Search Results (103)

Malassezia spp. has been recognized among neonatal intensive care unit (NICU) patients’ commensals and pathogens, accounting for a significant number of invasive fungal infections. The Random Amplified Polymorphic DNA (RAPD) may be used for Malassezia spp. strains typing from clinical isolates, demonstrating high resolution and specificity. Herein, we propose a retrospective analysis of Malassezia spp. isolates, aiming to investigate their identity and transmission pathways. Moreover, we documented Malassezia spp. prevalence within the University Hospital Policlinico of Catania, Italy. The analysis collected a total number of 16 M. pachydermatis and categorized them into four different clusters, hypothesizing a horizontal transmission. Although the essential role of microbiological sample cultures, our data suggested further environmental surveillance protocols to prevent NICU patients’ colonization due to the Malassezia spp. persistence and adhesion within healthcare surfaces. Full article

The genus Trifolium comprises numerous species that serve as globally important forage and ornamental crops. However, phenotypic difference between species were difficult to define in many cases because of the wide range of diversity caused by primary polymorphism. To effectively identify and differentiate Trifolium species, a total of 5288 candidate EST-SSR molecular markers were developed based on Trifolium repens transcriptome sequencing results, and 132 EST-SSRs that produced clear, reproducible, and highly polymorphic bands were verified after random selection and initial screening. Finally, 202 different bands were amplified by the 28 pairs of SSR primers, and variety identification and DNA fingerprinting were constructed for 16 Trifolium varieties mainly cultivated in China. The polymorphism information index (PIC) ranged from 0.117 to 0.432, with an average of 0.311. Cluster analysis and principal component analysis demonstrated that white clover clustered into a separate group, suggesting a relatively distant genetic relationship with the other 12 Trifolium materials. The DNA fingerprint map of Trifolium species constructed using highly polymorphic markers can effectively distinguish 16 different Trifolium materials. Notably, these markers developed from T. repens show high interspecific transferability, providing a powerful tool for further dissecting genetic diversity within the Trifolium genus, accelerating marker-assisted breeding programs, and reconstructing species domestication trajectories. Full article

Background: Bovine mastitis caused by Prototheca spp. is the most significant animal disease of algal origin, with an increasing number of cases reported worldwide. Currently, there is no effective treatment, so control requires the culling of infected animals. In Chile, information is limited, and a discrepancy remains in the literature regarding the Prototheca species involved in bovine mastitis. Methods: This study aimed to molecularly type and phenotypically characterize Prototheca isolates associated with bovine mastitis in Chile. Sixty-six Prototheca isolates obtained from individual bovine mastitis milk samples and bulk tank milk samples were analyzed through cytochrome b gene (cytb) sequencing, Random Amplified Polymorphic DNA–Polymerase Chain Reaction (RAPD-PCR) analysis, and phenotypic evaluation (morphology, antimicrobial susceptibility, and biofilm formation). Results: Sixty-five isolates were identified as P. bovis and one as P. ciferrii, marking the first report of the latter in bovine mastitis in Chile. RAPD analysis revealed a high genetic diversity in P. bovis. All strains exhibited resistance to the antibiotics tested from the Fluoroquinolone, β-lactam, and sulfonamide groups; however, 100% of the strains showed susceptibility to aminoglycosides, with gentamicin standing out as a potential therapeutic option. Most P. bovis strains formed weak (81.5%, 53/65) or moderate (15.4%, 10/65) biofilms, which could favor the persistence of infection. Conclusions: These findings provide novel insights into the molecular and phenotypic characteristics of Prototheca spp. in Chile, highlighting the predominance of P. bovis, the emergence of P. ciferri, and the implications for antimicrobial management and disease control. Full article

