested against conidial germination of C. gloeosporioides. Dithane M-45 and Redomil were the most effective when the conidia were immersed for 10~20 minutes at 500~1000 ppm concentrations. Antifungal activities of 13 plant extracts were tested against conidial germination of C. gloeosporioides. Conidial germination of C. gloeosporioides was completely inhibited in Curcuma longa (leaf and rhizome), Tagetes erecta (leaf) and Zingiber officinales (rhizome) after 15 minutes of incubation respectively.