In nature, orchid seed germination is extremely low, making in vitro asymbiotic seed germination essential for the propagation and conservation of endangered Vanda coerulea. This study optimized a micropropagation protocol and evaluated the genetic homogeneity of regenerated orchids. The synergistic effect of kinetin (KN) with auxins in the Mitra (M) medium best supported protocorm formation and seedling development. The highest shoot multiplication (5.62 ± 0.09) was achieved with 1.2 mg L⁻¹ KN and 0.6 mg L⁻¹ IBA (indole-3-butyric acid) in the medium. Enhanced leaf production (4.81 ± 0.37) was observed when 3.2 mg L⁻¹ KN was combined with 1.8 mg L⁻¹ IAA (indole-3-acetic acid), while root development was superior when 3.2 mg L⁻¹ KN together with 2.4 mg L⁻¹ IAA was incorporated in the medium. Anatomical sections confirmed well-developed leaf and root structures. Genetic fidelity assessment using random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), inter-primer binding site (iPBS), and start codon targeted (SCoT) markers revealed 97.17% monomorphism (240/247 bands) and low Nei’s genetic distances (0.000–0.039), indicating high similarity among the regenerants. Dendrogram clustering was supported by a high cophenetic correlation coefficient (CCC = 0.806) and strong resolution in Principal Coordinate Analysis (PCoA) (44.03% and 67.36% variation on the first two axes). The Mantel test revealed a significant correlation between both ISSR and SCoT markers with the pooled marker data. Flow cytometry confirmed the genome stability among the in vitro-propagated orchids, with consistently low CV (FL2-A) values (4.37–4.94%). This study demonstrated the establishment of a reliable in vitro protocol for rapidly propagating genetically identical V. coerulea via asymbiotic seed germination. Full article

The live microbiota of tea has not been extensively investigated. This study aimed to identify the live, culturable microbiota from four types of tea with varying oxidation levels, before and after brewing. Tea leaves and brews from oolong and fermented teas were analyzed for total viable counts of aerobic bacteria, lactobacilli, fungi, and Enterobacteriaceae. Cultivation was performed and isolates were identified by Sanger sequencing. Heat resistance was assessed at 70 °C and 90 °C. Random Amplified Polymorphic DNA (RAPD) was used to determine strain-level diversity. Fully oxidized, post-fermented Pu-erh tea had the highest viable bacterial count. Most isolates belonged to Bacillaceae, Staphylococcaceae, and Paenibacillaceae, families associated with soil or human skin. Only two potentially pathogenic species were identified: Staphylococcus epidermidis and Bacillus cereus. In Pu-erh, live bacteria were detected after brewing at 90 °C, including Heyndrickxia coagulans, a spore forming probiotic species. H. coagulans strains remained in vegetative state after hot water exposure and survived at 70 °C, indicating thermotolerance. RAPD-analysis revealed nine distinct H. coagulans strains across six Pu-erh teas. Conclusion: This study provides new insight into the viable microbiota of different teas and their survival during brewing, highlighting safety concerns and probiotic species like H. coagulans. Full article

Dengue fever is a mosquito-borne viral infection that recently appeared in Upper Egypt. Globally, more than 50 million new infections occur annually. It currently lacks effective treatment, necessitating vector control strategies targeting Aedes aegypti. This study investigates the potential of chlorophyllin as a control agent against dengue vectors. Chlorophyllin was characterized by FTIR analysis. The singlet oxygen quantum yield was determined by comparing the luminescence intensity at 1270 nm with that of phenalenone, yielding a value of 0.18. LC₅₀ and LC₉₀ values were calculated for chlorophyllin. Its larvicidal efficacy was assessed, revealing an LC₅₀ of 0.47 ppm in controlled laboratories and 93.3 ppm in semi-field conditions, demonstrating its superior potency against Aedes aegypti compared to pheophorbide and Bacillus sphaericus. Genotoxicity was analyzed through Random Amplified Polymorphic DNA (RAPD)-PCR, and histopathological changes were documented through microscopic examination. The genotoxicity results revealed high similarity in the DNA configurations of chlorophyllin-treated larvae and healthy individuals (similarity index of 0.8), whereas pheophorbide and Bacillus sphaericus exhibited substantial genetic deviations. Histopathological analysis demonstrated severe disruptions in chlorophyllin-treated larvae’s gut epithelial cells and muscle tissues, including epithelial detachment and irregular cell shapes. These findings position chlorophyllin as a promising gut toxin larvicide for Aedes aegypti control, with a more favorable genetic safety profile than conventional chemicals. Full article

Landraces are a critical genetic resource for resilience breeding, offering solutions to prepare agriculture for the challenges posed by climate change. Their efficient utilisation depends on understanding their history and genetic relationships. The current study investigates the phylogenetic relationships of barley landraces from Algeria, varieties from the Near and Middle East, traditional landraces, and modern cultivars from Europe. Using a core set of 33 varieties, including the wild ancestor Hordeum spontaneum from Armenia, genetic diversity was analysed with Random Amplified Polymorphic DNA (RAPD) and Simple Sequence Repeat (SSR) markers spanning all barley chromosomes. Based on the SSR-based phylogeny, the Algerian varieties are well clustered with those from the Near East, while distinct from the European varieties. The findings from RAPD markers partially support these results. Using exclusively traditional landraces, where a region of origin can be defined, the SSR markers are analysed separately for each chromosome individually, and the resulting clades are represented by the respective region of origin. This strategy resolves qualitative differences in geographic resolution, depending on the chromosome. While marker HvB23D (chromosome 4) separated the wild H. spontaneum from all domesticated genotypes, markers Bmag19 and Hv13GIII (chromosome 3) reveal four distinct geographic clusters (Maghreb, Near and Middle East, West Europe, Central Europe). These biogeographic patterns suggest a model, where divergence of domesticated barley due to human activity interacted with introgression of individual chromosomes from wild barley, yielding adaptive diversity. These biogeographic patterns suggest a model in which the divergence of domesticated barley, driven by human activity, interacts with the introgression of chromosomes from wild barley, resulting in the creation of adaptive genetic diversity. Our research advances our knowledge of barley landraces’ functional genomics and highlights their potential in molecular breeding, particularly for developing resilient varieties suited to diverse environmental conditions. Full article

The prevalence of plant parasitic nematodes (PPN) in the Irish peatlands was investigated in five different peatland habitats—raised bog, cutover scrub/woodlands, fens and peat grasslands, which were further sub-categorised into fourteen different sub-habitats. Within the raised bog habitat were healthy bog hummock (HBH), healthy bog lawn (HBL), degraded bog hummock (DBH) and degraded bog lawn (DBL) and the fen habitats were fen peat (FP) and rich fen peat (R-FP). Cutover scrub or woodland habitat included cutover scrub rewetted (C-RW), cutover scrub non-rewetted (C-NRW), woodlands rewetted (W-RW) and woodlands non-rewetted (W-NRW). Grassland included wasted peat (WP), rough grazing (RG-I) and improved fen peat grassland (IFPG-RW and IFPG-NRW). Soil samples from peatlands were all collected between July and December 2023 when the temperature ranged from 12 to 20 °C. One half of each sample was used for molecular nematode analysis and the other half for morphological identification of nematodes. For the morphological identification, a specific nematode extraction protocol was optimised for peatland soils, and the extracted nematodes were fixed onto slides to be studied under a high-power light microscope. Subsequently, the other part of the soil was processed to isolate total DNA, from which the 18S rRNA gene was sequenced for the identification of nematode taxa. The extracted DNA was also used for randomly amplified polymorphic DNA (RAPD) fingerprinting analysis to determine banding patterns that could classify different bog habitats based on PPN random primers. Compared to that in the climax habitats (HBH, HBL, DBH, DBL, FP, R-FP), PPN prevalence was recorded as being higher in grasslands (WP, RG-I, IFPG-RW and IFPG-NRW) and scrub/woodland ecosystems (C-RW, C-NRW, W-RW, W-NRW). The results indicate that nematode populations are different across the various bog habitats. Emerging and current quarantine PPN belonging to the families Pratylenchidae, Meloidogynidae, Anguinidae and Heteroderidae were noted to be above the threshold limits mentioned under EPPO guidelines, in grassland and wooded peatland habitats. Future actions for PPN management may need to be considered, along with the likelihood that these PPN might impact future paludiculture and other crops and trees growing in nearby agricultural lands. Full article

Fungi of the genus Aspergillus are widespread in the environment, where they produce large quantities of airborne conidia. Inhalation of Aspergillus spp. conidia in immunocompromised individuals can cause a wide spectrum of diseases, ranging from hypersensitivity responses to lethal invasive infections. Upon deposition in the lung epithelial surface, conidia encounter and interact with complex microbial communities that constitute the lung microbiota. The lung microbiota has been suggested to influence the establishment and growth of Aspergillus spp. in the human airways. However, the mechanisms underlying this interaction have not yet been sufficiently investigated. In this study, we aimed to enrich and isolate bacterial strains capable of inhibiting the germination and growth of A. fumigatus conidia from bronchoalveolar lavage fluid (BALF) samples of lung transplant recipients using a novel enrichment method. This method is based on a soft agar overlay plate assay in which bacteria are directly in contact with conidia, allowing inhibition to be readily observed during enrichment. We isolated a total of five clonal bacterial strains with identical genotypic fingerprints, as shown by random amplified polymorphic DNA PCR (RAPD–PCR). All strains were identified as Pseudomonas aeruginosa (strains b1–b5). The strains were able to inhibit the germination and growth of Aspergillus fumigatus in a soft agar confrontation assay, as well as in a germination multiplate assay. Moreover, when compared with ten P. aeruginosa strains isolated from expectoration through standard methods, no significant differences in inhibitory potential were observed. Additionally, we showed inhibition of A. fumigatus growth on Calu-3 cell culture monolayers. However, the isolated P. aeruginosa strains were shown to cause significant damage to the cell monolayers. Overall, although P. aeruginosa is a known opportunistic lung pathogen and antagonist of A. fumigatus, we validated this novel one-step enrichment approach for the isolation of bacterial strains antagonistic to A. fumigatus from BALF samples as a proof-of-concept. This opens up a new venue for the targeted enrichment of antagonistic bacterial strains against specific fungal pathogens. Full article

Jamun plant displays enormous diversity throughout Pakistan, which necessitates its screening, evaluation, and validation to document elite genotypes having better traits for the benefit of the fruit industry and farmers. Surveys were made in natural Jamun habitats across Punjab, Pakistan, and genotypes were marked based on visual diversity of trees and fruits. In total, 60 Jamun genotypes were selected for characterization based on phenotypic and genetic markers. Phenotypic characters related to trees, leaf, and flower along with fruit qualitative traits were assessed in situ. Results revealed significant diversity with high (>25%) coefficient of variance values and the first two components of correspondence analysis exhibited 41.71% variation among genotypes. A strong association was observed among traits like upright tree and round fruit shape (0.74), bluish-colored fruit and pinkish pulp (0.85), and elliptic-shaped fruit with low fruit waxiness (−0.72). Leaves of phenotypically characterized plants were brought to Wheat Biotechnology Lab., University of Agriculture, Faisalabad, Pakistan, where Jamun genotypes were investigated genetically using Random Amplified Polymorphic DNA (RAPD) and Inter Simple Sequence Repeat (ISSR) markers. A total of 132 bands were scored, of which 108 were polymorphic, corresponding to almost 81% polymorphism among collected genotypes. High polymorphism information content values were observed against RAPD (0.389) and ISSR (0.457) markers. Genotypes were compared in relation to genetic markers, which exhibited that almost 86% of genetic variability was attributed to differences among accessions, while 14% of variation was due to differences between collections of different areas. Findings of this study confirmed wide phenotypic and genetic distinctness of Jamun in Pakistan that can aid breeders for marker-assisted selection and germplasm enhancement for future crop improvement programs. Full article

The East African Highland banana (Mutika/Lujugira subgroup) is composed of triploid (AAA) cooking and beer banana varieties that are adapted to the high-altitude region of the Great Lakes region of East Africa. Banana production is affected by several biotic and abiotic factors. Breeding opportunities in bananas are limited due to female sterility and parthenocarpy. The genetic diversity of crops enables breeders to develop new germplasm. Molecular markers have been used widely to dissect crop plants’ genetic diversity. This study assessed the genetic variation in 27 varieties from the Mutika/Lujugira subgroup using random amplified polymorphic DNA (RAPD). No genetic variation was observed among the banana varieties, and the 18 ten-mer primers produced monomorphic banding profiles. The genetic homogeneity of this banana subgroup is not congruent with their extensive morphological variation. Domestication and the bottleneck effect are often cited as the cause of reduced diversity in crop plants. On the other hand, several mechanisms, including somatic mutations, transposable elements, polyploidy, genome plasticity, and epigenetic mechanisms, are known to increase plant phenotypic variability. Further in-depth research is needed to explain the puzzle between the genetic and morphological diversity in the Mutika/Lujugira subgroup. Full article

Acca sellowiana is a subtropical tree in the myrtle family (Myrtaceae) native to southern Brazil and northeastern Uruguay. It is recognized for its value as a fruit-bearing, ornamental, and medicinal species. Based on distinctive characteristics of fruits, seeds, and leaves, as well as its geographical distribution pattern, two variants of the species are distinguished: the “Brazilian type” and the “Uruguayan type”. The objective of this study was to characterize, for the first time, the diversity of 202 individuals from four wild populations in Uruguay, representative of the species’ most southern natural distribution. Twenty-three morphological descriptors (leaf, flower, and fruit) and 204 RAPD (Random Amplified Polymorphic DNA) markers were used. The morphological data collected validated the main criteria that distinguish “Uruguayan type” populations from “Brazilian type” populations, such as lower seed weight and fruit size, thin and slightly rough skin, high pulp percentage, and hairy white abaxial leaf surfaces. Analyses of both morphological and molecular data indicated wide diversity and strong population structuring, which is relevant information for designing conservation plans, sustainable utilization, and genetic improvement of the plant genetic resources of this species. Full article

This study discusses the challenge of distinguishing between two high-quality mandarin cultivars, ‘Asumi’ and ‘Asuki’, which have been introduced and cultivated in Korea after being developed through crossbreeding in Japan. Owing to genetic similarities resulting from crossbreeding between the same parent cultivars, it is challenging to differentiate them morphologically at the seedling stage. This difficulty poses challenges for cultivation and harvesting on farms. To address this issue, we developed a method using sequence characteristic amplification region (SCAR) markers for rapid and accurate differentiation between the two cultivars. We selected specific primer sets from random amplified polymorphic DNA–SCAR combinations and sequence-related amplified polymorphism contrast markers. The multiplex PCR system using these molecular markers was able to identify 16 mandarin cultivars, including ‘Asumi’ and ‘Asuki’, among 30 cultivars. The use of these SCAR markers is expected to enhance citrus cultivation by accurately identifying mixed cultivars and facilitating proper harvest timing for citrus distribution. Additionally, the markers can help identify the genetic traits of hybrid varieties at the seedling stage. Full article

Giant goldenrod (Solidago gigantea Aiton) is one of the most invasive plant species occurring in Europe. Since little is known about the molecular mechanisms contributing to its invasiveness, we examined the natural dynamics of the content of rhizome compounds, which can be crucial for plant resistance and adaptation to environmental stress. We focused on rhizomes because they are the main vector of giant goldenrod dispersion in invaded lands. Water-soluble sugars, proline, and abscisic acid (ABA) were quantified in rhizomes, as well as ABA in the rhizosphere from three different but geographically close natural locations in Poland (50°04′11.3″ N, 19°50′40.2″ E) under extreme light, thermal, and soil conditions, in early spring, late summer, and late autumn. The genetic diversity of plants between locations was checked using the random amplified polymorphic DNA (RAPD) markers. Sugar and proline content was assayed spectrophotometrically, and abscisic acid (ABA) with the ELISA immunomethod. It can be assumed that the accumulation of sugars in giant goldenrod rhizomes facilitated the process of plant adaptation to adverse environmental conditions (high temperature and/or water scarcity) caused by extreme weather in summer and autumn. The same was true for high levels of proline and ABA in summer. On the other hand, the lowering of proline and ABA in autumn did not confirm the previous assumptions about their synthesis in rhizomes during the acquisition of frost resistance by giant goldenrod. However, in the location with intensive sunlight and most extreme soil conditions, a constant amount of ABA in rhizomes was noticed as well as its exudation into the rhizosphere. This research indicates that soluble sugars, proline, and ABA alterations in rhizomes can participate in the mechanism of acclimation of S. gigantea to specific soil and meteorological conditions in the country of invasion irrespective of plant genetic variation. Full article

Nanopore sequencing is a third-generation biopolymer sequencing technique that relies on monitoring the changes in an electrical current that occur as nucleic acids are passed through a protein nanopore. Increasing quality of reads generated by nanopore sequencing systems encourages their application in genome-wide polymorphism detection and genotyping. In this study, we employed nanopore sequencing to identify genome-wide polymorphisms in the horse genome. To reduce the size and complexity of genome fragments for sequencing in a simple and cost-efficient manner, we amplified random DNA fragments using a modified DOP-PCR and sequenced the resulting products using the MinION system. After initial filtering, this generated 28,426 polymorphisms, which were validated at a 3% error rate. Upon further filtering for polymorphism and reproducibility, we identified 9495 SNPs that reflected the horse population structure. To conclude, the use of nanopore sequencing, in conjunction with a genome enrichment step, is a promising tool that can be practical in a variety of applications, including genotyping, population genomics, association studies, linkage mapping, and potentially genomic selection. Full article